Starting phenix.real_space_refine on Sat Aug 23 09:38:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tdv_41174/08_2025/8tdv_41174_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tdv_41174/08_2025/8tdv_41174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tdv_41174/08_2025/8tdv_41174_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tdv_41174/08_2025/8tdv_41174_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tdv_41174/08_2025/8tdv_41174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tdv_41174/08_2025/8tdv_41174.map" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.255 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 13 5.49 5 S 30 5.16 5 C 6733 2.51 5 N 2069 2.21 5 O 2110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10957 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3195 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 19, 'TRANS': 419} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 414 Unresolved non-hydrogen angles: 526 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 9, 'GLU:plan': 14, 'ASN:plan1': 4, 'TYR:plan': 6, 'GLN:plan1': 5, 'ARG:plan': 7, 'PHE:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 235 Chain: "B" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3122 Classifications: {'peptide': 417} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 18, 'TRANS': 398} Chain breaks: 5 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 394 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ASP:plan': 10, 'GLN:plan1': 4, 'GLU:plan': 8, 'ASN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 4, 'PHE:plan': 4, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 176 Chain: "E" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 2198 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 395} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 3 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1527 Unresolved non-hydrogen angles: 1950 Unresolved non-hydrogen dihedrals: 1294 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'ASN:plan1': 19, 'ASP:plan': 30, 'HIS:plan': 17, 'GLU:plan': 30, 'ARG:plan': 27, 'GLN:plan1': 18, 'PHE:plan': 21, 'TYR:plan': 22, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 875 Chain: "F" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 2169 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 390} Link IDs: {'PTRANS': 19, 'TRANS': 419} Chain breaks: 5 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1511 Unresolved non-hydrogen angles: 1930 Unresolved non-hydrogen dihedrals: 1278 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'ASP:plan': 33, 'ASN:plan1': 19, 'HIS:plan': 17, 'GLU:plan': 29, 'ARG:plan': 27, 'GLN:plan1': 17, 'PHE:plan': 21, 'TYR:plan': 21, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 869 Chain: "J" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4} Link IDs: {'rna2p': 5} Chain: "K" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 145 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 6} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.31, per 1000 atoms: 0.30 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: 1.07 Conformation dependent library (CDL) restraints added in 606.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.47 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: 1.76 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3949 1.34 - 1.46: 2025 1.46 - 1.58: 5057 1.58 - 1.69: 24 1.69 - 1.81: 46 Bond restraints: 11101 Sorted by residual: bond pdb=" C3' A K 9 " pdb=" O3' A K 9 " ideal model delta sigma weight residual 1.427 1.446 -0.019 1.50e-02 4.44e+03 1.55e+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 bond pdb=" CA ASP E 516 " pdb=" C ASP E 516 " ideal model delta sigma weight residual 1.531 1.523 0.008 1.12e-02 7.97e+03 5.68e-01 bond pdb=" C ARG F 366 " pdb=" O ARG F 366 " ideal model delta sigma weight residual 1.236 1.228 0.008 1.15e-02 7.56e+03 4.97e-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=" C3' A K 9 " pdb=" O3' A K 9 " pdb=" P C K 10 " ideal model delta sigma weight residual 120.20 125.58 -5.38 1.50e+00 4.44e-01 1.29e+01 angle pdb=" O3' A K 9 " pdb=" C3' A K 9 " pdb=" C2' A K 9 " ideal model delta sigma weight residual 109.50 114.73 -5.23 1.50e+00 4.44e-01 1.22e+01 angle pdb=" C ILE F 499 " pdb=" N VAL F 500 " pdb=" CA VAL F 500 " ideal model delta sigma weight residual 120.49 124.80 -4.31 1.38e+00 5.25e-01 9.75e+00 angle pdb=" CA TYR B 315 " pdb=" CB TYR B 315 " pdb=" CG