Starting phenix.real_space_refine on Wed Aug 5 18:36:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tdv_41174/08_2026/8tdv_41174_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tdv_41174/08_2026/8tdv_41174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tdv_41174/08_2026/8tdv_41174_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tdv_41174/08_2026/8tdv_41174_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tdv_41174/08_2026/8tdv_41174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tdv_41174/08_2026/8tdv_41174.map" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.255 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: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 13 5.49 5 S 30 5.16 5 C 6733 2.51 5 N 2069 2.21 5 O 2110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10957 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3195 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 19, 'TRANS': 419} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 414 Unresolved non-hydrogen angles: 526 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 9, 'GLU:plan': 14, 'ASN:plan1': 4, 'TYR:plan': 6, 'GLN:plan1': 5, 'ARG:plan': 7, 'PHE:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 235 Chain: "B" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3122 Classifications: {'peptide': 417} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 18, 'TRANS': 398} Chain breaks: 5 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 394 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ASP:plan': 10, 'GLN:plan1': 4, 'GLU:plan': 8, 'ASN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 4, 'PHE:plan': 4, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 176 Chain: "E" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 2198 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 395} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 3 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1527 Unresolved non-hydrogen angles: 1950 Unresolved non-hydrogen dihedrals: 1294 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'ASN:plan1': 19, 'ASP:plan': 30, 'HIS:plan': 17, 'GLU:plan': 30, 'ARG:plan': 27, 'GLN:plan1': 18, 'PHE:plan': 21, 'TYR:plan': 22, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 875 Chain: "F" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 2169 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 390} Link IDs: {'PTRANS': 19, 'TRANS': 419} Chain breaks: 5 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1511 Unresolved non-hydrogen angles: 1930 Unresolved non-hydrogen dihedrals: 1278 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'ASP:plan': 33, 'ASN:plan1': 19, 'HIS:plan': 17, 'GLU:plan': 29, 'ARG:plan': 27, 'GLN:plan1': 17, 'PHE:plan': 21, 'TYR:plan': 21, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 869 Chain: "J" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4} Link IDs: {'rna2p': 5} Chain: "K" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 145 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 6} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.97, per 1000 atoms: 0.27 Number of scatterers: 10957 At special positions: 0 Unit cell: (105.556, 109.154, 128.346, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 30 16.00 P 13 15.00 O 2110 8.00 N 2069 7.00 C 6733 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 645.2 milliseconds 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3268 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 15 sheets defined 60.0% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 163 through 182 removed outlier: 3.655A pdb=" N HIS A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 205 removed outlier: 3.734A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 220 removed outlier: 4.211A pdb=" N ASP A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.742A pdb=" N LEU A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 248 Processing helix chain 'A' and resid 249 through 257 removed outlier: 4.455A pdb=" N VAL A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 274 removed outlier: 4.409A pdb=" N CYS A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 removed outlier: 5.938A pdb=" N PHE A 296 " --> pdb=" O ASN A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 324 Processing helix chain 'A' and resid 330 through 337 removed outlier: 3.803A pdb=" N PHE A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 373 Processing helix chain 'A' and resid 376 through 393 Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.812A pdb=" N ILE A 413 " --> pdb=" O SER A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 removed outlier: 4.240A pdb=" N LYS A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 432 removed outlier: 3.853A pdb=" N LEU A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 438 through 450 Processing helix chain 'A' and resid 471 through 482 removed outlier: 3.959A pdb=" N SER A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) Proline residue: A 477 - end of helix Processing helix chain 'A' and resid 559 through 576 Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 150 through 156 Processing helix chain 'B' and resid 163 through 186 removed outlier: 3.646A pdb=" N HIS B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 190 Processing helix chain 'B' and resid 192 through 205 Processing helix chain 'B' and resid 214 through 220 removed outlier: 4.262A pdb=" N ASP B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 232 through 249 Processing helix chain 'B' and resid 249 through 257 removed outlier: 4.383A pdb=" N VAL B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 273 removed outlier: 4.490A pdb=" N CYS B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.538A pdb=" N SER B 295 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 300 removed outlier: 3.734A pdb=" N ILE B 300 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 324 Processing helix chain 'B' and resid 330 through 337 removed