Starting phenix.real_space_refine on Sat Feb 17 07:10:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7squ_25395/02_2024/7squ_25395.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7squ_25395/02_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_25395/02_2024/7squ_25395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7squ_25395/02_2024/7squ_25395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7squ_25395/02_2024/7squ_25395.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7squ_25395/02_2024/7squ_25395.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17856 Number of models: 1 Model: "" Number of chains: 12 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} Chain: "D" 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: "E" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 180 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "F" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 47 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "G" 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: "H" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 180 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "I" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 47 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "J" 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: "K" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 180 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "L" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 47 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} 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 - 3.50 Amino acid : False - 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: 5.93 Conformation dependent library (CDL) restraints added in 3.5 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: 1.99 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: 5.87 Time building geometry restraints manager: 6.56 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: 99.53 - 106.46: 555 106.46 - 113.39: 9842 113.39 - 120.32: 6873 120.32 - 127.25: 7354 127.25 - 134.18: 204 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 2.520 nonbonded pdb=" NE2 GLN D 137 " pdb=" OD1 ASN D 142 " model vdw 2.259 2.520 nonbonded pdb=" NE2 GLN J 137 " pdb=" OD1 ASN J 142 " model vdw 2.259 2.520 nonbonded pdb=" NE2 GLN A 137 " pdb=" OD1 ASN A 142 " model vdw 2.259 2.520 nonbonded pdb=" O ARG A 525 " pdb=" NH2 ARG A 533 " model vdw 2.337 2.520 ... (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 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: 0.650 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: 2.790 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 46.100 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.810 ------------------------------------------------------------------------------- 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 : 1.893 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: 1.5346 time to fit residues: 568.1613 Evaluate side-chains 216 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 212 time to evaluate : 1.965 ------------------------------------------------------------------------------- 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: 8.9990 chunk 169 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 90 optimal weight: 0.0050 chunk 175 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- 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: 0.8445 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18240 Z= 0.231 Angle : 0.559 9.169 24828 Z= 0.296 Chirality : 0.044 0.145 2780 Planarity : 0.005 0.049 3272 Dihedral : 4.108 19.442 2532 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.34 % Allowed : 17.59 % 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: 1.98 (0.20), residues: 772 sheet: 0.77 (0.22), residues: 548 loop : 0.13 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 519 HIS 0.003 0.001 HIS D 114 PHE 0.014 0.001 PHE G 401 TYR 0.014 0.002 TYR J 292 ARG 0.003 0.000 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 298 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 234 time to evaluate : 1.950 Fit side-chains revert: symmetry clash REVERT: A 106 MET cc_start: 0.8746 (mtm) cc_final: 0.8209 (mtp) REVERT: A 354 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.6882 (tpt) REVERT: A 378 MET cc_start: 0.6493 (OUTLIER) cc_final: 0.6271 (mpt) REVERT: A 452 LYS cc_start: 0.8594 (mttt) cc_final: 0.8365 (mtmm) REVERT: A 469 LYS cc_start: 0.8084 (tppt) cc_final: 0.7831 (mmtp) REVERT: A 507 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.6930 (mpm) REVERT: D 106 MET cc_start: 0.8744 (mtm) cc_final: 0.8168 (mtp) REVERT: D 292 TYR cc_start: 0.7734 (t80) cc_final: 0.7509 (t80) REVERT: D 354 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.6885 (tpt) REVERT: D 378 MET cc_start: 0.6511 (OUTLIER) cc_final: 0.6286 (mpt) REVERT: D 452 LYS cc_start: 0.8596 (mttt) cc_final: 0.8371 (mtmm) REVERT: D 469 LYS cc_start: 0.8085 (tppt) cc_final: 0.7839 (mmtp) REVERT: D 507 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.6989 (mpm) REVERT: G 106 MET cc_start: 0.8746 (mtm) cc_final: 0.8210 (mtp) REVERT: G 292 TYR cc_start: 0.7729 (t80) cc_final: 0.7506 (t80) REVERT: G 354 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.6889 (tpt) REVERT: G 378 MET cc_start: 0.6517 (OUTLIER) cc_final: 0.6302 (mpt) REVERT: G 452 LYS cc_start: 0.8604 (mttt) cc_final: 0.8378 (mtmm) REVERT: G 469 LYS cc_start: 0.8093 (tppt) cc_final: 0.7846 (mmtp) REVERT: G 507 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7180 (mpm) REVERT: J 106 MET cc_start: 0.8749 (mtm) cc_final: 0.8206 (mtp) REVERT: J 354 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.6886 (tpt) REVERT: J 378 MET cc_start: 0.6514 (OUTLIER) cc_final: 0.6301 (mpt) REVERT: J 452 LYS cc_start: 0.8598 (mttt) cc_final: 0.8372 (mtmm) REVERT: J 469 LYS cc_start: 0.8085 (tppt) cc_final: 0.7838 (mmtp) REVERT: J 507 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7182 (mpm) REVERT: J 521 ASP cc_start: 0.7946 (m-30) cc_final: 0.7684 (m-30) outliers start: 64 outliers final: 4 residues processed: 274 average time/residue: 1.6797 time to fit residues: 502.4037 Evaluate side-chains 226 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 210 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 507 MET Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain G residue 354 MET Chi-restraints excluded: chain G residue 378 MET Chi-restraints excluded: chain G residue 507 MET Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain J residue 354 MET 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: 0.0770 chunk 63 optimal weight: 0.5980 chunk 169 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 203 optimal weight: 8.9990 chunk 220 optimal weight: 9.9990 chunk 181 optimal weight: 8.9990 chunk 202 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 overall best weight: 1.7140 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2449 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 : 0.491 9.199 24828 Z= 0.254 Chirality : 0.042 0.142 2780 Planarity : 0.004 0.047 3272 Dihedral : 3.700 17.254 2524 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.30 % Allowed : 19.94 % Favored : 77.77 % 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: 1.44 (0.18), residues: 2268 helix: 2.09 (0.20), residues: 772 sheet: 0.98 (0.22), residues: 540 loop : 0.07 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 519 HIS 0.001 0.000 HIS G 538 PHE 0.017 0.001 PHE J 401 TYR 0.012 0.001 TYR J 292 ARG 0.011 0.000 ARG K 593 *********************** 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 259 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 215 time to evaluate : 2.168 Fit side-chains REVERT: A 354 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.6881 (tpt) REVERT: A 403 GLN cc_start: 0.8381 (mt0) cc_final: 0.7774 (tp-100) REVERT: A 452 LYS cc_start: 0.8601 (mttt) cc_final: 0.8348 (mtmm) REVERT: A 570 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: B 593 ARG cc_start: 0.7656 (mtp-110) cc_final: 0.7314 (mtm110) REVERT: D 354 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.6886 (tpt) REVERT: D 378 MET cc_start: 0.6735 (mpm) cc_final: 0.6534 (mpt) REVERT: D 403 GLN cc_start: 0.8377 (mt0) cc_final: 0.7763 (tp-100) REVERT: D 452 LYS cc_start: 0.8605 (mttt) cc_final: 0.8353 (mtmm) REVERT: D 570 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: G 354 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.6913 (tpt) REVERT: G 378 MET cc_start: 0.6736 (mpm) cc_final: 0.6535 (mpt) REVERT: G 403 GLN cc_start: 0.8376 (mt0) cc_final: 0.7772 (tp-100) REVERT: G 452 LYS cc_start: 0.8610 (mttt) cc_final: 0.8351 (mtmm) REVERT: G 570 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: J 354 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.6908 (tpt) REVERT: J 403 GLN cc_start: 0.8373 (mt0) cc_final: 0.7769 (tp-100) REVERT: J 452 LYS cc_start: 0.8604 (mttt) cc_final: 0.8352 (mtmm) REVERT: J 570 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7306 (mp0) outliers start: 44 outliers final: 9 residues processed: 242 average time/residue: 1.7636 time to fit residues: 464.2267 Evaluate side-chains 217 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 200 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 