TYR B 315 " ideal model delta sigma weight residual 113.90 119.50 -5.60 1.80e+00 3.09e-01 9.66e+00 angle pdb=" N LEU E 208 " pdb=" CA LEU E 208 " pdb=" C LEU E 208 " ideal model delta sigma weight residual 111.11 114.65 -3.54 1.20e+00 6.94e-01 8.70e+00 ... (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 2.260 nonbonded pdb=" OD1 ASP A 311 " pdb="FE FE A 701 " model vdw 2.001 2.260 nonbonded pdb=" OD1 ASP B 311 " pdb="FE FE B 701 " model vdw 2.026 2.260 nonbonded pdb=" OD2 ASP B 207 " pdb="FE FE B 701 " model vdw 2.057 2.260 nonbonded pdb=" O VAL A 117 " pdb=" O2' G J 8 " model vdw 2.113 3.040 ... (remaining 80212 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 114 through 123 and (name N or name CA or name C or name \ O or name CB )) or resid 124 or (resid 125 through 150 and (name N or name CA or \ name C or name O or name CB )) or resid 151 through 153 or (resid 154 through 1 \ 58 and (name N or name CA or name C or name O or name CB )) or (resid 159 throug \ h 169 and (name N or name CA or name C or name O or name CB )) or resid 170 or ( \ resid 171 and (name N or name CA or name C or name O or name CB )) or resid 172 \ or (resid 173 through 175 and (name N or name CA or name C or name O or name CB \ )) or resid 176 or (resid 177 through 182 and (name N or name CA or name C or na \ me O or name CB )) or resid 183 or (resid 184 through 202 and (name N or name CA \ or name C or name O or name CB )) or resid 203 or (resid 204 through 208 and (n \ ame N or name CA or name C or name O or name CB )) or resid 209 or (resid 210 an \ d (name N or name CA or name C or name O or name CB )) or resid 211 or (resid 21 \ 2 through 218 and (name N or name CA or name C or name O or name CB )) or resid \ 219 or (resid 220 through 235 and (name N or name CA or name C or name O or name \ CB )) or (resid 236 through 248 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 249 through 257 and (name N or name CA or name C or name O o \ r name CB )) or resid 258 or (resid 259 through 273 and (name N or name CA or na \ me C or name O or name CB )) or resid 274 or (resid 275 through 277 and (name N \ or name CA or name C or name O or name CB )) or (resid 282 through 288 and (name \ N or name CA or name C or name O or name CB )) or resid 289 or (resid 290 throu \ gh 306 and (name N or name CA or name C or name O or name CB )) or resid 307 or \ (resid 308 through 323 and (name N or name CA or name C or name O or name CB )) \ or resid 324 or (resid 325 through 356 and (name N or name CA or name C or name \ O or name CB )) or resid 357 or (resid 358 through 378 and (name N or name CA or \ name C or name O or name CB )) or resid 379 or (resid 380 through 400 and (name \ N or name CA or name C or name O or name CB )) or (resid 401 through 457 and (n \ ame N or name CA or name C or name O or name CB )) or resid 458 through 462 or r \ esid 469 through 487 or resid 492 through 504 or resid 514 through 520 or resid \ 549 through 579)) selection = (chain 'B' and ((resid 114 through 123 and (name N or name CA or name C or name \ O or name CB )) or resid 124 or (resid 125 through 150 and (name N or name CA or \ name C or name O or name CB )) or resid 151 through 153 or (resid 154 through 1 \ 58 and (name N or name CA or name C or name O or name CB )) or (resid 159 throug \ h 169 and (name N or name CA or name C or name O or name CB )) or resid 170 or ( \ resid 171 and (name N or name CA or name C or name O or name CB )) or resid 172 \ or (resid 173 through 175 and (name N or name CA or name C or name O or name CB \ )) or resid 176 or (resid 177 through 182 and (name N or name CA or name C or na \ me O or name CB )) or resid 183 or (resid 184 through 202 and (name N or name CA \ or name C or name O or name CB )) or resid 203 or (resid 204 through 208 and (n \ ame N or name CA or name C or name O or name CB )) or resid 209 or (resid 210 an \ d (name N or name CA or name C or name O or name CB )) or resid 211 or (resid 21 \ 2 through 218 and (name N or name CA or name C or name O or name CB )) or resid \ 219 or (resid 220 through 235 and (name N or name CA or name C or name O or name \ CB )) or resid 236 or (resid 237 through 248 and (name N or name CA or name C o \ r name O or name CB )) or resid 249 or (resid 250 through 257 and (name N or nam \ e CA or name C or name O or name CB )) or resid 258 or (resid 259 through 273 an \ d (name N or name CA or name C or name O or name CB )) or resid 274 or (resid 27 \ 5 through 