Starting phenix.real_space_refine on Sun Dec 29 19:14:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tdv_41174/12_2024/8tdv_41174_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tdv_41174/12_2024/8tdv_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tdv_41174/12_2024/8tdv_41174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tdv_41174/12_2024/8tdv_41174.map" model { file = "/net/cci-nas-00/data/ceres_data/8tdv_41174/12_2024/8tdv_41174_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tdv_41174/12_2024/8tdv_41174_neut.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.255 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-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 5, 'ARG:plan': 7, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 4, 'GLU:plan': 14, 'HIS:plan': 2} 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: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 4} 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: {'GLN:plan1': 18, 'ASP:plan': 30, 'TYR:plan': 22, 'ASN:plan1': 19, 'TRP:plan': 4, 'HIS:plan': 17, 'PHE:plan': 21, 'GLU:plan': 30, 'ARG:plan': 27} 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: {'GLN:plan1': 17, 'ASP:plan': 33, 'TYR:plan': 21, 'ASN:plan1': 19, 'TRP:plan': 4, 'HIS:plan': 17, 'PHE:plan': 21, 'GLU:plan': 29, 'ARG:plan': 27} 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: 8.14, per 1000 atoms: 0.74 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: 3.22 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.61 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: 3.75 Time building geometry restraints manager: 3.50 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: 1.560 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.120 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.220 ------------------------------------------------------------------------------- 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= 0.146 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (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 TRP 0.004 0.001 TRP B 231 HIS 0.003 0.001 HIS A 162 PHE 0.011 0.001 PHE A 141 TYR 0.025 0.001 TYR A 315 ARG 0.004 0.000 ARG A 333 *********************** 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 : 1.199 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: 0.2393 time to fit residues: 76.3600 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 : 1.391 ------------------------------------------------------------------------------- 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 144 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 81 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 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 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6123 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11101 Z= 0.269 Angle : 0.563 6.913 15247 Z= 0.307 Chirality : 0.045 0.238 1867 Planarity : 0.004 0.052 2033 Dihedral : 13.255 177.819 1999 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.56 % Allowed : 14.23 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.21), residues: 1698 helix: 0.95 (0.18), residues: 856 sheet: -1.23 (0.56), residues: 82 loop : -1.51 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 285 HIS 0.005 0.001 HIS A 167 PHE 0.019 0.002 PHE A 427 TYR 0.026 0.002 TYR A 315 ARG 0.005 0.000 ARG B 442 *********************** 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 201 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7327 (tm-30) cc_final: 0.6753 (tm-30) REVERT: A 384 THR cc_start: 0.7769 (m) cc_final: 0.7444 (m) REVERT: B 227 PRO cc_start: 0.7082 (Cg_endo) cc_final: 0.6735 (Cg_exo) REVERT: B 385 MET cc_start: 0.7542 (mtt) cc_final: 0.7304 (mtp) outliers start: 20 outliers final: 14 residues processed: 188 average time/residue: 0.2373 time to fit residues: 64.3602 Evaluate side-chains 181 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 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 86 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 42 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 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 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 11101 Z= 0.432 Angle : 0.668 8.217 15247 Z= 0.364 Chirality : 0.048 