Starting phenix.real_space_refine on Wed May 14 01:12:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tdv_41174/05_2025/8tdv_41174_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tdv_41174/05_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_41174/05_2025/8tdv_41174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tdv_41174/05_2025/8tdv_41174.map" model { file = "/net/cci-nas-00/data/ceres_data/8tdv_41174/05_2025/8tdv_41174_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tdv_41174/05_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-5687/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: 7.73, per 1000 atoms: 0.71 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: 2.87 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: 1.49 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: 3.19 Time building geometry restraints manager: 3.32 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: 1.150 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: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.350 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.850 ------------------------------------------------------------------------------- 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 : 1.148 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: 0.2171 time to fit residues: 68.8838 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 : 1.160 ------------------------------------------------------------------------------- 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 = 60)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.212377 restraints weight = 14541.216| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 3.46 r_work: 0.4187 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 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 : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7297 (tm-30) REVERT: A 326 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: A 384 THR cc_start: 0.7984 (m) cc_final: 0.7699 (m) REVERT: A 405 LYS cc_start: 0.7888 (ttmt) cc_final: 0.7615 (ttmm) REVERT: B 227 PRO cc_start: 0.7248 (Cg_endo) cc_final: 0.6890 (Cg_exo) REVERT: B 385 MET cc_start: 0.7778 (mtt) cc_final: 0.7502 (mtp) outliers start: 20 outliers final: 14 residues processed: 188 average time/residue: 0.2139 time to fit residues: 57.7053 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 : 1.123 ------------------------------------------------------------------------------- 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: 10.0000 chunk 124 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.244602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.208460 restraints weight = 15154.813| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 2.75 r_work: 0.4028 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.124 11101 Z= 0.594 Angle : 1.013 13.587 15247 Z= 0.552 Chirality : 0.058 0.286 1867 Planarity : 0.007 0.076 2033 Dihedral : 13.837 178.643 1999 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 5.34 % Allowed : 18.51 % Favored : 76.16 % 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: -2.35 (0.19), residues: 1698 helix: -0.92 (0.17), residues: 836 sheet: -1.11 (0.58), residues: 76 loop : -2.32 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP B 285 HIS 0.016 0.004 HIS A 167 PHE 0.045 0.004 PHE A 427 TYR 0.045 0.004 TYR A 315 ARG 0.007 0.001 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.07425 ( 656) hydrogen bonds : angle 6.69908 ( 1830) covalent geometry : bond 0.01310 (11101) covalent geometry : angle 1.01327 (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 192 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 1.206 Fit side-chains REVERT: A 115 MET cc_start: 0.6388 (mmm) cc_final: 0.5568 (mmm) REVERT: A 127 GLU cc_start: 0.8078 (tm-30) cc_final: 0.6969 (tm-30) REVERT: A 257 TYR cc_start: 0.8258 (m-80) cc_final: 0.8045 (m-80) REVERT: A 336 LYS cc_start: 0.7154 (tttt) cc_final: 0.6170 (mmtm) REVERT: A 415 ASP cc_start: 0.7897 (t0) cc_final: 0.7570 (t0) REVERT: B 326 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.6416 (mp10) REVERT: B 353 ASP cc_start: 0.6596 (m-30) cc_final: 0.5355 (t70) outliers start: 30 outliers final: 22 residues processed: 178 average time/residue: 0.2082 time to fit residues: 53.9880 Evaluate side-chains 180 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 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: 9.9990 chunk 111 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 156 optimal weight: 0.0570 chunk 163 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 2 optimal weight: 0.0980 chunk 96 optimal weight: 0.8980 overall best weight: 0.5700 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.259704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.210362 restraints weight = 14760.615| |-----------------------------------------------------------------------------| r_work (start): 0.4319 rms_B_bonded: 3.38 r_work: 0.4178 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11101 Z= 0.135 Angle : 0.547 7.720 15247 Z= 0.299 Chirality : 0.045 0.241 1867 Planarity : 0.003 0.045 2033 Dihedral : 12.987 176.949 1997 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.56 % Allowed : 21.17 % Favored : 75.27 % 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: -0.95 (0.21), residues: 1698 helix: 0.52 (0.19), residues: 815 sheet: -1.34 (0.54), residues: 88 loop : -1.80 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 231 HIS 0.007 0.001 HIS A 206 PHE 0.017 0.001 PHE A 141 TYR 0.028 0.001 TYR B 315 ARG 0.003 0.000 ARG A 318 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 656) hydrogen bonds : angle 4.76008 ( 1830) covalent geometry : bond 0.00295 (11101) covalent geometry : angle 0.54728 (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 195 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 1.330 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.6437 (mmm) cc_final: 0.5451 (mmm) REVERT: A 336 LYS cc_start: 0.7203 (tttt) cc_final: 0.6211 (mmtm) REVERT: A 415 ASP cc_start: 0.7281 (t0) cc_final: 0.7007 (t0) REVERT: A 417 GLU cc_start: 0.8336 (tp30) cc_final: 0.7927 (mm-30) REVERT: A 428 LEU cc_start: 0.9046 (mt) cc_final: 0.8825 (mt) REVERT: B 119 ASN cc_start: 0.8328 (t0) cc_final: 0.7779 (m110) REVERT: B 239 MET cc_start: 0.8295 (mtp) cc_final: 0.7979 (mtp) REVERT: B 347 LEU cc_start: 0.8738 (mt) cc_final: 0.8507 (mt) REVERT: B 353 ASP cc_start: 0.6459 (m-30) cc_final: 0.4919 (t70) REVERT: B 367 ASN cc_start: 0.7912 (m110) cc_final: 0.7511 (t0) REVERT: B 385 MET cc_start: 0.8027 (mtt) cc_final: 0.7650 (mtp) REVERT: B 391 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7846 (mp) outliers start: 20 outliers final: 14 residues processed: 185 average time/residue: 0.2095 time to fit residues: 56.3091 Evaluate side-chains 185 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 253 VAL Chi-restraints excluded: chain A residue 340 VAL 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 399 ILE Chi-restraints excluded: chain A residue 448 ILE 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: 20.0000 chunk 110 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 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 = 0.4749 r_free = 0.4749 target = 0.257148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.208774 restraints weight = 14555.407| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 3.27 r_work: 0.4139 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11101 Z= 0.200 Angle : 0.583 8.793 15247 Z= 0.316 Chirality : 0.045 0.249 1867 Planarity : 0.004 0.046 2033 Dihedral : 13.007 178.397 1997 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 4.98 % Allowed : 22.78 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.78 (0.21), residues: 1698 helix: 0.73 (0.19), residues: 800 sheet: -0.73 (0.60), residues: 76 loop : -1.81 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 231 HIS 0.007 0.002 HIS A 167 PHE 0.015 0.002 PHE A 241 TYR 0.029 0.002 TYR B 315 ARG 0.003 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 656) hydrogen bonds : angle 4.76562 ( 1830) covalent geometry : bond 0.00449 (11101) covalent geometry : angle 0.58292 (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 191 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.6443 (mmm) cc_final: 0.5446 (mmm) REVERT: A 336 LYS cc_start: 0.7006 (tttt) cc_final: 0.5932 (mmtm) REVERT: A 362 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7567 (ttm) REVERT: A 415 ASP cc_start: 0.7375 (t0) cc_final: 0.7045 (t0) REVERT: A 417 GLU cc_start: 0.8371 (tp30) cc_final: 0.7811 (mm-30) REVERT: B 155 TYR cc_start: 0.7959 (m-80) cc_final: 0.7648 (m-80) REVERT: B 239 MET cc_start: 0.8290 (mtp) cc_final: 0.8001 (mtp) REVERT: B 326 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6576 (mp10) REVERT: B 327 ASN cc_start: 0.8035 (t0) cc_final: 0.7761 (t0) REVERT: B 339 ARG cc_start: 0.7877 (mtp-110) cc_final: 0.7473 (mtp85) REVERT: B 347 LEU cc_start: 0.8737 (mt) cc_final: 0.8513 (mt) REVERT: B 353 ASP cc_start: 0.6404 (m-30) cc_final: 0.5150 (t70) REVERT: B 367 ASN cc_start: 0.7888 (m110) cc_final: 0.7480 (t0) REVERT: B 391 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8213 (mp) outliers start: 28 outliers final: 21 residues processed: 179 average time/residue: 0.2054 time to fit residues: 53.8740 Evaluate side-chains 184 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 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 365 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 326 GLN 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: 0.6980 chunk 85 optimal weight: 9.9990 chunk 