Starting phenix.real_space_refine on Tue Jul 29 09:10:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tdv_41174/07_2025/8tdv_41174_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tdv_41174/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tdv_41174/07_2025/8tdv_41174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tdv_41174/07_2025/8tdv_41174.map" model { file = "/net/cci-nas-00/data/ceres_data/8tdv_41174/07_2025/8tdv_41174_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tdv_41174/07_2025/8tdv_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-5711/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: 8.04, per 1000 atoms: 0.73 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: 3.20 Conformation dependent library (CDL) restraints added in 1.7 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: 1.78 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: 3.45 Time building geometry restraints manager: 3.59 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: 1.250 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.850 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.060 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.770 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.14623 ( 656) hydrogen bonds : angle 6.62510 ( 1830) covalent geometry : bond 0.00214 (11101) covalent geometry : angle 0.52528 (15247) *********************** 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 : 1.225 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: 0.2245 time to fit residues: 71.4650 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 : 1.244 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.262125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.212305 restraints weight = 14541.216| |-----------------------------------------------------------------------------| r_work (start): 0.4328 rms_B_bonded: 3.46 r_work: 0.4179 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 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= 0.181 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 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 656) hydrogen bonds : angle 4.85412 ( 1830) covalent geometry : bond 0.00398 (11101) covalent geometry : angle 0.56277 (15247) *********************** 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 : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7297 (tm-30) REVERT: A 326 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7361 (tm-30) REVERT: A 384 THR cc_start: 0.7981 (m) cc_final: 0.7696 (m) REVERT: A 405 LYS cc_start: 0.7888 (ttmt) cc_final: 0.7614 (ttmm) REVERT: B 227 PRO cc_start: 0.7243 (Cg_endo) cc_final: 0.6885 (Cg_exo) REVERT: B 385 MET cc_start: 0.7766 (mtt) cc_final: 0.7490 (mtp) outliers start: 20 outliers final: 14 residues processed: 188 average time/residue: 0.2870 time to fit residues: 79.1603 Evaluate side-chains 182 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 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 41 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 chunk 162 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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 119 ASN ** B 129 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 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.244402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.207978 restraints weight = 15077.129| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 2.79 r_work: 0.4031 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.128 11101 Z= 0.661 Angle : 1.099 15.193 15247 Z= 0.598 Chirality : 0.062 0.290 1867 Planarity : 0.008 0.087 2033 Dihedral : 14.003 178.999 1999 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.31 % Favored : 88.63 % Rotamer: Outliers : 6.23 % Allowed : 19.22 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.64 (0.19), residues: 1698 helix: -1.19 (0.16), residues: 828 sheet: -1.17 (0.58), residues: 76 loop : -2.41 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP A 231 HIS 0.017 0.004 HIS A 167 PHE 0.049 0.005 PHE A 427 TYR 0.047 0.004 TYR A 315 ARG 0.009 0.001 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.07989 ( 656) hydrogen bonds : angle 7.06889 ( 1830) covalent geometry : bond 0.01458 (11101) covalent geometry : angle 1.09901 (15247) *********************** 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 196 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 1.202 Fit side-chains REVERT: A 115 MET cc_start: 0.6291 (mmm) cc_final: 0.5343 (mmm) REVERT: A 127 GLU cc_start: 0.8116 (tm-30) cc_final: 0.6961 (tm-30) REVERT: A 415 