288 and (name N or name CA or name C or name O or name CB )) or resid \ 289 or (resid 290 through 306 and (name N or name CA or name C or name O or name \ CB )) or resid 307 or (resid 308 through 323 and (name N or name CA or name C o \ r name O or name CB )) or resid 324 or (resid 325 through 356 and (name N or nam \ e CA or name C or name O or name CB )) or resid 357 or (resid 358 through 378 an \ d (name N or name CA or name C or name O or name CB )) or resid 379 or (resid 38 \ 0 through 400 and (name N or name CA or name C or name O or name CB )) or (resid \ 401 through 457 and (name N or name CA or name C or name O or name CB )) or res \ id 458 through 487 or (resid 492 through 579 and (name N or name CA or name C or \ name O or name CB )))) selection = (chain 'E' and (resid 114 through 277 or resid 282 through 462 or resid 469 thro \ ugh 487 or resid 492 through 504 or resid 514 through 520 or resid 549 through 5 \ 79)) selection = (chain 'F' and (resid 114 through 462 or resid 469 through 487 or resid 492 thro \ ugh 504 or resid 514 through 520 or resid 549 through 579)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.320 Find NCS groups from input model: 0.330 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5999 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= 0.118 Angle : 0.525 5.738 15247 Z= 0.310 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 aren 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 covalent geometry : bond 0.00214 (11101) covalent geometry : angle 0.52528 (15247) hydrogen bonds : bond 0.14623 ( 656) hydrogen bonds : angle 6.62510 ( 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 : 0.382 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: 0.0968 time to fit residues: 30.9035 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 : 0.429 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 271 GLN ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4730 r_free = 0.4730 target = 0.256021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.218169 restraints weight = 14844.016| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 3.29 r_work: 0.4148 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 11101 Z= 0.274 Angle : 0.670 8.658 15247 Z= 0.364 Chirality : 0.048 0.257 1867 Planarity : 0.005 0.052 2033 Dihedral : 13.390 179.147 1999 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % 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 aren not related in a simple way. whole: -0.83 (0.20), residues: 1698 helix: 0.52 (0.18), residues: 844 sheet: -0.70 (0.63), residues: 66 loop : -1.76 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 145 TYR 0.030 0.002 TYR A 315 PHE 0.022 0.003 PHE A 427 TRP 0.010 0.002 TRP B 285 HIS 0.007 0.002 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00607 (11101) covalent geometry : angle 0.67031 (15247) hydrogen bonds : bond 0.04941 ( 656) hydrogen bonds : angle 5.24587 ( 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 200 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.307 Fit side-chains REVERT: A 127 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7304 (tm-30) REVERT: A 204 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6589 (mt) REVERT: A 233 HIS cc_start: 0.7779 (p-80) cc_final: 0.7445 (p-80) REVERT: A 257 TYR cc_start: 0.8207 (m-80) cc_final: 0.7850 (m-80) REVERT: A 326 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7358 (tm-30) REVERT: A 384 THR cc_start: 0.8117 (m) cc_final: 0.7833 (m) REVERT: A 415 ASP cc_start: 0.7474 (t0) cc_final: 0.7224 (t0) REVERT: A 443 GLU cc_start: 0.8244 (tp30) cc_final: 0.8042 (tp30) REVERT: A 447 GLN cc_start: 0.7820 (mm110) cc_final: 0.6964 (mt0) REVERT: B 142 GLN cc_start: 0.8507 (mm110) cc_final: 0.8301 (mm110) REVERT: B 347 LEU cc_start: 0.8524 (mt) cc_final: 0.8257 (mt) REVERT: B 353 ASP cc_start: 0.6466 (m-30) cc_final: 0.5087 (t70) REVERT: B 367 ASN cc_start: 0.7875 (m110) cc_final: 0.7429 (t0) REVERT: B 380 ASN cc_start: 0.7066 (m-40) cc_final: 0.6689 (p0) REVERT: B 385 MET cc_start: 0.8023 (mtt) cc_final: 0.7652 (mtp) REVERT: B 442 ARG cc_start: 0.8492 (ttp-110) cc_final: 0.7741 (ttm110) outliers start: 21 outliers final: 14 residues processed: 186 average time/residue: 0.0970 time to fit residues: 26.1475 Evaluate side-chains 188 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 204 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 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 