outlier: 3.610A pdb=" N PHE B 334 " --> pdb=" O ASP B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 373 Processing helix chain 'B' and resid 376 through 394 Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 409 through 414 removed outlier: 3.706A pdb=" N ALA B 412 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE B 413 " --> pdb=" O SER B 410 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 414 " --> pdb=" O THR B 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 409 through 414' Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 421 through 423 No H-bonds generated for 'chain 'B' and resid 421 through 423' Processing helix chain 'B' and resid 424 through 432 removed outlier: 3.930A pdb=" N LEU B 428 " --> pdb=" O ASP B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 450 removed outlier: 4.018A pdb=" N ILE B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR B 450 " --> pdb=" O LYS B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 474 Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.678A pdb=" N GLU B 479 " --> pdb=" O SER B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 497 Processing helix chain 'B' and resid 558 through 577 removed outlier: 4.271A pdb=" N TYR B 563 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA B 564 " --> pdb=" O LYS B 560 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN B 577 " --> pdb=" O CYS B 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 137 Processing helix chain 'E' and resid 138 through 143 Processing helix chain 'E' and resid 144 through 147 Processing helix chain 'E' and resid 163 through 182 removed outlier: 3.906A pdb=" N HIS E 167 " --> pdb=" O ASN E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 204 removed outlier: 3.535A pdb=" N VAL E 196 " --> pdb=" O SER E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 220 Processing helix chain 'E' and resid 221 through 226 Processing helix chain 'E' and resid 232 through 249 Processing helix chain 'E' and resid 250 through 257 Processing helix chain 'E' and resid 260 through 274 removed outlier: 4.337A pdb=" N CYS E 266 " --> pdb=" O GLU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 300 removed outlier: 6.000A pdb=" N PHE E 296 " --> pdb=" O ASN E 293 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE E 300 " --> pdb=" O LEU E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 324 removed outlier: 3.736A pdb=" N TRP E 313 " --> pdb=" O ASP E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 337 removed outlier: 3.957A pdb=" N PHE E 334 " --> pdb=" O ASP E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 373 Processing helix chain 'E' and resid 376 through 393 removed outlier: 3.764A pdb=" N ALA E 393 " --> pdb=" O ALA E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 405 removed outlier: 3.869A pdb=" N LYS E 405 " --> pdb=" O ALA E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 414 removed outlier: 4.027A pdb=" N ILE E 413 " --> pdb=" O SER E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 421 removed outlier: 4.391A pdb=" N LYS E 421 " --> pdb=" O GLU E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 432 removed outlier: 3.912A pdb=" N LEU E 428 " --> pdb=" O ASP E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 450 Processing helix chain 'E' and resid 471 through 483 removed outlier: 3.934A pdb=" N SER E 475 " --> pdb=" O GLU E 471 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU E 476 " --> pdb=" O ASP E 472 " (cutoff:3.500A) Proline residue: E 477 - end of helix removed outlier: 4.121A pdb=" N ALA E 483 " --> pdb=" O GLU E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 535 removed outlier: 4.055A pdb=" N LYS E 534 " --> pdb=" O ILE E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 576 Processing helix chain 'F' and resid 129 through 137 Processing helix chain 'F' and resid 138 through 143 Processing helix chain 'F' and resid 144 through 147 Processing helix chain 'F' and resid 150 through 156 Processing helix chain 'F' and resid 163 through 186 removed outlier: 3.661A pdb=" N HIS F 167 " --> pdb=" O ASN F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 190 Processing helix chain 'F' and resid 192 through 204 Processing helix chain 'F' and resid 214 through 220 removed outlier: 3.965A pdb=" N ASP F 218 " --> pdb=" O SER F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 226 Processing helix chain 'F' and resid 232 through 249 Processing helix chain 'F' and resid 249 through 258 removed outlier: 3.914A pdb=" N VAL F 253 " --> pdb=" O GLY F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 274 removed outlier: 4.583A pdb=" N CYS F 266 " --> pdb=" O GLU F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 295 removed outlier: 3.588A pdb=" N LYS F 294 " --> pdb=" O PRO F 291 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER F 295 " --> pdb=" O GLU F 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 291 through 295' Processing helix chain 'F' and resid 296 through 300 removed outlier: 3.601A pdb=" N ILE F 300 " --> pdb=" O LEU F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 324 Processing helix chain 'F' and resid 330 through 337 removed outlier: 3.809A pdb=" N PHE F 334 " --> pdb=" O ASP F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 374 Processing helix chain 'F' and resid 377 through 393 Processing helix chain 'F' and resid 394 through 397 removed outlier: 3.831A pdb=" N ILE F 397 " --> pdb=" O ASP F 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 394 through 397' Processing helix chain 'F' and resid 402 through 404 No H-bonds generated for 'chain 'F' and resid 402 through 404' Processing helix chain 'F' and resid 410 through 414 removed outlier: 4.278A pdb=" N ILE F 413 " --> pdb=" O SER F 410 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP F 414 " --> pdb=" O THR F 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 410 through 414' Processing helix chain 'F' and resid 415 through 420 Processing helix chain 'F' and