ASP cc_start: 0.7951 (t0) cc_final: 0.7628 (t0) REVERT: B 184 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7333 (pp20) REVERT: B 315 TYR cc_start: 0.8352 (p90) cc_final: 0.7659 (p90) REVERT: B 326 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.6367 (mp10) REVERT: B 353 ASP cc_start: 0.6696 (m-30) cc_final: 0.5349 (t70) outliers start: 35 outliers final: 25 residues processed: 182 average time/residue: 0.2147 time to fit residues: 57.4013 Evaluate side-chains 179 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 222 ILE 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 349 ILE 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 119 ASN Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 449 GLU 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 99 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 chunk 103 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 98 optimal weight: 0.0980 chunk 2 optimal weight: 0.2980 chunk 96 optimal weight: 0.7980 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 163 ASN B 210 HIS B 233 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN B 376 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.257135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.208731 restraints weight = 14829.952| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 3.79 r_work: 0.4134 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11101 Z= 0.140 Angle : 0.561 7.426 15247 Z= 0.307 Chirality : 0.045 0.242 1867 Planarity : 0.004 0.044 2033 Dihedral : 13.069 178.857 1997 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.74 % Allowed : 21.35 % Favored : 74.91 % 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: -1.19 (0.21), residues: 1698 helix: 0.26 (0.19), residues: 825 sheet: -1.25 (0.57), residues: 82 loop : -1.90 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 231 HIS 0.006 0.001 HIS A 206 PHE 0.016 0.002 PHE A 141 TYR 0.028 0.001 TYR B 315 ARG 0.004 0.001 ARG B 451 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 656) hydrogen bonds : angle 4.93158 ( 1830) covalent geometry : bond 0.00306 (11101) covalent geometry : angle 0.56093 (15247) *********************** 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 200 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.6326 (mmm) cc_final: 0.5308 (mmm) REVERT: A 233 HIS cc_start: 0.7599 (p-80) cc_final: 0.7313 (p-80) REVERT: A 336 LYS cc_start: 0.7042 (tttt) cc_final: 0.6110 (mmtm) REVERT: A 415 ASP cc_start: 0.7364 (t0) cc_final: 0.7074 (t0) REVERT: A 417 GLU cc_start: 0.8400 (tp30) cc_final: 0.7955 (mm-30) REVERT: B 119 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.7806 (m-40) REVERT: B 155 TYR cc_start: 0.7811 (m-80) cc_final: 0.7583 (m-80) REVERT: B 239 MET cc_start: 0.8279 (mtp) cc_final: 0.7948 (mtp) REVERT: B 339 ARG cc_start: 0.7828 (mtp-110) cc_final: 0.7440 (mtp85) REVERT: B 347 LEU cc_start: 0.8764 (mt) cc_final: 0.8532 (mt) REVERT: B 353 ASP cc_start: 0.6470 (m-30) cc_final: 0.4955 (t70) REVERT: B 367 ASN cc_start: 0.7923 (m110) cc_final: 0.7449 (t0) REVERT: B 385 MET cc_start: 0.8053 (mtt) cc_final: 0.7618 (mtp) REVERT: B 391 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7839 (mp) outliers start: 21 outliers final: 14 residues processed: 190 average time/residue: 0.2357 time to fit residues: 65.0898 Evaluate side-chains 184 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 1.318 ------------------------------------------------------------------------------- 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 167 HIS Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 391 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 141 optimal weight: 9.9990 chunk 165 optimal weight: 0.0370 chunk 110 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 82 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 overall best weight: 1.3060 ------------------------------------------------------------------------------- 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 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.255534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.205603 restraints weight = 14640.918| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 3.32 r_work: 0.4126 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 11101 Z= 0.213 Angle : 0.600 8.230 15247 Z= 0.325 Chirality : 0.046 0.251 1867 Planarity : 0.004 0.044 2033 Dihedral : 13.061 179.629 1997 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 5.87 % Allowed : 21.53 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.01 (0.21), residues: 1698 helix: 0.51 (0.19), residues: 