Starting phenix.real_space_refine on Fri Jul 3 00:43:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tdv_41174/07_2026/8tdv_41174_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tdv_41174/07_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_41174/07_2026/8tdv_41174_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tdv_41174/07_2026/8tdv_41174_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tdv_41174/07_2026/8tdv_41174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tdv_41174/07_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-dev-6108/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, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Time building chain proxies: 2.79, per 1000 atoms: 0.25 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: 0.90 Conformation dependent library (CDL) restraints added in 602.7 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: 0.27 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: 1.32 Time building geometry restraints manager: 1.21 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=" 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=" C3' A K 9 " pdb=" O3' A K 9 " ideal model delta sigma weight residual 1.427 1.446 -0.019 1.50e-02 4.44e+03 1.55e+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 - 1.15: 14693 1.15 - 2.30: 430 2.30 - 3.44: 89 3.44 - 4.59: 25 4.59 - 5.74: 10 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=" 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 angle pdb=" C1' C K 7 " pdb=" N1 C K 7 " pdb=" C2 C K 7 " ideal model delta sigma weight residual 118.80 122.97 -4.17 1.10e+00 8.26e-01 1.44e+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: 1372 0.046 - 0.091: 386 0.091 - 0.137: 105 0.137 - 0.183: 3 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 3.000 nonbonded pdb=" OD1 ASP A 311 " pdb="FE FE A 701 " model vdw 2.001 3.000 nonbonded pdb=" OD1 ASP B 311 " pdb="FE FE B 701 " model vdw 2.026 3.000 nonbonded pdb=" OD2 ASP B 207 " pdb="FE FE B 701 " model vdw 2.057 3.000 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.780 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.060 ------------------------------------------------------------------------------- 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= 0.122 Angle : 0.525 5.738 15247 Z= 0.336 Chirality : 0.043 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 0.00214 / 0.12 (11101) covalent geometry : angle 0.52531 / 0.34 (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 : 0.347 Fit side-chains REVERT: A 355 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6541 (mm-30) REVERT: A 384 THR cc_start: 0.7472 (m) cc_final: 0.7055 (m) REVERT: A 417 GLU cc_start: 0.7722 (tt0) cc_final: 0.7403 (tt0) REVERT: A 445 LEU cc_start: 0.8336 (mt) cc_final: 0.7973 (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: 0.6813 (Cg_exo) outliers start: 3 outliers final: 1 residues processed: 223 average time/residue: 0.0964 time to fit residues: 31.0225 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 : 0.482 ------------------------------------------------------------------------------- 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 = 0.4749 r_free = 0.4749 target = 0.258510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.223179 restraints weight = 14915.169| |-----------------------------------------------------------------------------| r_work (start): 0.4413 rms_B_bonded: 2.77 r_work: 0.4170 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 11101 Z= 0.276 Angle : 0.650 8.709 15247 Z= 0.362 Chirality : 0.048 0.251 1867 Planarity : 0.005 0.055 2033 Dihedral : 13.528 178.734 1999 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.74 % Allowed : 13.88 % Favored : 82.38 % 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: -0.77 (0.20), residues: 1698 helix: 0.59 (0.18), residues: 857 sheet: -1.30 (0.57), residues: 78 loop : -1.72 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 145 TYR 0.029 0.002 TYR A 315 PHE 0.026 0.003 PHE B 213 TRP 0.009 0.002 TRP B 285 HIS 0.011 0.002 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.28 (11101) covalent geometry : angle 0.65036 / 0.36 (15247) hydrogen bonds : bond 0.05008 / 3.41 ( 656) hydrogen bonds : angle 5.29129 / 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 194 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.410 Fit side-chains REVERT: A 326 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7335 (tm-30) REVERT: A 355 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6531 (mm-30) REVERT: A 384 THR cc_start: 0.7999 (m) cc_final: 0.7718 (m) REVERT: B 142 GLN cc_start: 0.8514 (mm110) cc_final: 0.8295 (mm110) REVERT: B 227 PRO cc_start: 0.7263 (Cg_endo) cc_final: 0.6932 (Cg_exo) outliers start: 21 outliers final: 13 residues processed: 181 average time/residue: 0.0990 time to fit residues: 26.2125 Evaluate side-chains 176 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 264 ASP 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: 6.9990 chunk 63 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 151 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN B 210 HIS B 233 HIS ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN B 376 HIS B 380 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.261634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.213811 restraints weight = 14900.067| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 3.33 r_work: 0.4181 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11101 Z= 0.195 Angle : 0.568 8.999 15247 Z= 0.314 Chirality : 0.046 0.244 1867 Planarity : 0.004 0.047 2033 Dihedral : 13.366 179.208 1999 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.38 % Allowed : 16.73 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.59 (0.21), residues: 1698 helix: 0.81 (0.18), residues: 840 sheet: -1.26 (0.58), residues: 78 loop : -1.68 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 318 TYR 0.027 0.002 TYR A 315 PHE 0.029 0.002 PHE B 329 TRP 0.006 0.001 TRP B 231 HIS 0.006 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (11101) covalent geometry : angle 0.56823 / 0.31 (15247) hydrogen bonds : bond 0.04231 / 2.90 ( 656) hydrogen bonds : angle 4.87087 / 3.67 ( 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 186 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7302 (tm-30) REVERT: A 257 TYR cc_start: 0.8128 (m-80) cc_final: 0.7837 (m-80) REVERT: A 326 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: A 336 LYS cc_start: 0.7152 (tttt) cc_final: 0.6368 (mmtm) REVERT: A 374 TYR cc_start: 0.8009 (m-80) cc_final: 0.7705 (m-80) REVERT: A 384 THR cc_start: 0.8000 (m) cc_final: 0.7712 (m) REVERT: B 194 ARG cc_start: 0.8057 (ttt90) cc_final: 0.7826 (ttt90) REVERT: B 227 PRO cc_start: 0.7240 (Cg_endo) cc_final: 0.6885 (Cg_exo) REVERT: B 228 GLU cc_start: 0.7997 (pp20) cc_final: 0.7692 (pp20) REVERT: B 326 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6216 (mp10) REVERT: B 347 LEU cc_start: 0.8630 (mt) cc_final: 0.8340 (mt) REVERT: B 367 ASN cc_start: 0.7869 (m110) cc_final: 0.7424 (t0) outliers start: 19 outliers final: 14 residues processed: 175 average time/residue: 0.0944 time to fit residues: 24.0406 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 : 0.380 ------------------------------------------------------------------------------- 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 326 GLN Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 381 ILE 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 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 420 THR 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: 0.7980 chunk 100 optimal weight: 0.1980 chunk 64 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 145 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 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 = 0.4789 r_free = 0.4789 target = 0.262946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.213557 restraints weight = 14838.977| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 3.46 r_work: 0.4206 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11101 Z= 0.140 Angle : 0.529 9.602 15247 Z= 0.287 Chirality : 0.045 0.238 1867 Planarity : 0.003 0.044 2033 Dihedral : 13.170 177.755 1999 