354 MET Chi-restraints excluded: chain G residue 393 GLN 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 20.0000 chunk 153 optimal weight: 0.8980 chunk 105 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 136 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 chunk 216 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18240 Z= 0.189 Angle : 0.499 9.429 24828 Z= 0.257 Chirality : 0.042 0.144 2780 Planarity : 0.005 0.076 3272 Dihedral : 3.684 15.648 2524 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.77 % Allowed : 20.20 % Favored : 77.04 % 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: 1.42 (0.18), residues: 2268 helix: 2.13 (0.20), residues: 776 sheet: 0.89 (0.22), residues: 548 loop : 0.03 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 519 HIS 0.001 0.000 HIS A 586 PHE 0.010 0.001 PHE G 401 TYR 0.008 0.001 TYR D 506 ARG 0.009 0.000 ARG E 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 264 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 211 time to evaluate : 1.913 Fit side-chains revert: symmetry clash REVERT: A 354 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.6919 (tpt) REVERT: A 403 GLN cc_start: 0.8410 (mt0) cc_final: 0.7857 (tp-100) REVERT: A 452 LYS cc_start: 0.8620 (mttt) cc_final: 0.8361 (mtmm) REVERT: A 570 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: B 593 ARG cc_start: 0.7650 (mtp-110) cc_final: 0.7307 (mtm110) REVERT: D 354 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.6925 (tpt) REVERT: D 403 GLN cc_start: 0.8395 (mt0) cc_final: 0.7840 (tp-100) REVERT: D 452 LYS cc_start: 0.8627 (mttt) cc_final: 0.8365 (mtmm) REVERT: D 570 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: E 593 ARG cc_start: 0.7876 (mtp-110) cc_final: 0.7564 (mtm110) REVERT: G 354 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.6929 (tpt) REVERT: G 403 GLN cc_start: 0.8410 (mt0) cc_final: 0.7858 (tp-100) REVERT: G 452 LYS cc_start: 0.8631 (mttt) cc_final: 0.8369 (mtmm) REVERT: G 570 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: H 593 ARG cc_start: 0.7875 (mtp-110) cc_final: 0.7565 (mtm110) REVERT: J 354 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.6920 (tpt) REVERT: J 403 GLN cc_start: 0.8398 (mt0) cc_final: 0.7844 (tp-100) REVERT: J 452 LYS cc_start: 0.8622 (mttt) cc_final: 0.8364 (mtmm) REVERT: J 570 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7252 (mp0) outliers start: 53 outliers final: 17 residues processed: 252 average time/residue: 1.6358 time to fit residues: 450.4798 Evaluate side-chains 199 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 174 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 393 GLN 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 354 MET Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 393 GLN 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 354 MET Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 393 GLN 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 354 MET Chi-restraints excluded: chain J residue 384 VAL Chi-restraints excluded: chain J residue 393 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 184 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 110 optimal weight: 0.0370 chunk 194 optimal weight: 1.9990 chunk 54 optimal weight: 30.0000 overall best weight: 4.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18240 Z= 0.298 Angle : 0.544 9.434 24828 Z= 0.282 Chirality : 0.044 0.152 2780 Planarity : 0.005 0.052 3272 Dihedral : 3.866 15.543 2524 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.24 % Allowed : 19.78 % Favored : 76.98 % 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: 1.26 (0.18), residues: 2268 helix: 2.09 (0.20), residues: 776 sheet: 0.76 (0.22), residues: 548 loop : -0.11 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 519 HIS 0.001 0.000 HIS D 538 PHE 0.010 0.001 PHE G 401 TYR 0.012 0.002 TYR A 506 ARG 0.004 0.000 ARG D 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 241 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 179 time to evaluate : 2.070 Fit side-chains REVERT: A 219 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8843 (mppt) REVERT: A 354 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.6905 (tpt) REVERT: A 403 GLN cc_start: 0.8414 (mt0) cc_final: 0.7994 (tp-100) REVERT: A 570 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: B 593 ARG cc_start: 0.7664 (mtp-110) cc_final: 0.7297 (mtm110) REVERT: D 219 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8807 (mppt) REVERT: D 354 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.6898 (tpt) REVERT: D 403 GLN cc_start: 0.8417 (mt0) cc_final: 0.7995 (tp-100) REVERT: D 570 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: E 593 ARG cc_start: 0.7849 (mtp-110) cc_final: 0.7567 (mtm110) REVERT: G 354 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.6893 (tpt) REVERT: G 403 GLN cc_start: 0.8417 (mt0) cc_final: 0.7958 (tp-100) REVERT: G 570 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: H 593 ARG cc_start: 0.7849 (mtp-110) cc_final: 0.7569 (mtm110) REVERT: J 219 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8806 (mppt) REVERT: J 354 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.6895 (tpt) REVERT: J 403 GLN cc_start: 0.8416 (mt0) cc_final: 0.7950 (tp-100) REVERT: J 570 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7328 (mp0) outliers start: 62 outliers final: 21 residues processed: 226 average time/residue: 1.3916 time to fit residues: 349.0400 Evaluate side-chains 199 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 167 time to evaluate : 2.003 ------------------------------------------------------------------------------- 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 384 VAL Chi-restraints excluded: chain A residue 514 ASP 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 384 VAL Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 514 ASP 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 354 MET Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 393 GLN Chi-restraints excluded: chain G residue 469 LYS Chi-restraints excluded: chain G residue 514 ASP 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: 10.0000 chunk 194 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 216 optimal weight: 0.4980 chunk 179 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN G 65 GLN J 65 GLN J 140 HIS J 316 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18240 Z= 0.207 Angle : 0.505 9.264 24828 Z= 0.260 Chirality : 0.043 0.146 2780 Planarity : 0.005 0.047 3272 Dihedral : 3.740 14.964 2524 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.35 % Allowed : 21.50 % Favored : 76.15 % 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: 1.29 (0.18), residues: 2268 helix: 2.14 (0.20), residues: 776 sheet: 0.71 (0.22), residues: 556 loop : -0.07 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 519 HIS 0.014 0.001 HIS J 140 PHE 0.006 0.001 PHE A 401 TYR 0.010 0.001 TYR G 472 ARG 0.007 0.000 ARG A 366 *********************** 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 231 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 186 time to evaluate : 2.153 Fit side-chains REVERT: A 64 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7140 (tm-30) REVERT: A 75 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8326 (tmmt) REVERT: A 403 GLN cc_start: 0.8418 (mt0) cc_final: 0.7907 (tp-100) REVERT: A 570 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: B 593 ARG cc_start: 0.7521 (mtp-110) cc_final: 0.7222 (mtm110) REVERT: D 75 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8329 (tmmt) REVERT: D 403 GLN cc_start: 0.8419 (mt0) cc_final: 0.7905 (tp-100) REVERT: D 570 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: E 593 ARG cc_start: 0.7569 (mtp-110) cc_final: 0.7352 (mtm110) REVERT: G 75 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8327 (tmmt) REVERT: G 219 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8780 (mppt) REVERT: G 403 GLN cc_start: 0.8502 (mt0) cc_final: 0.7980 (tp-100) REVERT: G 570 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: H 593 ARG cc_start: 0.7623 (mtp-110) cc_final: 0.7418 (mtm110) REVERT: J 75 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8326 (tmmt) REVERT: J 403 GLN cc_start: 0.8420 (mt0) cc_final: 0.7906 (tp-100) REVERT: J 570 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7270 (mp0) outliers start: 45 outliers final: 19 residues processed: 219 average time/residue: 1.4652 time to fit residues: 355.8533 Evaluate side-chains 204 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 175 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 514 ASP 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 75 LYS Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 514 ASP Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 219 LYS Chi-restraints excluded: chain G residue 393 GLN Chi-restraints excluded: chain G residue 469 LYS Chi-restraints excluded: chain G residue 514 ASP 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 60 ASN Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 393 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 158 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3431 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= 0.235 Angle : 0.505 