Starting phenix.real_space_refine on Wed Mar 4 16:38:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lba_0868/03_2026/6lba_0868.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lba_0868/03_2026/6lba_0868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lba_0868/03_2026/6lba_0868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lba_0868/03_2026/6lba_0868.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lba_0868/03_2026/6lba_0868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lba_0868/03_2026/6lba_0868.map" } resolution = 4.1 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= 0.004 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 100 5.16 5 C 9656 2.51 5 N 2624 2.21 5 O 2612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14992 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3748 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 20, 'TRANS': 445} Chain breaks: 12 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 5, 'PHE:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Restraints were copied for chains: C, B, D Time building chain proxies: 3.18, per 1000 atoms: 0.21 Number of scatterers: 14992 At special positions: 0 Unit cell: (108.443, 126.734, 103.217, 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 100 16.00 O 2612 8.00 N 2624 7.00 C 9656 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: 1.41 Conformation dependent library (CDL) restraints added in 424.7 milliseconds 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3592 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 4 sheets defined 64.2% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid -1 through 19 Processing helix chain 'A' and resid 30 through 53 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 65 through 88 Processing helix chain 'A' and resid 91 through 99 Processing helix chain 'A' and resid 104 through 118 removed outlier: 3.690A pdb=" N SER A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.912A pdb=" N ALA A 126 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 149 removed outlier: 3.916A pdb=" N MET A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 163 Processing helix chain 'A' and resid 170 through 171 No H-bonds generated for 'chain 'A' and resid 170 through 171' Processing helix chain 'A' and resid 173 through 174 No H-bonds generated for 'chain 'A' and resid 173 through 174' Processing helix chain 'A' and resid 175 through 198 removed outlier: 3.688A pdb=" N HIS A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG A 185 " --> pdb=" O TRP A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 Processing helix chain 'A' and resid 275 through 284 removed outlier: 3.609A pdb=" N SER A 280 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 320 removed outlier: 3.520A pdb=" N TYR A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 320 " --> pdb=" O GLN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 removed outlier: 4.290A pdb=" N ASP A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TYR A 349 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS A 351 " --> pdb=" O MET A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.698A pdb=" N TRP A 406 " --> pdb=" O PRO A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 432 through 447 removed outlier: 4.064A pdb=" N SER A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 478 through 490 removed outlier: 3.656A pdb=" N VAL A 482 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 484 " --> pdb=" O THR A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 516 removed outlier: 3.906A pdb=" N ARG A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ILE A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 541 removed outlier: 4.192A pdb=" N LEU A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 541 " --> pdb=" O ARG A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.609A pdb=" N TYR A 563 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 0 through 19 Processing helix chain 'C' and resid 30 through 53 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 65 through 88 Processing helix chain 'C' and resid 91 through 99 Processing helix chain 'C' and resid 104 through 118 removed outlier: 3.690A pdb=" N SER C 118 " --> pdb=" O PHE C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.912A pdb=" N ALA C 126 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 149 removed outlier: 3.916A pdb=" N MET C 138 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU C 139 " --> pdb=" O PRO C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 163 Processing helix chain 'C' and resid 170 through 171 No H-bonds generated for 'chain 'C' and resid 170 through 171' Processing helix chain 'C' and resid 173 through 174 No H-bonds generated for 'chain 'C' and resid 173 through 174' Processing helix chain 'C' and resid 175 through 198 removed outlier: 3.687A pdb=" N HIS C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG C 185 " --> pdb=" O TRP C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 275 through 284 removed outlier: 3.610A pdb=" N SER C 280 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU C 281 " --> pdb=" O ILE C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 320 removed outlier: 3.519A pdb=" N TYR C 318 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS C 320 " --> pdb=" O GLN C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 352 removed outlier: 4.290A pdb=" N ASP C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE C 343 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TYR C 349 " --> pdb=" O ARG C 345 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU C 350 " --> pdb=" O GLY C 346 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N HIS C 351 " --> pdb=" O MET C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.698A pdb=" N TRP C 406 " --> pdb=" O PRO C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 413 Processing helix chain 'C' and resid 432 through 447 removed outlier: 4.064A pdb=" N SER C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 478 through 490 removed outlier: 3.657A pdb=" N VAL C 482 " --> pdb=" O PRO C 478 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 484 " --> pdb=" O THR C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 516 removed outlier: 3.906A pdb=" N ARG C 504 " --> pdb=" O SER C 500 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ILE C 505 " --> pdb=" O SER C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 541 removed outlier: 4.193A pdb=" N LEU C 534 " --> pdb=" O ASP C 530 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG C 537 " --> pdb=" O ASP C 533 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS C 541 " --> pdb=" O ARG C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 555 through 570 removed outlier: 3.609A pdb=" N TYR C 563 " --> pdb=" O GLN C 559 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG C 564 " --> pdb=" O LEU C 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 0 through 19 Processing helix chain 'B' and resid 30 through 53 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 65 through 88 Processing helix chain 'B' and resid 91 through 99 Processing helix chain 'B' and resid 104 through 118 removed outlier: 3.690A pdb=" N SER B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.911A pdb=" N ALA B 126 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 149 removed outlier: 3.916A pdb=" N MET B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU B 139 " --> pdb=" O PRO B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 Processing helix chain 'B' and resid 170 through 171 No H-bonds generated for 'chain 'B' and resid 170 through 171' Processing helix chain 'B' and resid 173 through 174 No H-bonds generated for 'chain 'B' and resid 173 through 174' Processing helix chain 'B' and resid 175 through 198 removed outlier: 3.688A pdb=" N HIS B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG B 185 " --> pdb=" O TRP B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 218 Processing helix chain 'B' and resid 275 through 284 removed outlier: 3.609A pdb=" N SER B 280 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU B 281 " --> pdb=" O ILE B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 320 removed outlier: 3.519A pdb=" N TYR B 318 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 352 removed outlier: 4.290A pdb=" N ASP B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE B 343 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR B 349 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU B 350 " --> pdb=" O GLY B 346 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS B 351 " --> pdb=" O MET B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.698A pdb=" N TRP B 406 " --> pdb=" O PRO B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 413 Processing helix chain 'B' and resid 432 through 447 removed outlier: 4.063A pdb=" N SER B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 478 through 490 removed outlier: 3.657A pdb=" N