Starting phenix.real_space_refine on Sat Sep 28 00:44:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7squ_25395/09_2024/7squ_25395.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7squ_25395/09_2024/7squ_25395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7squ_25395/09_2024/7squ_25395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7squ_25395/09_2024/7squ_25395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7squ_25395/09_2024/7squ_25395.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7squ_25395/09_2024/7squ_25395.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 84 5.16 5 C 11256 2.51 5 N 3104 2.21 5 O 3412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17856 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4237 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 32, 'TRANS': 509} Chain: "B" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 180 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 47 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Restraints were copied for chains: E, H, K, D, G, J, F, I, L Time building chain proxies: 9.23, per 1000 atoms: 0.52 Number of scatterers: 17856 At special positions: 0 Unit cell: (147.538, 147.538, 91.0975, 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 84 16.00 O 3412 8.00 N 3104 7.00 C 11256 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: 4.13 Conformation dependent library (CDL) restraints added in 2.2 seconds 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4240 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 20 sheets defined 41.7% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 64 through 78 Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 154 through 170 Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.635A pdb=" N GLY A 175 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS A 219 " --> pdb=" O ARG A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA A 231 " --> pdb=" O GLY A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU A 360 " --> pdb=" O TRP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 372 through 375 removed outlier: 3.541A pdb=" N ALA A 375 " --> pdb=" O ASN A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 376 through 381 Processing helix chain 'A' and resid 394 through 403 Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 427 through 432 Processing helix chain 'A' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 503 through 511 Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 529 through 546 Processing helix chain 'A' and resid 561 through 575 Processing helix chain 'B' and resid 596 through 601 removed outlier: 4.344A pdb=" N ALA B 600 " --> pdb=" O MET B 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 596 through 601' Processing helix chain 'B' and resid 607 through 611 removed outlier: 3.856A pdb=" N ILE B 610 " --> pdb=" O SER B 607 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR B 611 " --> pdb=" O GLY B 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 607 through 611' Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 64 through 78 Processing helix chain 'D' and resid 148 through 153 Processing helix chain 'D' and resid 154 through 170 Processing helix chain 'D' and resid 171 through 175 removed outlier: 3.634A pdb=" N GLY D 175 " --> pdb=" O LYS D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 221 removed outlier: 6.277A pdb=" N ASP D 218 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYS D 219 " --> pdb=" O ARG D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA D 231 " --> pdb=" O GLY D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 351 Processing helix chain 'D' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU D 360 " --> pdb=" O TRP D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 367 No H-bonds generated for 'chain 'D' and resid 365 through 367' Processing helix chain 'D' and resid 372 through 375 removed outlier: 3.541A pdb=" N ALA D 375 " --> pdb=" O ASN D 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 372 through 375' Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 394 through 403 Processing helix chain 'D' and resid 422 through 427 Processing helix chain 'D' and resid 427 through 432 Processing helix chain 'D' and resid 448 through 462 removed outlier: 3.540A pdb=" N LYS D 452 " --> pdb=" O SER D 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR D 462 " --> pdb=" O PHE D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 470 Processing helix chain 'D' and resid 500 through 502 No H-bonds generated for 'chain 'D' and resid 500 through 502' Processing helix chain 'D' and resid 503 through 511 Processing helix chain 'D' and resid 512 through 525 Processing helix chain 'D' and resid 529 through 546 Processing helix chain 'D' and resid 561 through 575 Processing helix chain 'E' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA E 600 " --> pdb=" O MET E 596 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG E 601 " --> pdb=" O ALA E 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 596 through 601' Processing helix chain 'E' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE E 610 " --> pdb=" O SER E 607 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR E 611 " --> pdb=" O GLY E 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 607 through 611' Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 48 through 53 Processing helix chain 'G' and resid 64 through 78 Processing helix chain 'G' and resid 148 through 153 Processing helix chain 'G' and resid 154 through 170 Processing helix chain 'G' and resid 171 through 175 removed outlier: 3.635A pdb=" N GLY G 175 " --> pdb=" O LYS G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP G 218 " --> pdb=" O ILE G 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS G 219 " --> pdb=" O ARG G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 231 removed outlier: 3.568A pdb=" N ALA G 231 " --> pdb=" O GLY G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 351 Processing helix chain 'G' and resid 356 through 364 removed outlier: 4.320A pdb=" N LEU G 360 " --> pdb=" O TRP G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 367 No H-bonds generated for 'chain 'G' and resid 365 through 367' Processing helix chain 'G' and resid 372 through 375 removed outlier: 3.541A pdb=" N ALA G 375 " --> pdb=" O ASN G 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 372 through 375' Processing helix chain 'G' and resid 376 through 381 Processing helix chain 'G' and resid 394 