Starting phenix.real_space_refine on Fri Jul 3 23:34:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oqh_12701/07_2026/7oqh_12701.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oqh_12701/07_2026/7oqh_12701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oqh_12701/07_2026/7oqh_12701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oqh_12701/07_2026/7oqh_12701.map" model { file = "/net/cci-nas-00/data/ceres_data/7oqh_12701/07_2026/7oqh_12701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oqh_12701/07_2026/7oqh_12701.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7oqh_12701/07_2026/7oqh_12701.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oqh_12701/07_2026/7oqh_12701.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 P 18 5.49 5 Mg 5 5.21 5 S 54 5.16 5 C 10470 2.51 5 N 3042 2.21 5 O 3235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16824 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2770 Classifications: {'peptide': 363} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2787 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2775 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2797 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 341} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 2772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2772 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2732 Classifications: {'peptide': 356} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.86, per 1000 atoms: 0.23 Number of scatterers: 16824 At special positions: 0 Unit cell: (147.882, 131.451, 103.069, 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) S 54 16.00 P 18 15.00 Mg 5 11.99 O 3235 8.00 N 3042 7.00 C 10470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 772.2 milliseconds 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4010 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 14 sheets defined 43.8% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 331 through 341 removed outlier: 3.736A pdb=" N ARG A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 374 Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.504A pdb=" N VAL A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 432 removed outlier: 3.790A pdb=" N HIS A 414 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 469 through 478 removed outlier: 3.549A pdb=" N LYS A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 509 removed outlier: 3.796A pdb=" N THR A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.839A pdb=" N LEU A 545 " --> pdb=" O LYS A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 565 removed outlier: 4.140A pdb=" N LEU A 565 " --> pdb=" O VAL A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 575 Processing helix chain 'A' and resid 582 through 592 removed outlier: 3.559A pdb=" N GLU A 586 " --> pdb=" O LYS A 582 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 334 through 341 removed outlier: 3.862A pdb=" N LEU B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 374 Processing helix chain 'B' and resid 387 through 398 removed outlier: 3.875A pdb=" N THR B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 431 Processing helix chain 'B' and resid 441 through 453 removed outlier: 4.103A pdb=" N SER B 453 " --> pdb=" O TYR B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 469 Processing helix chain 'B' and resid 470 through 478 Processing helix chain 'B' and resid 500 through 510 removed outlier: 3.610A pdb=" N THR B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 527 Processing helix chain 'B' and resid 548 through 564 Processing helix chain 'B' and resid 566 through 581 removed outlier: 3.805A pdb=" N THR B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 592 Processing helix chain 'C' and resid 255 through 262 Processing helix chain 'C' and resid 334 through 341 Processing helix chain 'C' and resid 358 through 374 Processing helix chain 'C' and resid 387 through 398 removed outlier: 3.948A pdb=" N THR C 392 " --> pdb=" O PRO C 388 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 431 removed outlier: 3.606A pdb=" N GLN C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 453 removed outlier: 3.529A pdb=" N SER C 453 " --> pdb=" O TYR C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 477 removed outlier: 3.652A pdb=" N LYS C 473 " --> pdb=" O LEU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 510 removed outlier: 3.914A pdb=" N THR C 504 " --> pdb=" O SER C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 526 Processing helix chain 'C' and resid 542 through 546 removed outlier: 4.034A pdb=" N LEU C 545 " --> pdb=" O LYS C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 564 removed outlier: 4.066A pdb=" N GLY C 564 " --> pdb=" O ARG C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 579 Processing helix chain 'C' and resid 582 through 592 Processing helix chain 'D' and resid 254 through 261 Processing helix chain 'D' and resid 332 through 341 Processing helix chain 'D' and resid 358 through 374 removed outlier: 3.593A pdb=" N ILE D 362 " --> pdb=" O GLY D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 398 removed outlier: 3.777A pdb=" N THR D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 431 removed outlier: 3.688A pdb=" N GLN D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 453 removed outlier: 3.965A pdb=" N SER D 453 " --> pdb=" O TYR D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 468 No H-bonds generated for 'chain 'D' and resid 466 through 468' Processing helix chain 'D' and resid 469 through 478 removed outlier: 3.600A pdb=" N LYS D 473 " --> pdb=" O LEU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 510 removed outlier: 3.781A pdb=" N THR D 504 " --> pdb=" O SER