0.260 1867 Planarity : 0.004 0.048 2033 Dihedral : 13.336 178.289 1999 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 4.45 % Allowed : 16.73 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.21), residues: 1698 helix: 0.53 (0.18), residues: 820 sheet: -0.64 (0.58), residues: 76 loop : -1.80 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 285 HIS 0.008 0.002 HIS A 210 PHE 0.023 0.002 PHE A 427 TYR 0.031 0.002 TYR A 315 ARG 0.004 0.001 ARG A 145 *********************** 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: 25 poor density : 168 time to evaluate : 1.150 Fit side-chains REVERT: A 115 MET cc_start: 0.5654 (mmm) cc_final: 0.5091 (mmm) REVERT: A 127 GLU cc_start: 0.7482 (tm-30) cc_final: 0.6479 (tm-30) REVERT: A 233 HIS cc_start: 0.7561 (p-80) cc_final: 0.7232 (p-80) REVERT: A 257 TYR cc_start: 0.8019 (m-80) cc_final: 0.7750 (m-80) REVERT: A 384 THR cc_start: 0.8065 (m) cc_final: 0.7797 (m) REVERT: B 326 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.6389 (mp10) REVERT: B 353 ASP cc_start: 0.6447 (m-30) cc_final: 0.5514 (t70) REVERT: B 367 ASN cc_start: 0.7929 (m110) cc_final: 0.7497 (t0) REVERT: B 442 ARG cc_start: 0.8458 (ttp-110) cc_final: 0.8094 (ttp-110) outliers start: 25 outliers final: 18 residues processed: 181 average time/residue: 0.2351 time to fit residues: 63.1661 Evaluate side-chains 182 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 222 ILE Chi-restraints excluded: chain A residue 229 VAL 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 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 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 153 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 156 optimal weight: 0.0770 chunk 165 optimal weight: 20.0000 chunk 81 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- 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 B 119 ASN ** 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 328 ASN B 376 HIS B 380 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11101 Z= 0.254 Angle : 0.551 8.330 15247 Z= 0.298 Chirality : 0.045 0.241 1867 Planarity : 0.003 0.049 2033 Dihedral : 12.998 176.191 1997 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.09 % Allowed : 19.93 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1698 helix: 0.91 (0.19), residues: 826 sheet: -0.46 (0.65), residues: 66 loop : -1.67 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 231 HIS 0.008 0.001 HIS A 206 PHE 0.015 0.002 PHE A 427 TYR 0.026 0.001 TYR A 315 ARG 0.002 0.000 ARG B 408 *********************** 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 196 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.5665 (mmm) cc_final: 0.5118 (mmm) REVERT: A 127 GLU cc_start: 0.7673 (tm-30) cc_final: 0.6814 (tm-30) REVERT: A 233 HIS cc_start: 0.7419 (p-80) cc_final: 0.7111 (p-80) REVERT: A 384 THR cc_start: 0.7918 (m) cc_final: 0.7602 (m) REVERT: B 326 GLN cc_start: 0.6924 (OUTLIER) cc_final: 0.6224 (mp10) REVERT: B 353 ASP cc_start: 0.6509 (m-30) cc_final: 0.5443 (t70) REVERT: B 367 ASN cc_start: 0.7892 (m110) cc_final: 0.7468 (t0) REVERT: B 385 MET cc_start: 0.7771 (mtt) cc_final: 0.7378 (mtp) REVERT: B 442 ARG cc_start: 0.8415 (ttp-110) cc_final: 0.8099 (ttp-110) outliers start: 23 outliers final: 17 residues processed: 185 average time/residue: 0.2185 time to fit residues: 60.5590 Evaluate side-chains 182 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 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 399 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 420 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 2.9990 chunk 93 optimal weight: 0.2980 chunk 2 optimal weight: 0.6980 chunk 123 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11101 Z= 0.284 Angle : 0.567 9.148 15247 Z= 0.304 Chirality : 0.045 0.245 1867 Planarity : 0.003 0.047 2033 Dihedral : 12.937 176.645 1997 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 4.63 % Allowed : 21.17 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.21), residues: 1698 helix: 0.91 (0.19), residues: 821 sheet: -0.93 (0.63), residues: 72 loop : -1.68 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 231 HIS 0.006 0.001 HIS A 206 PHE 0.015 0.002 PHE A 427 TYR 0.026 0.001 TYR B 315 ARG 0.003 0.000 ARG B 290 *********************** 