resid 421 through 423 No H-bonds generated for 'chain 'F' and resid 421 through 423' Processing helix chain 'F' and resid 424 through 432 removed outlier: 3.893A pdb=" N LEU F 428 " --> pdb=" O ASP F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 437 No H-bonds generated for 'chain 'F' and resid 435 through 437' Processing helix chain 'F' and resid 438 through 450 removed outlier: 3.635A pdb=" N ILE F 448 " --> pdb=" O ILE F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 474 No H-bonds generated for 'chain 'F' and resid 472 through 474' Processing helix chain 'F' and resid 475 through 484 Processing helix chain 'F' and resid 559 through 576 removed outlier: 4.463A pdb=" N TYR F 563 " --> pdb=" O ARG F 559 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA F 564 " --> pdb=" O LYS F 560 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 120 Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 342 Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AA4, first strand: chain 'A' and resid 459 through 460 removed outlier: 3.695A pdb=" N TYR A 553 " --> pdb=" O ILE A 499 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 499 " --> pdb=" O TYR A 553 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 120 Processing sheet with id=AA6, first strand: chain 'B' and resid 338 through 342 Processing sheet with id=AA7, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AA8, first strand: chain 'B' and resid 459 through 460 removed outlier: 3.761A pdb=" N TYR B 553 " --> pdb=" O ILE B 499 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 116 through 120 Processing sheet with id=AB1, first strand: chain 'E' and resid 338 through 342 Processing sheet with id=AB2, first strand: chain 'E' and resid 456 through 460 removed outlier: 5.116A pdb=" N GLY E 458 " --> pdb=" O VAL E 552 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR E 553 " --> pdb=" O ILE E 499 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE E 499 " --> pdb=" O TYR E 553 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 116 through 120 Processing sheet with id=AB4, first strand: chain 'F' and resid 338 through 342 Processing sheet with id=AB5, first strand: chain 'F' and resid 399 through 400 Processing sheet with id=AB6, first strand: chain 'F' and resid 501 through 502 656 hydrogen bonds defined for protein. 1830 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: 1.45 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3949 1.34 - 1.46: 2025 1.46 - 1.58: 5057 1.58 - 1.69: 24 1.69 - 1.81: 46 Bond restraints: 11101 Sorted by residual: bond pdb=" C3' A K 9 " pdb=" O3' A K 9 " ideal model delta sigma weight residual 1.427 1.446 -0.019 1.20e-02 6.94e+03 2.42e+00 bond pdb=" N1 C K 11 " pdb=" C2 C K 11 " ideal model delta sigma weight residual 1.397 1.410 -0.013 1.00e-02 1.00e+04 1.64e+00 bond pdb=" N9 G J 8 " pdb=" C4 G J 8 " ideal model delta sigma weight residual 1.375 1.385 -0.010 8.00e-03 1.56e+04 1.48e+00 bond pdb=" C VAL E 457 " pdb=" N GLY E 458 " ideal model delta sigma weight residual 1.322 1.334 -0.012 1.20e-02 6.94e+03 9.55e-01 bond pdb=" CA ILE A 222 " pdb=" CB ILE A 222 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 8.76e-01 ... (remaining 11096 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 14697 1.18 - 2.35: 431 2.35 - 3.53: 86 3.53 - 4.70: 25 4.70 - 5.88: 8 Bond angle restraints: 15247 Sorted by residual: angle pdb=" N1 C K 11 " pdb=" C2 C K 11 " pdb=" O2 C K 11 " ideal model delta sigma weight residual 118.90 122.03 -3.13 6.00e-01 2.78e+00 2.71e+01 angle pdb=" C1' C K 11 " pdb=" N1 C K 11 " pdb=" C2 C K 11 " ideal model delta sigma weight residual 118.80 124.39 -5.59 1.10e+00 8.26e-01 2.58e+01 angle pdb=" C3' A K 9 " pdb=" O3' A K 9 " pdb=" P C K 10 " ideal model delta sigma weight residual 119.70 125.58 -5.88 1.20e+00 6.94e-01 2.40e+01 angle pdb=" N1 C K 7 " pdb=" C2 C K 7 " pdb=" O2 C K 7 " ideal model delta sigma weight residual 118.90 121.48 -2.58 6.00e-01 2.78e+00 1.84e+01 angle pdb=" O2 C K 11 " pdb=" C2 C K 11 " pdb=" N3 C K 11 " ideal model delta sigma weight residual 121.90 119.00 2.90 7.00e-01 2.04e+00 1.72e+01 ... (remaining 15242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 6459 35.82 - 71.63: 89 71.63 - 107.45: 18 107.45 - 143.27: 1 143.27 - 179.08: 4 Dihedral angle restraints: 6571 sinusoidal: 1551 harmonic: 5020 Sorted by residual: dihedral pdb=" O4' C J 10 " pdb=" C1' C J 10 " pdb=" N1 C J 10 " pdb=" C2 C J 10 " ideal model delta sinusoidal sigma weight residual -128.00 51.08 -179.08 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C K 7 " pdb=" C1' C K 7 " pdb=" N1 C K 7 " pdb=" C2 C K 7 " ideal model delta sinusoidal sigma weight residual 232.00 68.82 163.18 1 1.70e+01 3.46e-03 6.50e+01 dihedral pdb=" O4' C K 11 " pdb=" C1' C K 11 " pdb=" N1 C K 11 " pdb=" C2 C K 11 " ideal model delta sinusoidal sigma weight residual 232.00 76.53 155.47 1 1.70e+01 3.46e-03 6.34e+01 ... (remaining 6568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1359 0.046 - 0.091: 397 0.091 - 0.137: 106 0.137 - 0.183: 4 0.183 - 0.228: 1 Chirality restraints: 1867 Sorted by residual: chirality pdb=" C3' A K 9 " pdb=" C4' A K 9 " pdb=" O3' A K 9 " pdb=" C2' A K 9 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA TYR B 315 " pdb=" N TYR B 315 " pdb=" C TYR B 315 " pdb=" CB TYR B 315 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA TYR A 315 " pdb=" N TYR A 315 " pdb=" C TYR A 315 " pdb=" CB TYR A 315 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.26e-01 ... (remaining 1864 not shown) Planarity restraints: 2033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER F 368 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" C SER F 368 " 0.041 2.00e-02 2.50e+03 pdb=" O SER F 368 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU F 369 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 129 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO B 130 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 130 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 