through 403 Processing helix chain 'G' and resid 422 through 427 Processing helix chain 'G' and resid 427 through 432 Processing helix chain 'G' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS G 452 " --> pdb=" O SER G 448 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR G 462 " --> pdb=" O PHE G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 465 through 470 Processing helix chain 'G' and resid 500 through 502 No H-bonds generated for 'chain 'G' and resid 500 through 502' Processing helix chain 'G' and resid 503 through 511 Processing helix chain 'G' and resid 512 through 525 Processing helix chain 'G' and resid 529 through 546 Processing helix chain 'G' and resid 561 through 575 Processing helix chain 'H' and resid 596 through 601 removed outlier: 4.345A pdb=" N ALA H 600 " --> pdb=" O MET H 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG H 601 " --> pdb=" O ALA H 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 596 through 601' Processing helix chain 'H' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE H 610 " --> pdb=" O SER H 607 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR H 611 " --> pdb=" O GLY H 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 607 through 611' Processing helix chain 'J' and resid 45 through 47 No H-bonds generated for 'chain 'J' and resid 45 through 47' Processing helix chain 'J' and resid 48 through 53 Processing helix chain 'J' and resid 64 through 78 Processing helix chain 'J' and resid 148 through 153 Processing helix chain 'J' and resid 154 through 170 Processing helix chain 'J' and resid 171 through 175 removed outlier: 3.635A pdb=" N GLY J 175 " --> pdb=" O LYS J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 221 removed outlier: 6.277A pdb=" N ASP J 218 " --> pdb=" O ILE J 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS J 219 " --> pdb=" O ARG J 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA J 231 " --> pdb=" O GLY J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 351 Processing helix chain 'J' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU J 360 " --> pdb=" O TRP J 356 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 367 No H-bonds generated for 'chain 'J' and resid 365 through 367' Processing helix chain 'J' and resid 372 through 375 removed outlier: 3.542A pdb=" N ALA J 375 " --> pdb=" O ASN J 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 372 through 375' Processing helix chain 'J' and resid 376 through 381 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 422 through 427 Processing helix chain 'J' and resid 427 through 432 Processing helix chain 'J' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS J 452 " --> pdb=" O SER J 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR J 462 " --> pdb=" O PHE J 458 " (cutoff:3.500A) Processing helix chain 'J' and resid 465 through 470 Processing helix chain 'J' and resid 500 through 502 No H-bonds generated for 'chain 'J' and resid 500 through 502' Processing helix chain 'J' and resid 503 through 511 Processing helix chain 'J' and resid 512 through 525 Processing helix chain 'J' and resid 529 through 546 Processing helix chain 'J' and resid 561 through 575 Processing helix chain 'K' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA K 600 " --> pdb=" O MET K 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG K 601 " --> pdb=" O ALA K 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 596 through 601' Processing helix chain 'K' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE K 610 " --> pdb=" O SER K 607 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR K 611 " --> pdb=" O GLY K 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 607 through 611' Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 91 removed outlier: 6.947A pdb=" N ASN A 115 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG A 178 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE A 117 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA A 180 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY A 119 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU A 182 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 121 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 137 Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 498 removed outlier: 7.188A pdb=" N THR A 480 " --> pdb=" O ASP A 559 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ASP A 559 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASN A 482 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG A 557 " --> pdb=" O ASN A 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS A 488 " --> pdb=" O GLN A 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN A 551 " --> pdb=" O HIS A 488 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE A 412 " --> pdb=" O PHE A 560 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N SER A 325 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 14.477A pdb=" N TYR A 327 " --> pdb=" O PRO A 417 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR A 285 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA A 326 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA A 283 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU A 281 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN A 278 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE A 268 " --> pdb=" O GLN A 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG A 280 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN A 266 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 282 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN A 234 " --> pdb=" O ARG A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 248 through 249 removed outlier: 3.518A pdb=" N ASP A 248 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 305 through 306 Processing sheet with id=AA6, first strand: chain 'D' and resid 87 through 91 removed outlier: 6.947A pdb=" N ASN D 115 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG D 178 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE D 117 " --> pdb=" O ARG D 178 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA D 180 " --> pdb=" O PHE D 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY D 119 " --> pdb=" O ALA D 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU D 182 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL D 121 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 134 through 137 Processing sheet with id=AA8, first strand: chain 'D' and resid 496 through 498 removed outlier: 