VAL B 482 " --> pdb=" O PRO B 478 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 484 " --> pdb=" O THR B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 516 removed outlier: 3.906A pdb=" N ARG B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ILE B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 541 removed outlier: 4.192A pdb=" N LEU B 534 " --> pdb=" O ASP B 530 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 537 " --> pdb=" O ASP B 533 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 541 " --> pdb=" O ARG B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 554 No H-bonds generated for 'chain 'B' and resid 552 through 554' Processing helix chain 'B' and resid 555 through 570 removed outlier: 3.609A pdb=" N TYR B 563 " --> pdb=" O GLN B 559 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 0 through 19 Processing helix chain 'D' and resid 30 through 53 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 65 through 88 Processing helix chain 'D' and resid 91 through 99 Processing helix chain 'D' and resid 104 through 118 removed outlier: 3.689A pdb=" N SER D 118 " --> pdb=" O PHE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.912A pdb=" N ALA D 126 " --> pdb=" O ALA D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 149 removed outlier: 3.916A pdb=" N MET D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU D 139 " --> pdb=" O PRO D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'D' and resid 170 through 171 No H-bonds generated for 'chain 'D' and resid 170 through 171' Processing helix chain 'D' and resid 173 through 174 No H-bonds generated for 'chain 'D' and resid 173 through 174' Processing helix chain 'D' and resid 175 through 198 removed outlier: 3.687A pdb=" N HIS D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG D 185 " --> pdb=" O TRP D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 218 Processing helix chain 'D' and resid 275 through 284 removed outlier: 3.610A pdb=" N SER D 280 " --> pdb=" O GLU D 277 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU D 281 " --> pdb=" O ILE D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 320 removed outlier: 3.521A pdb=" N TYR D 318 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS D 320 " --> pdb=" O GLN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 352 removed outlier: 4.290A pdb=" N ASP D 338 " --> pdb=" O PRO D 334 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE D 343 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR D 349 " --> pdb=" O ARG D 345 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU D 350 " --> pdb=" O GLY D 346 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N HIS D 351 " --> pdb=" O MET D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 407 removed outlier: 3.697A pdb=" N TRP D 406 " --> pdb=" O PRO D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 413 Processing helix chain 'D' and resid 432 through 447 removed outlier: 4.064A pdb=" N SER D 436 " --> pdb=" O ALA D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 478 through 490 removed outlier: 3.656A pdb=" N VAL D 482 " --> pdb=" O PRO D 478 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU D 484 " --> pdb=" O THR D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 516 removed outlier: 3.906A pdb=" N ARG D 504 " --> pdb=" O SER D 500 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ILE D 505 " --> pdb=" O SER D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 541 removed outlier: 4.192A pdb=" N LEU D 534 " --> pdb=" O ASP D 530 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG D 537 " --> pdb=" O ASP D 533 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS D 541 " --> pdb=" O ARG D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 554 No H-bonds generated for 'chain 'D' and resid 552 through 554' Processing helix chain 'D' and resid 555 through 570 removed outlier: 3.608A pdb=" N TYR D 563 " --> pdb=" O GLN D 559 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG D 564 " --> pdb=" O LEU D 560 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA2, first strand: chain 'C' and resid 365 through 366 Processing sheet with id=AA3, first strand: chain 'B' and resid 365 through 366 Processing sheet with id=AA4, first strand: chain 'D' and resid 365 through 366 737 hydrogen bonds defined for protein. 2091 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: 2.21 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4816 1.34 - 1.46: 3305 1.46 - 1.58: 7047 1.58 - 1.69: 0 1.69 - 1.81: 152 Bond restraints: 15320 Sorted by residual: bond pdb=" N PRO A 403 " pdb=" CD PRO A 403 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.49e+01 bond pdb=" N PRO B 403 " pdb=" CD PRO B 403 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.49e+01 bond pdb=" N PRO D 403 " pdb=" CD PRO D 403 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.47e+01 bond pdb=" N PRO C 403 " pdb=" CD PRO C 403 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.46e+01 bond pdb=" N PHE C 331 " pdb=" CA PHE C 331 " ideal model delta sigma weight residual 1.458 1.425 0.032 1.22e-02 6.72e+03 7.02e+00 ... (remaining 15315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 19936 2.61 - 5.21: 596 5.21 - 7.82: 88 7.82 - 10.43: 16 10.43 - 13.04: 4 Bond angle restraints: 20640 Sorted by residual: angle pdb=" CA PRO B 403 " pdb=" N PRO B 403 " pdb=" CD PRO B 403 " ideal model delta sigma weight residual 112.00 98.96 13.04 1.40e+00 5.10e-01 8.67e+01 angle pdb=" CA PRO C 403 " pdb=" N PRO C 403 " pdb=" CD PRO C 403 " ideal model delta sigma weight residual 112.00 98.97 13.03 1.40e+00 5.10e-01 8.67e+01 angle pdb=" CA PRO A 403 " pdb=" N PRO A 403 " pdb=" CD PRO A 403 " ideal model delta sigma weight residual 112.00 98.98 13.02 1.40e+00 5.10e-01 8.64e+01 angle pdb=" N ARG B 540 " pdb=" CA ARG B 540 " pdb=" C ARG B 540 " ideal model delta sigma weight residual 111.07 121.01 -9.94 1.07e+00 8.73e-01 8.64e+01 angle pdb=" CA PRO D 403 " pdb=" N PRO D 403 " pdb=" CD PRO D 403 " ideal model delta sigma weight residual 112.00 99.00 13.00 1.40e+00 5.10e-01 8.62e+01 ... (remaining 20635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 8056 16.04 - 32.08: 884 32.08 - 48.12: 228 48.12 - 64.16: 32 64.16 - 80.20: 12 Dihedral angle restraints: 9212 sinusoidal: 3760 harmonic: 5452 Sorted by residual: dihedral pdb=" CA HIS C 100 " pdb=" C HIS C 100 " pdb=" N GLN C 101 " pdb=" CA GLN C 101 " ideal model delta harmonic sigma weight residual 180.00 134.30 45.70 0 5.00e+00 4.00e-02 8.36e+01 dihedral pdb=" CA HIS D 100 " pdb=" C HIS D 100 " pdb=" N GLN D 101 " pdb=" CA GLN D 101 " ideal model delta harmonic sigma weight residual 180.00 134.30 45.70 0 5.00e+00 4.00e-02 8.35e+01 dihedral pdb=" CA HIS A 100 " pdb=" C HIS A 100 " pdb=" N GLN A 101 " pdb=" CA GLN A 101 " ideal model delta harmonic sigma weight residual 180.00 134.32 45.68 0 5.00e+00 4.00e-02 8.35e+01 ... (remaining 9209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1944 0.077 - 0.154: 254 0.154 - 0.230: 51 0.230 - 0.307: 11 0.307 - 0.384: 8 Chirality restraints: 2268 Sorted by residual: chirality pdb=" CA THR D 206 " pdb=" N THR D 206 " pdb=" C THR D 206 " pdb=" CB THR D 206 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA THR A 206 " pdb=" N THR A 206 " pdb=" C THR A 206 " pdb=" CB THR A 206 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CA THR B 206 " pdb=" N THR B 206 " pdb=" C THR B 206 " pdb=" CB THR B 206 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.67e+00 ... (remaining 2265 not shown) Planarity restraints: 2596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 333 " 0.082 5.00e-02 4.00e+02 1.25e-01 2.52e+01 pdb=" N PRO D 334 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO D 334 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO D 334 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 333 " -0.082 5.00e-02 4.00e+02 1.25e-01 2.52e+01 pdb=" N PRO A 334 " 0.217 5.00e-02 4.00e+02 pdb=" CA PRO A 334 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 334 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 333 " 0.082 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO C 334 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO C 334 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO C 334 " 0.073 5.00e-02 4.00e+02 ... (remaining 2593 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.26: 93 2.26 - 2.92: 7786 2.92 - 3.58: 22983 3.58 - 4.24: 33090 4.24 - 4.90: 53716 Nonbonded interactions: 117668 Sorted by model distance: nonbonded pdb=" O LEU C 539 " pdb=" CG PRO C 543 " model vdw 1.605 3.440 nonbonded pdb=" O LEU D 539 " pdb=" CG PRO D 543 " model vdw 1.605 3.440 nonbonded pdb=" O LEU A 539 " pdb=" CG PRO A 543 " model vdw 1.606 3.440 nonbonded pdb=" O LEU B 539 " pdb=" CG PRO B 543 " model vdw 1.606 3.440 nonbonded pdb=" O LEU D 360 " pdb=" OD1 ASN D 361 " model vdw 1.858 3.040 ... (remaining 117663 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 'C' selection = chain 'B' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.980 