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: 9.9990 chunk 63 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 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** ** B 376 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 = 0.4715 r_free = 0.4715 target = 0.253699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.217020 restraints weight = 14996.609| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 3.06 r_work: 0.4124 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 11101 Z= 0.318 Angle : 0.695 8.435 15247 Z= 0.379 Chirality : 0.049 0.264 1867 Planarity : 0.005 0.050 2033 Dihedral : 13.359 177.232 1999 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 4.63 % Allowed : 19.22 % Favored : 76.16 % 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 aren not related in a simple way. whole: -1.25 (0.20), residues: 1698 helix: 0.16 (0.18), residues: 829 sheet: -0.90 (0.57), residues: 76 loop : -1.93 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 145 TYR 0.030 0.002 TYR A 315 PHE 0.025 0.002 PHE A 427 TRP 0.010 0.002 TRP A 231 HIS 0.009 0.002 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00709 (11101) covalent geometry : angle 0.69534 (15247) hydrogen bonds : bond 0.05145 ( 656) hydrogen bonds : angle 5.37203 ( 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 193 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.380 Fit side-chains REVERT: A 115 MET cc_start: 0.6208 (mmm) cc_final: 0.5125 (mmm) REVERT: A 127 GLU cc_start: 0.7894 (tm-30) cc_final: 0.6774 (tm-30) REVERT: A 233 HIS cc_start: 0.7841 (p-80) cc_final: 0.7550 (p-80) REVERT: A 257 TYR cc_start: 0.8177 (m-80) cc_final: 0.7959 (m-80) REVERT: A 336 LYS cc_start: 0.7083 (tttt) cc_final: 0.6066 (mmtm) REVERT: A 384 THR cc_start: 0.8146 (m) cc_final: 0.7936 (m) REVERT: A 415 ASP cc_start: 0.7670 (t0) cc_final: 0.7317 (t0) REVERT: B 119 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.8057 (m-40) REVERT: B 142 GLN cc_start: 0.8526 (mm110) cc_final: 0.8253 (mm110) REVERT: B 326 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6367 (mp10) REVERT: B 347 LEU cc_start: 0.8554 (mt) cc_final: 0.8305 (mt) REVERT: B 353 ASP cc_start: 0.6388 (m-30) cc_final: 0.5150 (t70) REVERT: B 380 ASN cc_start: 0.6986 (m-40) cc_final: 0.6615 (p0) REVERT: B 442 ARG cc_start: 0.8447 (ttp-110) cc_final: 0.8165 (ttp-110) outliers start: 26 outliers final: 19 residues processed: 178 average time/residue: 0.1086 time to fit residues: 27.7433 Evaluate side-chains 183 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 381 ILE 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 156 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 420 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 12 optimal weight: 0.5980 chunk 100 optimal weight: 0.0870 chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 37 optimal weight: 30.0000 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 145 optimal weight: 0.0570 chunk 0 optimal weight: 0.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN A 321 HIS A 452 ASN B 210 HIS B 233 HIS ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 HIS B 376 HIS 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 = 0.261714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.212705 restraints weight = 14783.746| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 3.39 r_work: 0.4192 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11101 Z= 0.116 Angle : 0.503 7.233 15247 Z= 0.273 Chirality : 0.044 0.234 1867 Planarity : 0.003 0.046 2033 Dihedral : 12.880 175.639 1997 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.56 % Allowed : 21.00 % Favored : 75.44 % 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 aren not related in a simple way. whole: -0.44 (0.21), residues: 1698 helix: 1.02 (0.19), residues: 829 sheet: -1.08 (0.61), residues: 78 loop : -1.68 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 451 TYR 0.023 0.001 TYR B 315 PHE 0.013 0.002 PHE A 141 TRP 0.005 0.001 TRP B 231 HIS 0.013 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00253 (11101) covalent geometry : angle 0.50323 (15247) hydrogen bonds : bond 0.03207 ( 656) hydrogen bonds : angle 4.30784 ( 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 199 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.6294 (mmm) cc_final: 0.5639 (mmm) REVERT: A 127 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7065 (tm-30) REVERT: A 233 HIS cc_start: 0.7624 (p-80) cc_final: 0.7321 (p-80) REVERT: A 304 