52 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 0.0570 chunk 30 optimal weight: 0.9990 chunk 139 optimal weight: 8.9990 chunk 169 optimal weight: 0.0060 chunk 133 optimal weight: 10.0000 chunk 135 optimal weight: 0.6980 overall best weight: 0.4114 ------------------------------------------------------------------------------- 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 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN B 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.262319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.212525 restraints weight = 14843.417| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 3.43 r_work: 0.4194 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11101 Z= 0.108 Angle : 0.502 7.820 15247 Z= 0.272 Chirality : 0.044 0.233 1867 Planarity : 0.003 0.045 2033 Dihedral : 12.778 177.328 1997 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.09 % Allowed : 23.67 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.22), residues: 1698 helix: 1.25 (0.19), residues: 811 sheet: -1.07 (0.57), residues: 88 loop : -1.59 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 231 HIS 0.013 0.001 HIS A 206 PHE 0.012 0.001 PHE B 213 TYR 0.023 0.001 TYR B 315 ARG 0.002 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03104 ( 656) hydrogen bonds : angle 4.20606 ( 1830) covalent geometry : bond 0.00234 (11101) covalent geometry : angle 0.50236 (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 188 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6670 (mmm) cc_final: 0.5900 (mmm) REVERT: A 127 GLU cc_start: 0.7750 (tm-30) cc_final: 0.6826 (tm-30) REVERT: A 304 LYS cc_start: 0.7044 (mmtm) cc_final: 0.6452 (mtmt) REVERT: A 336 LYS cc_start: 0.7191 (tttt) cc_final: 0.6211 (mmtm) REVERT: A 362 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7559 (ttm) REVERT: A 374 TYR cc_start: 0.8019 (m-80) cc_final: 0.7548 (m-80) REVERT: A 406 LYS cc_start: 0.8287 (mppt) cc_final: 0.7829 (mptt) REVERT: A 415 ASP cc_start: 0.7187 (t0) cc_final: 0.6933 (t0) REVERT: A 417 GLU cc_start: 0.8336 (tp30) cc_final: 0.7843 (mm-30) REVERT: B 119 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7847 (m-40) REVERT: B 194 ARG cc_start: 0.8102 (ttt90) cc_final: 0.7685 (ttt-90) REVERT: B 239 MET cc_start: 0.8253 (mtp) cc_final: 0.7944 (mtp) REVERT: B 326 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6358 (mp10) REVERT: B 339 ARG cc_start: 0.7799 (mtp-110) cc_final: 0.7463 (mtm110) REVERT: B 347 LEU cc_start: 0.8710 (mt) cc_final: 0.8500 (mt) REVERT: B 353 ASP cc_start: 0.6731 (m-30) cc_final: 0.5022 (t70) REVERT: B 385 MET cc_start: 0.7955 (mtt) cc_final: 0.7552 (mtp) outliers start: 23 outliers final: 16 residues processed: 177 average time/residue: 0.2073 time to fit residues: 53.1924 Evaluate side-chains 178 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 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 199 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 328 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 140 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 chunk 105 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.256046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.205477 restraints weight = 14947.649| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 3.39 r_work: 0.4123 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11101 Z= 0.232 Angle : 0.602 9.293 15247 Z= 0.324 Chirality : 0.046 0.248 1867 Planarity : 0.004 0.044 2033 Dihedral : 12.960 176.686 1997 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 5.34 % Allowed : 24.38 % Favored : 70.28 % 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: -0.57 (0.21), residues: 1698 helix: 0.91 (0.19), residues: 812 sheet: -0.95 (0.60), residues: 82 loop : -1.72 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 285 HIS 0.007 0.002 HIS A 167 PHE 0.017 0.002 PHE A 427 TYR 0.029 0.002 TYR B 315 ARG 0.004 0.001 ARG B 290 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 656) hydrogen bonds : angle 4.63746 ( 1830) covalent geometry : bond 0.00523 (11101) covalent geometry : angle 0.60228 (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 194 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6716 (mmm) cc_final: 0.5833 (mmm) REVERT: A 127 GLU cc_start: 0.7862 (tm-30) cc_final: 0.6895 (tm-30) REVERT: A 304 LYS cc_start: 0.7127 (mmtm) cc_final: 0.6522 (mtmt) REVERT: A 336 LYS cc_start: 0.6976 (tttt) cc_final: 0.5951 (mmtm) REVERT: A 415 ASP cc_start: 0.7452 (t0) cc_final: 0.7115 (t0) REVERT: A 417 GLU cc_start: 0.8347 (tp30) cc_final: 0.7822 (mm-30) REVERT: B 119 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.8076 (m-40) REVERT: B 239 MET cc_start: 0.8223 (mtp) cc_final: 0.7924 (mtp) REVERT: B 326 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.6522 (mp10) REVERT: B 339 ARG cc_start: 0.7834 (mtp-110) cc_final: 0.7610 (mtp85) REVERT: B 347 LEU cc_start: 0.8756 (mt) cc_final: 0.8513 (mt) REVERT: B 353 ASP cc_start: 0.6739 (m-30) cc_final: 0.5055 (t70) outliers start: 30 outliers final: 26 residues processed: 179 average time/residue: 0.2276 time to fit residues: 59.5207 Evaluate side-chains 189 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 ASN 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: 1.9990 chunk 156 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 63 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 47 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.261862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.212135 restraints weight = 14782.542| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 3.39 r_work: 0.4190 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11101 Z= 0.116 Angle : 0.510 8.334 15247 Z= 0.274 Chirality : 0.044 0.232 1867 Planarity : 0.003 0.044 2033 Dihedral : 12.705 178.978 1997 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.80 % Allowed : 24.38 % 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: -0.19 (0.22), residues: 1698 helix: 1.29 (0.19), residues: 824 sheet: -0.93 (0.60), residues: 82 loop : -1.63 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 231 HIS 0.010 0.001 HIS A 206 PHE 0.014 0.001 PHE B 213 TYR 0.023 0.001 TYR B 315 ARG 0.002 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03054 ( 656) hydrogen bonds : angle 4.16407 ( 1830) covalent geometry : bond 0.00258 (11101) covalent geometry : angle 0.50980 (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 187 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6713 (mmm) cc_final: 0.5925 (mmm) REVERT: A 127 GLU cc_start: 0.7800 (tm-30) cc_final: 0.6904 (tm-30) REVERT: A 304 LYS cc_start: 0.7031 (mmtm) cc_final: 0.6439 (mtmt) REVERT: A 336 LYS cc_start: 0.7107 (tttt) cc_final: 0.6178 (mmtm) REVERT: A 374 TYR cc_start: 0.7949 (m-80) cc_final: 0.7561 (m-80) REVERT: A 415 ASP cc_start: 0.7255 (t0) cc_final: 0.6947 (t0) REVERT: A 417 GLU cc_start: 0.8346 (tp30) cc_final: 0.7773 (mm-30) REVERT: B 119 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.8000 (m-40) REVERT: B 239 MET cc_start: 0.8122 (mtp) cc_final: 0.7807 (mtp) REVERT: B 326 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.6414 (mp10) REVERT: B 339 ARG cc_start: 0.7779 (mtp-110) cc_final: 0.7530 (mtm110) REVERT: B 347 LEU cc_start: 0.8701 (mt) cc_final: 0.8469 (mt) REVERT: B 353 ASP cc_start: 0.6655 (m-30) cc_final: 0.4886 (t70) REVERT: B 385 MET cc_start: 0.7798 (mtt) cc_final: 0.7455 (mtp) outliers start: 27 outliers final: 23 residues processed: 174 average time/residue: 0.2133 time to fit residues: 54.2889 Evaluate side-chains 176 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 399 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 199 VAL 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 420 THR 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: 1.9990 chunk 149 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 168 optimal weight: 0.0370 chunk 8 optimal weight: 0.9990 chunk 114 optimal weight: 0.4980 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.260460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.210587 restraints weight = 14866.106| |-----------------------------------------------------------------------------| r_work (start): 0.4331 rms_B_bonded: 3.38 r_work: 0.4180 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11101 Z= 0.131 Angle : 0.533 8.696 15247 Z= 0.286 Chirality : 0.044 0.236 1867 Planarity : 0.003 0.045 2033 Dihedral : 12.681 179.369 1997 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 4.45 % Allowed : 24.38 % 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: -0.03 (0.22), residues: 1698 helix: 1.41 (0.19), residues: 819 sheet: -0.51 (0.63), residues: 76 loop : -1.56 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 231 HIS 0.008 0.001 HIS A 206 PHE 0.011 0.001 PHE A 329 TYR 0.024 0.001 TYR B 315 ARG 0.002 0.000 ARG B 290 Details of bonding type rmsd hydrogen bonds : bond 0.03170 ( 656) hydrogen bonds : angle 4.14663 ( 1830) covalent geometry : bond 0.00297 (11101) covalent geometry : angle 0.53341 (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: 25 poor density : 155 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6763 (mmm) cc_final: 0.5989 (mmm) REVERT: A 127 GLU cc_start: 0.7801 (tm-30) cc_final: 0.6865 (tm-30) REVERT: A 304 LYS cc_start: 0.7052 (mmtm) cc_final: 0.6506 (mtmt) REVERT: A 336 LYS cc_start: 0.7067 (tttt) cc_final: 0.6138 (mmtm) REVERT: A 374 TYR cc_start: 0.8030 (m-80) cc_final: 0.7633 (m-80) REVERT: A 415 ASP cc_start: 0.7299 (t0) cc_final: 0.6981 (t0) REVERT: A 417 GLU cc_start: 0.8362 (tp30) cc_final: 0.7775 (mm-30) REVERT: A 443 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7447 (tt0) REVERT: B 119 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.8002 (m-40) REVERT: B 185 LYS cc_start: 0.7847 (mtpt) cc_final: 0.7609 (mttt) REVERT: B 239 MET cc_start: 0.8198 (mtp) cc_final: 0.7894 (mtp) REVERT: B 255 GLU cc_start: 0.7701 (pp20) cc_final: 0.7465 (pp20) REVERT: B 326 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.6447 (mp10) REVERT: B 347 LEU cc_start: 0.8728 (mt) cc_final: 0.8486 (mt) REVERT: B 353 ASP cc_start: 0.6573 (m-30) cc_final: 0.4870 (t70) outliers start: 25 outliers final: 23 residues processed: 169 average time/residue: 0.2129 time to fit residues: 52.1067 Evaluate side-chains 179 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 399 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 199 VAL 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 420 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 87 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 98 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 71 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 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 = 0.4777 r_free = 0.4777 target = 0.260836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.211484 restraints weight = 14696.638| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 3.31 r_work: 0.4179 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11101 Z= 0.134 Angle : 0.537 10.186 15247 Z= 0.285 Chirality : 0.044 0.236 1867 Planarity : 0.003 0.044 2033 Dihedral : 12.649 179.502 1997 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.80 % Allowed : 24.20 % 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: -0.02 (0.22), residues: 1698 helix: 1.45 (0.19), residues: 825 sheet: -0.46 (0.64), residues: 76 loop : -1.62 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 231 HIS 0.007 0.001 HIS A 206 PHE 0.012 0.001 PHE A 329 TYR 0.024 0.001 TYR B 315 ARG 0.002 0.000 ARG B 339 Details of bonding type rmsd hydrogen bonds : bond 0.03134 ( 656) hydrogen bonds : angle 4.13535 ( 1830) covalent geometry : bond 0.00303 (11101) covalent geometry : angle 0.53684 (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 179 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6534 (mmm) cc_final: 0.5025 (mmm) REVERT: A 127 GLU cc_start: 0.7767 (tm-30) cc_final: 0.6677 (tm-30) REVERT: A 304 LYS cc_start: 0.7004 (mmtm) cc_final: 0.6490 (mtmt) REVERT: A 336 LYS cc_start: 0.7042 (tttt) cc_final: 0.6113 (mmtm) REVERT: A 374 TYR cc_start: 0.8075 (m-80) cc_final: 0.7697 (m-80) REVERT: A 384 THR cc_start: 0.7741 (m) cc_final: 0.7443 (m) REVERT: A 415 ASP cc_start: 0.7283 (t0) cc_final: 0.6967 (t0) REVERT: A 417 GLU cc_start: 0.8354 (tp30) cc_final: 0.7769 (mm-30) REVERT: A 443 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7454 (tt0) REVERT: B 119 ASN cc_start: 0.8245 (OUTLIER) cc_final: 0.7965 (m-40) REVERT: B 185 LYS cc_start: 0.7839 (mtpt) cc_final: 0.7591 (mttt) REVERT: B 239 MET cc_start: 0.8220 (mtp) cc_final: 0.7920 (mtp) REVERT: B 326 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.6470 (mp10) REVERT: B 347 LEU cc_start: 0.8725 (mt) cc_final: 0.8488 (mt) REVERT: B 353 ASP cc_start: 0.6648 (m-30) cc_final: 0.4731 (t70) outliers start: 27 outliers final: 23 residues processed: 170 average time/residue: 0.2120 time to fit residues: 52.5647 Evaluate side-chains 175 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 399 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 199 VAL 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 349 ILE Chi-restraints excluded: chain B residue 380 ASN 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: 20.0000 chunk 86 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 78 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.258598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.208658 restraints weight = 14724.474| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 3.33 r_work: 0.4163 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11101 Z= 0.166 Angle : 0.557 9.199 15247 Z= 0.297 Chirality : 0.045 0.241 1867 Planarity : 0.003 0.044 2033 Dihedral : 12.686 179.119 1997 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 4.45 % Allowed : 24.56 % 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: -0.13 (0.22), residues: 1698 helix: 1.30 (0.19), residues: 832 sheet: -0.47 (0.64), residues: 76 loop : -1.62 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 231 HIS 0.005 0.001 HIS A 206 PHE 0.012 0.001 PHE A 427 TYR 0.025 0.001 TYR B 315 ARG 0.002 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 656) hydrogen bonds : angle 4.25193 ( 1830) covalent geometry : bond 0.00378 (11101) covalent geometry : angle 0.55729 (15247) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5893.33 seconds wall clock time: 102 minutes 5.70 seconds (6125.70 seconds total)