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15320 Z= 0.316 Angle : 1.039 13.037 20640 Z= 0.716 Chirality : 0.062 0.384 2268 Planarity : 0.007 0.125 2596 Dihedral : 14.227 80.205 5620 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 70.19 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.91 % Favored : 88.64 % Rotamer: Outliers : 3.56 % Allowed : 6.87 % Favored : 89.57 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.46 (0.19), residues: 1760 helix: -1.28 (0.15), residues: 1060 sheet: -1.66 (0.75), residues: 56 loop : -2.03 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 74 TYR 0.011 0.002 TYR C 82 PHE 0.011 0.001 PHE B 117 TRP 0.011 0.001 TRP C 186 HIS 0.005 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00538 (15320) covalent geometry : angle 1.03870 (20640) hydrogen bonds : bond 0.24352 ( 737) hydrogen bonds : angle 7.55577 ( 2091) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 455 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.8235 (tp30) cc_final: 0.7809 (tp30) REVERT: A 28 GLN cc_start: 0.7879 (pt0) cc_final: 0.7652 (pp30) REVERT: A 31 CYS cc_start: 0.8266 (p) cc_final: 0.7496 (p) REVERT: A 54 LYS cc_start: 0.8452 (mttt) cc_final: 0.8008 (mttp) REVERT: A 84 LYS cc_start: 0.9394 (mtpt) cc_final: 0.8785 (ttpt) REVERT: A 148 LYS cc_start: 0.8677 (tttt) cc_final: 0.8454 (ttpp) REVERT: A 171 ARG cc_start: 0.7339 (mtt180) cc_final: 0.7011 (mtt90) REVERT: A 178 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7643 (tm-30) REVERT: A 186 TRP cc_start: 0.6976 (m-90) cc_final: 0.6742 (m-10) REVERT: A 190 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7124 (tm-30) REVERT: A 430 HIS cc_start: 0.6897 (OUTLIER) cc_final: 0.6338 (p-80) REVERT: A 439 MET cc_start: 0.7961 (mmm) cc_final: 0.7613 (mmm) REVERT: A 487 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6769 (mmm160) REVERT: A 514 VAL cc_start: 0.9180 (t) cc_final: 0.8876 (m) REVERT: A 534 LEU cc_start: 0.7152 (mt) cc_final: 0.6893 (mt) REVERT: C 1 MET cc_start: 0.9036 (tpt) cc_final: 0.8825 (tpt) REVERT: C 2 GLU cc_start: 0.8309 (tp30) cc_final: 0.7936 (tp30) REVERT: C 31 CYS cc_start: 0.8293 (p) cc_final: 0.7511 (p) REVERT: C 54 LYS cc_start: 0.8542 (mttt) cc_final: 0.8129 (mttp) REVERT: C 84 LYS cc_start: 0.9357 (mtpt) cc_final: 0.8729 (ttpt) REVERT: C 148 LYS cc_start: 0.8795 (tttt) cc_final: 0.8578 (ttpp) REVERT: C 171 ARG cc_start: 0.7532 (mtt180) cc_final: 0.7128 (mtt90) REVERT: C 178 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7743 (tm-30) REVERT: C 186 TRP cc_start: 0.6928 (m-90) cc_final: 0.6572 (m-10) REVERT: C 190 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7187 (tm-30) REVERT: C 439 MET cc_start: 0.7958 (mmm) cc_final: 0.7401 (mmm) REVERT: C 487 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6844 (mmm160) REVERT: C 514 VAL cc_start: 0.9230 (t) cc_final: 0.8961 (m) REVERT: B 1 MET cc_start: 0.8969 (tpt) cc_final: 0.8767 (tpt) REVERT: B 2 GLU cc_start: 0.8295 (tp30) cc_final: 0.7934 (tp30) REVERT: B 54 LYS cc_start: 0.8606 (mttt) cc_final: 0.8177 (mttp) REVERT: B 171 ARG cc_start: 0.7640 (mtt180) cc_final: 0.7209 (mtt90) REVERT: B 178 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7900 (tm-30) REVERT: B 212 ASP cc_start: 0.9156 (m-30) cc_final: 0.8952 (m-30) REVERT: B 345 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7748 (tpm170) REVERT: B 439 MET cc_start: 0.7919 (mmm) cc_final: 0.7405 (mmm) REVERT: B 514 VAL cc_start: 0.9281 (t) cc_final: 0.9002 (m) REVERT: D 2 GLU cc_start: 0.8231 (tp30) cc_final: 0.7833 (tp30) REVERT: D 24 ILE cc_start: 0.7826 (mm) cc_final: 0.7623 (mt) REVERT: D 28 GLN cc_start: 0.7931 (pt0) cc_final: 0.7723 (pp30) REVERT: D 31 CYS cc_start: 0.8435 (p) cc_final: 0.7629 (p) REVERT: D 54 LYS cc_start: 0.8487 (mttt) cc_final: 0.8017 (mttp) REVERT: D 84 LYS cc_start: 0.9313 (mtpt) cc_final: 0.8721 (ttpt) REVERT: D 171 ARG cc_start: 0.7369 (mtt180) cc_final: 0.6960 (mtt90) REVERT: D 178 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7641 (tm-30) REVERT: D 190 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7236 (tm-30) REVERT: D 439 MET cc_start: 0.7950 (mmm) cc_final: 0.7364 (mmm) REVERT: D 487 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6847 (mmm160) REVERT: D 514 VAL cc_start: 0.9147 (t) cc_final: 0.8874 (m) outliers start: 56 outliers final: 25 residues processed: 479 average time/residue: 0.1443 time to fit residues: 96.4594 Evaluate side-chains 375 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 345 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS C 21 GLN C 28 GLN C 109 HIS C 312 HIS B 21 GLN B 28 GLN B 30 GLN B 51 GLN ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 HIS ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 GLN D 21 GLN D 30 GLN D 51 GLN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.129004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.107785 restraints weight = 33477.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.110147 restraints weight = 22382.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.111863 restraints weight = 16928.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.112975 restraints weight = 13838.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.113860 restraints weight = 12039.135| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15320 Z= 0.173 Angle : 0.719 6.299 20640 Z= 0.376 Chirality : 0.044 0.216 2268 Planarity : 0.005 0.054 2596 Dihedral : 5.964 42.193 1976 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.13 % Allowed : 4.83 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.02 (0.20), residues: 1760 helix: 0.11 (0.15), residues: 1096 sheet: -1.21 (0.78), residues: 56 loop : -2.01 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 142 TYR 0.019 0.002 TYR D 376 PHE 0.020 0.002 PHE C 442 TRP 0.015 0.002 TRP B 489 HIS 0.005 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00395 (15320) covalent geometry : angle 0.71922 (20640) hydrogen bonds : bond 0.05335 ( 737) hydrogen bonds : angle 5.18925 ( 2091) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 492 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.7721 (tp30) cc_final: 0.7205 (tp30) REVERT: A 28 GLN cc_start: 0.8053 (pt0) cc_final: 0.7652 (pp30) REVERT: A 31 CYS cc_start: 0.8194 (p) cc_final: 0.7487 (p) REVERT: A 54 LYS cc_start: 0.8392 (mttt) cc_final: 0.7970 (mttp) REVERT: A 84 LYS cc_start: 0.9356 (mtpt) cc_final: 0.8641 (ttpt) REVERT: A 148 LYS cc_start: 0.8731 (tttt) cc_final: 0.8128 (ttpp) REVERT: A 149 TYR cc_start: 0.8464 (m-10) cc_final: 0.7925 (m-10) REVERT: A 186 TRP cc_start: 0.6827 (m-10) cc_final: 0.6604 (m-10) REVERT: A 187 ASN cc_start: 0.8700 (t0) cc_final: 0.8467 (t0) REVERT: A 190 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7135 (tm-30) REVERT: A 311 MET cc_start: 0.8359 (pmm) cc_final: 0.7611 (pmm) REVERT: A 340 MET cc_start: 0.8343 (mtm) cc_final: 0.8094 (mtt) REVERT: A 366 HIS cc_start: 0.8006 (m-70) cc_final: 0.7513 (m170) REVERT: A 487 ARG cc_start: 0.8337 (mmt90) cc_final: 0.7776 (mmm160) REVERT: A 534 LEU cc_start: 0.8587 (mt) cc_final: 0.8350 (mt) REVERT: A 563 TYR cc_start: 0.8700 (m-80) cc_final: 0.8357 (m-10) REVERT: C 2 GLU cc_start: 0.7759 (tp30) cc_final: 0.7290 (tp30) REVERT: C 54 LYS cc_start: 0.8399 (mttt) cc_final: 0.8083 (mttp) REVERT: C 84 LYS cc_start: 0.9350 (mtpt) cc_final: 0.8726 (ttpt) REVERT: C 148 LYS cc_start: 0.8781 (tttt) cc_final: 0.8279 (ttpp) REVERT: C 149 TYR cc_start: 0.8542 (m-10) cc_final: 0.7969 (m-10) REVERT: C 184 ASP cc_start: 0.7998 (p0) cc_final: 0.7797 (p0) REVERT: C 186 TRP cc_start: 0.6792 (m-10) cc_final: 0.6538 (m-10) REVERT: C 187 ASN cc_start: 0.8659 (t0) cc_final: 0.8422 (t0) REVERT: C 190 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7146 (tm-30) REVERT: C 311 MET cc_start: 0.8456 (pmm) cc_final: 0.7752 (pmm) REVERT: C 366 HIS cc_start: 0.8104 (m-70) cc_final: 0.7682 (m170) REVERT: C 431 LYS cc_start: 0.9037 (mttt) cc_final: 0.8741 (mmtm) REVERT: C 487 ARG cc_start: 0.8342 (mmt90) cc_final: 0.8033 (mmm160) REVERT: B 2 GLU cc_start: 0.7796 (tp30) cc_final: 0.7300 (tp30) REVERT: B 49 ILE cc_start: 0.9518 (mt) cc_final: 0.9301 (mm) REVERT: B 54 LYS cc_start: 0.8449 (mttt) cc_final: 0.8097 (mttp) REVERT: B 84 LYS cc_start: 0.9307 (mtpt) cc_final: 0.8724 (ttpt) REVERT: B 148 LYS cc_start: 0.8725 (ttpp) cc_final: 0.8426 (tttp) REVERT: B 149 TYR cc_start: 0.8513 (m-10) cc_final: 0.7979 (m-10) REVERT: B 171 ARG cc_start: 0.7114 (mtt180) cc_final: 0.6764 (mtt90) REVERT: B 190 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7109 (tm-30) REVERT: B 311 MET cc_start: 0.8514 (pmm) cc_final: 0.7297 (ptp) REVERT: B 366 HIS cc_start: 0.7878 (m-70) cc_final: 0.5214 (m-70) REVERT: B 367 LEU cc_start: 0.8766 (mp) cc_final: 0.8562 (mt) REVERT: B 435 TYR cc_start: 0.7494 (t80) cc_final: 0.7153 (t80) REVERT: B 563 TYR cc_start: 0.8652 (m-80) cc_final: 0.8335 (m-10) REVERT: D 2 GLU cc_start: 0.7783 (tp30) cc_final: 0.7268 (tp30) REVERT: D 28 GLN cc_start: 0.8213 (pt0) cc_final: 0.7611 (pp30) REVERT: D 54 LYS cc_start: 0.8371 (mttt) cc_final: 0.8010 (mttp) REVERT: D 84 LYS cc_start: 0.9364 (mtpt) cc_final: 0.8729 (ttpt) REVERT: D 149 TYR cc_start: 0.8483 (m-10) cc_final: 0.8028 (m-10) REVERT: D 155 ASP cc_start: 0.7790 (t70) cc_final: 0.7261 (t0) REVERT: D 171 ARG cc_start: 0.7150 (mtt180) cc_final: 0.6791 (mtt90) REVERT: D 190 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7251 (tm-30) REVERT: D 311 MET cc_start: 0.8407 (pmm) cc_final: 0.7487 (pmm) REVERT: D 366 HIS cc_start: 0.7949 (m-70) cc_final: 0.7316 (m170) REVERT: D 563 TYR cc_start: 0.8611 (m-80) cc_final: 0.8294 (m-10) outliers start: 2 outliers final: 0 residues processed: 492 average time/residue: 0.1331 time to fit residues: 93.1121 Evaluate side-chains 355 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 154 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 178 optimal weight: 0.9990 chunk 77 optimal weight: 0.0470 chunk 66 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 150 optimal weight: 0.0000 overall best weight: 0.5486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 59 HIS ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN C 59 HIS C 111 HIS ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 GLN D 21 GLN D 59 HIS ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 HIS ** D 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.128681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.106766 restraints weight = 33157.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109134 restraints weight = 22449.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.110823 restraints weight = 17049.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.111758 restraints weight = 13970.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.112746 restraints weight = 12286.230| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15320 Z= 0.147 Angle : 0.670 8.149 20640 Z= 0.348 Chirality : 0.042 0.205 2268 Planarity : 0.004 0.042 2596 Dihedral : 5.812 39.008 1976 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 0.19 % Allowed : 3.82 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -0.29 (0.21), residues: 1760 helix: 0.71 (0.16), residues: 1076 sheet: -1.12 (0.79), residues: 56 loop : -1.67 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 507 TYR 0.022 0.002 TYR D 435 PHE 0.043 0.002 PHE A 442 TRP 0.030 0.002 TRP D 489 HIS 0.006 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00326 (15320) covalent geometry : angle 0.67008 (20640) hydrogen bonds : bond 0.04416 ( 737) hydrogen bonds : angle 4.67054 ( 2091) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 462 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8095 (pt0) cc_final: 0.7508 (pp30) REVERT: A 31 CYS cc_start: 0.8199 (p) cc_final: 0.7292 (p) REVERT: A 54 LYS cc_start: 0.8477 (mttt) cc_final: 0.8061 (mttp) REVERT: A 84 LYS cc_start: 0.9357 (mtpt) cc_final: 0.8745 (ttpt) REVERT: A 92 TRP cc_start: 0.8597 (t60) cc_final: 0.8102 (t60) REVERT: A 148 LYS cc_start: 0.8712 (tttt) cc_final: 0.8306 (ttpt) REVERT: A 149 TYR cc_start: 0.8429 (m-10) cc_final: 0.8026 (m-10) REVERT: A 155 ASP cc_start: 0.7343 (t0) cc_final: 0.6904 (m-30) REVERT: A 158 MET cc_start: 0.8225 (tmm) cc_final: 0.8019 (tmm) REVERT: A 184 ASP cc_start: 0.8313 (p0) cc_final: 0.7900 (p0) REVERT: A 187 ASN cc_start: 0.8963 (t0) cc_final: 0.8593 (t0) REVERT: A 190 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7167 (tm-30) REVERT: A 407 TYR cc_start: 0.6526 (m-80) cc_final: 0.6186 (m-80) REVERT: A 431 LYS cc_start: 0.9180 (mttt) cc_final: 0.8592 (mmtm) REVERT: A 442 PHE cc_start: 0.6025 (m-80) cc_final: 0.5658 (m-80) REVERT: A 494 SER cc_start: 0.8961 (m) cc_final: 0.8244 (t) REVERT: C 2 GLU cc_start: 0.7857 (tp30) cc_final: 0.7391 (tp30) REVERT: C 31 CYS cc_start: 0.8388 (p) cc_final: 0.7512 (p) REVERT: C 37 LEU cc_start: 0.9691 (mt) cc_final: 0.9292 (tp) REVERT: C 54 LYS cc_start: 0.8610 (mttt) cc_final: 0.7940 (mttp) REVERT: C 84 LYS cc_start: 0.9367 (mtpt) cc_final: 0.8758 (ttpt) REVERT: C 92 TRP cc_start: 0.8651 (t60) cc_final: 0.8070 (t60) REVERT: C 148 LYS cc_start: 0.8878 (tttt) cc_final: 0.8601 (ttpt) REVERT: C 149 TYR cc_start: 0.8464 (m-10) cc_final: 0.8073 (m-10) REVERT: C 155 ASP cc_start: 0.7535 (t0) cc_final: 0.7044 (m-30) REVERT: C 158 MET cc_start: 0.8365 (ttp) cc_final: 0.8039 (ttp) REVERT: C 184 ASP cc_start: 0.8351 (p0) cc_final: 0.7999 (p0) REVERT: C 186 TRP cc_start: 0.6859 (m-10) cc_final: 0.6602 (m-10) REVERT: C 190 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7190 (tm-30) REVERT: C 431 LYS cc_start: 0.9097 (mttt) cc_final: 0.8598 (mmtm) REVERT: C 563 TYR cc_start: 0.8258 (m-80) cc_final: 0.8028 (m-10) REVERT: B 2 GLU cc_start: 0.7774 (tp30) cc_final: 0.7295 (tp30) REVERT: B 31 CYS cc_start: 0.8020 (p) cc_final: 0.7011 (p) REVERT: B 54 LYS cc_start: 0.8585 (mttt) cc_final: 0.7800 (mttp) REVERT: B 84 LYS cc_start: 0.9321 (mtpt) cc_final: 0.8691 (ttpt) REVERT: B 92 TRP cc_start: 0.8860 (t60) cc_final: 0.8506 (t60) REVERT: B 148 LYS cc_start: 0.8815 (ttpp) cc_final: 0.8532 (ttpt) REVERT: B 155 ASP cc_start: 0.7466 (t0) cc_final: 0.7229 (m-30) REVERT: B 190 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7159 (tm-30) REVERT: B 410 GLU cc_start: 0.8835 (pm20) cc_final: 0.8492 (tm-30) REVERT: B 539 LEU cc_start: 0.9196 (pp) cc_final: 0.8815 (mm) REVERT: D 28 GLN cc_start: 0.8104 (pt0) cc_final: 0.7527 (pp30) REVERT: D 37 LEU cc_start: 0.9600 (mt) cc_final: 0.9217 (tp) REVERT: D 54 LYS cc_start: 0.8663 (mttt) cc_final: 0.8009 (mttp) REVERT: D 84 LYS cc_start: 0.9334 (mtpt) cc_final: 0.8960 (ttpt) REVERT: D 149 TYR cc_start: 0.8419 (m-10) cc_final: 0.8110 (m-10) REVERT: D 155 ASP cc_start: 0.7088 (t70) cc_final: 0.6647 (m-30) REVERT: D 158 MET cc_start: 0.8400 (tmm) cc_final: 0.8118 (tmm) REVERT: D 184 ASP cc_start: 0.8209 (p0) cc_final: 0.7931 (p0) REVERT: D 190 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7296 (tm-30) REVERT: D 431 LYS cc_start: 0.9101 (mttt) cc_final: 0.8434 (mmmm) REVERT: D 493 PRO cc_start: 0.7761 (Cg_endo) cc_final: 0.6902 (Cg_exo) outliers start: 3 outliers final: 0 residues processed: 462 average time/residue: 0.1180 time to fit residues: 80.5046 Evaluate side-chains 339 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 48 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 175 optimal weight: 0.0870 chunk 146 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 164 optimal weight: 0.0970 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 109 HIS ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN C 187 ASN ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN B 59 HIS B 109 HIS B 111 HIS B 187 ASN ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 GLN D 109 HIS ** D 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.129740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.108360 restraints weight = 33502.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.110536 restraints weight = 23099.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.112087 restraints weight = 17868.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.113063 restraints weight = 14881.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.113516 restraints weight = 13114.976| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15320 Z= 0.135 Angle : 0.634 7.086 20640 Z= 0.329 Chirality : 0.041 0.159 2268 Planarity : 0.005 0.089 2596 Dihedral : 5.633 35.848 1976 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.09 (0.21), residues: 1760 helix: 0.98 (0.16), residues: 1076 sheet: -0.76 (0.80), residues: 56 loop : -1.45 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 507 TYR 0.020 0.002 TYR D 435 PHE 0.035 0.002 PHE B 442 TRP 0.033 0.002 TRP A 186 HIS 0.003 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00308 (15320) covalent geometry : angle 0.63356 (20640) hydrogen bonds : bond 0.04042 ( 737) hydrogen bonds : angle 4.32413 ( 2091) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8084 (pt0) cc_final: 0.7540 (pp30) REVERT: A 31 CYS cc_start: 0.8213 (p) cc_final: 0.7435 (p) REVERT: A 54 LYS cc_start: 0.8782 (mttt) cc_final: 0.8037 (mttp) REVERT: A 84 LYS cc_start: 0.9372 (mtpt) cc_final: 0.8816 (ttpt) REVERT: A 92 TRP cc_start: 0.8712 (t60) cc_final: 0.8127 (t60) REVERT: A 148 LYS cc_start: 0.8706 (tttt) cc_final: 0.8490 (ttpt) REVERT: A 155 ASP cc_start: 0.7359 (t0) cc_final: 0.6807 (m-30) REVERT: A 158 MET cc_start: 0.8324 (tmm) cc_final: 0.8083 (tmm) REVERT: A 184 ASP cc_start: 0.8201 (p0) cc_final: 0.7682 (p0) REVERT: A 186 TRP cc_start: 0.6926 (m-10) cc_final: 0.6594 (m-10) REVERT: A 187 ASN cc_start: 0.8919 (t0) cc_final: 0.8514 (t0) REVERT: A 190 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7170 (tm-30) REVERT: A 431 LYS cc_start: 0.9173 (mttt) cc_final: 0.8736 (mmtm) REVERT: A 435 TYR cc_start: 0.7921 (t80) cc_final: 0.7553 (t80) REVERT: A 463 ILE cc_start: 0.9133 (mt) cc_final: 0.8709 (pt) REVERT: C 2 GLU cc_start: 0.7721 (tp30) cc_final: 0.7343 (tp30) REVERT: C 28 GLN cc_start: 0.8211 (pt0) cc_final: 0.7465 (pp30) REVERT: C 37 LEU cc_start: 0.9714 (mt) cc_final: 0.9304 (tp) REVERT: C 54 LYS cc_start: 0.8271 (mttt) cc_final: 0.7679 (mttp) REVERT: C 84 LYS cc_start: 0.9350 (mtpt) cc_final: 0.9016 (ttpt) REVERT: C 92 TRP cc_start: 0.8724 (t60) cc_final: 0.8241 (t60) REVERT: C 155 ASP cc_start: 0.7475 (t0) cc_final: 0.6947 (m-30) REVERT: C 190 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7179 (tm-30) REVERT: C 431 LYS cc_start: 0.9075 (mttt) cc_final: 0.8591 (mmtm) REVERT: C 442 PHE cc_start: 0.6218 (m-80) cc_final: 0.5809 (m-80) REVERT: B 2 GLU cc_start: 0.7645 (tp30) cc_final: 0.7214 (tp30) REVERT: B 28 GLN cc_start: 0.8154 (pt0) cc_final: 0.7418 (pp30) REVERT: B 54 LYS cc_start: 0.8213 (mttt) cc_final: 0.7740 (mttp) REVERT: B 55 LEU cc_start: 0.8955 (mp) cc_final: 0.8730 (mp) REVERT: B 84 LYS cc_start: 0.9319 (mtpt) cc_final: 0.8774 (ttpt) REVERT: B 92 TRP cc_start: 0.8875 (t60) cc_final: 0.8589 (t60) REVERT: B 138 MET cc_start: 0.8584 (mmt) cc_final: 0.8225 (mmt) REVERT: B 148 LYS cc_start: 0.8768 (ttpp) cc_final: 0.8474 (ttpt) REVERT: B 155 ASP cc_start: 0.7389 (t0) cc_final: 0.7125 (m-30) REVERT: B 184 ASP cc_start: 0.8162 (p0) cc_final: 0.7794 (p0) REVERT: B 190 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7116 (tm-30) REVERT: B 218 LEU cc_start: 0.9102 (mp) cc_final: 0.8774 (tt) REVERT: B 442 PHE cc_start: 0.6128 (m-80) cc_final: 0.5806 (m-80) REVERT: B 539 LEU cc_start: 0.9204 (pp) cc_final: 0.8761 (mt) REVERT: D 28 GLN cc_start: 0.8139 (pt0) cc_final: 0.7196 (pp30) REVERT: D 54 LYS cc_start: 0.8640 (mttt) cc_final: 0.7788 (mttp) REVERT: D 80 GLU cc_start: 0.8255 (tm-30) cc_final: 0.8053 (tm-30) REVERT: D 84 LYS cc_start: 0.9352 (mtpt) cc_final: 0.8648 (ttmt) REVERT: D 122 GLU cc_start: 0.7734 (tp30) cc_final: 0.7345 (tm-30) REVERT: D 158 MET cc_start: 0.8512 (tmm) cc_final: 0.8234 (tmm) REVERT: D 184 ASP cc_start: 0.8091 (p0) cc_final: 0.7577 (p0) REVERT: D 190 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7275 (tm-30) REVERT: D 431 LYS cc_start: 0.9056 (mttt) cc_final: 0.8626 (mmtm) REVERT: D 442 PHE cc_start: 0.6337 (m-80) cc_final: 0.5949 (m-80) REVERT: D 539 LEU cc_start: 0.9143 (pp) cc_final: 0.8620 (mt) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.1272 time to fit residues: 78.0001 Evaluate side-chains 333 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 38 optimal weight: 0.1980 chunk 138 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 162 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS C 187 ASN ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN B 187 ASN ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 HIS D 21 GLN D 27 ASN D 30 GLN ** D 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.127926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.107072 restraints weight = 33962.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109256 restraints weight = 23381.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.110805 restraints weight = 18046.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.111911 restraints weight = 14932.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.112517 restraints weight = 13003.308| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15320 Z= 0.150 Angle : 0.645 9.890 20640 Z= 0.329 Chirality : 0.041 0.144 2268 Planarity : 0.004 0.058 2596 Dihedral : 5.523 35.338 1976 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.10 (0.21), residues: 1760 helix: 0.82 (0.16), residues: 1116 sheet: -0.76 (0.77), residues: 56 loop : -1.24 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 470 TYR 0.018 0.001 TYR C 376 PHE 0.024 0.002 PHE D 442 TRP 0.039 0.002 TRP C 186 HIS 0.003 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00350 (15320) covalent geometry : angle 0.64523 (20640) hydrogen bonds : bond 0.03817 ( 737) hydrogen bonds : angle 4.22968 ( 2091) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8107 (pt0) cc_final: 0.7412 (pp30) REVERT: A 54 LYS cc_start: 0.8432 (mttt) cc_final: 0.7812 (mttp) REVERT: A 71 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7547 (mm-30) REVERT: A 84 LYS cc_start: 0.9312 (mtpt) cc_final: 0.8890 (ttmt) REVERT: A 92 TRP cc_start: 0.8735 (t60) cc_final: 0.8374 (t60) REVERT: A 155 ASP cc_start: 0.7374 (t0) cc_final: 0.6776 (m-30) REVERT: A 158 MET cc_start: 0.8362 (tmm) cc_final: 0.8059 (tmm) REVERT: A 184 ASP cc_start: 0.8302 (p0) cc_final: 0.7848 (p0) REVERT: A 186 TRP cc_start: 0.7089 (m-10) cc_final: 0.6631 (m-10) REVERT: A 190 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7230 (tm-30) REVERT: A 410 GLU cc_start: 0.8951 (pm20) cc_final: 0.8338 (tm-30) REVERT: A 435 TYR cc_start: 0.8171 (t80) cc_final: 0.7752 (t80) REVERT: A 439 MET cc_start: 0.8209 (mmp) cc_final: 0.7971 (mmm) REVERT: A 442 PHE cc_start: 0.6340 (m-80) cc_final: 0.5976 (m-80) REVERT: A 467 MET cc_start: 0.8845 (mpp) cc_final: 0.8633 (mpp) REVERT: C 2 GLU cc_start: 0.7772 (tp30) cc_final: 0.7468 (tp30) REVERT: C 28 GLN cc_start: 0.8278 (pt0) cc_final: 0.7571 (pp30) REVERT: C 37 LEU cc_start: 0.9720 (mt) cc_final: 0.9342 (tp) REVERT: C 54 LYS cc_start: 0.8646 (mttt) cc_final: 0.7771 (mttp) REVERT: C 84 LYS cc_start: 0.9361 (mtpt) cc_final: 0.9018 (ttpt) REVERT: C 92 TRP cc_start: 0.8790 (t60) cc_final: 0.8277 (t60) REVERT: C 155 ASP cc_start: 0.7554 (t0) cc_final: 0.6958 (m-30) REVERT: C 158 MET cc_start: 0.8125 (ttp) cc_final: 0.7800 (ttp) REVERT: C 184 ASP cc_start: 0.8183 (p0) cc_final: 0.7944 (p0) REVERT: C 190 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7261 (tm-30) REVERT: C 431 LYS cc_start: 0.9024 (mttt) cc_final: 0.8613 (mmtm) REVERT: C 435 TYR cc_start: 0.7776 (t80) cc_final: 0.7365 (t80) REVERT: C 442 PHE cc_start: 0.5936 (m-80) cc_final: 0.5606 (m-80) REVERT: B 2 GLU cc_start: 0.7722 (tp30) cc_final: 0.7446 (tp30) REVERT: B 28 GLN cc_start: 0.8293 (pt0) cc_final: 0.7352 (pp30) REVERT: B 37 LEU cc_start: 0.9507 (mt) cc_final: 0.9184 (tp) REVERT: B 54 LYS cc_start: 0.8679 (mttt) cc_final: 0.7823 (mttp) REVERT: B 84 LYS cc_start: 0.9336 (mtpt) cc_final: 0.8974 (ttpt) REVERT: B 92 TRP cc_start: 0.8961 (t60) cc_final: 0.8614 (t60) REVERT: B 148 LYS cc_start: 0.8778 (ttpp) cc_final: 0.8401 (ttpt) REVERT: B 155 ASP cc_start: 0.7542 (t0) cc_final: 0.7092 (m-30) REVERT: B 158 MET cc_start: 0.7782 (ttp) cc_final: 0.7526 (tmm) REVERT: B 165 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8433 (mptt) REVERT: B 178 GLU cc_start: 0.8397 (mp0) cc_final: 0.8066 (mp0) REVERT: B 184 ASP cc_start: 0.8185 (p0) cc_final: 0.7851 (p0) REVERT: B 190 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7303 (tm-30) REVERT: B 218 LEU cc_start: 0.9007 (mp) cc_final: 0.8729 (tt) REVERT: B 461 MET cc_start: 0.5626 (mpp) cc_final: 0.4841 (mmp) REVERT: D 24 ILE cc_start: 0.7914 (mm) cc_final: 0.7590 (mt) REVERT: D 28 GLN cc_start: 0.8230 (pt0) cc_final: 0.7249 (pp30) REVERT: D 54 LYS cc_start: 0.8382 (mttt) cc_final: 0.7775 (mttp) REVERT: D 84 LYS cc_start: 0.9338 (mtpt) cc_final: 0.9010 (ttpt) REVERT: D 158 MET cc_start: 0.8534 (tmm) cc_final: 0.8148 (tmm) REVERT: D 184 ASP cc_start: 0.8240 (p0) cc_final: 0.7791 (p0) REVERT: D 190 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7308 (tm-30) REVERT: D 431 LYS cc_start: 0.9038 (mttt) cc_final: 0.8616 (mmtm) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.1084 time to fit residues: 64.3192 Evaluate side-chains 323 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 154 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN C 51 GLN ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 HIS D 27 ASN ** D 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.128149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.107519 restraints weight = 33008.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.109778 restraints weight = 22483.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.111359 restraints weight = 17119.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.112299 restraints weight = 14155.