LYS cc_start: 0.6913 (mmtm) cc_final: 0.6599 (mtmt) REVERT: A 336 LYS cc_start: 0.7102 (tttt) cc_final: 0.6153 (mmtm) REVERT: A 374 TYR cc_start: 0.8033 (m-80) cc_final: 0.7622 (m-80) REVERT: A 384 THR cc_start: 0.8071 (m) cc_final: 0.7788 (m) REVERT: A 415 ASP cc_start: 0.7294 (t0) cc_final: 0.7003 (t0) REVERT: B 119 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7866 (m-40) REVERT: B 194 ARG cc_start: 0.7945 (ttt90) cc_final: 0.7704 (ttt90) REVERT: B 326 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6177 (mp10) REVERT: B 339 ARG cc_start: 0.7814 (mtp-110) cc_final: 0.7592 (mtm110) REVERT: B 353 ASP cc_start: 0.6315 (m-30) cc_final: 0.4898 (t70) REVERT: B 367 ASN cc_start: 0.7853 (m110) cc_final: 0.7394 (t0) REVERT: B 385 MET cc_start: 0.7938 (mtt) cc_final: 0.7520 (mtp) outliers start: 20 outliers final: 12 residues processed: 191 average time/residue: 0.0996 time to fit residues: 27.4573 Evaluate side-chains 183 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 311 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 119 ASN 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: 9.9990 chunk 93 optimal weight: 0.0470 chunk 44 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 chunk 167 optimal weight: 0.0050 chunk 155 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 overall best weight: 2.2098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.252487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.202166 restraints weight = 14860.768| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 3.34 r_work: 0.4088 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 11101 Z= 0.329 Angle : 0.710 10.106 15247 Z= 0.382 Chirality : 0.049 0.260 1867 Planarity : 0.005 0.047 2033 Dihedral : 13.187 179.358 1997 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.66 % Favored : 90.28 % Rotamer: Outliers : 5.34 % Allowed : 21.89 % 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 aren not related in a simple way. whole: -1.08 (0.21), residues: 1698 helix: 0.31 (0.18), residues: 826 sheet: -0.76 (0.60), residues: 76 loop : -1.84 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 145 TYR 0.032 0.002 TYR A 315 PHE 0.027 0.003 PHE A 241 TRP 0.010 0.002 TRP B 231 HIS 0.011 0.002 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00737 (11101) covalent geometry : angle 0.71038 (15247) hydrogen bonds : bond 0.05106 ( 656) hydrogen bonds : angle 5.21603 ( 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 198 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6464 (mmm) cc_final: 0.5718 (mmm) REVERT: A 127 GLU cc_start: 0.7935 (tm-30) cc_final: 0.6975 (tm-30) REVERT: A 233 HIS cc_start: 0.7881 (p-80) cc_final: 0.7603 (p-80) REVERT: A 336 LYS cc_start: 0.6977 (tttt) cc_final: 0.5981 (mmtm) REVERT: A 415 ASP cc_start: 0.7647 (t0) cc_final: 0.7263 (t0) REVERT: B 353 ASP cc_start: 0.6440 (m-30) cc_final: 0.5205 (t70) REVERT: B 385 MET cc_start: 0.8188 (mtt) cc_final: 0.7962 (mtt) REVERT: B 409 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8375 (tt) outliers start: 30 outliers final: 25 residues processed: 184 average time/residue: 0.0949 time to fit residues: 25.9744 Evaluate side-chains 181 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 191 ILE 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 264 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 448 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 199 VAL Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 420 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 116 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 170 optimal weight: 7.9990 chunk 63 optimal weight: 0.5980 chunk 138 optimal weight: 8.9990 chunk 94 optimal weight: 0.0370 chunk 6 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 37 optimal weight: 30.0000 chunk 11 optimal weight: 0.5980 chunk 107 optimal weight: 10.0000 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 380 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.261561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.212437 restraints weight = 14766.153| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 3.38 r_work: 0.4187 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11101 Z= 0.116 Angle : 0.520 7.948 15247 Z= 0.279 Chirality : 0.044 0.230 1867 Planarity : 0.003 0.044 2033 Dihedral : 12.737 178.176 1997 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.91 % Allowed : 24.02 % Favored : 72.06 % 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 