D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 527 removed outlier: 3.565A pdb=" N ARG D 527 " --> pdb=" O LYS D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 546 removed outlier: 4.087A pdb=" N LEU D 545 " --> pdb=" O LYS D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 565 removed outlier: 3.912A pdb=" N LEU D 565 " --> pdb=" O VAL D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 578 Processing helix chain 'D' and resid 583 through 592 removed outlier: 3.726A pdb=" N SER D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 262 Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 358 through 374 Processing helix chain 'E' and resid 387 through 398 removed outlier: 3.784A pdb=" N THR E 392 " --> pdb=" O PRO E 388 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP E 393 " --> pdb=" O GLU E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 432 Processing helix chain 'E' and resid 441 through 453 removed outlier: 3.799A pdb=" N SER E 453 " --> pdb=" O TYR E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 468 Processing helix chain 'E' and resid 469 through 477 removed outlier: 3.752A pdb=" N LYS E 473 " --> pdb=" O LEU E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 510 removed outlier: 3.746A pdb=" N THR E 504 " --> pdb=" O SER E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 526 Processing helix chain 'E' and resid 542 through 546 removed outlier: 3.839A pdb=" N LEU E 545 " --> pdb=" O LYS E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 565 removed outlier: 3.578A pdb=" N LEU E 565 " --> pdb=" O VAL E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 580 removed outlier: 4.032A pdb=" N ASP E 572 " --> pdb=" O HIS E 568 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS E 580 " --> pdb=" O SER E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 592 removed outlier: 3.583A pdb=" N SER E 592 " --> pdb=" O LEU E 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 262 Processing helix chain 'F' and resid 309 through 313 removed outlier: 3.693A pdb=" N LYS F 313 " --> pdb=" O GLU F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 341 removed outlier: 3.853A pdb=" N ARG F 335 " --> pdb=" O ARG F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 374 Processing helix chain 'F' and resid 387 through 398 removed outlier: 3.530A pdb=" N THR F 392 " --> pdb=" O PRO F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 431 removed outlier: 3.749A pdb=" N GLN F 431 " --> pdb=" O ARG F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 451 removed outlier: 3.574A pdb=" N LEU F 445 " --> pdb=" O SER F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 468 No H-bonds generated for 'chain 'F' and resid 466 through 468' Processing helix chain 'F' and resid 469 through 478 removed outlier: 3.871A pdb=" N LYS F 473 " --> pdb=" O LEU F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 510 Processing helix chain 'F' and resid 521 through 527 Processing helix chain 'F' and resid 548 through 564 Processing helix chain 'F' and resid 566 through 581 removed outlier: 3.783A pdb=" N THR F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 589 Processing sheet with id=AA1, first strand: chain 'A' and resid 251 through 253 removed outlier: 3.965A pdb=" N ALA A 227 " --> pdb=" O VAL A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 322 through 323 removed outlier: 4.503A pdb=" N ILE A 343 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 401 through 403 removed outlier: 7.054A pdb=" N LEU A 379 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE A 403 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL A 381 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 436 " --> pdb=" O HIS A 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 401 through 403 removed outlier: 7.054A pdb=" N LEU A 379 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE A 403 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL A 381 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 436 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA A 349 " --> pdb=" O ALA A 492 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA A 494 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE A 351 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ARG A 348 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU A 518 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU A 350 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU A 520 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL A 352 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 9.642A pdb=" N GLU A 517 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N ASN A 536 " --> pdb=" O GLU A 517 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS A 519 " --> pdb=" O ASP A 534 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 250 through 253 removed outlier: 3.561A pdb=" N ALA B 237 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY B 228 " --> pdb=" O ARG B 240 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA B 268 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE B 297 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N THR B 270 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B 293 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 401 through 406 removed outlier: 6.731A pdb=" N LEU B 379 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE B 403 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL B 381 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N SER B 405 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU B 383 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N HIS B 378 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU B 438 " --> pdb=" O HIS B 378 