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.113170 restraints weight = 12434.504| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15320 Z= 0.129 Angle : 0.620 9.199 20640 Z= 0.317 Chirality : 0.040 0.148 2268 Planarity : 0.004 0.038 2596 Dihedral : 5.367 34.214 1976 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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 (0.21), residues: 1760 helix: 0.90 (0.16), residues: 1116 sheet: -0.68 (0.75), residues: 56 loop : -1.15 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 182 TYR 0.015 0.001 TYR D 116 PHE 0.028 0.002 PHE D 442 TRP 0.052 0.002 TRP B 186 HIS 0.004 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00296 (15320) covalent geometry : angle 0.62014 (20640) hydrogen bonds : bond 0.03635 ( 737) hydrogen bonds : angle 4.16856 ( 2091) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8104 (pt0) cc_final: 0.7392 (pp30) REVERT: A 54 LYS cc_start: 0.8417 (mttt) cc_final: 0.7848 (mttp) REVERT: A 55 LEU cc_start: 0.8754 (mp) cc_final: 0.8228 (mp) REVERT: A 71 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7324 (mm-30) REVERT: A 84 LYS cc_start: 0.9317 (mtpt) cc_final: 0.8878 (ttmt) REVERT: A 92 TRP cc_start: 0.8777 (t60) cc_final: 0.8397 (t60) REVERT: A 155 ASP cc_start: 0.7215 (t0) cc_final: 0.6573 (m-30) REVERT: A 158 MET cc_start: 0.8382 (tmm) cc_final: 0.8075 (tmm) REVERT: A 184 ASP cc_start: 0.8250 (p0) cc_final: 0.7813 (p0) REVERT: A 186 TRP cc_start: 0.6969 (m-10) cc_final: 0.6560 (m-10) REVERT: A 190 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7248 (tm-30) REVERT: A 347 MET cc_start: 0.8027 (tpp) cc_final: 0.7483 (tpp) REVERT: A 410 GLU cc_start: 0.8951 (pm20) cc_final: 0.8288 (tm-30) REVERT: A 435 TYR cc_start: 0.7984 (t80) cc_final: 0.6540 (t80) REVERT: C 21 GLN cc_start: 0.8285 (tt0) cc_final: 0.8073 (tt0) REVERT: C 28 GLN cc_start: 0.8303 (pt0) cc_final: 0.7220 (pp30) REVERT: C 37 LEU cc_start: 0.9735 (mt) cc_final: 0.9352 (tp) REVERT: C 54 LYS cc_start: 0.8391 (mttt) cc_final: 0.7811 (mttp) REVERT: C 71 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7438 (mm-30) REVERT: C 84 LYS cc_start: 0.9363 (mtpt) cc_final: 0.8737 (ttmt) REVERT: C 155 ASP cc_start: 0.7248 (t0) cc_final: 0.6742 (m-30) REVERT: C 178 GLU cc_start: 0.8410 (mp0) cc_final: 0.8187 (mp0) REVERT: C 184 ASP cc_start: 0.8171 (p0) cc_final: 0.7835 (p0) REVERT: C 190 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7315 (tm-30) REVERT: C 218 LEU cc_start: 0.9003 (mp) cc_final: 0.8797 (tt) REVERT: C 435 TYR cc_start: 0.8130 (t80) cc_final: 0.7920 (t80) REVERT: C 487 ARG cc_start: 0.8154 (mmt90) cc_final: 0.7949 (mmm160) REVERT: B 28 GLN cc_start: 0.8331 (pt0) cc_final: 0.7412 (pp30) REVERT: B 54 LYS cc_start: 0.8326 (mttt) cc_final: 0.7709 (mttp) REVERT: B 84 LYS cc_start: 0.9328 (mtpt) cc_final: 0.8986 (ttpt) REVERT: B 92 TRP cc_start: 0.8929 (t60) cc_final: 0.8636 (t60) REVERT: B 155 ASP cc_start: 0.7330 (t0) cc_final: 0.6926 (m-30) REVERT: B 158 MET cc_start: 0.7783 (ttp) cc_final: 0.7449 (tmm) REVERT: B 184 ASP cc_start: 0.8121 (p0) cc_final: 0.7868 (p0) REVERT: B 190 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7290 (tm-30) REVERT: B 347 MET cc_start: 0.7924 (ttp) cc_final: 0.7033 (ttp) REVERT: B 410 GLU cc_start: 0.8864 (pm20) cc_final: 0.8257 (tm-30) REVERT: B 461 MET cc_start: 0.5679 (mpp) cc_final: 0.5025 (mmp) REVERT: B 539 LEU cc_start: 0.9198 (pp) cc_final: 0.8720 (mt) REVERT: D 18 MET cc_start: 0.9291 (tpt) cc_final: 0.9076 (tpt) REVERT: D 24 ILE cc_start: 0.7849 (mm) cc_final: 0.7622 (mt) REVERT: D 28 GLN cc_start: 0.8169 (pt0) cc_final: 0.7175 (pp30) REVERT: D 54 LYS cc_start: 0.8666 (mttt) cc_final: 0.7798 (mttp) REVERT: D 84 LYS cc_start: 0.9351 (mtpt) cc_final: 0.8883 (ttmt) REVERT: D 158 MET cc_start: 0.8495 (tmm) cc_final: 0.7992 (tmm) REVERT: D 165 LYS cc_start: 0.8679 (mmmt) cc_final: 0.8320 (mptt) REVERT: D 184 ASP cc_start: 0.8203 (p0) cc_final: 0.7706 (p0) REVERT: D 190 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7233 (tm-30) REVERT: D 431 LYS cc_start: 0.8926 (mttt) cc_final: 0.8593 (mmmm) REVERT: D 442 PHE cc_start: 0.6745 (m-80) cc_final: 0.6423 (m-80) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.1064 time to fit residues: 64.5661 Evaluate side-chains 332 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 160 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 34 optimal weight: 0.0000 chunk 148 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 177 optimal weight: 8.9990 chunk 131 optimal weight: 0.5980 chunk 152 optimal weight: 6.9990 chunk 134 optimal weight: 0.0870 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 0.0870 overall best weight: 0.3340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 HIS ** 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 = 0.3752 r_free = 0.3752 target = 0.131272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.111816 restraints weight = 33599.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.113811 restraints weight = 23940.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.115262 restraints weight = 18814.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116324 restraints weight = 15717.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.116965 restraints weight = 13753.703| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.6028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15320 Z= 0.124 Angle : 0.645 9.885 20640 Z= 0.327 Chirality : 0.040 0.164 2268 Planarity : 0.004 0.061 2596 Dihedral : 5.316 33.296 1976 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.18 (0.21), residues: 1760 helix: 0.80 (0.16), residues: 1120 sheet: -0.27 (0.76), residues: 56 loop : -1.09 (0.28), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 74 TYR 0.016 0.001 TYR B 116 PHE 0.039 0.002 PHE C 442 TRP 0.086 0.002 TRP B 186 HIS 0.003 0.001 HIS B 351 Details of bonding type rmsd covalent geometry : bond 0.00272 (15320) covalent geometry : angle 0.64530 (20640) hydrogen bonds : bond 0.03599 ( 737) hydrogen bonds : angle 4.18083 ( 2091) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8162 (pt0) cc_final: 0.7572 (pp30) REVERT: A 54 LYS cc_start: 0.8448 (mttt) cc_final: 0.7985 (mttp) REVERT: A 71 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7255 (mm-30) REVERT: A 84 LYS cc_start: 0.9303 (mtpt) cc_final: 0.8882 (ttmt) REVERT: A 92 TRP cc_start: 0.8766 (t60) cc_final: 0.8403 (t60) REVERT: A 155 ASP cc_start: 0.6918 (t0) cc_final: 0.6358 (m-30) REVERT: A 184 ASP cc_start: 0.8079 (p0) cc_final: 0.7628 (p0) REVERT: A 190 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7280 (tm-30) REVERT: A 216 LYS cc_start: 0.8427 (tptt) cc_final: 0.7785 (tppt) REVERT: A 347 MET cc_start: 0.7886 (tpp) cc_final: 0.7661 (tpp) REVERT: A 363 MET cc_start: 0.8737 (mtp) cc_final: 0.8521 (mtm) REVERT: A 410 GLU cc_start: 0.8890 (pm20) cc_final: 0.8257 (tm-30) REVERT: A 435 TYR cc_start: 0.8149 (t80) cc_final: 0.7894 (t80) REVERT: A 439 MET cc_start: 0.7920 (mmp) cc_final: 0.7693 (mmm) REVERT: A 442 PHE cc_start: 0.6504 (m-80) cc_final: 0.6268 (m-80) REVERT: C 24 ILE cc_start: 0.7803 (mm) cc_final: 0.7555 (mt) REVERT: C 28 GLN cc_start: 0.8297 (pt0) cc_final: 0.7490 (pp30) REVERT: C 37 LEU cc_start: 0.9698 (mt) cc_final: 0.9324 (tp) REVERT: C 54 LYS cc_start: 0.8659 (mttt) cc_final: 0.7887 (mttp) REVERT: C 71 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7372 (mm-30) REVERT: C 84 LYS cc_start: 0.9326 (mtpt) cc_final: 0.8936 (ttmt) REVERT: C 148 LYS cc_start: 0.8412 (ttpt) cc_final: 0.7792 (tmmt) REVERT: C 155 ASP cc_start: 0.7016 (t0) cc_final: 0.6630 (m-30) REVERT: C 184 ASP cc_start: 0.8150 (p0) cc_final: 0.7719 (p0) REVERT: C 190 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7325 (tm-30) REVERT: C 338 ASP cc_start: 0.9423 (t0) cc_final: 0.9145 (t70) REVERT: C 410 GLU cc_start: 0.8857 (pm20) cc_final: 0.8175 (tm-30) REVERT: C 487 ARG cc_start: 0.8111 (mmt90) cc_final: 0.7853 (mmm160) REVERT: B 24 ILE cc_start: 0.7789 (mm) cc_final: 0.7438 (mt) REVERT: B 28 GLN cc_start: 0.8181 (pt0) cc_final: 0.7361 (pp30) REVERT: B 37 LEU cc_start: 0.9426 (mt) cc_final: 0.9135 (tp) REVERT: B 54 LYS cc_start: 0.8659 (mttt) cc_final: 0.7874 (mttp) REVERT: B 84 LYS cc_start: 0.9335 (mtpt) cc_final: 0.8883 (ttmt) REVERT: B 92 TRP cc_start: 0.8960 (t60) cc_final: 0.8597 (t60) REVERT: B 155 ASP cc_start: 0.7129 (t0) cc_final: 0.6692 (m-30) REVERT: B 158 MET cc_start: 0.7832 (ttp) cc_final: 0.7630 (tmm) REVERT: B 190 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7266 (tm-30) REVERT: B 340 MET cc_start: 0.8072 (mtm) cc_final: 0.7773 (mtt) REVERT: B 435 TYR cc_start: 0.7459 (t80) cc_final: 0.7046 (t80) REVERT: B 439 MET cc_start: 0.8033 (mmp) cc_final: 0.7782 (mmm) REVERT: B 461 MET cc_start: 0.5789 (mpp) cc_final: 0.5347 (mmp) REVERT: B 463 ILE cc_start: 0.8473 (mp) cc_final: 0.7796 (pt) REVERT: B 539 LEU cc_start: 0.9133 (pp) cc_final: 0.8692 (mt) REVERT: D 28 GLN cc_start: 0.8131 (pt0) cc_final: 0.7542 (pp30) REVERT: D 54 LYS cc_start: 0.8487 (mttt) cc_final: 0.7826 (mttp) REVERT: D 84 LYS cc_start: 0.9329 (mtpt) cc_final: 0.8926 (ttmt) REVERT: D 155 ASP cc_start: 0.7124 (t0) cc_final: 0.6608 (m-30) REVERT: D 158 MET cc_start: 0.8429 (tmm) cc_final: 0.7909 (tmm) REVERT: D 165 LYS cc_start: 0.8587 (mmmt) cc_final: 0.8288 (mptt) REVERT: D 184 ASP cc_start: 0.8107 (p0) cc_final: 0.7692 (p0) REVERT: D 190 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7243 (tm-30) REVERT: D 431 LYS cc_start: 0.8834 (mttt) cc_final: 0.8521 (mmmm) REVERT: D 442 PHE cc_start: 0.6658 (m-80) cc_final: 0.6131 (m-80) REVERT: D 461 MET cc_start: 0.5870 (mpp) cc_final: 0.5070 (mmp) REVERT: D 463 ILE cc_start: 0.8469 (mp) cc_final: 0.7616 (pt) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.1116 time to fit residues: 70.7421 Evaluate side-chains 338 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 183 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 2 optimal weight: 0.0770 chunk 138 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 169 optimal weight: 0.6980 chunk 152 optimal weight: 0.9980 chunk 182 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 HIS C 27 ASN C 312 HIS B 312 HIS D 312 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.129148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108200 restraints weight = 33362.