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % 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: -0.29 (0.21), residues: 1698 helix: 1.05 (0.19), residues: 840 sheet: -1.22 (0.58), residues: 78 loop : -1.50 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.025 0.001 TYR A 315 PHE 0.021 0.002 PHE B 329 TRP 0.006 0.001 TRP B 231 HIS 0.008 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (11101) covalent geometry : angle 0.52907 / 0.29 (15247) hydrogen bonds : bond 0.03602 / 2.49 ( 656) hydrogen bonds : angle 4.52505 / 3.40 ( 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 189 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.392 Fit side-chains REVERT: A 127 GLU cc_start: 0.7804 (tm-30) cc_final: 0.6927 (tm-30) REVERT: A 257 TYR cc_start: 0.8103 (m-80) cc_final: 0.7788 (m-80) REVERT: A 326 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: A 336 LYS cc_start: 0.7127 (tttt) cc_final: 0.6286 (mmtm) REVERT: A 374 TYR cc_start: 0.7961 (m-80) cc_final: 0.7604 (m-80) REVERT: A 384 THR cc_start: 0.7990 (m) cc_final: 0.7694 (m) REVERT: A 443 GLU cc_start: 0.8408 (tp30) cc_final: 0.7759 (tt0) REVERT: B 119 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7786 (m-40) REVERT: B 194 ARG cc_start: 0.7943 (ttt90) cc_final: 0.7715 (ttt90) REVERT: B 227 PRO cc_start: 0.7237 (Cg_endo) cc_final: 0.6897 (Cg_exo) REVERT: B 228 GLU cc_start: 0.7933 (pp20) cc_final: 0.7688 (pp20) REVERT: B 239 MET cc_start: 0.8225 (mtp) cc_final: 0.7907 (mtp) REVERT: B 326 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6313 (mp10) REVERT: B 353 ASP cc_start: 0.6571 (m-30) cc_final: 0.5060 (t70) REVERT: B 367 ASN cc_start: 0.7852 (m110) cc_final: 0.7400 (t0) REVERT: B 385 MET cc_start: 0.7797 (mtt) cc_final: 0.7540 (mtp) REVERT: B 442 ARG cc_start: 0.8421 (ttp-110) cc_final: 0.8182 (ttp-110) outliers start: 19 outliers final: 13 residues processed: 180 average time/residue: 0.0896 time to fit residues: 23.5958 Evaluate side-chains 176 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 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 326 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 83 optimal weight: 10.0000 chunk 93 optimal weight: 0.0670 chunk 44 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 167 optimal weight: 0.0670 chunk 155 optimal weight: 0.1980 chunk 77 optimal weight: 9.9990 chunk 78 optimal weight: 0.0670 chunk 158 optimal weight: 4.9990 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN B 200 GLN B 233 HIS B 321 HIS B 367 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.266081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.217722 restraints weight = 14725.760| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 3.46 r_work: 0.4231 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11101 Z= 0.101 Angle : 0.497 8.765 15247 Z= 0.268 Chirality : 0.044 0.231 1867 Planarity : 0.003 0.043 2033 Dihedral : 12.936 179.989 1997 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.20 % Allowed : 20.28 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.40 (0.19), residues: 835 sheet: -0.81 (0.55), residues: 86 loop : -1.31 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 408 TYR 0.024 0.001 TYR A 315 PHE 0.041 0.002 PHE A 329 TRP 0.005 0.001 TRP B 231 HIS 0.009 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (11101) covalent geometry : angle 0.49665 / 0.27 (15247) hydrogen bonds : bond 0.03051 / 2.12 ( 656) hydrogen bonds : angle 4.13536 / 3.10 ( 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 184 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6178 (mmm) cc_final: 0.5942 (mmm) REVERT: A 127 GLU cc_start: 0.7705 (tm-30) cc_final: 0.6833 (tm-30) REVERT: A 257 TYR cc_start: 0.8018 (m-80) cc_final: 0.7791 (m-80) REVERT: A 259 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6421 (mt) REVERT: A 304 LYS cc_start: 0.7064 (mmtm) cc_final: 0.6471 (mtmt) REVERT: A 312 LYS cc_start: 0.7874 (mttp) cc_final: 0.7446 (mtmm) REVERT: A 326 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: A 336 LYS cc_start: 0.7140 (tttt) cc_final: 0.6215 (mmtm) REVERT: A 374 TYR cc_start: 0.7944 (m-80) cc_final: 0.7553 (m-80) REVERT: A 384 THR cc_start: 0.7978 (m) cc_final: 0.7674 (m) REVERT: A 415 ASP cc_start: 0.7193 (t0) cc_final: 0.6878 (t0) REVERT: A 443 GLU cc_start: 0.8349 (tp30) cc_final: 0.7668 (tt0) REVERT: B 194 ARG cc_start: 0.7883 (ttt90) cc_final: 0.7642 (ttt90) REVERT: B 227 PRO cc_start: 0.7242 (Cg_endo) cc_final: 0.6891 (Cg_exo) REVERT: B 228 GLU cc_start: 0.7867 (pp20) cc_final: 0.7641 (pp20) REVERT: B 239 MET cc_start: 0.8166 (mtp) cc_final: 0.7873 (mtp) REVERT: B 326 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6216 (mp10) REVERT: B 367 ASN cc_start: 0.7909 (m-40) cc_final: 0.7405 (t0) outliers start: 18 outliers final: 10 residues processed: 177 average time/residue: 0.0885 time to fit residues: 22.6470 Evaluate side-chains 171 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 448 ILE 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 326 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 116 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 94 optimal weight: 0.0870 chunk 6 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 overall best weight: 1.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.259680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.210088 restraints weight = 14732.461| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 3.39 r_work: 0.4166 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11101 Z= 0.214 Angle : 0.571 7.751 15247 Z= 0.311 Chirality : 0.046 0.253 1867 Planarity : 0.003 0.045 2033 Dihedral : 13.024 179.335 1997 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.27 % Allowed : 19.93 % Favored : 75.80 % 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: -0.10 (0.21), residues: 1698 helix: 1.16 (0.19), residues: 829 sheet: -0.75 (0.60), residues: 76 loop : -1.35 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 408 TYR 0.026 0.002 TYR B 315 PHE 0.029 0.002 PHE A 329 TRP 0.008 0.002 TRP B 285 HIS 0.006 0.002 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (11101) covalent geometry : angle 0.57096 / 0.31 (15247) hydrogen bonds : bond 0.03897 / 2.68 ( 656) hydrogen bonds : angle 4.43795 / 3.31 ( 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 184 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.6348 (mmm) cc_final: 0.5818 (mmm) REVERT: A 116 LYS cc_start: 0.8257 (mmtt) cc_final: 0.8012 (mmtt) REVERT: A 257 TYR cc_start: 0.8026 (m-80) cc_final: 0.7804 (m-80) REVERT: A 259 LEU cc_start: 0.6660 (OUTLIER) cc_final: 0.6374 (mt) REVERT: A 326 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: A 336 LYS cc_start: 0.7190 (tttt) cc_final: 0.6392 (mmtm) REVERT: A 384 THR cc_start: 0.8226 (m) cc_final: 0.7931 (m) REVERT: A 415 ASP cc_start: 0.7463 (t0) cc_final: 0.7161 (t0) REVERT: A 417 GLU cc_start: 0.8275 (tt0) cc_final: 0.7790 (tp30) REVERT: B 119 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7909 (m-40) REVERT: B 227 PRO cc_start: 0.7266 (Cg_endo) cc_final: 0.6941 (Cg_exo) REVERT: B 239 MET cc_start: 0.8105 (mtp) cc_final: 0.7830 (mtp) REVERT: B 353 ASP cc_start: 0.6365 (m-30) cc_final: 0.5117 (t70) REVERT: B 367 ASN cc_start: 0.7964 (m-40) cc_final: 0.7466 (t0) REVERT: B 385 MET cc_start: 0.7905 (mtt) cc_final: 0.7569 (mtp) outliers start: 24 outliers final: 18 residues processed: 173 average time/residue: 0.0821 time to fit residues: 21.1756 Evaluate side-chains 177 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 229 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 LEU 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 382 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 119 ASN Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 150 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 71 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 152 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.259875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.209821 restraints weight = 14711.032| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 3.41 r_work: 0.4178 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11101 Z= 0.180 Angle : 0.547 8.318 15247 Z= 0.298 Chirality : 0.045 0.244 1867 Planarity : 