7.188A pdb=" N THR D 480 " --> pdb=" O ASP D 559 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ASP D 559 " --> pdb=" O THR D 480 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASN D 482 " --> pdb=" O ARG D 557 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG D 557 " --> pdb=" O ASN D 482 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N HIS D 488 " --> pdb=" O GLN D 551 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLN D 551 " --> pdb=" O HIS D 488 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE D 412 " --> pdb=" O PHE D 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER D 325 " --> pdb=" O ASP D 415 " (cutoff:3.500A) removed outlier: 14.478A pdb=" N TYR D 327 " --> pdb=" O PRO D 417 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR D 285 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA D 326 " --> pdb=" O ALA D 283 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA D 283 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU D 281 " --> pdb=" O PRO D 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN D 278 " --> pdb=" O ILE D 268 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE D 268 " --> pdb=" O GLN D 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG D 280 " --> pdb=" O ASN D 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN D 266 " --> pdb=" O ARG D 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL D 282 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN D 234 " --> pdb=" O ARG D 267 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 248 through 249 removed outlier: 3.518A pdb=" N ASP D 248 " --> pdb=" O VAL D 256 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 305 through 306 Processing sheet with id=AB2, first strand: chain 'G' and resid 87 through 91 removed outlier: 6.947A pdb=" N ASN G 115 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ARG G 178 " --> pdb=" O ASN G 115 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE G 117 " --> pdb=" O ARG G 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA G 180 " --> pdb=" O PHE G 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY G 119 " --> pdb=" O ALA G 180 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU G 182 " --> pdb=" O GLY G 119 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL G 121 " --> pdb=" O LEU G 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 134 through 137 Processing sheet with id=AB4, first strand: chain 'G' and resid 496 through 498 removed outlier: 7.188A pdb=" N THR G 480 " --> pdb=" O ASP G 559 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ASP G 559 " --> pdb=" O THR G 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN G 482 " --> pdb=" O ARG G 557 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG G 557 " --> pdb=" O ASN G 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS G 488 " --> pdb=" O GLN G 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN G 551 " --> pdb=" O HIS G 488 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE G 412 " --> pdb=" O PHE G 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER G 325 " --> pdb=" O ASP G 415 " (cutoff:3.500A) removed outlier: 14.478A pdb=" N TYR G 327 " --> pdb=" O PRO G 417 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR G 285 " --> pdb=" O THR G 324 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA G 326 " --> pdb=" O ALA G 283 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA G 283 " --> pdb=" O ALA G 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU G 281 " --> pdb=" O PRO G 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN G 278 " --> pdb=" O ILE G 268 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE G 268 " --> pdb=" O GLN G 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG G 280 " --> pdb=" O ASN G 266 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN G 266 " --> pdb=" O ARG G 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL G 282 " --> pdb=" O ILE G 264 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN G 234 " --> pdb=" O ARG G 267 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP G 248 " --> pdb=" O VAL G 256 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 305 through 306 Processing sheet with id=AB7, first strand: chain 'J' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN J 115 " --> pdb=" O THR J 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG J 178 " --> pdb=" O ASN J 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE J 117 " --> pdb=" O ARG J 178 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA J 180 " --> pdb=" O PHE J 117 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLY J 119 " --> pdb=" O ALA J 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU J 182 " --> pdb=" O GLY J 119 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL J 121 " --> pdb=" O LEU J 182 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 134 through 137 Processing sheet with id=AB9, first strand: chain 'J' and resid 496 through 498 removed outlier: 7.189A pdb=" N THR J 480 " --> pdb=" O ASP J 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP J 559 " --> pdb=" O THR J 480 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASN J 482 " --> pdb=" O ARG J 557 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG J 557 " --> pdb=" O ASN J 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS J 488 " --> pdb=" O GLN J 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN J 551 " --> pdb=" O HIS J 488 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE J 412 " --> pdb=" O PHE J 560 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N SER J 325 " --> pdb=" O ASP J 415 " (cutoff:3.500A) removed outlier: 14.478A pdb=" N TYR J 327 " --> pdb=" O PRO J 417 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR J 285 " --> pdb=" O THR J 324 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA J 326 " --> pdb=" O ALA J 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA J 283 " --> pdb=" O ALA J 326 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU J 281 " --> pdb=" O PRO J 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN J 278 " --> pdb=" O ILE J 268 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE J 268 " --> pdb=" O GLN J 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG J 280 " --> pdb=" O ASN J 266 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN J 266 " --> pdb=" O ARG J 280 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL J 282 " --> pdb=" O ILE J 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN J 234 " --> pdb=" O ARG J 267 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 248 through 249 removed outlier: 3.518A pdb=" N ASP J 248 " --> pdb=" O VAL J 256 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 305 through 306 772 hydrogen bonds defined for protein. 