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 192 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.5824 (mmm) cc_final: 0.5194 (mmm) REVERT: A 127 GLU cc_start: 0.7701 (tm-30) cc_final: 0.6880 (tm-30) REVERT: A 233 HIS cc_start: 0.7516 (p-80) cc_final: 0.7203 (p-80) REVERT: A 304 LYS cc_start: 0.6539 (mmtm) cc_final: 0.6196 (ttpt) REVERT: A 336 LYS cc_start: 0.7583 (tttt) cc_final: 0.6753 (mmtm) REVERT: A 384 THR cc_start: 0.7965 (m) cc_final: 0.7693 (m) REVERT: B 326 GLN cc_start: 0.6851 (OUTLIER) cc_final: 0.6238 (mp10) REVERT: B 353 ASP cc_start: 0.6424 (m-30) cc_final: 0.5446 (t70) REVERT: B 367 ASN cc_start: 0.7889 (m110) cc_final: 0.7460 (t0) outliers start: 26 outliers final: 22 residues processed: 181 average time/residue: 0.2091 time to fit residues: 55.5126 Evaluate side-chains 187 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 311 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 448 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 380 ASN 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 55 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 165 optimal weight: 20.0000 chunk 137 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 0.0050 chunk 86 optimal weight: 9.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- 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 210 HIS B 233 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN B 380 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11101 Z= 0.247 Angle : 0.544 8.266 15247 Z= 0.291 Chirality : 0.045 0.241 1867 Planarity : 0.003 0.046 2033 Dihedral : 12.806 178.258 1997 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.63 % Allowed : 22.42 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.21), residues: 1698 helix: 1.13 (0.19), residues: 822 sheet: -0.72 (0.64), residues: 72 loop : -1.52 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 231 HIS 0.006 0.001 HIS A 206 PHE 0.013 0.002 PHE A 427 TYR 0.025 0.001 TYR B 315 ARG 0.003 0.000 ARG A 220 *********************** 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 191 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6038 (mmm) cc_final: 0.5419 (mmm) REVERT: A 127 GLU cc_start: 0.7337 (tm-30) cc_final: 0.6585 (tm-30) REVERT: A 233 HIS cc_start: 0.7458 (p-80) cc_final: 0.7227 (p-80) REVERT: A 304 LYS cc_start: 0.6596 (mmtm) cc_final: 0.6182 (mtmt) REVERT: A 336 LYS cc_start: 0.7534 (tttt) cc_final: 0.6816 (mmtm) REVERT: A 384 THR cc_start: 0.8115 (m) cc_final: 0.7694 (m) REVERT: B 353 ASP cc_start: 0.6445 (m-30) cc_final: 0.5439 (t70) REVERT: B 367 ASN cc_start: 0.7883 (m110) cc_final: 0.7463 (t0) REVERT: B 385 MET cc_start: 0.7814 (mtt) cc_final: 0.7448 (mtp) outliers start: 26 outliers final: 22 residues processed: 178 average time/residue: 0.2174 time to fit residues: 56.8030 Evaluate side-chains 183 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 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 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 254 MET Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 420 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 93 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 100 optimal weight: 0.0020 chunk 76 optimal weight: 2.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- 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 271 GLN B 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11101 Z= 0.268 Angle : 0.553 8.918 15247 Z= 0.297 Chirality : 0.045 0.243 1867 Planarity : 0.003 0.046 2033 Dihedral : 12.780 178.343 1997 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.80 % Allowed : 23.31 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.21), residues: 1698 helix: 1.18 (0.19), residues: 821 sheet: -0.68 (0.65), residues: 72 loop : -1.53 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 231 HIS 0.006 0.001 HIS B 376 PHE 0.016 0.002 PHE A 241 TYR 0.025 0.001 TYR B 315 ARG 0.002 0.000 ARG B 290 *********************** 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 191 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6118 (mmm) cc_final: 0.4885 (mmm) REVERT: A 127 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6178 (tm-30) REVERT: A 233 HIS cc_start: 0.7494 (p-80) cc_final: 0.7232 (p-80) REVERT: A 304 LYS cc_start: 0.6672 (mmtm) cc_final: 