0.003 0.044 2033 Dihedral : 12.987 179.421 1997 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.74 % Allowed : 22.42 % 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: -0.12 (0.21), residues: 1698 helix: 1.21 (0.19), residues: 817 sheet: -1.15 (0.59), residues: 78 loop : -1.37 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 290 TYR 0.025 0.001 TYR B 315 PHE 0.017 0.002 PHE A 427 TRP 0.008 0.001 TRP B 231 HIS 0.005 0.002 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (11101) covalent geometry : angle 0.54661 / 0.30 (15247) hydrogen bonds : bond 0.03651 / 2.51 ( 656) hydrogen bonds : angle 4.39549 / 3.28 ( 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 181 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6262 (mmm) cc_final: 0.5619 (mmm) REVERT: A 116 LYS cc_start: 0.8243 (mmtt) cc_final: 0.8033 (mmtt) REVERT: A 257 TYR cc_start: 0.8009 (m-80) cc_final: 0.7784 (m-80) REVERT: A 259 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6406 (mt) REVERT: A 304 LYS cc_start: 0.7037 (mmtm) cc_final: 0.6170 (mtmt) REVERT: A 312 LYS cc_start: 0.8287 (mttp) cc_final: 0.7895 (mtmm) REVERT: A 326 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7378 (tm-30) REVERT: A 336 LYS cc_start: 0.7189 (tttt) cc_final: 0.6391 (mmtm) REVERT: A 384 THR cc_start: 0.8130 (m) cc_final: 0.7843 (m) REVERT: A 415 ASP cc_start: 0.7370 (t0) cc_final: 0.7089 (t0) REVERT: A 417 GLU cc_start: 0.8319 (tt0) cc_final: 0.7870 (tp30) REVERT: B 119 ASN cc_start: 0.8144 (OUTLIER) cc_final: 0.7814 (m-40) REVERT: B 312 LYS cc_start: 0.8222 (mttp) cc_final: 0.7975 (mttm) REVERT: B 353 ASP cc_start: 0.6370 (m-30) cc_final: 0.5118 (t70) REVERT: B 367 ASN cc_start: 0.7975 (m-40) cc_final: 0.7479 (t0) outliers start: 21 outliers final: 17 residues processed: 171 average time/residue: 0.0853 time to fit residues: 21.6059 Evaluate side-chains 179 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 382 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 150 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 420 THR 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: 0.0470 chunk 146 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 135 optimal weight: 0.0030 chunk 117 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 147 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.5088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** 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 = 0.264326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.214913 restraints weight = 14771.640| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 3.45 r_work: 0.4211 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.2810 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= 0.116 Angle : 0.508 8.730 15247 Z= 0.274 Chirality : 0.044 0.235 1867 Planarity : 0.003 0.043 2033 Dihedral : 12.817 179.500 1997 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.38 % Allowed : 22.95 % Favored : 73.67 % 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 (0.22), residues: 1698 helix: 1.42 (0.19), residues: 830 sheet: -0.64 (0.62), residues: 76 loop : -1.30 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 352 TYR 0.023 0.001 TYR B 315 PHE 0.019 0.002 PHE A 329 TRP 0.007 0.001 TRP B 231 HIS 0.009 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (11101) covalent geometry : angle 0.50792 / 0.27 (15247) hydrogen bonds : bond 0.03059 / 2.12 ( 656) hydrogen bonds : angle 4.12104 / 3.09 ( 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 178 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.6292 (mmm) cc_final: 0.5122 (mmm) REVERT: A 127 GLU cc_start: 0.7938 (tm-30) cc_final: 0.6667 (tm-30) REVERT: A 255 GLU cc_start: 0.5075 (pt0) cc_final: 0.4853 (pt0) REVERT: A 259 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6562 (mt) REVERT: A 304 LYS cc_start: 0.7009 (mmtm) cc_final: 0.6242 (mtmt) REVERT: A 312 LYS cc_start: 0.8196 (mttp) cc_final: 0.7802 (mtmm) REVERT: A 326 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: A 336 LYS cc_start: 0.7074 (tttt) cc_final: 0.6323 (mmtm) REVERT: A 374 TYR cc_start: 0.7989 (m-80) cc_final: 0.7592 (m-80) REVERT: A 384 THR cc_start: 0.8009 (m) cc_final: 0.7728 (m) REVERT: A 415 ASP cc_start: 0.7283 (t0) cc_final: 0.7014 (t0) REVERT: A 443 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7336 (tt0) REVERT: B 119 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7822 (m-40) REVERT: B 312 LYS cc_start: 0.8100 (mttp) cc_final: 0.7873 (mttm) REVERT: B 326 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6394 (mp10) REVERT: B 353 ASP cc_start: 0.6329 (m-30) cc_final: 0.4888 (t70) REVERT: B 362 MET cc_start: 0.6092 (ttp) cc_final: 0.5540 (tpp) REVERT: B 367 ASN cc_start: 0.7961 (m-40) cc_final: 0.7466 (t0) REVERT: B 442 ARG cc_start: 0.8422 (ttp-110) cc_final: 0.7677 (ttm110) REVERT: B 456 TYR cc_start: 0.7041 (t80) cc_final: 0.6470 (t80) outliers start: 19 outliers final: 14 residues processed: 171 average time/residue: 0.0813 time to fit residues: 20.8905 Evaluate side-chains 172 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU 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 411 THR Chi-restraints excluded: chain A residue 448 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 311 ASP Chi-restraints excluded: chain B residue 326 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 37 optimal weight: 30.0000 chunk 76 optimal weight: 0.0670 chunk 41 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 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 = 0.4786 r_free = 0.4786 target = 0.262121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.212441 restraints weight = 14784.159| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 3.42 r_work: 0.4191 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11101 Z= 0.150 Angle : 0.545 14.595 15247 Z= 0.291 Chirality : 0.044 0.242 1867 Planarity : 0.003 0.045 2033 Dihedral : 12.797 179.742 1997 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.56 % Allowed : 23.67 % Favored : 72.78 % 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: 0.13 (0.22), residues: 1698 helix: 1.40 (0.19), residues: 825 sheet: -0.57 (0.63), residues: 76 loop : -1.30 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 164 TYR 0.025 0.002 TYR B 315 PHE 0.024 0.002 PHE A 329 TRP 0.007 0.001 TRP A 313 HIS 0.005 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (11101) covalent geometry : angle 0.54469 / 0.29 (15247) hydrogen bonds : bond 0.03322 / 2.30 ( 656) hydrogen bonds : angle 4.19426 / 3.13 ( 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 179 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6347 (mmm) cc_final: 0.5138 (mmm) REVERT: A 127 GLU cc_start: 0.7951 (tm-30) cc_final: 0.6723 (tm-30) REVERT: A 259 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6537 (mt) REVERT: A 304 LYS cc_start: 0.7043 (mmtm) cc_final: 0.6211 (mtmt) REVERT: A 312 LYS cc_start: 0.8251 (mttp) cc_final: 0.7842 (mtmm) REVERT: A 326 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: A 336 LYS cc_start: 0.7107 (tttt) cc_final: 0.6238 (mmtm) REVERT: A 384 THR cc_start: 0.8140 (m) cc_final: 0.7881 (m) REVERT: A 415 ASP cc_start: 0.7372 (t0) cc_final: 0.7107 (t0) REVERT: A 443 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7370 (tt0) REVERT: B 119 ASN cc_start: 0.8147 (OUTLIER) cc_final: 0.7818 (m-40) REVERT: B 155 TYR cc_start: 0.7886 (m-80) cc_final: 0.7588 (m-80) REVERT: B 312 LYS cc_start: 0.8251 (mttp) cc_final: 0.8011 (mttm) REVERT: B 326 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.6410 (mp10) REVERT: B 353 ASP cc_start: 0.6328 (m-30) cc_final: 0.4903 (t70) REVERT: B 362 MET cc_start: 0.5914 (ttp) cc_final: 0.5505 (tpp) REVERT: B 367 ASN cc_start: 0.7955 (m-40) cc_final: 0.7482 (t0) REVERT: B 456 TYR cc_start: 0.7075 (t80) cc_final: 0.6509 (t80) outliers start: 20 outliers final: 14 residues processed: 171 average time/residue: 0.0855 time to fit residues: 21.2896 Evaluate side-chains 174 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 326 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 59 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 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 = 0.262980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.213503 