2160 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: 5.26 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5887 1.33 - 1.45: 2406 1.45 - 1.57: 9783 1.57 - 1.69: 0 1.69 - 1.81: 164 Bond restraints: 18240 Sorted by residual: bond pdb=" N VAL J 66 " pdb=" CA VAL J 66 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.42e+00 bond pdb=" N VAL A 66 " pdb=" CA VAL A 66 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.42e+00 bond pdb=" N VAL D 66 " pdb=" CA VAL D 66 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.42e+00 bond pdb=" N THR J 61 " pdb=" CA THR J 61 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.31e-02 5.83e+03 7.16e+00 bond pdb=" N THR D 61 " pdb=" CA THR D 61 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.31e-02 5.83e+03 7.13e+00 ... (remaining 18235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 23081 1.24 - 2.49: 1449 2.49 - 3.73: 234 3.73 - 4.97: 48 4.97 - 6.21: 16 Bond angle restraints: 24828 Sorted by residual: angle pdb=" N THR J 437 " pdb=" CA THR J 437 " pdb=" C THR J 437 " ideal model delta sigma weight residual 110.20 103.99 6.21 1.58e+00 4.01e-01 1.55e+01 angle pdb=" N THR A 437 " pdb=" CA THR A 437 " pdb=" C THR A 437 " ideal model delta sigma weight residual 110.20 104.00 6.20 1.58e+00 4.01e-01 1.54e+01 angle pdb=" N THR G 437 " pdb=" CA THR G 437 " pdb=" C THR G 437 " ideal model delta sigma weight residual 110.20 104.00 6.20 1.58e+00 4.01e-01 1.54e+01 angle pdb=" N THR D 437 " pdb=" CA THR D 437 " pdb=" C THR D 437 " ideal model delta sigma weight residual 110.20 104.01 6.19 1.58e+00 4.01e-01 1.54e+01 angle pdb=" CA GLY G 62 " pdb=" C GLY G 62 " pdb=" O GLY G 62 " ideal model delta sigma weight residual 122.65 118.10 4.55 1.28e+00 6.10e-01 1.26e+01 ... (remaining 24823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 9453 16.10 - 32.21: 1075 32.21 - 48.31: 304 48.31 - 64.42: 64 64.42 - 80.52: 36 Dihedral angle restraints: 10932 sinusoidal: 4308 harmonic: 6624 Sorted by residual: dihedral pdb=" N GLU J 570 " pdb=" CA GLU J 570 " pdb=" CB GLU J 570 " pdb=" CG GLU J 570 " ideal model delta sinusoidal sigma weight residual -180.00 -122.27 -57.73 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N GLU A 570 " pdb=" CA GLU A 570 " pdb=" CB GLU A 570 " pdb=" CG GLU A 570 " ideal model delta sinusoidal sigma weight residual -180.00 -122.27 -57.73 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N GLU G 570 " pdb=" CA GLU G 570 " pdb=" CB GLU G 570 " pdb=" CG GLU G 570 " ideal model delta sinusoidal sigma weight residual -180.00 -122.30 -57.70 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 10929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1233 0.033 - 0.065: 882 0.065 - 0.098: 465 0.098 - 0.131: 156 0.131 - 0.164: 44 Chirality restraints: 2780 Sorted by residual: chirality pdb=" CA PRO D 513 " pdb=" N PRO D 513 " pdb=" C PRO D 513 " pdb=" CB PRO D 513 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA PRO A 513 " pdb=" N PRO A 513 " pdb=" C PRO A 513 " pdb=" CB PRO A 513 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" CA PRO G 513 " pdb=" N PRO G 513 " pdb=" C PRO G 513 " pdb=" CB PRO G 513 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 2777 not shown) Planarity restraints: 3272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 335 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO D 336 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 336 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 336 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 335 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO J 336 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO J 336 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO J 336 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 335 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO A 336 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 336 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 336 " 0.030 5.00e-02 4.00e+02 ... (remaining 3269 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4004 2.79 - 3.32: 15043 3.32 - 3.84: 27177 3.84 - 4.37: 32521 4.37 - 4.90: 56217 Nonbonded interactions: 134962 Sorted by model distance: nonbonded pdb=" NE2 GLN G 137 " pdb=" OD1 ASN G 142 " model vdw 2.259 3.120 nonbonded pdb=" NE2 GLN D 137 " pdb=" OD1 ASN D 142 " model vdw 2.259 3.120 nonbonded pdb=" NE2 GLN J 137 " pdb=" OD1 ASN J 142 " model vdw 2.259 3.120 nonbonded pdb=" NE2 GLN A 137 " pdb=" OD1 ASN A 142 " model vdw 2.259 3.120 nonbonded pdb=" O ARG A 525 " pdb=" NH2 ARG A 533 " model vdw 2.337 3.120 ... (remaining 134957 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 37.300 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 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:11.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 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 : 0.010 0.053 18240 Z= 0.641 Angle : 0.698 6.214 24828 Z= 0.406 Chirality : 0.055 0.164 2780 Planarity : 0.005 0.054 3272 Dihedral : 15.781 80.523 6692 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.04 % Allowed : 15.66 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.17), residues: 2268 helix: 1.96 (0.20), residues: 772 sheet: 1.14 (0.22), residues: 536 loop : -0.01 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 424 HIS 0.005 0.001 HIS G 491 PHE 0.011 0.002 PHE G 339 TYR 0.016 0.002 TYR D 455 ARG 0.007 0.001 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 326 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.8813 (mtm) cc_final: 0.8345 (mtp) REVERT: A 384 VAL cc_start: 0.7762 (t) cc_final: 0.7515 (t) REVERT: A 452 LYS cc_start: 0.8671 (mttt) cc_final: 0.8433 (mtmm) REVERT: D 106 MET cc_start: 0.8772 (mtm) cc_final: 0.8311 (mtp) REVERT: D 384 VAL cc_start: 0.7760 (t) cc_final: 0.7519 (t) REVERT: D 452 LYS cc_start: 0.8669 (mttt) cc_final: 0.8431 (mtmm) REVERT: G 106 MET cc_start: 0.8754 (mtm) cc_final: 0.8292 (mtp) REVERT: G 384 VAL cc_start: 0.7768 (t) cc_final: 0.7528 (t) REVERT: G 452 LYS cc_start: 0.8675 (mttt) cc_final: 0.8464 (mtmm) REVERT: J 106 MET cc_start: 0.8799 (mtm) cc_final: 0.8330 (mtp) REVERT: J 384 VAL cc_start: 0.7774 (t) cc_final: 0.7530 (t) REVERT: J 452 LYS cc_start: 0.8673 (mttt) cc_final: 0.8437 (mtmm) outliers start: 