0.6246 (mtmt) REVERT: A 336 LYS cc_start: 0.7542 (tttt) cc_final: 0.6828 (mmtm) REVERT: A 384 THR cc_start: 0.7966 (m) cc_final: 0.7668 (m) REVERT: B 353 ASP cc_start: 0.6467 (m-30) cc_final: 0.5435 (t70) REVERT: B 367 ASN cc_start: 0.7892 (m110) cc_final: 0.7467 (t0) REVERT: B 409 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8087 (tt) outliers start: 27 outliers final: 23 residues processed: 178 average time/residue: 0.2163 time to fit residues: 56.7986 Evaluate side-chains 183 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 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 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 197 LEU Chi-restraints excluded: chain B residue 254 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 31 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 112 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 15 optimal weight: 0.4980 chunk 129 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11101 Z= 0.215 Angle : 0.531 8.935 15247 Z= 0.285 Chirality : 0.044 0.238 1867 Planarity : 0.003 0.045 2033 Dihedral : 12.656 179.309 1997 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 4.98 % Allowed : 23.49 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.22), residues: 1698 helix: 1.30 (0.19), residues: 833 sheet: -0.17 (0.70), residues: 66 loop : -1.54 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 231 HIS 0.006 0.001 HIS A 206 PHE 0.025 0.002 PHE A 241 TYR 0.024 0.001 TYR B 315 ARG 0.002 0.000 ARG B 290 *********************** 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 189 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6198 (mmm) cc_final: 0.4657 (mmm) REVERT: A 127 GLU cc_start: 0.7338 (tm-30) cc_final: 0.6532 (tm-30) REVERT: A 233 HIS cc_start: 0.7366 (p-80) cc_final: 0.7067 (p-80) REVERT: A 304 LYS cc_start: 0.6583 (mmtm) cc_final: 0.6217 (mtmt) REVERT: A 336 LYS cc_start: 0.7486 (tttt) cc_final: 0.6820 (mmtm) REVERT: A 384 THR cc_start: 0.7930 (m) cc_final: 0.7638 (m) REVERT: A 406 LYS cc_start: 0.8080 (mppt) cc_final: 0.7729 (mmtp) REVERT: B 194 ARG cc_start: 0.7915 (ttt90) cc_final: 0.7703 (ttt-90) REVERT: B 326 GLN cc_start: 0.6845 (OUTLIER) cc_final: 0.6464 (mp10) REVERT: B 353 ASP cc_start: 0.6432 (m-30) cc_final: 0.5227 (t70) REVERT: B 367 ASN cc_start: 0.7880 (m110) cc_final: 0.7464 (t0) REVERT: B 385 MET cc_start: 0.7754 (mtt) cc_final: 0.7381 (mtp) outliers start: 28 outliers final: 24 residues processed: 175 average time/residue: 0.2334 time to fit residues: 59.3809 Evaluate side-chains 184 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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 311 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 370 HIS 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 197 LEU Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 420 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 153 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 145 optimal weight: 0.3980 chunk 100 optimal weight: 0.0770 overall best weight: 2.4944 ------------------------------------------------------------------------------- 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 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 11101 Z= 0.543 Angle : 0.744 10.041 15247 Z= 0.402 Chirality : 0.050 0.265 1867 Planarity : 0.005 0.045 2033 Dihedral : 13.142 176.992 1997 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 5.87 % Allowed : 24.02 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.21), residues: 1698 helix: 0.25 (0.18), residues: 829 sheet: -1.18 (0.60), residues: 83 loop : -1.90 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 231 HIS 0.010 0.002 HIS B 210 PHE 0.054 0.003 PHE A 329 TYR 0.033 0.003 TYR A 315 ARG 0.007 0.001 ARG A 408 *********************** 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 199 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 1.231 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.6058 (mmm) cc_final: 0.4512 (mmm) REVERT: A 127 GLU cc_start: 0.7582 (tm-30) cc_final: 0.6233 (tm-30) REVERT: A 304 LYS cc_start: 0.6785 (mmtm) cc_final: 0.6413 (mtmt) REVERT: A 336 LYS cc_start: 0.7536 (tttt) cc_final: 0.6710 (mmtm) REVERT: A 384 THR cc_start: 0.8010 (m) cc_final: 0.7759 (m) REVERT: B 218 ASP cc_start: 0.8094 (p0) cc_final: 