130 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 480 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C VAL B 480 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL B 480 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA B 481 " -0.011 2.00e-02 2.50e+03 ... (remaining 2030 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 74 2.58 - 3.16: 9274 3.16 - 3.74: 16550 3.74 - 4.32: 20242 4.32 - 4.90: 34077 Nonbonded interactions: 80217 Sorted by model distance: nonbonded pdb=" OD2 ASP A 207 " pdb="FE FE A 701 " model vdw 2.000 2.260 nonbonded pdb=" OD1 ASP A 311 " pdb="FE FE A 701 " model vdw 2.001 2.260 nonbonded pdb=" OD1 ASP B 311 " pdb="FE FE B 701 " model vdw 2.026 2.260 nonbonded pdb=" OD2 ASP B 207 " pdb="FE FE B 701 " model vdw 2.057 2.260 nonbonded pdb=" O VAL A 117 " pdb=" O2' G J 8 " model vdw 2.113 3.040 ... (remaining 80212 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 114 through 123 and (name N or name CA or name C or name \ O or name CB )) or resid 124 or (resid 125 through 150 and (name N or name CA or \ name C or name O or name CB )) or resid 151 through 153 or (resid 154 through 1 \ 58 and (name N or name CA or name C or name O or name CB )) or (resid 159 throug \ h 169 and (name N or name CA or name C or name O or name CB )) or resid 170 or ( \ resid 171 and (name N or name CA or name C or name O or name CB )) or resid 172 \ or (resid 173 through 175 and (name N or name CA or name C or name O or name CB \ )) or resid 176 or (resid 177 through 182 and (name N or name CA or name C or na \ me O or name CB )) or resid 183 or (resid 184 through 202 and (name N or name CA \ or name C or name O or name CB )) or resid 203 or (resid 204 through 208 and (n \ ame N or name CA or name C or name O or name CB )) or resid 209 or (resid 210 an \ d (name N or name CA or name C or name O or name CB )) or resid 211 or (resid 21 \ 2 through 218 and (name N or name CA or name C or name O or name CB )) or resid \ 219 or (resid 220 through 235 and (name N or name CA or name C or name O or name \ CB )) or (resid 236 through 248 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 249 through 257 and (name N or name CA or name C or name O o \ r name CB )) or resid 258 or (resid 259 through 273 and (name N or name CA or na \ me C or name O or name CB )) or resid 274 or (resid 275 through 277 and (name N \ or name CA or name C or name O or name CB )) or (resid 282 through 288 and (name \ N or name CA or name C or name O or name CB )) or resid 289 or (resid 290 throu \ gh 306 and (name N or name CA or name C or name O or name CB )) or resid 307 or \ (resid 308 through 323 and (name N or name CA or name C or name O or name CB )) \ or resid 324 or (resid 325 through 356 and (name N or name CA or name C or name \ O or name CB )) or resid 357 or (resid 358 through 378 and (name N or name CA or \ name C or name O or name CB )) or resid 379 or (resid 380 through 400 and (name \ N or name CA or name C or name O or name CB )) or (resid 401 through 457 and (n \ ame N or name CA or name C or name O or name CB )) or resid 458 through 462 or r \ esid 469 through 487 or resid 492 through 504 or resid 514 through 520 or resid \ 549 through 579)) selection = (chain 'B' and ((resid 114 through 123 and (name N or name CA or name C or name \ O or name CB )) or resid 124 or (resid 125 through 150 and (name N or name CA or \ name C or name O or name CB )) or resid 151 through 153 or (resid 154 through 1 \ 58 and (name N or name CA or name C or name O or name CB )) or (resid 159 throug \ h 169 and (name N or name CA or name C or name O or name CB )) or resid 170 or ( \ resid 171 and (name N or name CA or name C or name O or name CB )) or resid 172 \ or (resid 173 through 175 and (name N or name CA or name C or name O or name CB \ )) or resid 176 or (resid 177 through 182 and (name N or name CA or name C or na \ me O or name CB )) or resid 183 or (resid 184 through 202 and (name N or name CA \ or name C or name O or name CB )) or resid 203 or (resid 204 through 208 and (n \ ame N or name CA or name C or name O or name CB )) or resid 209 or (resid 210 an \ d (name N or name CA or name C or name O or name CB )) or resid 211 or (resid 21 \ 2 through 218 and (name N or name CA or name C or name O or name CB )) or resid \ 219 or (resid 220 through 235 and (name N or name CA or name C or name O or name \ CB )) or resid 236 or (resid 237 through 248 and (name N or name CA or name C o \ r name O or name CB )) or resid 249 or (resid 250 through 257 and (name N or nam \ e CA or name C or name O or name CB )) or resid 258 or (resid 259 through 273 an \ d (name N or name CA or name C or name O or name CB )) or resid 274 or (resid 27 \ 5 through 288 and (name N or name CA or name C or name O or name CB )) or resid \ 289 or (resid 290 through 306 and (name N or name CA or name C or name O or name \ CB )) or resid 307 or (resid 308 through 323 and (name N or name CA or name C o \ r name O or name CB )) or resid 324 or (resid 325 through 356 and (name N or nam \ e CA or name C or name O or name CB )) or resid 357 or (resid 358 through 378 an \ d (name N or name CA or name C or name O or name CB )) or resid 379 or (resid 38 \ 0 through 400 and (name N or name CA or name C or name O or name CB )) or (resid \ 401 through 457 and (name N or name CA or name C or name O or name CB )) or res \ id 458 through 487 or (resid 492 through 579 and (name N or name CA or name C or \ name O or name CB )))) selection = (chain 'E' and (resid 114 through 277 or resid 282 through 462 or resid 469 thro \ ugh 487 or resid 492 through 504 or resid 514 through 520 or resid 549 through 5 \ 79)) selection = (chain 'F' and (resid 114 through 462 or resid 469 through 487 or resid 492 thro \ ugh 504 or resid 514 through 520 or resid 549 through 579)) } 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.540 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 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 : 0.002 0.028 