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N MET B 380 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASP B 440 " --> pdb=" O MET B 380 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL B 382 " --> pdb=" O ASP B 440 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ALA B 349 " --> pdb=" O ALA B 492 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA B 494 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE B 351 " --> pdb=" O ALA B 494 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG B 348 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N LEU B 518 " --> pdb=" O ARG B 348 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B 350 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU B 520 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 352 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N GLU B 517 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N ASN B 536 " --> pdb=" O GLU B 517 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS B 519 " --> pdb=" O ASP B 534 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 253 through 254 removed outlier: 4.222A pdb=" N GLY C 228 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA C 268 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE C 297 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR C 270 " --> pdb=" O ASP C 295 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP C 295 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 401 through 406 removed outlier: 3.575A pdb=" N ASP C 385 " --> pdb=" O SER C 405 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N HIS C 378 " --> pdb=" O VAL C 436 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU C 438 " --> pdb=" O HIS C 378 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N MET C 380 " --> pdb=" O LEU C 438 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASP C 440 " --> pdb=" O MET C 380 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL C 382 " --> pdb=" O ASP C 440 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 493 " --> pdb=" O LEU C 439 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA C 349 " --> pdb=" O ALA C 492 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ALA C 494 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ILE C 351 " --> pdb=" O ALA C 494 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ARG C 348 " --> pdb=" O ALA C 516 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N LEU C 518 " --> pdb=" O ARG C 348 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU C 350 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU C 520 " --> pdb=" O LEU C 350 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL C 352 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N GLU C 517 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N ASN C 536 " --> pdb=" O GLU C 517 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LYS C 519 " --> pdb=" O ASP C 534 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 238 through 240 removed outlier: 3.901A pdb=" N GLY D 228 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA D 268 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE D 297 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR D 270 " --> pdb=" O ASP D 295 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG D 293 " --> pdb=" O ALA D 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 401 through 406 removed outlier: 6.755A pdb=" N LEU D 379 " --> pdb=" O GLU D 401 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE D 403 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VAL D 381 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N SER D 405 " --> pdb=" O VAL D 381 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU D 383 " --> pdb=" O SER D 405 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL D 384 " --> pdb=" O ASP D 440 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR D 493 " --> pdb=" O LEU D 439 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA D 349 " --> pdb=" O ALA D 492 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA D 494 " --> pdb=" O ALA D 349 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE D 351 " --> pdb=" O ALA D 494 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ARG D 348 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N LEU D 518 " --> pdb=" O ARG D 348 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU D 350 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU D 520 " --> pdb=" O LEU D 350 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL D 352 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 9.623A pdb=" N GLU D 517 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ASN D 536 " --> pdb=" O GLU D 517 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS D 519 " --> pdb=" O ASP D 534 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 251 through 254 removed outlier: 4.089A pdb=" N GLY E 228 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA E 227 " --> pdb=" O VAL E 269 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 401 through 406 removed outlier: 6.996A pdb=" N LEU E 379 " --> pdb=" O GLU E 401 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE E 403 " --> pdb=" O LEU E 379 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL E 381 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER E 405 " --> pdb=" O VAL E 381 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU E 383 " --> pdb=" O SER E 405 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL E 436 " --> pdb=" O HIS E 378 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL E 382 " --> pdb=" O LEU E 438 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL E 384 " --> pdb=" O ASP E 440 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL E 435 " --> pdb=" O THR E 489 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE E 491 " --> pdb=" O VAL E 435 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL E 437 " --> pdb=" O ILE E 491 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N THR E 493 " --> pdb=" O VAL E 437 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU E 439 " --> pdb=" O THR E 493 " (cutoff:3.500A) removed outlier: 9.504A pdb=" N MET E 495 " --> pdb=" O LEU E 439 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA E 349 " --> pdb=" O ALA E 492 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ALA E 494 " --> pdb=" O ALA E 349 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE E 351 " --> pdb=" O ALA E 494 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA E 516 " --> pdb=" O ARG E 348 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 289 through 290 removed outlier: 3.814A pdb=" N VAL F 251 " --> pdb=" O VAL F 239 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY F 228 " --> pdb=" O ARG F 240 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER F 296 " --> pdb=" O THR F 270 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 401 through 406 removed outlier: 6.810A pdb=" N LEU F 379 " --> pdb=" O GLU F 401 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE F 403 " --> pdb=" O LEU F 379 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL F 381 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N SER F 405 " --> pdb=" O VAL F 381 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU F 383 " --> pdb=" O SER F 405 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL F 384 " --> pdb=" O ASP F 440 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 439 " --> pdb=" O ILE F 491 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA F 492 " --> pdb=" O ALA F 349 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA F 516 " --> pdb=" O ARG F 348 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N GLU F 517 " --> pdb=" O ASN F 536 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ASN F 536 " --> pdb=" O GLU F 517 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS F 519 " --> pdb=" O ASP F 534 " (cutoff:3.500A) 703 hydrogen bonds defined for protein. 2034 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: 2.40 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5732 1.34 - 1.46: 2062 1.46 - 1.57: 9154 1.57 - 1.69: 27 1.69 - 1.81: 101 Bond restraints: 17076 Sorted by residual: bond pdb=" CB PRO E 248 " pdb=" CG PRO E 248 " ideal model delta sigma weight residual 1.492 1.631 -0.139 5.00e-02 4.00e+02 7.69e+00 bond pdb=" C GLN E 224 " pdb=" N PRO E 225 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.19e+00 bond pdb=" N PRO E 248 " pdb=" CA PRO E 248 " ideal model delta sigma weight residual 1.473 1.461 0.011 8.50e-03 1.38e+04 1.83e+00 bond pdb=" CA ASP C 543 " pdb=" CB ASP C 543 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.68e-02 3.54e+03 1.20e+00 bond pdb=" C TYR F 318 " pdb=" N PRO F 319 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.92e-01 ... (remaining 17071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 22709 1.87 - 3.74: 370 3.74 - 5.62: 58 5.62 - 7.49: 17 7.49 - 9.36: 5 Bond angle restraints: 23159 Sorted by residual: angle pdb=" CA PRO E 248 " pdb=" N PRO E 248 " pdb=" CD PRO E 248 " ideal model delta sigma weight residual 112.00 104.79 7.21 1.40e+00 5.10e-01 2.65e+01 angle pdb=" N TYR E 318 " pdb=" CA TYR E 318 " pdb=" C TYR E 318 " ideal model delta sigma weight residual 109.81 118.41 -8.60 2.21e+00 2.05e-01 1.51e+01 angle pdb=" C SER B 242 " pdb=" N GLY B 243 " pdb=" CA GLY B 243 " ideal model delta sigma weight residual 121.70 128.67 -6.97 1.80e+00 3.09e-01 1.50e+01 angle pdb=" C LEU E 317 " pdb=" N TYR E 318 " pdb=" CA TYR E 318 " ideal model delta sigma weight residual 121.80 131.16 -9.36 2.44e+00 1.68e-01 1.47e+01 angle pdb=" C LYS D 580 " pdb=" N THR D 581 " pdb=" CA THR D 581 " ideal model delta sigma weight residual 121.54 128.17 -6.63 1.91e+00 2.74e-01 1.21e+01 ... (remaining 23154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9483 17.98 - 35.97: 844 35.97 - 53.95: 147 53.95 - 71.93: 15 71.93 - 89.91: 12 Dihedral angle restraints: 10501 sinusoidal: 4293 harmonic: 6208 Sorted by residual: dihedral pdb=" CA TYR D 318 " pdb=" C TYR D 318 " pdb=" N PRO D 319 " pdb=" CA PRO D 319 " ideal model delta harmonic sigma weight residual 180.00 151.32 28.68 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA TYR E 318 " pdb=" C TYR E 318 " pdb=" N PRO E 319 " pdb=" CA PRO E 319 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA GLN E 224 " pdb=" C GLN E 224 " pdb=" N PRO E 225 " pdb=" CA PRO E 225 " ideal model delta harmonic sigma weight residual 180.00 -159.48 -20.52 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 10498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2055 0.047 - 0.093: 492 0.093 - 0.140: 155 0.140 - 0.186: 5 0.186 - 0.232: 2 Chirality restraints: 2709 Sorted by residual: chirality pdb=" CA TYR D 318 " pdb=" N TYR D 318 " pdb=" C TYR D 318 " pdb=" CB TYR D 318 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA TYR E 318 " pdb=" N TYR E 318 " pdb=" C TYR E 318 " pdb=" CB TYR E 318 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.20e-01 chirality pdb=" CA PRO E 225 " pdb=" N PRO E 225 " pdb=" C PRO E 225 " pdb=" CB PRO E 225 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 2706 not shown) Planarity restraints: 3003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 536 " -0.056 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO B 537 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO B 537 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 537 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 308 