813 sheet: -0.78 (0.61), residues: 76 loop : -1.94 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 285 HIS 0.007 0.002 HIS A 167 PHE 0.017 0.002 PHE B 213 TYR 0.030 0.002 TYR B 315 ARG 0.003 0.001 ARG B 318 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 656) hydrogen bonds : angle 4.91488 ( 1830) covalent geometry : bond 0.00481 (11101) covalent geometry : angle 0.59984 (15247) *********************** 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 196 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6493 (mmm) cc_final: 0.5417 (mmm) REVERT: A 233 HIS cc_start: 0.7740 (p-80) cc_final: 0.7387 (p-80) REVERT: A 241 PHE cc_start: 0.8335 (t80) cc_final: 0.8022 (t80) REVERT: A 336 LYS cc_start: 0.6912 (tttt) cc_final: 0.5964 (mmtm) REVERT: A 415 ASP cc_start: 0.7404 (t0) cc_final: 0.7087 (t0) REVERT: A 417 GLU cc_start: 0.8358 (tp30) cc_final: 0.7746 (mm-30) REVERT: B 119 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.7943 (m110) REVERT: B 239 MET cc_start: 0.8309 (mtp) cc_final: 0.8006 (mtp) REVERT: B 255 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7231 (pp20) REVERT: B 326 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.6543 (mp10) REVERT: B 339 ARG cc_start: 0.7812 (mtp-110) cc_final: 0.7531 (mtp85) REVERT: B 347 LEU cc_start: 0.8745 (mt) cc_final: 0.8517 (mt) REVERT: B 353 ASP cc_start: 0.6781 (m-30) cc_final: 0.5091 (t70) REVERT: B 367 ASN cc_start: 0.7837 (m110) cc_final: 0.7404 (t0) REVERT: B 385 MET cc_start: 0.8200 (mtt) cc_final: 0.7937 (mtt) REVERT: B 391 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8219 (mp) outliers start: 33 outliers final: 21 residues processed: 182 average time/residue: 0.2747 time to fit residues: 74.0533 Evaluate side-chains 187 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 349 ILE 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 399 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 391 LEU 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 54 optimal weight: 0.7980 chunk 85 optimal weight: 9.9990 chunk 52 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 101 optimal weight: 0.0670 chunk 30 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 chunk 169 optimal weight: 0.3980 chunk 133 optimal weight: 9.9990 chunk 135 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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** B 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.261080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.211137 restraints weight = 14870.485| |-----------------------------------------------------------------------------| r_work (start): 0.4328 rms_B_bonded: 3.42 r_work: 0.4181 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11101 Z= 0.119 Angle : 0.529 10.239 15247 Z= 0.282 Chirality : 0.044 0.235 1867 Planarity : 0.003 0.042 2033 Dihedral : 12.829 175.131 1997 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.27 % Allowed : 23.31 % Favored : 72.42 % 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: -0.48 (0.21), residues: 1698 helix: 1.06 (0.19), residues: 808 sheet: -0.78 (0.59), residues: 82 loop : -1.77 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 285 HIS 0.012 0.001 HIS A 206 PHE 0.016 0.001 PHE B 213 TYR 0.024 0.001 TYR B 315 ARG 0.002 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03265 ( 656) hydrogen bonds : angle 4.36171 ( 1830) covalent geometry : bond 0.00266 (11101) covalent geometry : angle 0.52881 (15247) *********************** 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 192 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6571 (mmm) cc_final: 0.5467 (mmm) REVERT: A 233 HIS cc_start: 0.7611 (p-80) cc_final: 0.7334 (p-80) REVERT: A 304 LYS cc_start: 0.7058 (mmtm) cc_final: 0.6672 (mtmt) REVERT: A 336 LYS cc_start: 0.7069 (tttt) cc_final: 0.6169 (mmtm) REVERT: A 415 ASP cc_start: 0.7242 (t0) cc_final: 0.6951 (t0) REVERT: A 417 GLU cc_start: 0.8397 (tp30) cc_final: 0.7823 (mm-30) REVERT: B 194 ARG cc_start: 0.8025 (ttt90) cc_final: 0.7660 (ttt-90) REVERT: B 239 MET cc_start: 0.8266 (mtp) cc_final: 0.7931 (mtp) REVERT: B 326 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.6543 (mp10) REVERT: B 339 ARG cc_start: 0.7773 (mtp-110) cc_final: 0.7445 (mtm110) REVERT: B 347 LEU cc_start: 0.8711 (mt) cc_final: 0.8510 (mt) REVERT: B 353 ASP cc_start: 0.6714 (m-30) cc_final: 0.5046 (t70) REVERT: B 367 ASN cc_start: 0.7828 (m110) cc_final: 0.7401 (t0) REVERT: B 385 MET cc_start: 0.8014 (mtt) cc_final: 0.7760 (mtt) REVERT: B 391 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8151 (mp) outliers start: 24 outliers