11101 Z= 0.124 Angle : 0.533 5.878 15247 Z= 0.348 Chirality : 0.044 0.228 1867 Planarity : 0.004 0.056 2033 Dihedral : 14.036 179.084 3303 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.53 % Allowed : 6.23 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.21), residues: 1698 helix: 0.71 (0.19), residues: 849 sheet: -0.96 (0.56), residues: 92 loop : -1.49 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 333 TYR 0.025 0.001 TYR A 315 PHE 0.011 0.001 PHE A 141 TRP 0.004 0.001 TRP B 231 HIS 0.003 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.12 (11101) covalent geometry : angle 0.53313 / 0.35 (15247) hydrogen bonds : bond 0.14623 / 9.56 ( 656) hydrogen bonds : angle 6.62510 / 4.96 ( 1830) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 221 time to evaluate : 0.379 Fit side-chains REVERT: A 355 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6540 (mm-30) REVERT: A 384 THR cc_start: 0.7472 (m) cc_final: 0.7056 (m) REVERT: A 417 GLU cc_start: 0.7722 (tt0) cc_final: 0.7402 (tt0) REVERT: A 445 LEU cc_start: 0.8336 (mt) cc_final: 0.7972 (mp) REVERT: A 447 GLN cc_start: 0.7423 (mm110) cc_final: 0.7035 (mt0) REVERT: B 135 ILE cc_start: 0.8128 (mt) cc_final: 0.7922 (mt) REVERT: B 227 PRO cc_start: 0.7102 (Cg_endo) cc_final: 0.6811 (Cg_exo) outliers start: 3 outliers final: 1 residues processed: 223 average time/residue: 0.0993 time to fit residues: 32.1947 Evaluate side-chains 167 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 450 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.0050 chunk 91 optimal weight: 0.0870 chunk 149 optimal weight: 10.0000 overall best weight: 1.7976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 ASN A 271 GLN B 163 ASN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 GLN B 248 ASN B 293 ASN ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN B 375 GLN ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.258108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.220005 restraints weight = 14842.906| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 2.84 r_work: 0.4167 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 11101 Z= 0.273 Angle : 0.647 8.928 15247 Z= 0.357 Chirality : 0.049 0.444 1867 Planarity : 0.005 0.052 2033 Dihedral : 13.432 178.431 1999 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.38 % Allowed : 14.77 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.20), residues: 1698 helix: 0.60 (0.18), residues: 857 sheet: -1.31 (0.57), residues: 78 loop : -1.71 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 442 TYR 0.028 0.002 TYR A 315 PHE 0.024 0.003 PHE B 213 TRP 0.009 0.002 TRP B 285 HIS 0.008 0.002 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.27 (11101) covalent geometry : angle 0.64672 / 0.36 (15247) hydrogen bonds : bond 0.05073 / 3.44 ( 656) hydrogen bonds : angle 5.29571 / 4.00 ( 1830) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.397 Fit side-chains REVERT: A 326 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: A 355 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6490 (mm-30) REVERT: A 384 THR cc_start: 0.8007 (m) cc_final: 0.7728 (m) REVERT: A 405 LYS cc_start: 0.8001 (ttmt) cc_final: 0.7776 (ttmt) REVERT: A 416 MET cc_start: 0.8247 (mmp) cc_final: 0.7936 (mmp) REVERT: B 142 GLN cc_start: 0.8512 (mm110) cc_final: 0.8275 (mm110) REVERT: B 227 PRO cc_start: 0.7273 (Cg_endo) cc_final: 0.6945 (Cg_exo) outliers start: 19 outliers final: 12 residues processed: 181 average time/residue: 0.0949 time to fit residues: 25.3122 Evaluate side-chains 177 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 450 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 83 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 92 optimal weight: 8.9990 chunk 137 optimal weight: 0.0470 chunk 84 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 151 optimal weight: 0.0970 chunk 158 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 ASN A 321 HIS A 452 ASN B 210 HIS B 233 HIS B 321 HIS B 328 ASN B 376 HIS B 380 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.264100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.214489 restraints weight = 14822.994| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 3.47 r_work: 0.4204 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11101 Z= 0.127 Angle : 0.522 9.229 15247 Z= 0.287 Chirality : 0.045 0.420 1867 Planarity : 0.003 0.047 2033 Dihedral : 13.242 179.325 1999 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.56 % Allowed : 15.66 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.21), residues: 1698 helix: 1.06 (0.19), residues: 845 sheet: -1.25 (0.57), residues: 82 loop : -1.48 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 318 TYR 0.025 0.001 TYR A 315 PHE 0.030 0.002 PHE B 329 TRP 0.007 0.001 TRP A 313 HIS 0.006 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (11101) covalent geometry : angle 0.52188 / 0.29 (15247) hydrogen bonds : bond 0.03733 / 2.56 ( 656) hydrogen bonds : angle 4.64430 / 3.52 ( 1830) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.277 Fit side-chains REVERT: A 127 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7239 (tm-30) REVERT: A 257 TYR cc_start: 0.8111 (m-80) cc_final: 0.7812 (m-80) REVERT: A 326 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: A 336 LYS cc_start: 0.7160 (tttt) cc_final: 0.6267 (mmtm) REVERT: A 384 THR cc_start: 0.7945 (m) cc_final: 0.7657 (m) REVERT: A 405 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7594 (ttmm) REVERT: A 443 GLU cc_start: 0.8440 (tp30) cc_final: 0.7793 (tt0) REVERT: B 227 PRO cc_start: 0.7215 (Cg_endo) cc_final: 0.6863 (Cg_exo) REVERT: B 326 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.5898 (mp10) REVERT: B 385 MET cc_start: 0.7697 (mtt) cc_final: 0.7413 (mtp) outliers start: 20 outliers final: 12 residues processed: 185 average time/residue: 0.0821 time to fit residues: 22.2952 Evaluate side-chains 178 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 450 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 12 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 131 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 145 optimal weight: 0.0060 chunk 0 optimal weight: 2.