9.331 24828 Z= 0.259 Chirality : 0.043 0.147 2780 Planarity : 0.005 0.048 3272 Dihedral : 3.749 15.133 2524 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.82 % Allowed : 21.29 % Favored : 75.89 % 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: 1.31 (0.18), residues: 2268 helix: 2.16 (0.20), residues: 776 sheet: 0.70 (0.22), residues: 556 loop : -0.06 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 519 HIS 0.001 0.000 HIS G 538 PHE 0.008 0.001 PHE J 401 TYR 0.010 0.001 TYR A 506 ARG 0.007 0.000 ARG A 366 *********************** 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 235 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 181 time to evaluate : 1.869 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8331 (tmmt) REVERT: A 219 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.8813 (mppt) REVERT: A 351 ASN cc_start: 0.8455 (m-40) cc_final: 0.8032 (t0) REVERT: A 403 GLN cc_start: 0.8520 (mt0) cc_final: 0.8019 (tp-100) REVERT: A 570 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: B 593 ARG cc_start: 0.7532 (mtp-110) cc_final: 0.7228 (mtm110) REVERT: D 75 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8331 (tmmt) REVERT: D 219 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8812 (mppt) REVERT: D 351 ASN cc_start: 0.8457 (m-40) cc_final: 0.8033 (t0) REVERT: D 403 GLN cc_start: 0.8541 (mt0) cc_final: 0.7986 (tp-100) REVERT: D 570 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: G 75 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8329 (tmmt) REVERT: G 219 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8760 (mppt) REVERT: G 351 ASN cc_start: 0.8454 (m-40) cc_final: 0.8030 (t0) REVERT: G 403 GLN cc_start: 0.8519 (mt0) cc_final: 0.7963 (tp-100) REVERT: G 570 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: H 593 ARG cc_start: 0.7531 (mtp-110) cc_final: 0.7290 (mtm180) REVERT: J 75 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8329 (tmmt) REVERT: J 219 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8810 (mppt) REVERT: J 351 ASN cc_start: 0.8456 (m-40) cc_final: 0.8032 (t0) REVERT: J 403 GLN cc_start: 0.8488 (mt0) cc_final: 0.8041 (tp-100) REVERT: J 570 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7295 (mp0) outliers start: 54 outliers final: 24 residues processed: 220 average time/residue: 1.3832 time to fit residues: 338.1068 Evaluate side-chains 211 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 175 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 514 ASP 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 60 ASN Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 219 LYS Chi-restraints excluded: chain G residue 230 MET Chi-restraints excluded: chain G residue 393 GLN Chi-restraints excluded: chain G residue 469 LYS Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 570 GLU Chi-restraints excluded: chain J residue 60 ASN Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 219 LYS Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain J residue 514 ASP 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: 10.0000 chunk 86 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 147 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 20 optimal weight: 0.0170 chunk 169 optimal weight: 20.0000 overall best weight: 3.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN D 316 GLN G 316 GLN J 140 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18240 Z= 0.221 Angle : 0.501 8.806 24828 Z= 0.258 Chirality : 0.043 0.145 2780 Planarity : 0.005 0.048 3272 Dihedral : 3.720 15.003 2524 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.18 % Allowed : 20.98 % Favored : 75.84 % 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: 1.30 (0.18), residues: 2268 helix: 2.14 (0.20), residues: 780 sheet: 0.69 (0.22), residues: 556 loop : -0.07 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 519 HIS 0.016 0.001 HIS J 140 PHE 0.005 0.001 PHE J 339 TYR 0.010 0.001 TYR J 472 ARG 0.010 0.000 ARG K 593 *********************** 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 239 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 178 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8332 (tmmt) REVERT: A 351 ASN cc_start: 0.8406 (m-40) cc_final: 0.7972 (t0) REVERT: A 403 GLN cc_start: 0.8473 (mt0) cc_final: 0.8198 (tm-30) REVERT: A 570 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: B 593 ARG cc_start: 0.7455 (mtp-110) cc_final: 0.7115 (mtm110) REVERT: D 75 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8331 (tmmt) REVERT: D 351 ASN cc_start: 0.8431 (m-40) cc_final: 0.7980 (t0) REVERT: D 403 GLN cc_start: 0.8516 (mt0) cc_final: 0.8219 (tm-30) REVERT: D 570 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: G 75 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8329 (tmmt) REVERT: G 219 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8764 (mppt) REVERT: G 351 ASN cc_start: 0.8429 (m-40) cc_final: 0.7978 (t0) REVERT: G 403 GLN cc_start: 0.8501 (mt0) cc_final: 0.8211 (tm-30) REVERT: G 570 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: J 75 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8329 (tmmt) REVERT: J 351 ASN cc_start: 0.8430 (m-40) cc_final: 0.7979 (t0) REVERT: J 403 GLN cc_start: 0.8477 (mt0) cc_final: 0.8196 (tm-30) REVERT: J 570 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7274 (mp0) outliers start: 61 outliers final: 28 residues processed: 223 average time/residue: 1.5052 time to fit residues: 370.9080 Evaluate side-chains 217 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 180 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 514 ASP 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 A residue 585 GLN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 514 ASP 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 60 ASN Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 219 LYS Chi-restraints excluded: chain G residue 230 MET Chi-restraints excluded: chain G residue 469 LYS Chi-restraints excluded: chain G residue 514 ASP 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 G residue 585 GLN Chi-restraints excluded: chain J residue 60 ASN Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain J residue 514 ASP Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 548 SER Chi-restraints excluded: chain J residue 570 GLU Chi-restraints excluded: chain J residue 585 GLN 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: 4.9990 chunk 201 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 200 optimal weight: 0.0060 overall best weight: 2.2004 ------------------------------------------------------------------------------- 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: 0.8478 moved from start: 0.3672 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= 0.171 Angle : 0.500 8.664 24828 Z= 0.254 Chirality : 0.042 0.139 2780 Planarity : 0.005 0.070 3272 Dihedral : 3.655 14.748 2524 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.19 % Allowed : 21.66 % Favored : 76.15 % 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: 1.38 (0.18), residues: 2268 helix: 2.25 (0.20), residues: 780 sheet: 0.74 (0.22), residues: 556 loop : -0.07 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 519 HIS 0.002 0.000 HIS A 114 PHE 0.005 0.001 PHE A 577 TYR 0.009 0.001 TYR J 472 ARG 0.012 0.000 ARG K 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 225 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 183 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8348 (tmmt) REVERT: A 351 ASN cc_start: 0.8371 (m-40) cc_final: 0.7965 (t0) REVERT: A 403 GLN cc_start: 0.8453 (mt0) cc_final: 0.8202 (tm-30) REVERT: A 570 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: B 593 ARG cc_start: 0.7373 (mtp-110) cc_final: 0.7075 (mtm110) REVERT: D 75 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8347 (tmmt) REVERT: D 351 ASN cc_start: 0.8388 (m-40) cc_final: 0.7982 (t0) REVERT: D 403 GLN cc_start: 0.8504 (mt0) cc_final: 0.8219 (tm-30) REVERT: D 570 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: G 75 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8345 (tmmt) REVERT: G 351 ASN cc_start: 0.8387 (m-40) cc_final: 0.7982 (t0) REVERT: G 354 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.6846 (tpt) REVERT: G 403 GLN cc_start: 0.8479 (mt0) cc_final: 0.8198 (tm-30) REVERT: G 570 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: J 75 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8345 (tmmt) REVERT: J 351 ASN cc_start: 0.8388 (m-40) cc_final: 0.7982 (t0) REVERT: J 354 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.6847 (tpt) REVERT: J 403 GLN cc_start: 0.8453 (mt0) cc_final: 0.8205 (tm-30) REVERT: J 570 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7247 (mp0) outliers start: 42 outliers final: 20 residues processed: 212 average time/residue: 1.4217 time to fit residues: 334.6288 Evaluate side-chains 208 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 178 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 514 ASP 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 60 ASN Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 514 ASP 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 D residue 585 GLN Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 230 MET Chi-restraints excluded: chain G