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.110674 restraints weight = 21709.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112341 restraints weight = 16078.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113533 restraints weight = 13072.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.114222 restraints weight = 11251.416| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15320 Z= 0.133 Angle : 0.654 10.346 20640 Z= 0.332 Chirality : 0.040 0.146 2268 Planarity : 0.004 0.048 2596 Dihedral : 5.275 31.737 1976 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 (0.21), residues: 1760 helix: 0.73 (0.16), residues: 1120 sheet: -0.43 (0.75), residues: 56 loop : -1.04 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 507 TYR 0.011 0.001 TYR D 435 PHE 0.029 0.001 PHE B 442 TRP 0.066 0.002 TRP B 186 HIS 0.003 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00305 (15320) covalent geometry : angle 0.65366 (20640) hydrogen bonds : bond 0.03547 ( 737) hydrogen bonds : angle 4.21106 ( 2091) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8255 (pt0) cc_final: 0.7602 (pp30) REVERT: A 37 LEU cc_start: 0.9588 (mt) cc_final: 0.9263 (tp) REVERT: A 54 LYS cc_start: 0.8586 (mttt) cc_final: 0.7976 (mttp) REVERT: A 71 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7263 (mm-30) REVERT: A 84 LYS cc_start: 0.9296 (mtpt) cc_final: 0.8864 (ttmt) REVERT: A 92 TRP cc_start: 0.8776 (t60) cc_final: 0.8393 (t60) REVERT: A 148 LYS cc_start: 0.8554 (ttpt) cc_final: 0.7971 (tmmt) REVERT: A 155 ASP cc_start: 0.7087 (t0) cc_final: 0.6459 (m-30) REVERT: A 158 MET cc_start: 0.7744 (tmm) cc_final: 0.7391 (tmm) REVERT: A 184 ASP cc_start: 0.8205 (p0) cc_final: 0.7840 (p0) REVERT: A 190 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7253 (tm-30) REVERT: A 216 LYS cc_start: 0.8445 (tptt) cc_final: 0.7821 (tppt) REVERT: A 338 ASP cc_start: 0.9431 (t0) cc_final: 0.9075 (t0) REVERT: A 347 MET cc_start: 0.8017 (tpp) cc_final: 0.7682 (tpp) REVERT: A 363 MET cc_start: 0.8924 (mtp) cc_final: 0.8703 (mtm) REVERT: C 24 ILE cc_start: 0.7826 (mm) cc_final: 0.7585 (mt) REVERT: C 28 GLN cc_start: 0.8328 (pt0) cc_final: 0.7528 (pp30) REVERT: C 37 LEU cc_start: 0.9633 (mt) cc_final: 0.9327 (tp) REVERT: C 54 LYS cc_start: 0.8400 (mttt) cc_final: 0.7843 (mttp) REVERT: C 84 LYS cc_start: 0.9331 (mtpt) cc_final: 0.8902 (ttmt) REVERT: C 148 LYS cc_start: 0.8447 (ttpt) cc_final: 0.7777 (tmmt) REVERT: C 155 ASP cc_start: 0.7128 (t0) cc_final: 0.6648 (m-30) REVERT: C 158 MET cc_start: 0.7892 (ttp) cc_final: 0.7599 (tmm) REVERT: C 184 ASP cc_start: 0.8295 (p0) cc_final: 0.7949 (p0) REVERT: C 190 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7388 (tm-30) REVERT: C 435 TYR cc_start: 0.8062 (t80) cc_final: 0.7795 (t80) REVERT: B 1 MET cc_start: 0.8762 (tpt) cc_final: 0.8527 (tpt) REVERT: B 24 ILE cc_start: 0.7970 (mm) cc_final: 0.7596 (mt) REVERT: B 28 GLN cc_start: 0.8295 (pt0) cc_final: 0.7489 (pp30) REVERT: B 37 LEU cc_start: 0.9472 (mt) cc_final: 0.9126 (tp) REVERT: B 54 LYS cc_start: 0.8423 (mttt) cc_final: 0.7625 (mttp) REVERT: B 84 LYS cc_start: 0.9309 (mtpt) cc_final: 0.8840 (ttmt) REVERT: B 155 ASP cc_start: 0.7244 (t0) cc_final: 0.6765 (m-30) REVERT: B 158 MET cc_start: 0.7990 (ttp) cc_final: 0.7788 (tmm) REVERT: B 186 TRP cc_start: 0.6943 (m-90) cc_final: 0.6687 (m-90) REVERT: B 190 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7317 (tm-30) REVERT: B 340 MET cc_start: 0.8392 (mtm) cc_final: 0.8119 (mtt) REVERT: B 410 GLU cc_start: 0.8798 (pm20) cc_final: 0.8316 (tm-30) REVERT: B 435 TYR cc_start: 0.7715 (t80) cc_final: 0.7236 (t80) REVERT: B 442 PHE cc_start: 0.6309 (m-80) cc_final: 0.5273 (m-80) REVERT: B 461 MET cc_start: 0.5883 (mpp) cc_final: 0.5430 (mmp) REVERT: B 567 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8134 (tm-30) REVERT: D 18 MET cc_start: 0.9286 (tpt) cc_final: 0.9032 (tpt) REVERT: D 28 GLN cc_start: 0.8212 (pt0) cc_final: 0.7574 (pp30) REVERT: D 54 LYS cc_start: 0.8500 (mttt) cc_final: 0.7726 (mttp) REVERT: D 84 LYS cc_start: 0.9315 (mtpt) cc_final: 0.8875 (ttmt) REVERT: D 155 ASP cc_start: 0.7223 (t0) cc_final: 0.6581 (m-30) REVERT: D 158 MET cc_start: 0.8512 (tmm) cc_final: 0.7957 (tmm) REVERT: D 165 LYS cc_start: 0.8615 (mmmt) cc_final: 0.8373 (mptt) REVERT: D 184 ASP cc_start: 0.8183 (p0) cc_final: 0.7864 (p0) REVERT: D 190 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7250 (tm-30) REVERT: D 363 MET cc_start: 0.8941 (mtp) cc_final: 0.8689 (mtm) REVERT: D 431 LYS cc_start: 0.8806 (mttt) cc_final: 0.8550 (mmmm) REVERT: D 442 PHE cc_start: 0.6681 (m-80) cc_final: 0.6056 (m-80) REVERT: D 461 MET cc_start: 0.6203 (mpp) cc_final: 0.5306 (mmp) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.1009 time to fit residues: 64.3009 Evaluate side-chains 327 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 0.0040 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 102 optimal weight: 0.2980 chunk 120 optimal weight: 1.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 HIS C 21 GLN C 27 ASN C 312 HIS ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.128605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.107610 restraints weight = 33078.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.110159 restraints weight = 21322.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.111959 restraints weight = 15634.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113201 restraints weight = 12514.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.113960 restraints weight = 10667.749| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.6260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15320 Z= 0.133 Angle : 0.659 8.885 20640 Z= 0.336 Chirality : 0.041 0.139 2268 Planarity : 0.004 0.048 2596 Dihedral : 5.282 32.662 1976 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 (0.21), residues: 1760 helix: 0.71 (0.16), residues: 1120 sheet: -0.25 (0.76), residues: 56 loop : -1.03 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 74 TYR 0.010 0.001 TYR D 435 PHE 0.025 0.002 PHE C 499 TRP 0.060 0.002 TRP B 186 HIS 0.004 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00307 (15320) covalent geometry : angle 0.65863 (20640) hydrogen bonds : bond 0.03566 ( 737) hydrogen bonds : angle 4.18897 ( 2091) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8284 (pt0) cc_final: 0.7631 (pp30) REVERT: A 37 LEU cc_start: 0.9566 (mt) cc_final: 0.9220 (tp) REVERT: A 53 LEU cc_start: 0.9170 (mt) cc_final: 0.8955 (mt) REVERT: A 54 LYS cc_start: 0.8559 (mttt) cc_final: 0.7837 (mttp) REVERT: A 71 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7307 (mm-30) REVERT: A 84 LYS cc_start: 0.9332 (mtpt) cc_final: 0.8897 (ttmt) REVERT: A 148 LYS cc_start: 0.8507 (ttpt) cc_final: 0.7912 (tmmt) REVERT: A 155 ASP cc_start: 0.7041 (t0) cc_final: 0.6519 (m-30) REVERT: A 158 MET cc_start: 0.7714 (tmm) cc_final: 0.7323 (tmm) REVERT: A 184 ASP cc_start: 0.8185 (p0) cc_final: 0.7843 (p0) REVERT: A 190 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7274 (tm-30) REVERT: A 216 LYS cc_start: 0.8435 (tptt) cc_final: 0.7812 (tppt) REVERT: A 338 ASP cc_start: 0.9427 (t0) cc_final: 0.9076 (t0) REVERT: A 363 MET cc_start: 0.8931 (mtp) cc_final: 0.8698 (mtm) REVERT: A 407 TYR cc_start: 0.6283 (m-80) cc_final: 0.6017 (m-80) REVERT: A 410 GLU cc_start: 0.9033 (pm20) cc_final: 0.8283 (tm-30) REVERT: A 435 TYR cc_start: 0.8143 (t80) cc_final: 0.7797 (t80) REVERT: A 442 PHE cc_start: 0.6586 (m-80) cc_final: 0.6208 (m-80) REVERT: A 461 MET cc_start: 0.5393 (mpp) cc_final: 0.4431 (mmp) REVERT: A 487 ARG cc_start: 0.8256 (mmt90) cc_final: 0.7844 (mmm160) REVERT: A 539 LEU cc_start: 0.9140 (pp) cc_final: 0.8575 (mt) REVERT: C 24 ILE cc_start: 0.7953 (mm) cc_final: 0.7638 (mt) REVERT: C 28 GLN cc_start: 0.8375 (pt0) cc_final: 0.7276 (pp30) REVERT: C 37 LEU cc_start: 0.9651 (mt) cc_final: 0.9297 (tp) REVERT: C 54 LYS cc_start: 0.8507 (mttt) cc_final: 0.7771 (mttp) REVERT: C 84 LYS cc_start: 0.9333 (mtpt) cc_final: 0.8909 (ttmt) REVERT: C 87 MET cc_start: 0.8363 (mtm) cc_final: 0.8149 (mtp) REVERT: C 148 LYS cc_start: 0.8610 (ttpt) cc_final: 0.7954 (tmmt) REVERT: C 155 ASP cc_start: 0.7117 (t0) cc_final: 0.6637 (m-30) REVERT: C 158 MET cc_start: 0.7919 (ttp) cc_final: 0.7663 (tmm) REVERT: C 184 ASP cc_start: 0.8238 (p0) cc_final: 0.7878 (p0) REVERT: C 190 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7347 (tm-30) REVERT: C 216 LYS cc_start: 0.8414 (tptt) cc_final: 0.7794 (tppt) REVERT: C 410 GLU cc_start: 0.8943 (pm20) cc_final: 0.8334 (tm-30) REVERT: C 435 TYR cc_start: 0.8212 (t80) cc_final: 0.7811 (t80) REVERT: C 487 ARG cc_start: 0.8420 (mmt90) cc_final: 0.7871 (mmm160) REVERT: B 24 ILE cc_start: 0.7971 (mm) cc_final: 0.7632 (mt) REVERT: B 28 GLN cc_start: 0.8293 (pt0) cc_final: 0.7491 (pp30) REVERT: B 37 LEU cc_start: 0.9478 (mt) cc_final: 