final: 19 residues processed: 182 average time/residue: 0.2729 time to fit residues: 71.6853 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 : 1.399 ------------------------------------------------------------------------------- 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 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 340 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 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 311 ASP 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 391 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 140 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 18 optimal weight: 0.0170 chunk 144 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 45 optimal weight: 0.5980 chunk 119 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.9224 ------------------------------------------------------------------------------- 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** ** 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 = 0.4707 r_free = 0.4707 target = 0.252212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.214859 restraints weight = 14910.627| |-----------------------------------------------------------------------------| r_work (start): 0.4341 rms_B_bonded: 3.09 r_work: 0.4114 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 11101 Z= 0.292 Angle : 0.675 9.239 15247 Z= 0.365 Chirality : 0.048 0.256 1867 Planarity : 0.004 0.042 2033 Dihedral : 13.117 179.478 1997 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 5.52 % Allowed : 23.84 % 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: -1.03 (0.21), residues: 1698 helix: 0.47 (0.19), residues: 814 sheet: -0.75 (0.63), residues: 76 loop : -1.94 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 285 HIS 0.009 0.002 HIS A 167 PHE 0.020 0.002 PHE A 427 TYR 0.032 0.002 TYR B 315 ARG 0.005 0.001 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.04710 ( 656) hydrogen bonds : angle 5.07572 ( 1830) covalent geometry : bond 0.00656 (11101) covalent geometry : angle 0.67502 (15247) *********************** 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 197 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6464 (mmm) cc_final: 0.5338 (mmm) REVERT: A 127 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7037 (tm-30) REVERT: A 233 HIS cc_start: 0.7847 (p-80) cc_final: 0.7539 (p-80) REVERT: A 241 PHE cc_start: 0.8339 (t80) cc_final: 0.8131 (t80) REVERT: A 304 LYS cc_start: 0.6979 (mmtm) cc_final: 0.6636 (mtmt) REVERT: A 336 LYS cc_start: 0.6886 (tttt) cc_final: 0.5983 (mmtm) REVERT: A 374 TYR cc_start: 0.8325 (m-80) cc_final: 0.8023 (m-80) REVERT: A 384 THR cc_start: 0.8150 (m) cc_final: 0.7924 (m) REVERT: A 415 ASP cc_start: 0.7433 (t0) cc_final: 0.7133 (t0) REVERT: A 417 GLU cc_start: 0.8270 (tp30) cc_final: 0.7846 (mm-30) REVERT: B 119 ASN cc_start: 0.8356 (OUTLIER) cc_final: 0.8121 (m-40) REVERT: B 239 MET cc_start: 0.8235 (mtp) cc_final: 0.7946 (mtp) REVERT: B 347 LEU cc_start: 0.8735 (mt) cc_final: 0.8513 (mt) REVERT: B 353 ASP cc_start: 0.6868 (m-30) cc_final: 0.5169 (t70) REVERT: B 385 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7976 (mtt) REVERT: B 391 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8340 (mp) outliers start: 31 outliers final: 24 residues processed: 183 average time/residue: 0.2564 time to fit residues: 70.5071 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 : 1.773 ------------------------------------------------------------------------------- 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 349 ILE 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 119 ASN 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 365 THR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 391 LEU 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 154 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 156 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 47 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 B 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.259767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.210049 restraints weight = 14684.804| |-----------------------------------------------------------------------------| r_work (start): 0.4322 rms_B_bonded: 3.44 r_work: 0.4171 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11101 Z= 0.121 Angle : 0.533 8.330 15247 Z= 0.285 Chirality : 0.044 0.233 1867 Planarity : 0.003 0.041 2033 Dihedral : 12.798 177.618 1997 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.38 % Allowed : 25.80 % Favored : 70.82 % 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: 