aren not related in a simple way. whole: -0.34 (0.21), residues: 1698 helix: 1.07 (0.19), residues: 828 sheet: -0.39 (0.68), residues: 66 loop : -1.66 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 408 TYR 0.023 0.001 TYR B 315 PHE 0.019 0.002 PHE B 213 TRP 0.008 0.001 TRP B 231 HIS 0.013 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00256 (11101) covalent geometry : angle 0.51952 (15247) hydrogen bonds : bond 0.03111 ( 656) hydrogen bonds : angle 4.23896 ( 1830) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6463 (mmm) cc_final: 0.5676 (mmm) REVERT: A 127 GLU cc_start: 0.7718 (tm-30) cc_final: 0.6808 (tm-30) REVERT: A 233 HIS cc_start: 0.7610 (p-80) cc_final: 0.7307 (p-80) REVERT: A 240 MET cc_start: 0.7938 (tpp) cc_final: 0.6970 (tpp) REVERT: A 304 LYS cc_start: 0.7047 (mmtm) cc_final: 0.6558 (mtmt) REVERT: A 312 LYS cc_start: 0.8225 (mttp) cc_final: 0.7818 (mtmm) REVERT: A 336 LYS cc_start: 0.7071 (tttt) cc_final: 0.6160 (mmtm) REVERT: A 374 TYR cc_start: 0.8019 (m-80) cc_final: 0.7547 (m-80) REVERT: B 194 ARG cc_start: 0.8060 (ttt90) cc_final: 0.7775 (ttt90) REVERT: B 339 ARG cc_start: 0.7735 (mtp-110) cc_final: 0.7264 (mtp85) REVERT: B 353 ASP cc_start: 0.6713 (m-30) cc_final: 0.4827 (t70) REVERT: B 367 ASN cc_start: 0.7856 (m110) cc_final: 0.7456 (t0) REVERT: B 385 MET cc_start: 0.8028 (mtt) cc_final: 0.7768 (mtt) outliers start: 22 outliers final: 17 residues processed: 179 average time/residue: 0.0971 time to fit residues: 24.9500 Evaluate side-chains 174 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 382 ILE 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 199 VAL Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 380 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 71 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 13 optimal weight: 0.4980 chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 30.0000 chunk 148 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 HIS ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN B 380 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.255281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.204912 restraints weight = 14804.554| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 3.37 r_work: 0.4113 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 11101 Z= 0.257 Angle : 0.635 8.637 15247 Z= 0.342 Chirality : 0.047 0.252 1867 Planarity : 0.004 0.044 2033 Dihedral : 12.947 176.595 1997 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 5.16 % Allowed : 25.62 % Favored : 69.22 % 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 aren not related in a simple way. whole: -0.81 (0.21), residues: 1698 helix: 0.62 (0.19), residues: 833 sheet: -0.71 (0.63), residues: 76 loop : -1.83 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 164 TYR 0.030 0.002 TYR B 315 PHE 0.022 0.002 PHE A 241 TRP 0.008 0.002 TRP B 231 HIS 0.007 0.002 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00579 (11101) covalent geometry : angle 0.63457 (15247) hydrogen bonds : bond 0.04396 ( 656) hydrogen bonds : angle 4.79069 ( 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 199 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6577 (mmm) cc_final: 0.5751 (mmm) REVERT: A 127 GLU cc_start: 0.7913 (tm-30) cc_final: 0.6879 (tm-30) REVERT: A 233 HIS cc_start: 0.7826 (p-80) cc_final: 0.7529 (p-80) REVERT: A 256 GLN cc_start: 0.7657 (tm-30) cc_final: 0.7401 (tm-30) REVERT: A 304 LYS cc_start: 0.7064 (mmtm) cc_final: 0.6644 (mtmt) REVERT: A 336 LYS cc_start: 0.6982 (tttt) cc_final: 0.6026 (mmtm) REVERT: A 355 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6930 (mm-30) REVERT: A 415 ASP cc_start: 0.7452 (t0) cc_final: 0.7145 (t0) REVERT: A 417 GLU cc_start: 0.8204 (tt0) cc_final: 0.7886 (tp30) REVERT: B 353 ASP cc_start: 0.6686 (m-30) cc_final: 0.4972 (t70) REVERT: B 385 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7921 (mtt) REVERT: B 409 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8346 (tt) outliers start: 29 outliers final: 24 residues processed: 185 average time/residue: 0.1040 time to fit residues: 27.7719 Evaluate side-chains 191 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 191 ILE 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 340 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 368 SER 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 156 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 409 ILE 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: 