20 outliers final: 4 residues processed: 338 average time/residue: 1.5462 time to fit residues: 572.7921 Evaluate side-chains 216 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 212 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain J residue 60 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 90 optimal weight: 0.0020 chunk 175 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 203 optimal weight: 5.9990 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18240 Z= 0.248 Angle : 0.581 9.096 24828 Z= 0.306 Chirality : 0.045 0.147 2780 Planarity : 0.005 0.049 3272 Dihedral : 4.072 19.255 2532 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.13 % Allowed : 17.80 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.17), residues: 2268 helix: 1.97 (0.20), residues: 772 sheet: 0.73 (0.21), residues: 556 loop : 0.18 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 519 HIS 0.003 0.001 HIS D 114 PHE 0.016 0.001 PHE D 401 TYR 0.012 0.002 TYR A 292 ARG 0.003 0.001 ARG G 456 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 228 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.8746 (mtm) cc_final: 0.8215 (mtp) REVERT: A 292 TYR cc_start: 0.7779 (t80) cc_final: 0.7514 (t80) REVERT: A 378 MET cc_start: 0.6488 (OUTLIER) cc_final: 0.6226 (mpt) REVERT: A 452 LYS cc_start: 0.8602 (mttt) cc_final: 0.8373 (mtmm) REVERT: A 507 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7012 (mpm) REVERT: A 520 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7219 (tt0) REVERT: A 521 ASP cc_start: 0.7936 (m-30) cc_final: 0.7676 (m-30) REVERT: D 106 MET cc_start: 0.8745 (mtm) cc_final: 0.8218 (mtp) REVERT: D 292 TYR cc_start: 0.7777 (t80) cc_final: 0.7505 (t80) REVERT: D 378 MET cc_start: 0.6513 (OUTLIER) cc_final: 0.6251 (mpt) REVERT: D 452 LYS cc_start: 0.8602 (mttt) cc_final: 0.8370 (mtmm) REVERT: D 507 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7017 (mpm) REVERT: D 520 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7198 (tt0) REVERT: D 521 ASP cc_start: 0.7921 (m-30) cc_final: 0.7656 (m-30) REVERT: G 106 MET cc_start: 0.8746 (mtm) cc_final: 0.8216 (mtp) REVERT: G 292 TYR cc_start: 0.7770 (t80) cc_final: 0.7503 (t80) REVERT: G 378 MET cc_start: 0.6525 (OUTLIER) cc_final: 0.6274 (mpt) REVERT: G 452 LYS cc_start: 0.8609 (mttt) cc_final: 0.8377 (mtmm) REVERT: G 507 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7242 (mpm) REVERT: G 520 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7195 (tt0) REVERT: G 521 ASP cc_start: 0.7927 (m-30) cc_final: 0.7667 (m-30) REVERT: J 106 MET cc_start: 0.8751 (mtm) cc_final: 0.8173 (mtp) REVERT: J 292 TYR cc_start: 0.7798 (t80) cc_final: 0.7531 (t80) REVERT: J 378 MET cc_start: 0.6521 (OUTLIER) cc_final: 0.6272 (mpt) REVERT: J 452 LYS cc_start: 0.8605 (mttt) cc_final: 0.8372 (mtmm) REVERT: J 507 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7173 (mpm) REVERT: J 521 ASP cc_start: 0.7960 (m-30) cc_final: 0.7695 (m-30) outliers start: 60 outliers final: 4 residues processed: 268 average time/residue: 1.5634 time to fit residues: 458.9119 Evaluate side-chains 218 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 203 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 507 MET Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain G residue 378 MET Chi-restraints excluded: chain G residue 507 MET Chi-restraints excluded: chain G residue 520 GLU Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain J residue 378 MET Chi-restraints excluded: chain J residue 507 MET Chi-restraints excluded: chain J residue 545 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 169 optimal weight: 0.7980 chunk 138 optimal weight: 7.9990 chunk 56 optimal weight: 20.0000 chunk 203 optimal weight: 0.0170 chunk 220 optimal weight: 8.9990 chunk 181 optimal weight: 8.9990 chunk 202 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 overall best weight: 2.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18240 Z= 0.176 Angle : 0.514 9.169 24828 Z= 0.264 Chirality : 0.043 0.144 2780 Planarity : 0.005 0.045 3272 Dihedral : 3.740 16.496 2524 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.83 % Allowed : 20.35 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.18), residues: 2268 helix: 2.11 (0.20), residues: 772 sheet: 0.82 (0.22), residues: 548 loop : 0.08 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 519 HIS 0.002 0.000 HIS D 114 PHE 0.019 0.001 PHE J 401 TYR 0.010 0.001 TYR J 292 ARG 0.002 0.000 ARG E 613 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 213 time to evaluate : 1.992 Fit side-chains REVERT: A 51 ARG cc_start: 0.7966 (mpp80) cc_final: 0.7752 (mpp80) REVERT: A 106 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8176 (mtp) REVERT: A 354 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.6972 (tpt) REVERT: A 378 MET cc_start: 0.6735 (mpm) cc_final: 0.6534 (mpt) REVERT: A 403 GLN cc_start: 0.8428 (mt0) cc_final: 0.7799 (tp-100) REVERT: A 452 LYS cc_start: 0.8605 (mttt) cc_final: 0.8355 (mtmm) REVERT: D 51 ARG cc_start: 0.7966 (mpp80) cc_final: 0.7750 (mpp80) REVERT: D 354 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.6971 (tpt) REVERT: D 378 MET cc_start: 0.6749 (mpm) cc_final: 0.6547 (mpt) REVERT: D 403 GLN cc_start: 0.8390 (mt0) cc_final: 0.7764 (tp-100) REVERT: D 452 LYS cc_start: 0.8605 (mttt) cc_final: 0.8354 (mtmm) REVERT: G 51 ARG cc_start: 0.7961 (mpp80) cc_final: 0.7747 (mpp80) REVERT: G 354 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.6977 (tpt) REVERT: G 403 GLN cc_start: 0.8387 (mt0) cc_final: 0.7777 (tp-100) REVERT: G 452 LYS cc_start: 0.8612 (mttt) cc_final: 0.8357 (mtmm) REVERT: J 51 ARG cc_start: 0.7959 (mpp80) cc_final: 0.7744 (mpp80) REVERT: J 354 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.6968 (tpt) REVERT: J 403 GLN cc_start: 0.8387 (mt0) cc_final: 0.7774 (tp-100) REVERT: J 452 LYS cc_start: 0.8605 (mttt) cc_final: 0.8355 (mtmm) outliers start: 35 outliers final: 8 residues processed: 240 average time/residue: 1.6022 time to fit residues: 421.4270 Evaluate side-chains 209 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 196 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain G residue 354 MET Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain J residue 354 MET Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 548 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 136 optimal weight: 8.9990 chunk 204 optimal weight: 1.9990 chunk 216 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 193 optimal weight: 0.0870 chunk 58 optimal