restraints weight = 14700.485| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 3.42 r_work: 0.4206 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11101 Z= 0.137 Angle : 0.523 9.131 15247 Z= 0.282 Chirality : 0.044 0.239 1867 Planarity : 0.003 0.044 2033 Dihedral : 12.734 179.748 1997 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.20 % Allowed : 23.49 % Favored : 73.31 % 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: 0.14 (0.22), residues: 1698 helix: 1.40 (0.19), residues: 831 sheet: -0.83 (0.61), residues: 82 loop : -1.27 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 339 TYR 0.025 0.002 TYR B 315 PHE 0.046 0.002 PHE A 329 TRP 0.006 0.001 TRP B 231 HIS 0.007 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (11101) covalent geometry : angle 0.52295 / 0.28 (15247) hydrogen bonds : bond 0.03225 / 2.23 ( 656) hydrogen bonds : angle 4.13905 / 3.09 ( 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 174 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.6354 (mmm) cc_final: 0.5241 (mmm) REVERT: A 127 GLU cc_start: 0.7903 (tm-30) cc_final: 0.6649 (tm-30) REVERT: A 259 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6527 (mt) REVERT: A 304 LYS cc_start: 0.7051 (mmtm) cc_final: 0.6250 (mtmt) REVERT: A 312 LYS cc_start: 0.8260 (mttp) cc_final: 0.7844 (mtmm) REVERT: A 326 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: A 336 LYS cc_start: 0.7110 (tttt) cc_final: 0.6203 (mmtm) REVERT: A 384 THR cc_start: 0.8126 (m) cc_final: 0.7865 (m) REVERT: A 405 LYS cc_start: 0.7974 (ttmt) cc_final: 0.7588 (ptmm) REVERT: A 415 ASP cc_start: 0.7371 (t0) cc_final: 0.7088 (t0) REVERT: A 417 GLU cc_start: 0.8328 (tt0) cc_final: 0.7835 (tp30) REVERT: A 443 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7372 (tt0) REVERT: B 119 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7773 (m-40) REVERT: B 312 LYS cc_start: 0.8236 (mttp) cc_final: 0.7998 (mttm) REVERT: B 326 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.6326 (mp10) REVERT: B 353 ASP cc_start: 0.6334 (m-30) cc_final: 0.4906 (t70) REVERT: B 362 MET cc_start: 0.5884 (ttp) cc_final: 0.5518 (tpp) REVERT: B 367 ASN cc_start: 0.7950 (m-40) cc_final: 0.7470 (t0) REVERT: B 385 MET cc_start: 0.7793 (mtt) cc_final: 0.7452 (mtp) REVERT: B 456 TYR cc_start: 0.6939 (t80) cc_final: 0.6437 (t80) outliers start: 18 outliers final: 14 residues processed: 167 average time/residue: 0.0907 time to fit residues: 22.2364 Evaluate side-chains 174 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 381 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 411 THR 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 311 ASP Chi-restraints excluded: chain B residue 326 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 134 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 33 optimal weight: 0.4980 chunk 156 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 66 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** 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 = 0.4779 r_free = 0.4779 target = 0.260854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.211571 restraints weight = 14715.660| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 3.38 r_work: 0.4175 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11101 Z= 0.184 Angle : 0.568 9.031 15247 Z= 0.308 Chirality : 0.045 0.245 1867 Planarity : 0.003 0.045 2033 Dihedral : 12.786 179.664 1997 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 3.91 % Allowed : 23.13 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.21), residues: 1698 helix: 1.27 (0.19), residues: 825 sheet: -0.67 (0.65), residues: 72 loop : -1.36 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 164 TYR 0.035 0.002 TYR B 298 PHE 0.050 0.002 PHE A 329 TRP 0.007 0.001 TRP B 231 HIS 0.006 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (11101) covalent geometry : angle 0.56788 / 0.31 (15247) hydrogen bonds : bond 0.03612 / 2.50 ( 656) hydrogen bonds : angle 4.31307 / 3.21 ( 1830) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2680.71 seconds wall clock time: 46 minutes 26.35 seconds (2786.35 seconds total)