0.4980 chunk 146 optimal weight: 0.0470 chunk 52 optimal weight: 0.5980 chunk 135 optimal weight: 0.0040 chunk 117 optimal weight: 9.9990 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 147 optimal weight: 9.9990 chunk 91 optimal weight: 0.0000 chunk 61 optimal weight: 0.9990 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS B 248 ASN B 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.263251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.214486 restraints weight = 14750.550| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 3.40 r_work: 0.4211 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.3439 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= 0.100 Angle : 0.510 8.348 15247 Z= 0.273 Chirality : 0.043 0.229 1867 Planarity : 0.003 0.044 2033 Dihedral : 12.569 179.913 1997 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.74 % Allowed : 26.87 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.21), residues: 1698 helix: 1.24 (0.19), residues: 838 sheet: -0.38 (0.70), residues: 66 loop : -1.68 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 352 TYR 0.022 0.001 TYR B 315 PHE 0.015 0.001 PHE B 213 TRP 0.008 0.001 TRP B 231 HIS 0.010 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00214 (11101) covalent geometry : angle 0.50981 (15247) hydrogen bonds : bond 0.02881 ( 656) hydrogen bonds : angle 4.08231 ( 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 184 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6482 (mmm) cc_final: 0.5721 (mmm) REVERT: A 127 GLU cc_start: 0.7763 (tm-30) cc_final: 0.6926 (tm-30) REVERT: A 233 HIS cc_start: 0.7551 (p-80) cc_final: 0.7247 (p-80) REVERT: A 304 LYS cc_start: 0.7126 (mmtm) cc_final: 0.6650 (mtmt) REVERT: A 312 LYS cc_start: 0.8235 (mttp) cc_final: 0.7831 (mtmm) REVERT: A 336 LYS cc_start: 0.6984 (tttt) cc_final: 0.6145 (mmtm) REVERT: A 355 GLU cc_start: 0.6821 (mm-30) cc_final: 0.6575 (mm-30) REVERT: A 374 TYR cc_start: 0.8001 (m-80) cc_final: 0.7566 (m-80) REVERT: A 405 LYS cc_start: 0.7857 (ttmt) cc_final: 0.7614 (ptmm) REVERT: A 406 LYS cc_start: 0.8276 (mppt) cc_final: 0.7975 (mmtt) REVERT: A 415 ASP cc_start: 0.7292 (t0) cc_final: 0.7023 (t0) REVERT: B 353 ASP cc_start: 0.6565 (m-30) cc_final: 0.4690 (t70) REVERT: B 367 ASN cc_start: 0.7829 (m110) cc_final: 0.7361 (t0) outliers start: 21 outliers final: 12 residues processed: 174 average time/residue: 0.1038 time to fit residues: 26.2893 Evaluate side-chains 171 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 380 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 10 optimal weight: 0.0060 chunk 9 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 37 optimal weight: 0.0170 chunk 76 optimal weight: 0.0060 chunk 41 optimal weight: 20.0000 chunk 148 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 18 optimal weight: 0.0270 chunk 57 optimal weight: 0.9990 overall best weight: 0.2108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.264782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.215984 restraints weight = 14781.990| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 3.41 r_work: 0.4229 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11101 Z= 0.100 Angle : 0.528 12.691 15247 Z= 0.278 Chirality : 0.043 0.214 1867 Planarity : 0.003 0.044 2033 Dihedral : 12.318 178.901 1997 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.14 % Allowed : 28.83 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.22), residues: 1698 helix: 1.50 (0.19), residues: 839 sheet: -0.50 (0.62), residues: 82 loop : -1.45 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 143 TYR 0.022 0.001 TYR B 315 PHE 0.012 0.001 PHE A 221 TRP 0.009 0.001 TRP A 313 HIS 0.011 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00214 (11101) covalent geometry : angle 0.52752 (15247) hydrogen bonds : bond 0.02763 ( 656) hydrogen bonds : angle 3.95166 ( 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 167 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6623 (mmm) cc_final: 0.4753 (mmm) REVERT: A 304 LYS cc_start: 0.7306 (mmtm) cc_final: 0.6782 (mtmt) REVERT: A 312 LYS cc_start: 0.8175 (mttp) cc_final: 0.7832 (mtmm) REVERT: A 336 LYS cc_start: 0.6961 (tttt) cc_final: 0.6171 (mmtm) REVERT: A 374 TYR cc_start: 0.8024 (m-80) cc_final: 0.7575 (m-80) REVERT: A 405 LYS cc_start: 0.7767 (ttmt) cc_final: 0.7510 (ptmm) REVERT: A 406 LYS cc_start: 0.8241 (mppt) cc_final: 0.7931 (mmtt) REVERT: A 415 ASP cc_start: 0.7247 (t0) cc_final: 