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.263262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.213986 restraints weight = 14660.407| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 3.42 r_work: 0.4213 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11101 Z= 0.135 Angle : 0.512 9.269 15247 Z= 0.279 Chirality : 0.045 0.431 1867 Planarity : 0.003 0.045 2033 Dihedral : 13.186 179.359 1999 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.38 % Allowed : 19.04 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.21), residues: 1698 helix: 1.09 (0.19), residues: 849 sheet: -1.10 (0.58), residues: 82 loop : -1.36 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 442 TYR 0.024 0.001 TYR B 315 PHE 0.022 0.002 PHE B 329 TRP 0.005 0.001 TRP B 231 HIS 0.008 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (11101) covalent geometry : angle 0.51232 / 0.28 (15247) hydrogen bonds : bond 0.03520 / 2.42 ( 656) hydrogen bonds : angle 4.45797 / 3.36 ( 1830) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7182 (tm-30) REVERT: A 257 TYR cc_start: 0.8087 (m-80) cc_final: 0.7780 (m-80) REVERT: A 326 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7367 (tm-30) REVERT: A 336 LYS cc_start: 0.7082 (tttt) cc_final: 0.6278 (mmtm) REVERT: A 384 THR cc_start: 0.8011 (m) cc_final: 0.7718 (m) REVERT: A 405 LYS cc_start: 0.7845 (ttmt) cc_final: 0.7597 (ttmm) REVERT: A 415 ASP cc_start: 0.7435 (t0) cc_final: 0.7007 (t0) REVERT: A 443 GLU cc_start: 0.8442 (tp30) cc_final: 0.7820 (tt0) REVERT: B 227 PRO cc_start: 0.7226 (Cg_endo) cc_final: 0.6886 (Cg_exo) REVERT: B 326 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.5950 (mp10) REVERT: B 385 MET cc_start: 0.7806 (mtt) cc_final: 0.7551 (mtp) outliers start: 19 outliers final: 14 residues processed: 178 average time/residue: 0.0852 time to fit residues: 22.6074 Evaluate side-chains 181 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 450 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 83 optimal weight: 9.9990 chunk 93 optimal weight: 0.0970 chunk 44 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 155 optimal weight: 0.6980 chunk 77 optimal weight: 0.0040 chunk 78 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN B 380 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.260243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.210407 restraints weight = 14694.505| |-----------------------------------------------------------------------------| r_work (start): 0.4311 rms_B_bonded: 3.36 r_work: 0.4162 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11101 Z= 0.189 Angle : 0.550 8.374 15247 Z= 0.300 Chirality : 0.046 0.444 1867 Planarity : 0.003 0.045 2033 Dihedral : 13.159 179.698 1999 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.27 % Allowed : 20.11 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.21), residues: 1698 helix: 1.10 (0.19), residues: 829 sheet: -0.75 (0.60), residues: 76 loop : -1.46 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.025 0.002 TYR B 315 PHE 0.024 0.002 PHE A 329 TRP 0.007 0.001 TRP B 231 HIS 0.006 0.002 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (11101) covalent geometry : angle 0.54976 / 0.30 (15247) hydrogen bonds : bond 0.03840 / 2.64 ( 656) hydrogen bonds : angle 4.47940 / 3.35 ( 1830) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.245 Fit side-chains REVERT: A 115 MET cc_start: 0.6200 (mmm) cc_final: 0.5890 (mmm) REVERT: A 127 GLU cc_start: 0.7838 (tm-30) cc_final: 0.6956 (tm-30) REVERT: A 257 TYR cc_start: 0.8055 (m-80) cc_final: 0.7821 (m-80) REVERT: A 259 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6478 (mt) REVERT: A 326 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7357 (tm-30) REVERT: A 336 LYS cc_start: 0.7146 (tttt) cc_final: 0.6351 (mmtm) REVERT: A 384 THR cc_start: 0.8141 (m) cc_final: 0.7874 (m) REVERT: A 415 ASP cc_start: 0.7530 (t0) cc_final: 0.7133 (t0) REVERT: A 443 GLU cc_start: 0.8440 (tp30) cc_final: 0.7759 (tt0) REVERT: B 119 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7890 (m-40) REVERT: B 367 ASN cc_start: 0.7976 (m-40) cc_final: 0.7464 (t0) outliers start: 24 outliers final: 17 residues processed: 174 average time/residue: 0.0712 time to fit residues: 18.8562 Evaluate side-chains 177 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 450 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 116 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 170 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 37 optimal weight: 0.0170 chunk 11 optimal weight: 0.1980 chunk 107 optimal weight: 6.9990 overall best weight: 0.6424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.262661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.213292 restraints weight = 14609.224| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 3.37 r_work: 0.4200 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11101 Z= 0.127 Angle : 0.511 9.742 15247 Z= 0.275 Chirality : 0.045 0.426 1867 Planarity : 0.003 0.044 2033 Dihedral : 13.000 179.686 1999 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.56 % Allowed : 21.89 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.21), residues: 1698 helix: 1.24 (0.19), residues: 841 sheet: -1.12 (0.58), residues: 82 loop : -1.38 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 442 TYR 0.024 0.001 TYR B 315 PHE 0.039 0.002 PHE A 329 TRP 0.007 0.001 TRP B 231 HIS 0.008 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (11101) covalent geometry : angle 0.51090 / 0.28 (15247) hydrogen bonds : bond 0.03332 / 2.31 ( 656) hydrogen bonds : angle 4.26435 / 3.19 ( 1830) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.365 Fit side-chains REVERT: A 115 MET cc_start: 0.6222 (mmm) cc_final: 0.5881 (mmm) REVERT: A 127 GLU cc_start: 0.7715 (tm-30) cc_final: 0.6809 (tm-30) REVERT: A 