1.03 (0.19), residues: 816 sheet: -0.65 (0.63), residues: 76 loop : -1.83 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 231 HIS 0.011 0.001 HIS A 206 PHE 0.017 0.001 PHE B 213 TYR 0.024 0.001 TYR B 315 ARG 0.002 0.000 ARG A 352 Details of bonding type rmsd hydrogen bonds : bond 0.03193 ( 656) hydrogen bonds : angle 4.36070 ( 1830) covalent geometry : bond 0.00269 (11101) covalent geometry : angle 0.53343 (15247) *********************** 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 188 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6678 (mmm) cc_final: 0.5779 (mmm) REVERT: A 127 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.6932 (tm-30) REVERT: A 233 HIS cc_start: 0.7692 (p-80) cc_final: 0.7415 (p-80) REVERT: A 241 PHE cc_start: 0.8231 (t80) cc_final: 0.8002 (t80) REVERT: A 304 LYS cc_start: 0.6943 (mmtm) cc_final: 0.6560 (mtmt) REVERT: A 336 LYS cc_start: 0.6984 (tttt) cc_final: 0.6134 (mmtm) REVERT: A 374 TYR cc_start: 0.8105 (m-80) cc_final: 0.7698 (m-80) REVERT: A 384 THR cc_start: 0.7921 (m) cc_final: 0.7537 (m) REVERT: A 415 ASP cc_start: 0.7273 (t0) cc_final: 0.6962 (t0) REVERT: A 417 GLU cc_start: 0.8404 (tp30) cc_final: 0.7888 (mm-30) REVERT: A 443 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7393 (tt0) REVERT: B 255 GLU cc_start: 0.7851 (pp20) cc_final: 0.7596 (pp20) REVERT: B 347 LEU cc_start: 0.8747 (mt) cc_final: 0.8520 (mt) REVERT: B 353 ASP cc_start: 0.6604 (m-30) cc_final: 0.4893 (t70) REVERT: B 367 ASN cc_start: 0.7801 (m110) cc_final: 0.7405 (t0) REVERT: B 370 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.6275 (m90) REVERT: B 391 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8127 (mp) outliers start: 19 outliers final: 14 residues processed: 177 average time/residue: 0.2088 time to fit residues: 54.1073 Evaluate side-chains 185 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU 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 368 SER 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 311 ASP Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 391 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 133 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 149 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 chunk 109 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 114 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4759 r_free = 0.4759 target = 0.258725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.209053 restraints weight = 14861.983| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 3.35 r_work: 0.4163 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11101 Z= 0.149 Angle : 0.569 16.147 15247 Z= 0.301 Chirality : 0.045 0.239 1867 Planarity : 0.003 0.041 2033 Dihedral : 12.787 178.487 1997 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 3.02 % Allowed : 25.98 % Favored : 71.00 % 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 (0.22), residues: 1698 helix: 1.14 (0.19), residues: 820 sheet: -0.55 (0.64), residues: 76 loop : -1.71 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 313 HIS 0.007 0.002 HIS A 206 PHE 0.019 0.002 PHE B 213 TYR 0.025 0.001 TYR B 315 ARG 0.002 0.000 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 656) hydrogen bonds : angle 4.35478 ( 1830) covalent geometry : bond 0.00339 (11101) covalent geometry : angle 0.56883 (15247) *********************** 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 180 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6664 (mmm) cc_final: 0.5602 (mmm) REVERT: A 127 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.6846 (tm-30) REVERT: A 233 HIS cc_start: 0.7707 (p-80) cc_final: 0.7425 (p-80) REVERT: A 241 PHE cc_start: 0.8284 (t80) cc_final: 0.8022 (t80) REVERT: A 304 LYS cc_start: 0.6925 (mmtm) cc_final: 0.6557 (mtmt) REVERT: A 336 LYS cc_start: 0.6944 (tttt) cc_final: 0.6132 (mmtm) REVERT: A 374 TYR cc_start: 0.8138 (m-80) cc_final: 0.7756 (m-80) REVERT: A 384 THR cc_start: 0.8010 (m) cc_final: 0.7714 (m) REVERT: A 415 ASP cc_start: 0.7313 (t0) cc_final: 0.7042 (t0) REVERT: A 417 GLU cc_start: 0.8379 (tp30) cc_final: 0.7867 (mm-30) REVERT: B 185 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7669 (mttt) REVERT: B 228 GLU cc_start: 0.8106 (pp20) cc_final: 0.7900 (pp20) REVERT: B 255 GLU cc_start: 0.7820 (pp20) cc_final: 0.7543 (pp20) REVERT: B 347 LEU cc_start: 0.8763 (mt) cc_final: 0.8542 (mt) REVERT: B 353 ASP cc_start: 0.6642 (m-30) cc_final: 0.4858 (t70) REVERT: B 367 ASN cc_start: 0.7838 (m110) cc_final: 0.7431 (t0) REVERT: B 370 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.6277 (m90) REVERT: B 391 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8206 (mp) outliers start: 17 outliers final: 14 residues processed: 172 average time/residue: 0.2124 time to fit residues: 53.4861 Evaluate side-chains 179 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU 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 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 311 ASP Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 87 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.259310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.209716 restraints weight = 14756.583| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 3.27 r_work: 0.4175 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11101 Z= 0.183 Angle : 0.583 9.173 15247 Z= 0.314 Chirality : 0.045 0.243 1867 Planarity : 0.003 0.041 2033 Dihedral : 12.825 178.109 1997 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 3.20 % Allowed : 25.62 % Favored : 71.17 % 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: 0.99 (0.19), residues: 820 sheet: -0.57 (0.65), residues: 76 loop : -1.81 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 231 HIS 0.005 0.002 HIS A 210 PHE 0.047 0.002 PHE A 329 TYR 0.026 0.001 TYR B 315 ARG 0.003 0.000 ARG B 290 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 656) hydrogen bonds : angle 4.54304 ( 1830) covalent geometry : bond 0.00413 (11101) covalent geometry : angle 0.58287 (15247) ********************** 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 185 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6551 (mmm) cc_final: 0.5467 (mmm) REVERT: A 127 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: A 233 HIS cc_start: 0.7765 (p-80) cc_final: 0.7453 (p-80) REVERT: A 241 PHE cc_start: 0.8377 (t80) cc_final: 0.8129 (t80) REVERT: A 304 LYS cc_start: 0.6943 (mmtm) cc_final: 0.6596 (mtmt) REVERT: A 336 LYS cc_start: 0.6894 (tttt) cc_final: 0.6096 (mmtm) REVERT: A 374 TYR cc_start: 0.8249 (m-80) cc_final: 0.7913 (m-80) REVERT: A 384 THR cc_start: 0.8055 (m) cc_final: 0.7775 (m) REVERT: A 415 ASP cc_start: 0.7385 (t0) cc_final: 0.7139 (t0) REVERT: A 443 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7331 (tt0) REVERT: B 155 TYR cc_start: 0.7959 (m-80) cc_final: 0.7678 (m-80) REVERT: B 185 LYS cc_start: 0.7773 (mtpt) cc_final: 0.7540 (mttt) REVERT: B 255 GLU cc_start: 0.7829 (pp20) cc_final: 0.7579 (pp20) REVERT: B 347 LEU cc_start: 0.8789 (mt) cc_final: 0.8562 (mt) REVERT: B 353 ASP cc_start: 0.6670 (m-30) cc_final: 0.4877 (t70) REVERT: B 367 ASN cc_start: 0.7874 (m110) cc_final: 0.7459 (t0) REVERT: B 370 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.6320 (m90) REVERT: B 391 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8210 (mp) outliers start: 18 outliers final: 15 residues processed: 176 average time/residue: 0.2147 time to fit residues: 54.9249 Evaluate side-chains 184 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU 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 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 311 ASP Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 391 LEU 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 119 optimal weight: 0.0000 chunk 86 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 78 optimal weight: 0.5980 chunk 112 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 = 0.4764 r_free = 0.4764 target = 0.259355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.210480 restraints weight = 14558.739| |-----------------------------------------------------------------------------| r_work (start): 0.4322 rms_B_bonded: 3.35 r_work: 0.4171 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.3769 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= 0.130 Angle : 0.543 8.935 15247 Z= 0.289 Chirality : 0.044 0.236 1867 Planarity : 0.003 0.040 2033 Dihedral : 12.671 179.528 1997 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.56 % Allowed : 25.80 % 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: -0.22 (0.22), residues: 1698 helix: 1.25 (0.19), residues: 828 sheet: -0.45 (0.66), residues: 76 loop : -1.70 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 313 HIS 0.008 0.001 HIS A 206 PHE 0.040 0.002 PHE A 329 TYR 0.024 0.001 TYR B 315 ARG 0.003 0.000 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.03111 ( 656) hydrogen bonds : angle 4.24342 ( 1830) covalent geometry : bond 0.00293 (11101) covalent geometry : angle 0.54269 (15247) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6314.75 seconds wall clock time: 112 minutes 55.58 seconds (6775.58 seconds total)