residue 354 MET Chi-restraints excluded: chain G residue 514 ASP 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 60 ASN Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 230 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.8980 chunk 212 optimal weight: 9.9990 chunk 129 optimal weight: 0.0980 chunk 100 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 223 optimal weight: 20.0000 chunk 205 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 137 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 overall best weight: 2.9184 ------------------------------------------------------------------------------- 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: 0.8483 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18240 Z= 0.203 Angle : 0.517 9.123 24828 Z= 0.263 Chirality : 0.043 0.143 2780 Planarity : 0.005 0.062 3272 Dihedral : 3.685 14.516 2524 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.62 % Allowed : 22.34 % Favored : 76.04 % 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: 1.36 (0.18), residues: 2268 helix: 2.21 (0.20), residues: 780 sheet: 0.74 (0.22), residues: 556 loop : -0.06 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 519 HIS 0.007 0.001 HIS J 140 PHE 0.005 0.001 PHE A 88 TYR 0.010 0.001 TYR D 472 ARG 0.013 0.000 ARG E 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 212 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 2.053 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8348 (tmmt) REVERT: A 351 ASN cc_start: 0.8413 (m-40) cc_final: 0.8006 (t0) REVERT: A 403 GLN cc_start: 0.8476 (mt0) cc_final: 0.8215 (tm-30) REVERT: A 570 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: B 593 ARG cc_start: 0.7369 (mtp-110) cc_final: 0.7062 (mtm110) REVERT: D 75 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8350 (tmmt) REVERT: D 351 ASN cc_start: 0.8421 (m-40) cc_final: 0.8007 (t0) REVERT: D 403 GLN cc_start: 0.8510 (mt0) cc_final: 0.8216 (tm-30) REVERT: D 570 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: G 75 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8348 (tmmt) REVERT: G 351 ASN cc_start: 0.8419 (m-40) cc_final: 0.8005 (t0) REVERT: G 354 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.6858 (tpt) REVERT: G 403 GLN cc_start: 0.8513 (mt0) cc_final: 0.8227 (tm-30) REVERT: G 570 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: J 75 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8347 (tmmt) REVERT: J 351 ASN cc_start: 0.8420 (m-40) cc_final: 0.8007 (t0) REVERT: J 354 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.6853 (tpt) REVERT: J 403 GLN cc_start: 0.8486 (mt0) cc_final: 0.8213 (tm-30) REVERT: J 570 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7257 (mp0) outliers start: 31 outliers final: 20 residues processed: 202 average time/residue: 1.5546 time to fit residues: 346.1560 Evaluate side-chains 204 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 174 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 514 ASP 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 A residue 585 GLN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 469 LYS 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 D residue 585 GLN Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 354 MET Chi-restraints excluded: chain G residue 514 ASP 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 G residue 585 GLN Chi-restraints excluded: chain J residue 60 ASN Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 140 HIS 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 Chi-restraints excluded: chain J residue 585 GLN 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: 5.9990 chunk 54 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 182 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.110468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.076283 restraints weight = 34262.401| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.62 r_work: 0.2987 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18240 Z= 0.218 Angle : 0.523 9.099 24828 Z= 0.266 Chirality : 0.043 0.143 2780 Planarity : 0.005 0.094 3272 Dihedral : 3.704 14.566 2524 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.67 % Allowed : 22.13 % Favored : 76.20 % 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: 2.19 (0.20), residues: 780 sheet: 0.72 (0.22), residues: 556 loop : -0.06 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 519 HIS 0.010 0.000 HIS J 140 PHE 0.005 0.001 PHE D 88 TYR 0.011 0.001 TYR A 472 ARG 0.015 0.000 ARG E 593 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6627.59 seconds wall clock time: 118 minutes 1.96 seconds (7081.96 seconds total)