257 TYR cc_start: 0.7991 (m-80) cc_final: 0.7776 (m-80) REVERT: A 259 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6329 (mt) REVERT: A 304 LYS cc_start: 0.7023 (mmtm) cc_final: 0.6355 (mtmt) REVERT: A 326 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7351 (tm-30) REVERT: A 336 LYS cc_start: 0.7170 (tttt) cc_final: 0.6288 (mmtm) REVERT: A 384 THR cc_start: 0.8067 (m) cc_final: 0.7719 (m) REVERT: A 415 ASP cc_start: 0.7245 (t0) cc_final: 0.6940 (t0) REVERT: A 443 GLU cc_start: 0.8419 (tp30) cc_final: 0.7715 (tt0) REVERT: B 119 ASN cc_start: 0.8131 (OUTLIER) cc_final: 0.7803 (m-40) REVERT: B 227 PRO cc_start: 0.7231 (Cg_endo) cc_final: 0.6891 (Cg_exo) REVERT: B 353 ASP cc_start: 0.6509 (m-30) cc_final: 0.5134 (t70) REVERT: B 367 ASN cc_start: 0.7957 (m-40) cc_final: 0.7440 (t0) REVERT: B 408 ARG cc_start: 0.7540 (mtm-85) cc_final: 0.7323 (ttp-170) outliers start: 20 outliers final: 14 residues processed: 177 average time/residue: 0.0777 time to fit residues: 20.5929 Evaluate side-chains 178 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 311 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 71 optimal weight: 0.4980 chunk 77 optimal weight: 9.9990 chunk 152 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 0.0070 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.261128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.212678 restraints weight = 14545.532| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 3.32 r_work: 0.4173 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11101 Z= 0.174 Angle : 0.550 12.029 15247 Z= 0.296 Chirality : 0.046 0.438 1867 Planarity : 0.003 0.044 2033 Dihedral : 12.968 179.566 1997 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 4.27 % Allowed : 21.89 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.21), residues: 1698 helix: 1.19 (0.19), residues: 829 sheet: -1.20 (0.57), residues: 82 loop : -1.39 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 290 TYR 0.026 0.001 TYR A 315 PHE 0.021 0.002 PHE A 329 TRP 0.007 0.001 TRP B 231 HIS 0.005 0.002 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (11101) covalent geometry : angle 0.54952 / 0.30 (15247) hydrogen bonds : bond 0.03690 / 2.56 ( 656) hydrogen bonds : angle 4.39041 / 3.27 ( 1830) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.6270 (mmm) cc_final: 0.5788 (mmm) REVERT: A 127 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7170 (tm-30) REVERT: A 259 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6493 (mt) REVERT: A 304 LYS cc_start: 0.7015 (mmtm) cc_final: 0.6286 (mtmt) REVERT: A 312 LYS cc_start: 0.8258 (mttp) cc_final: 0.7842 (mtmm) REVERT: A 326 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7403 (tm-30) REVERT: A 336 LYS cc_start: 0.7180 (tttt) cc_final: 0.6256 (mmtm) REVERT: A 374 TYR cc_start: 0.8071 (m-80) cc_final: 0.7778 (m-80) REVERT: A 384 THR cc_start: 0.8093 (m) cc_final: 0.7827 (m) REVERT: A 405 LYS cc_start: 0.8065 (ttmm) cc_final: 0.7504 (ttpt) REVERT: A 415 ASP cc_start: 0.7412 (t0) cc_final: 0.7008 (t0) REVERT: A 443 GLU cc_start: 0.8420 (tp30) cc_final: 0.8214 (tm-30) REVERT: B 119 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7822 (m-40) REVERT: B 228 GLU cc_start: 0.8022 (pp20) cc_final: 0.7800 (pp20) REVERT: B 353 ASP cc_start: 0.6363 (m-30) cc_final: 0.5106 (t70) REVERT: B 367 ASN cc_start: 0.7982 (m-40) cc_final: 0.7474 (t0) outliers start: 24 outliers final: 19 residues processed: 172 average time/residue: 0.0820 time to fit residues: 21.0637 Evaluate side-chains 181 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 450 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 89 optimal weight: 6.9990 chunk 50 optimal weight: 0.0980 chunk 146 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 135 optimal weight: 0.4980 chunk 117 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.263029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.213645 restraints weight = 14680.699| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 3.44 r_work: 0.4203 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11101 Z= 0.119 Angle : 0.502 9.224 15247 Z= 0.271 Chirality : 0.045 0.420 1867 Planarity : 0.003 0.044 2033 Dihedral : 12.843 179.871 1997 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.85 % Allowed : 24.56 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.22), residues: 1698 helix: 1.38 (0.19), residues: 835 sheet: -1.09 (0.58), residues: 82 loop : -1.31 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 366 TYR 0.024 0.001 TYR A 315 PHE 0.034 0.002 PHE A 329 TRP 0.007 0.001 TRP B 231 HIS 0.007 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (11101) covalent geometry : angle 0.50239 / 0.27 (15247) hydrogen bonds : bond 0.03139 / 2.17 ( 656) hydrogen bonds : angle 4.16585 / 3.11 ( 1830) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.398 Fit side-chains REVERT: A 115 MET cc_start: 0.6305 (mmm) cc_final: 0.5033 (mmm) REVERT: A 127 GLU cc_start: 0.7963 (tm-30) cc_final: 0.6669 (tm-30) REVERT: A 259 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6640 (mt) REVERT: A 304 LYS cc_start: 0.7148 (mmtm) cc_final: 0.6416 (mtmt) REVERT: A 312 LYS cc_start: 0.8186 (mttp) cc_final: 0.7784 (mtmm) REVERT: A 326 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7374 (tm-30) REVERT: A 336 LYS cc_start: 0.7178 (tttt) cc_final: 0.6255 (mmtm) REVERT: A 374 TYR cc_start: 0.8050 (m-80) cc_final: 0.7707 (m-80) REVERT: A 384 THR cc_start: 0.8022 (m) cc_final: 0.7745 (m) REVERT: A 415 ASP cc_start: 0.7359 (t0) cc_final: 0.7024 (t0) REVERT: A 443 GLU cc_start: 0.8401 (tp30) cc_final: 0.8189 (tm-30) REVERT: B 353 ASP cc_start: 0.6453 (m-30) cc_final: 0.5026 (t70) REVERT: B 367 ASN cc_start: 0.7958 (m-40) cc_final: 0.7457 (t0) outliers start: 16 outliers final: 14 residues processed: 165 average time/residue: 0.0845 time to fit residues: 20.9300 Evaluate side-chains 171 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 311 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 10 optimal weight: 