weight: 10.0000 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18240 Z= 0.294 Angle : 0.563 9.424 24828 Z= 0.292 Chirality : 0.045 0.153 2780 Planarity : 0.005 0.045 3272 Dihedral : 3.910 15.284 2524 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.34 % Allowed : 19.26 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.18), residues: 2268 helix: 1.90 (0.20), residues: 776 sheet: 0.73 (0.22), residues: 548 loop : -0.06 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 519 HIS 0.002 0.001 HIS J 586 PHE 0.012 0.001 PHE A 401 TYR 0.012 0.002 TYR A 506 ARG 0.004 0.001 ARG B 593 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 176 time to evaluate : 1.774 Fit side-chains REVERT: A 51 ARG cc_start: 0.8039 (mpp80) cc_final: 0.7777 (mpp80) REVERT: A 354 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7017 (tpt) REVERT: A 403 GLN cc_start: 0.8439 (mt0) cc_final: 0.7969 (tp-100) REVERT: A 570 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: D 51 ARG cc_start: 0.8037 (mpp80) cc_final: 0.7807 (mpp80) REVERT: D 354 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7022 (tpt) REVERT: D 403 GLN cc_start: 0.8444 (mt0) cc_final: 0.7968 (tp-100) REVERT: D 570 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: G 51 ARG cc_start: 0.8035 (mpp80) cc_final: 0.7779 (mpp80) REVERT: G 354 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7020 (tpt) REVERT: G 403 GLN cc_start: 0.8420 (mt0) cc_final: 0.7987 (tp-100) REVERT: G 507 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7180 (mpm) REVERT: G 570 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: J 51 ARG cc_start: 0.8035 (mpp80) cc_final: 0.7779 (mpp80) REVERT: J 354 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7014 (tpt) REVERT: J 403 GLN cc_start: 0.8421 (mt0) cc_final: 0.7951 (tp-100) REVERT: J 507 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7178 (mpm) REVERT: J 570 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7416 (mp0) outliers start: 64 outliers final: 13 residues processed: 224 average time/residue: 1.3462 time to fit residues: 335.5874 Evaluate side-chains 195 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 172 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain B residue 593 ARG Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 354 MET Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 507 MET Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 570 GLU Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 354 MET Chi-restraints excluded: chain J residue 384 VAL Chi-restraints excluded: chain J residue 507 MET Chi-restraints excluded: chain J residue 548 SER Chi-restraints excluded: chain J residue 570 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 184 optimal weight: 9.9990 chunk 149 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 110 optimal weight: 0.3980 chunk 194 optimal weight: 0.0270 chunk 54 optimal weight: 8.9990 overall best weight: 4.2844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN D 65 GLN G 65 GLN J 65 GLN J 140 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18240 Z= 0.271 Angle : 0.542 7.775 24828 Z= 0.283 Chirality : 0.044 0.151 2780 Planarity : 0.005 0.045 3272 Dihedral : 3.908 15.291 2524 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.14 % Allowed : 20.35 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.18), residues: 2268 helix: 1.93 (0.20), residues: 776 sheet: 0.68 (0.22), residues: 556 loop : -0.07 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 519 HIS 0.014 0.001 HIS J 140 PHE 0.009 0.001 PHE A 401 TYR 0.011 0.001 TYR G 472 ARG 0.005 0.000 ARG G 366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 188 time to evaluate : 2.062 Fit side-chains REVERT: A 51 ARG cc_start: 0.8104 (mpp80) cc_final: 0.7834 (mpp80) REVERT: A 219 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8958 (mppt) REVERT: A 354 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7148 (tpt) REVERT: A 403 GLN cc_start: 0.8441 (mt0) cc_final: 0.7970 (tp-100) REVERT: A 570 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: D 51 ARG cc_start: 0.8101 (mpp80) cc_final: 0.7864 (mpp80) REVERT: D 219 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8969 (mppt) REVERT: D 354 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7150 (tpt) REVERT: D 403 GLN cc_start: 0.8446 (mt0) cc_final: 0.7974 (tp-100) REVERT: D 570 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: G 51 ARG cc_start: 0.8101 (mpp80) cc_final: 0.7864 (mpp80) REVERT: G 219 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.8969 (mppt) REVERT: G 354 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7164 (tpt) REVERT: G 403 GLN cc_start: 0.8454 (mt0) cc_final: 0.7935 (tp-100) REVERT: G 507 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7224 (mpm) REVERT: G 570 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: J 51 ARG cc_start: 0.8099 (mpp80) cc_final: 0.7830 (mpp80) REVERT: J 219 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8966 (mppt) REVERT: J 354 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7159 (tpt) REVERT: J 403 GLN cc_start: 0.8530 (mt0) cc_final: 0.8004 (tp-100) REVERT: J 570 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7427 (mp0) outliers start: 41 outliers final: 12 residues processed: 217 average time/residue: 1.3379 time to fit residues: 322.9320 Evaluate side-chains 204 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 179 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 219 LYS Chi-restraints excluded: chain G residue 354 MET Chi-restraints excluded: chain G residue 507 MET Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 570 GLU Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 219 LYS Chi-restraints excluded: chain J residue 354 MET Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 548 SER Chi-restraints excluded: chain J residue 570 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 216 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 18240 Z= 0.381 Angle : 0.579 8.245 24828 Z= 0.301 Chirality : 0.046 0.157 2780 Planarity : 0.005 0.048 3272 Dihedral : 4.104 15.819 2524 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.56 % Allowed : 20.56 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.18), residues: 2268 helix: 1.77 (0.19), residues: 772 sheet: 0.56 (0.22), residues: 556 loop : -0.14 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 549 HIS 0.002 0.001 HIS J 538 PHE 0.010 0.001 PHE J 88 TYR 0.016 0.002 TYR J 506 ARG 0.007 0.001 ARG B 593 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 