0.9097 (tp) REVERT: B 54 LYS cc_start: 0.8665 (mttt) cc_final: 0.7723 (mttp) REVERT: B 84 LYS cc_start: 0.9306 (mtpt) cc_final: 0.8817 (ttmt) REVERT: B 92 TRP cc_start: 0.8739 (t60) cc_final: 0.8220 (t60) REVERT: B 155 ASP cc_start: 0.7268 (t0) cc_final: 0.6874 (m-30) REVERT: B 158 MET cc_start: 0.8074 (ttp) cc_final: 0.7781 (tmm) REVERT: B 186 TRP cc_start: 0.6963 (m-90) cc_final: 0.6652 (m-90) REVERT: B 190 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7336 (tm-30) REVERT: B 340 MET cc_start: 0.8541 (mtm) cc_final: 0.8283 (mtt) REVERT: B 442 PHE cc_start: 0.6866 (m-80) cc_final: 0.5765 (m-80) REVERT: B 461 MET cc_start: 0.5709 (mpp) cc_final: 0.5378 (mmp) REVERT: B 539 LEU cc_start: 0.9203 (pp) cc_final: 0.8707 (mt) REVERT: B 567 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8123 (tm-30) REVERT: D 28 GLN cc_start: 0.8251 (pt0) cc_final: 0.7619 (pp30) REVERT: D 54 LYS cc_start: 0.8502 (mttt) cc_final: 0.7761 (mttp) REVERT: D 84 LYS cc_start: 0.9323 (mtpt) cc_final: 0.8878 (ttmt) REVERT: D 92 TRP cc_start: 0.8873 (t60) cc_final: 0.8613 (t60) REVERT: D 155 ASP cc_start: 0.7204 (t0) cc_final: 0.6601 (m-30) REVERT: D 158 MET cc_start: 0.8531 (tmm) cc_final: 0.7939 (tmm) REVERT: D 184 ASP cc_start: 0.8182 (p0) cc_final: 0.7905 (p0) REVERT: D 190 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7214 (tm-30) REVERT: D 363 MET cc_start: 0.8913 (mtp) cc_final: 0.8707 (mtm) REVERT: D 442 PHE cc_start: 0.6513 (m-80) cc_final: 0.5918 (m-80) REVERT: D 461 MET cc_start: 0.6077 (mpp) cc_final: 0.5659 (mpp) outliers start: 0 outliers final: 0 residues processed: 404 average time/residue: 0.0980 time to fit residues: 61.0644 Evaluate side-chains 333 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 42 optimal weight: 0.2980 chunk 147 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 136 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 176 optimal weight: 0.0570 chunk 3 optimal weight: 0.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 ASN ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.130196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.109234 restraints weight = 33247.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111716 restraints weight = 21672.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.113426 restraints weight = 16048.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.114573 restraints weight = 13002.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.115423 restraints weight = 11219.339| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.6459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15320 Z= 0.124 Angle : 0.649 8.944 20640 Z= 0.331 Chirality : 0.040 0.173 2268 Planarity : 0.004 0.048 2596 Dihedral : 5.184 31.371 1976 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.15 (0.21), residues: 1760 helix: 0.73 (0.16), residues: 1120 sheet: -0.21 (0.76), residues: 56 loop : -1.00 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 74 TYR 0.009 0.001 TYR D 435 PHE 0.030 0.001 PHE B 442 TRP 0.058 0.002 TRP B 186 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00282 (15320) covalent geometry : angle 0.64923 (20640) hydrogen bonds : bond 0.03452 ( 737) hydrogen bonds : angle 4.21660 ( 2091) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8263 (pt0) cc_final: 0.7619 (pp30) REVERT: A 37 LEU cc_start: 0.9592 (mt) cc_final: 0.9218 (tp) REVERT: A 54 LYS cc_start: 0.8570 (mttt) cc_final: 0.7891 (mttp) REVERT: A 71 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7339 (mm-30) REVERT: A 84 LYS cc_start: 0.9325 (mtpt) cc_final: 0.8876 (ttmt) REVERT: A 148 LYS cc_start: 0.8477 (ttpt) cc_final: 0.7909 (tmmt) REVERT: A 155 ASP cc_start: 0.6946 (t0) cc_final: 0.6403 (m-30) REVERT: A 158 MET cc_start: 0.7629 (tmm) cc_final: 0.7276 (tmm) REVERT: A 184 ASP cc_start: 0.8135 (p0) cc_final: 0.7745 (p0) REVERT: A 190 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7256 (tm-30) REVERT: A 216 LYS cc_start: 0.8434 (tptt) cc_final: 0.7816 (tppt) REVERT: A 363 MET cc_start: 0.8840 (mtp) cc_final: 0.8606 (mtm) REVERT: A 410 GLU cc_start: 0.8993 (pm20) cc_final: 0.8365 (tm-30) REVERT: A 435 TYR cc_start: 0.7760 (t80) cc_final: 0.7503 (t80) REVERT: A 442 PHE cc_start: 0.6472 (m-80) cc_final: 0.6122 (m-80) REVERT: A 461 MET cc_start: 0.5815 (mpp) cc_final: 0.4902 (mmp) REVERT: A 487 ARG cc_start: 0.8141 (mmt90) cc_final: 0.7843 (mmm160) REVERT: A 539 LEU cc_start: 0.9122 (pp) cc_final: 0.8498 (mt) REVERT: C 24 ILE cc_start: 0.7972 (mm) cc_final: 0.7718 (mt) REVERT: C 28 GLN cc_start: 0.8312 (pt0) cc_final: 0.7532 (pp30) REVERT: C 37 LEU cc_start: 0.9666 (mt) cc_final: 0.9299 (tp) REVERT: C 54 LYS cc_start: 0.8515 (mttt) cc_final: 0.7847 (mttp) REVERT: C 84 LYS cc_start: 0.9309 (mtpt) cc_final: 0.8881 (ttmt) REVERT: C 148 LYS cc_start: 0.8548 (ttpt) cc_final: 0.7908 (tmmt) REVERT: C 155 ASP cc_start: 0.7004 (t0) cc_final: 0.6566 (m-30) REVERT: C 158 MET cc_start: 0.7888 (ttp) cc_final: 0.7668 (tmm) REVERT: C 184 ASP cc_start: 0.8217 (p0) cc_final: 0.7842 (p0) REVERT: C 190 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7339 (tm-30) REVERT: C 197 LYS cc_start: 0.7973 (mmpt) cc_final: 0.7420 (ttpp) REVERT: C 216 LYS cc_start: 0.8403 (tptt) cc_final: 0.7793 (tppt) REVERT: C 410 GLU cc_start: 0.8969 (pm20) cc_final: 0.8329 (tm-30) REVERT: C 435 TYR cc_start: 0.8014 (t80) cc_final: 0.7531 (t80) REVERT: C 442 PHE cc_start: 0.7671 (t80) cc_final: 0.7199 (t80) REVERT: C 487 ARG cc_start: 0.8180 (mmt90) cc_final: 0.7825 (mmm160) REVERT: B 24 ILE cc_start: 0.7954 (mm) cc_final: 0.7626 (mt) REVERT: B 28 GLN cc_start: 0.8235 (pt0) cc_final: 0.7503 (pp30) REVERT: B 37 LEU cc_start: 0.9399 (mt) cc_final: 0.9021 (tp) REVERT: B 54 LYS cc_start: 0.8520 (mttt) cc_final: 0.7749 (mttp) REVERT: B 84 LYS cc_start: 0.9301 (mtpt) cc_final: 0.8811 (ttmt) REVERT: B 92 TRP cc_start: 0.8568 (t60) cc_final: 0.8194 (t60) REVERT: B 149 TYR cc_start: 0.8497 (m-10) cc_final: 0.8073 (m-10) REVERT: B 155 ASP cc_start: 0.7114 (t0) cc_final: 0.6703 (m-30) REVERT: B 190 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7521 (tm-30) REVERT: B 347 MET cc_start: 0.7623 (ttp) cc_final: 0.7281 (ttp) REVERT: B 349 TYR cc_start: 0.8038 (t80) cc_final: 0.7785 (t80) REVERT: B 461 MET cc_start: 0.5890 (mpp) cc_final: 0.5575 (mmp) REVERT: B 539 LEU cc_start: 0.9169 (pp) cc_final: 0.8696 (mt) REVERT: B 567 GLU cc_start: 0.8269 (tm-30) cc_final: 0.8034 (tm-30) REVERT: D 18 MET cc_start: 0.9273 (tpt) cc_final: 0.9033 (tpt) REVERT: D 28 GLN cc_start: 0.8235 (pt0) cc_final: 0.7571 (pp30) REVERT: D 54 LYS cc_start: 0.8530 (mttt) cc_final: 0.7867 (mttp) REVERT: D 84 LYS cc_start: 0.9298 (mtpt) cc_final: 0.8844 (ttmt) REVERT: D 92 TRP cc_start: 0.8831 (t60) cc_final: 0.8621 (t60) REVERT: D 155 ASP cc_start: 0.7108 (t0) cc_final: 0.6537 (m-30) REVERT: D 158 MET cc_start: 0.8518 (tmm) cc_final: 0.7973 (tmm) REVERT: D 184 ASP cc_start: 0.8146 (p0) cc_final: 0.7848 (p0) REVERT: D 190 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7402 (tm-30) REVERT: D 216 LYS cc_start: 0.8451 (tptt) cc_final: 0.7779 (tppt) REVERT: D 363 MET cc_start: 0.8860 (mtp) cc_final: 0.8643 (mtm) REVERT: D 442 PHE cc_start: 0.6454 (m-80) cc_final: 0.5845 (m-80) REVERT: D 461 MET cc_start: 0.6194 (mpp) cc_final: 0.5844 (mpp) outliers start: 0 outliers final: 0 residues processed: 411 average time/residue: 0.1047 time to fit residues: 66.3243 Evaluate side-chains 335 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 131 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 172 optimal weight: 0.0770 chunk 157 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 177 optimal weight: 0.7980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.129174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.108162 restraints weight = 33633.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110636 restraints weight = 21872.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.112324 restraints weight = 16201.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.113401 restraints weight = 13148.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.114269 restraints weight = 11393.324| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.6542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15320 Z= 0.130 Angle : 0.649 10.951 20640 Z= 0.332 Chirality : 0.040 0.145 2268 Planarity : 0.004 0.048 2596 Dihedral : 5.141 31.436 1976 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.15 (0.21), residues: 1760 helix: 0.73 (0.16), residues: 1120 sheet: -0.29 (0.77), residues: 56 loop : -0.97 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 74 TYR 0.018 0.001 TYR B 116 PHE 0.025 0.001 PHE B 442 TRP 0.055 0.002 TRP B 186 HIS 0.004 0.001 HIS D 351 Details of bonding type rmsd covalent geometry : bond 0.00300 (15320) covalent geometry : angle 0.64936 (20640) hydrogen bonds : bond 0.03472 ( 737) hydrogen bonds : angle 4.25353 ( 2091) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2341.01 seconds wall clock time: 41 minutes 19.64 seconds (2479.64 seconds total)