0.0370 chunk 9 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 37 optimal weight: 0.0870 chunk 76 optimal weight: 0.3980 chunk 41 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.263194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.213889 restraints weight = 14587.353| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 3.46 r_work: 0.4204 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11101 Z= 0.114 Angle : 0.504 9.645 15247 Z= 0.272 Chirality : 0.045 0.420 1867 Planarity : 0.003 0.044 2033 Dihedral : 12.802 179.622 1997 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.56 % Allowed : 24.20 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.22), residues: 1698 helix: 1.48 (0.19), residues: 835 sheet: -0.58 (0.62), residues: 76 loop : -1.28 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 290 TYR 0.023 0.001 TYR A 315 PHE 0.025 0.002 PHE A 329 TRP 0.008 0.001 TRP A 313 HIS 0.007 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (11101) covalent geometry : angle 0.50375 / 0.27 (15247) hydrogen bonds : bond 0.03084 / 2.14 ( 656) hydrogen bonds : angle 4.09650 / 3.06 ( 1830) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6331 (mmm) cc_final: 0.5189 (mmm) REVERT: A 127 GLU cc_start: 0.7897 (tm-30) cc_final: 0.6681 (tm-30) REVERT: A 259 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6703 (mt) REVERT: A 304 LYS cc_start: 0.7127 (mmtm) cc_final: 0.6394 (mtmt) REVERT: A 312 LYS cc_start: 0.7956 (mttp) cc_final: 0.7576 (mtmm) REVERT: A 326 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7371 (tm-30) REVERT: A 336 LYS cc_start: 0.7145 (tttt) cc_final: 0.6341 (mmtm) REVERT: A 374 TYR cc_start: 0.8009 (m-80) cc_final: 0.7629 (m-80) REVERT: A 384 THR cc_start: 0.8025 (m) cc_final: 0.7746 (m) REVERT: A 415 ASP cc_start: 0.7313 (t0) cc_final: 0.6956 (t0) REVERT: A 443 GLU cc_start: 0.8355 (tp30) cc_final: 0.8147 (tm-30) REVERT: B 119 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7754 (m-40) REVERT: B 194 ARG cc_start: 0.8096 (ttt90) cc_final: 0.7647 (ttt-90) REVERT: B 353 ASP cc_start: 0.6423 (m-30) cc_final: 0.4982 (t70) REVERT: B 367 ASN cc_start: 0.7941 (m-40) cc_final: 0.7461 (t0) outliers start: 20 outliers final: 15 residues processed: 171 average time/residue: 0.0810 time to fit residues: 20.7367 Evaluate side-chains 173 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 311 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 59 optimal weight: 0.0570 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.262996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.213674 restraints weight = 14570.689| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 3.39 r_work: 0.4201 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11101 Z= 0.129 Angle : 0.507 9.084 15247 Z= 0.275 Chirality : 0.045 0.424 1867 Planarity : 0.003 0.044 2033 Dihedral : 12.791 179.735 1997 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.56 % Allowed : 23.84 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.22), residues: 1698 helix: 1.49 (0.19), residues: 835 sheet: -0.49 (0.63), residues: 76 loop : -1.28 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 442 TYR 0.029 0.002 TYR B 298 PHE 0.060 0.002 PHE A 329 TRP 0.007 0.001 TRP A 313 HIS 0.007 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (11101) covalent geometry : angle 0.50692 / 0.28 (15247) hydrogen bonds : bond 0.03147 / 2.19 ( 656) hydrogen bonds : angle 4.08139 / 3.04 ( 1830) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.6362 (mmm) cc_final: 0.5132 (mmm) REVERT: A 127 GLU cc_start: 0.7863 (tm-30) cc_final: 0.6682 (tm-30) REVERT: A 259 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6757 (mt) REVERT: A 304 LYS cc_start: 0.7137 (mmtm) cc_final: 0.6423 (mtmt) REVERT: A 312 LYS cc_start: 0.8228 (mttp) cc_final: 0.7819 (mtmm) REVERT: A 326 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7322 (tm-30) REVERT: A 336 LYS cc_start: 0.7162 (tttt) cc_final: 0.6383 (mmtm) REVERT: A 374 TYR cc_start: 0.8060 (m-80) cc_final: 0.7735 (m-80) REVERT: A 384 THR cc_start: 0.8138 (m) cc_final: 0.7875 (m) REVERT: A 415 ASP cc_start: 0.7349 (t0) cc_final: 0.7013 (t0) REVERT: A 443 GLU cc_start: 0.8343 (tp30) cc_final: 0.8134 (tm-30) REVERT: B 119 ASN cc_start: 0.8100 (OUTLIER) cc_final: 0.7773 (m-40) REVERT: B 353 ASP cc_start: 0.6440 (m-30) cc_final: 0.5004 (t70) REVERT: B 362 MET cc_start: 0.6040 (ttp) cc_final: 0.5504 (tpp) REVERT: B 367 ASN cc_start: 0.7953 (m-40) cc_final: 0.7471 (t0) outliers start: 20 outliers final: 16 residues processed: 168 average time/residue: 0.0794 time to fit residues: 20.2747 Evaluate side-chains 175 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 311 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 134 optimal weight: 2.9990 chunk 122 optimal weight: 0.0870 chunk 42 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 66 optimal weight: 0.2980 chunk 70 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.264503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.215374 restraints weight = 14673.063| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 3.41 r_work: 0.4214 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11101 Z= 0.112 Angle : 0.503 8.904 15247 Z= 0.271 Chirality : 0.044 0.417 1867 Planarity : 0.003 0.045 2033 Dihedral : 12.721 179.570 1997 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.20 % Allowed : 24.56 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.22), residues: 1698 helix: 1.55 (0.19), residues: 837 sheet: -0.40 (0.63), residues: 76 loop : -1.23 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.023 0.001 TYR A 315 PHE 0.054 0.002 PHE A 329 TRP 0.008 0.001 TRP B 231 HIS 0.009 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (11101) covalent geometry : angle 0.50289 / 0.27 (15247) hydrogen bonds : bond 0.02952 / 2.05 ( 656) hydrogen bonds : angle 4.01069 / 2.99 ( 1830) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2516.99 seconds wall clock time: 43 minutes 30.84 seconds (2610.84 seconds total)