178 time to evaluate : 2.000 Fit side-chains REVERT: A 51 ARG cc_start: 0.8150 (mpp80) cc_final: 0.7876 (mpp80) REVERT: A 354 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7138 (tpt) REVERT: A 403 GLN cc_start: 0.8575 (mt0) cc_final: 0.8116 (tp-100) REVERT: A 570 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: D 51 ARG cc_start: 0.8158 (mpp80) cc_final: 0.7885 (mpp80) REVERT: D 354 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7141 (tpt) REVERT: D 403 GLN cc_start: 0.8595 (mt0) cc_final: 0.8098 (tp-100) REVERT: D 570 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: G 51 ARG cc_start: 0.8158 (mpp80) cc_final: 0.7888 (mpp80) REVERT: G 354 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7144 (tpt) REVERT: G 403 GLN cc_start: 0.8575 (mt0) cc_final: 0.8071 (tp-100) REVERT: G 507 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7279 (mpm) REVERT: G 570 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: J 51 ARG cc_start: 0.8145 (mpp80) cc_final: 0.7872 (mpp80) REVERT: J 354 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7138 (tpt) REVERT: J 403 GLN cc_start: 0.8571 (mt0) cc_final: 0.8068 (tp-100) REVERT: J 570 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7454 (mp0) outliers start: 49 outliers final: 10 residues processed: 210 average time/residue: 1.3561 time to fit residues: 317.0493 Evaluate side-chains 191 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 354 MET Chi-restraints excluded: chain G residue 507 MET Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 570 GLU Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 354 MET Chi-restraints excluded: chain J residue 548 SER Chi-restraints excluded: chain J residue 570 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 0.0060 chunk 24 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 HIS J 316 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18240 Z= 0.165 Angle : 0.518 9.902 24828 Z= 0.265 Chirality : 0.042 0.139 2780 Planarity : 0.005 0.046 3272 Dihedral : 3.829 16.197 2524 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.72 % Allowed : 21.09 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.18), residues: 2268 helix: 2.08 (0.20), residues: 776 sheet: 0.65 (0.22), residues: 556 loop : -0.10 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 519 HIS 0.009 0.001 HIS J 140 PHE 0.005 0.001 PHE G 577 TYR 0.009 0.001 TYR D 472 ARG 0.006 0.000 ARG H 593 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 189 time to evaluate : 2.079 Fit side-chains REVERT: A 51 ARG cc_start: 0.8149 (mpp80) cc_final: 0.7874 (mpp80) REVERT: A 351 ASN cc_start: 0.8468 (m-40) cc_final: 0.8019 (t0) REVERT: A 354 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7092 (tpt) REVERT: A 403 GLN cc_start: 0.8503 (mt0) cc_final: 0.8231 (tm-30) REVERT: A 570 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: D 51 ARG cc_start: 0.8156 (mpp80) cc_final: 0.7873 (mpp80) REVERT: D 351 ASN cc_start: 0.8469 (m-40) cc_final: 0.8021 (t0) REVERT: D 354 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7095 (tpt) REVERT: D 403 GLN cc_start: 0.8505 (mt0) cc_final: 0.8230 (tm-30) REVERT: D 570 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: G 51 ARG cc_start: 0.8158 (mpp80) cc_final: 0.7877 (mpp80) REVERT: G 351 ASN cc_start: 0.8466 (m-40) cc_final: 0.8020 (t0) REVERT: G 354 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7095 (tpt) REVERT: G 403 GLN cc_start: 0.8498 (mt0) cc_final: 0.8211 (tm-30) REVERT: G 570 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: J 51 ARG cc_start: 0.8145 (mpp80) cc_final: 0.7872 (mpp80) REVERT: J 351 ASN cc_start: 0.8466 (m-40) cc_final: 0.8020 (t0) REVERT: J 354 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7091 (tpt) REVERT: J 403 GLN cc_start: 0.8495 (mt0) cc_final: 0.8240 (tm-30) REVERT: J 570 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7388 (mp0) outliers start: 33 outliers final: 8 residues processed: 208 average time/residue: 1.4931 time to fit residues: 344.7542 Evaluate side-chains 198 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 182 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain G residue 230 MET Chi-restraints excluded: chain G residue 354 MET Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 570 GLU Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain J residue 354 MET Chi-restraints excluded: chain J residue 548 SER Chi-restraints excluded: chain J residue 570 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 137 optimal weight: 0.0980 chunk 147 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 169 optimal weight: 0.8980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18240 Z= 0.184 Angle : 0.520 9.014 24828 Z= 0.263 Chirality : 0.043 0.141 2780 Planarity : 0.005 0.058 3272 Dihedral : 3.741 15.346 2524 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.10 % Allowed : 21.82 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.18), residues: 2268 helix: 2.11 (0.20), residues: 776 sheet: 0.67 (0.22), residues: 556 loop : -0.07 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 519 HIS 0.001 0.000 HIS D 491 PHE 0.005 0.001 PHE G 401 TYR 0.008 0.001 TYR A 317 ARG 0.009 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 2.110 Fit side-chains REVERT: A 51 ARG cc_start: 0.8161 (mpp80) cc_final: 0.7872 (mpp80) REVERT: A 351 ASN cc_start: 0.8388 (m-40) cc_final: 0.7958 (t0) REVERT: A 403 GLN cc_start: 0.8474 (mt0) cc_final: 0.8220 (tm-30) REVERT: A 570 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: D 51 ARG cc_start: 0.8159 (mpp80) cc_final: 0.7870 (mpp80) REVERT: D 351 ASN cc_start: 0.8389 (m-40) cc_final: 0.7961 (t0) REVERT: D 403 GLN cc_start: 0.8479 (mt0) cc_final: 0.8222 (tm-30) REVERT: D 570 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: G 51 ARG cc_start: 0.8159 (mpp80) cc_final: 0.7872 (mpp80) REVERT: G 351 ASN cc_start: 0.8388 (m-40) cc_final: 0.7961 (t0) REVERT: G 403 GLN cc_start: 0.8499 (mt0) cc_final: 0.8217 (tm-30) REVERT: G 570 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: J 51 ARG cc_start: 0.8156 (mpp80) cc_final: 0.7868 (mpp80) REVERT: J 351 ASN cc_start: 0.8387 (m-40) cc_final: 0.7961 (t0) REVERT: J 403 GLN cc_start: 0.8477 (mt0) cc_final: 0.8216 (tm-30) REVERT: J 570 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7402 (mp0) outliers start: 21 outliers final: 12 residues processed: 195 average time/residue: 1.3876 time to fit residues: 301.2202 Evaluate side-chains 190 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 174 