0.7787 (p0) REVERT: B 353 ASP cc_start: 0.6993 (m-30) cc_final: 0.5427 (t70) REVERT: B 385 MET cc_start: 0.7915 (mtt) cc_final: 0.7521 (mtp) outliers start: 33 outliers final: 26 residues processed: 181 average time/residue: 0.2387 time to fit residues: 63.7963 Evaluate side-chains 189 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 1.319 ------------------------------------------------------------------------------- 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 191 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 266 CYS 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 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 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 197 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 365 THR 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 162 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 170 optimal weight: 20.0000 chunk 156 optimal weight: 0.4980 chunk 135 optimal weight: 0.0670 chunk 14 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 overall best weight: 0.8120 ------------------------------------------------------------------------------- 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 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11101 Z= 0.233 Angle : 0.581 13.117 15247 Z= 0.310 Chirality : 0.045 0.237 1867 Planarity : 0.003 0.046 2033 Dihedral : 12.793 178.402 1997 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.09 % Allowed : 25.27 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.21), residues: 1698 helix: 0.88 (0.19), residues: 840 sheet: -0.73 (0.63), residues: 76 loop : -1.74 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 231 HIS 0.007 0.002 HIS A 206 PHE 0.034 0.002 PHE A 329 TYR 0.025 0.002 TYR B 315 ARG 0.002 0.000 ARG A 220 ********************** 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 184 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6042 (mmm) cc_final: 0.4477 (mmm) REVERT: A 127 GLU cc_start: 0.7269 (tm-30) cc_final: 0.6432 (tm-30) REVERT: A 233 HIS cc_start: 0.7523 (p-80) cc_final: 0.7216 (p-80) REVERT: A 304 LYS cc_start: 0.6636 (mmtm) cc_final: 0.6335 (mtmt) REVERT: A 336 LYS cc_start: 0.7424 (tttt) cc_final: 0.6809 (mmtm) REVERT: A 374 TYR cc_start: 0.8084 (m-80) cc_final: 0.7871 (m-80) REVERT: A 384 THR cc_start: 0.7968 (m) cc_final: 0.7663 (m) REVERT: A 405 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7774 (pttp) REVERT: B 326 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6492 (mp10) REVERT: B 353 ASP cc_start: 0.6823 (m-30) cc_final: 0.5292 (t70) REVERT: B 367 ASN cc_start: 0.7806 (m110) cc_final: 0.7403 (t0) REVERT: B 385 MET cc_start: 0.7800 (mtt) cc_final: 0.7404 (mtp) outliers start: 23 outliers final: 20 residues processed: 175 average time/residue: 0.2230 time to fit residues: 56.7745 Evaluate side-chains 182 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 311 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 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 405 LYS 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 197 LEU Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 326 GLN 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 144 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 17 optimal weight: 0.0980 chunk 25 optimal weight: 0.8980 chunk 119 optimal weight: 20.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.263069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.214588 restraints weight = 14542.507| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 3.25 r_work: 0.4206 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11101 Z= 0.190 Angle : 0.550 12.449 15247 Z= 0.291 Chirality : 0.044 0.236 1867 Planarity : 0.003 0.045 2033 Dihedral : 12.624 179.882 1997 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.91 % Allowed : 26.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.22), residues: 1698 helix: 1.36 (0.19), residues: 834 sheet: -0.33 (0.70), residues: 66 loop : -1.62 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 231 HIS 0.008 0.001 HIS A 206 PHE 0.026 0.002 PHE B 213 TYR 0.023 0.001 TYR B 315 ARG 0.001 0.000 ARG B 290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2235.30 seconds wall clock time: 41 minutes 39.56 seconds (2499.56 seconds total)