0.7029 (t0) REVERT: A 417 GLU cc_start: 0.8267 (tt0) cc_final: 0.7983 (tt0) REVERT: A 443 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7337 (tt0) REVERT: B 185 LYS cc_start: 0.7872 (mtpt) cc_final: 0.7624 (mttt) REVERT: B 255 GLU cc_start: 0.7742 (pp20) cc_final: 0.7501 (pp20) REVERT: B 326 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.6643 (mp10) REVERT: B 353 ASP cc_start: 0.6579 (m-30) cc_final: 0.4678 (t70) REVERT: B 367 ASN cc_start: 0.7828 (m110) cc_final: 0.7369 (t0) outliers start: 12 outliers final: 10 residues processed: 165 average time/residue: 0.1032 time to fit residues: 24.9880 Evaluate side-chains 161 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 199 VAL 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: 1.9990 chunk 58 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 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: 0.6980 chunk 8 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4787 r_free = 0.4787 target = 0.262545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.213167 restraints weight = 14696.513| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 3.40 r_work: 0.4200 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11101 Z= 0.128 Angle : 0.523 9.649 15247 Z= 0.279 Chirality : 0.044 0.195 1867 Planarity : 0.003 0.043 2033 Dihedral : 12.284 179.564 1997 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.31 % Allowed : 28.11 % Favored : 69.57 % 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 aren not related in a simple way. whole: 0.25 (0.22), residues: 1698 helix: 1.55 (0.19), residues: 838 sheet: -0.56 (0.61), residues: 86 loop : -1.37 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 164 TYR 0.028 0.002 TYR B 298 PHE 0.028 0.002 PHE A 329 TRP 0.007 0.001 TRP B 231 HIS 0.008 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00286 (11101) covalent geometry : angle 0.52314 (15247) hydrogen bonds : bond 0.03070 ( 656) hydrogen bonds : angle 4.04607 ( 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 169 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6582 (mmm) cc_final: 0.5052 (mmm) REVERT: A 127 GLU cc_start: 0.7710 (tm-30) cc_final: 0.6671 (tm-30) REVERT: A 304 LYS cc_start: 0.7257 (mmtm) cc_final: 0.6747 (mtmt) REVERT: A 312 LYS cc_start: 0.8304 (mttp) cc_final: 0.7890 (mtmm) REVERT: A 336 LYS cc_start: 0.6920 (tttt) cc_final: 0.6139 (mmtm) REVERT: A 374 TYR cc_start: 0.8100 (m-80) cc_final: 0.7676 (m-80) REVERT: A 405 LYS cc_start: 0.7837 (ttmt) cc_final: 0.7568 (ptmm) REVERT: A 406 LYS cc_start: 0.8263 (mppt) cc_final: 0.7863 (mmtt) REVERT: A 415 ASP cc_start: 0.7375 (t0) cc_final: 0.7104 (t0) REVERT: A 417 GLU cc_start: 0.8265 (tt0) cc_final: 0.7887 (tp30) REVERT: B 185 LYS cc_start: 0.7861 (mtpt) cc_final: 0.7618 (mttt) REVERT: B 255 GLU cc_start: 0.7778 (pp20) cc_final: 0.7487 (pp20) REVERT: B 353 ASP cc_start: 0.6598 (m-30) cc_final: 0.4691 (t70) REVERT: B 367 ASN cc_start: 0.7856 (m110) cc_final: 0.7465 (t0) outliers start: 13 outliers final: 11 residues processed: 163 average time/residue: 0.1050 time to fit residues: 24.8340 Evaluate side-chains 164 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 420 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 134 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 38 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.259496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.209274 restraints weight = 14827.540| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 3.40 r_work: 0.4162 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 11101 Z= 0.217 Angle : 0.608 10.682 15247 Z= 0.324 Chirality : 0.046 0.171 1867 Planarity : 0.004 0.043 2033 Dihedral : 12.444 178.594 1997 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 3.38 % Allowed : 26.87 % Favored : 69.75 % 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 aren not related in a simple way. whole: -0.22 (0.21), residues: 1698 helix: 1.11 (0.19), residues: 842 sheet: -0.40 (0.68), residues: 71 loop : -1.57 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 318 TYR 0.030 0.002 TYR B 287 PHE 0.042 0.002 PHE A 329 TRP 0.009 0.002 TRP B 231 HIS 0.006 0.002 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00491 (11101) covalent geometry : angle 0.60817 (15247) hydrogen bonds : bond 0.03904 ( 656) hydrogen bonds : angle 4.48356 ( 1830) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3051.15 seconds wall clock time: 52 minutes 43.00 seconds (3163.00 seconds total)