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain G residue 230 MET Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 570 GLU Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 548 SER Chi-restraints excluded: chain J residue 570 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 201 optimal weight: 0.8980 chunk 121 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 157 optimal weight: 0.0040 chunk 61 optimal weight: 8.9990 chunk 181 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 200 optimal weight: 0.0770 overall best weight: 1.7954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 140 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18240 Z= 0.161 Angle : 0.521 9.443 24828 Z= 0.262 Chirality : 0.042 0.138 2780 Planarity : 0.005 0.084 3272 Dihedral : 3.642 14.543 2524 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.89 % Allowed : 22.18 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.18), residues: 2268 helix: 2.15 (0.20), residues: 776 sheet: 0.83 (0.22), residues: 548 loop : -0.06 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 519 HIS 0.009 0.000 HIS J 140 PHE 0.005 0.001 PHE G 577 TYR 0.008 0.001 TYR J 287 ARG 0.019 0.000 ARG B 593 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 176 time to evaluate : 1.964 Fit side-chains REVERT: A 51 ARG cc_start: 0.8156 (mpp80) cc_final: 0.7867 (mpp80) REVERT: A 351 ASN cc_start: 0.8348 (m-40) cc_final: 0.7941 (t0) REVERT: A 403 GLN cc_start: 0.8554 (mt0) cc_final: 0.8222 (tm-30) REVERT: A 570 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: D 51 ARG cc_start: 0.8156 (mpp80) cc_final: 0.7868 (mpp80) REVERT: D 351 ASN cc_start: 0.8349 (m-40) cc_final: 0.7943 (t0) REVERT: D 403 GLN cc_start: 0.8513 (mt0) cc_final: 0.8221 (tm-30) REVERT: D 570 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7409 (mp0) REVERT: G 51 ARG cc_start: 0.8157 (mpp80) cc_final: 0.7870 (mpp80) REVERT: G 351 ASN cc_start: 0.8347 (m-40) cc_final: 0.7941 (t0) REVERT: G 403 GLN cc_start: 0.8510 (mt0) cc_final: 0.8201 (tm-30) REVERT: G 570 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: J 51 ARG cc_start: 0.8151 (mpp80) cc_final: 0.7863 (mpp80) REVERT: J 351 ASN cc_start: 0.8346 (m-40) cc_final: 0.7941 (t0) REVERT: J 403 GLN cc_start: 0.8509 (mt0) cc_final: 0.8200 (tm-30) REVERT: J 570 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7408 (mp0) outliers start: 17 outliers final: 13 residues processed: 188 average time/residue: 1.4174 time to fit residues: 295.4985 Evaluate side-chains 190 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 173 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain G residue 230 MET Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 570 GLU Chi-restraints excluded: chain J residue 140 HIS Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 548 SER Chi-restraints excluded: chain J residue 570 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 7.9990 chunk 212 optimal weight: 10.0000 chunk 129 optimal weight: 0.0970 chunk 100 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 223 optimal weight: 4.9990 chunk 205 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 18 optimal weight: 0.0370 chunk 137 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 overall best weight: 4.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 140 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18240 Z= 0.260 Angle : 0.559 10.056 24828 Z= 0.281 Chirality : 0.044 0.145 2780 Planarity : 0.005 0.087 3272 Dihedral : 3.749 14.605 2524 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.94 % Allowed : 21.82 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.18), residues: 2268 helix: 2.02 (0.20), residues: 776 sheet: 0.70 (0.22), residues: 556 loop : -0.05 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP J 149 HIS 0.013 0.001 HIS J 140 PHE 0.007 0.001 PHE J 88 TYR 0.010 0.001 TYR G 506 ARG 0.014 0.001 ARG K 593 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 182 time to evaluate : 2.062 Fit side-chains REVERT: A 51 ARG cc_start: 0.8171 (mpp80) cc_final: 0.7870 (mpp80) REVERT: A 351 ASN cc_start: 0.8467 (m-40) cc_final: 0.8017 (t0) REVERT: A 403 GLN cc_start: 0.8521 (mt0) cc_final: 0.8211 (tm-30) REVERT: B 593 ARG cc_start: 0.7253 (mtm180) cc_final: 0.6936 (mtp180) REVERT: D 51 ARG cc_start: 0.8170 (mpp80) cc_final: 0.7869 (mpp80) REVERT: D 351 ASN cc_start: 0.8469 (m-40) cc_final: 0.8019 (t0) REVERT: D 403 GLN cc_start: 0.8525 (mt0) cc_final: 0.8233 (tm-30) REVERT: E 596 MET cc_start: 0.8318 (mmp) cc_final: 0.8092 (mmp) REVERT: G 51 ARG cc_start: 0.8161 (mpp80) cc_final: 0.7867 (mpp80) REVERT: G 351 ASN cc_start: 0.8467 (m-40) cc_final: 0.8018 (t0) REVERT: G 403 GLN cc_start: 0.8500 (mt0) cc_final: 0.8213 (tm-30) REVERT: H 593 ARG cc_start: 0.7532 (mtp-110) cc_final: 0.7326 (mtm180) REVERT: H 596 MET cc_start: 0.8314 (mmp) cc_final: 0.8086 (mmp) REVERT: J 51 ARG cc_start: 0.8166 (mpp80) cc_final: 0.7867 (mpp80) REVERT: J 351 ASN cc_start: 0.8467 (m-40) cc_final: 0.8018 (t0) REVERT: J 403 GLN cc_start: 0.8496 (mt0) cc_final: 0.8212 (tm-30) outliers start: 18 outliers final: 9 residues processed: 194 average time/residue: 1.4238 time to fit residues: 306.4631 Evaluate side-chains 185 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 176 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 548 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 5.9990 chunk 189 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 163 optimal weight: 5.9990 chunk 26 optimal weight: 0.0010 chunk 49 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 overall best weight: 2.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.110642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.076497 restraints weight = 34208.141| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.61 r_work: 0.2993 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18240 Z= 0.194 Angle : 0.542 10.138 24828 Z= 0.272 Chirality : 0.043 0.140 2780 Planarity : 0.005 0.076 3272 Dihedral : 3.644 14.297 2524 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.68 % Allowed : 22.18 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.18), residues: 2268 helix: 2.16 (0.20), residues: 776 sheet: 0.70 (0.22), residues: 556 loop : -0.04 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 519 HIS 0.002 0.000 HIS D 114 PHE 0.005 0.001 PHE J 577 TYR 0.009 0.001 TYR J 472 ARG 0.013 0.000 ARG E 593 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6430.41 seconds wall clock time: 112 minutes 48.84 seconds (6768.84 seconds total)