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.01e+00 pdb=" N PRO B 309 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 309 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 309 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 548 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.69e+00 pdb=" N PRO C 549 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 549 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 549 " -0.030 5.00e-02 4.00e+02 ... (remaining 3000 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 151 2.55 - 3.14: 13346 3.14 - 3.73: 25644 3.73 - 4.31: 34974 4.31 - 4.90: 59588 Nonbonded interactions: 133703 Sorted by model distance: nonbonded pdb=" O2B ATP F 701 " pdb="MG MG F 702 " model vdw 1.967 2.170 nonbonded pdb=" O2B ATP D 701 " pdb="MG MG D 702 " model vdw 1.977 2.170 nonbonded pdb=" O2B ATP E 701 " pdb="MG MG E 702 " model vdw 1.978 2.170 nonbonded pdb=" O2G ATP B 701 " pdb="MG MG B 702 " model vdw 1.983 2.170 nonbonded pdb=" O2G ATP F 701 " pdb="MG MG F 702 " model vdw 2.007 2.170 ... (remaining 133698 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 223 through 262 or (resid 263 and (name N or name CA or na \ me C or name O or name CB or name CG or name SD )) or resid 264 through 276 or r \ esid 288 through 330 or (resid 331 and (name N or name CA or name C or name O or \ name CB )) or resid 332 through 423 or (resid 424 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ )) or resid \ 425 through 455 or (resid 460 and (name N or name CA or name C or name O or nam \ e CB )) or resid 461 through 466 or (resid 467 and (name N or name CA or name C \ or name O or name CB or name OG1)) or resid 468 through 481 or (resid 482 and (n \ ame N or name CA or name C or name O or name CB or name CG1 or name CG2)) or res \ id 483 through 589)) selection = (chain 'B' and (resid 223 through 276 or resid 288 through 306 or (resid 307 thr \ ough 308 and (name N or name CA or name C or name O or name CB )) or resid 309 t \ hrough 330 or (resid 331 and (name N or name CA or name C or name O or name CB ) \ ) or resid 332 through 348 or (resid 349 and (name N or name CA or name C or nam \ e O )) or resid 350 through 360 or (resid 361 and (name N or name CA or name C o \ r name O or name CB or name OG1)) or resid 362 through 455 or (resid 460 and (na \ me N or name CA or name C or name O or name CB )) or resid 461 through 466 or (r \ esid 467 and (name N or name CA or name C or name O or name CB or name OG1)) or \ resid 468 through 481 or (resid 482 and (name N or name CA or name C or name O o \ r name CB or name CG1 or name CG2)) or resid 483 through 526 or (resid 527 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD or name N \ E or name CZ )) or resid 528 through 556 or (resid 557 and (name N or name CA or \ name C or name O or name CB )) or resid 558 through 589)) selection = (chain 'C' and (resid 223 through 262 or (resid 263 and (name N or name CA or na \ me C or name O or name CB or name CG or name SD )) or resid 264 through 276 or r \ esid 288 through 306 or (resid 307 through 308 and (name N or name CA or name C \ or name O or name CB )) or resid 309 through 330 or (resid 331 and (name N or na \ me CA or name C or name O or name CB )) or resid 332 through 348 or (resid 349 a \ nd (name N or name CA or name C or name O )) or resid 350 through 360 or (resid \ 361 and (name N or name CA or name C or name O or name CB or name OG1)) or resid \ 362 through 423 or (resid 424 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD or name NE or name CZ )) or resid 425 through 455 or \ (resid 460 and (name N or name CA or name C or name O or name CB )) or resid 461 \ through 481 or (resid 482 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2)) or resid 483 through 526 or (resid 527 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ )) or resid 528 through 556 or (resid 557 and (name N or name CA or name C o \ r name O or name CB )) or resid 558 through 589)) selection = (chain 'D' and (resid 223 through 262 or (resid 263 and (name N or name CA or na \ me C or name O or name CB or name CG or name SD )) or resid 264 through 276 or r \ esid 288 through 306 or (resid 307 through 308 and (name N or name CA or name C \ or name O or name CB )) or resid 309 through 330 or (resid 331 and (name N or na \ me CA or name C or name O or name CB )) or resid 332 through 348 or (resid 349 a \ nd (name N or name CA or name C or name O )) or resid 350 through 360 or (resid \ 361 and (name N or name CA or name C or name O or name CB or name OG1)) or resid \ 362 through 423 or (resid 424 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD or name NE or name CZ )) or resid 425 through 455 or \ (resid 460 and (name N or name CA or name C or name O or name CB )) or resid 461 \ through 466 or (resid 467 and (name N or name CA or name C or name O or name CB \ or name OG1)) or resid 468 through 481 or (resid 482 and (name N or name CA or \ name C or name O or name CB or name CG1 or name CG2)) or resid 483 through 526 o \ r (resid 527 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name NE or name CZ )) or resid 528 through 556 or (resid 557 and (na \ me N or name CA or name C or name O or name CB )) or resid 558 through 589)) selection = (chain 'E' and (resid 223 through 262 or (resid 263 and (name N or name CA or na \ me C or name O or name CB or name CG or name SD )) or resid 264 through 276 or r \ esid 288 through 306 or (resid 307 through 308 and (name N or name CA or name C \ or name O or name CB )) or resid 309 through 348 or (resid 349 and (name N or na \ me CA or name C or name O )) or resid 350 through 360 or (resid 361 and (name N \ or name CA or name C or name O or name CB or name OG1)) or resid 362 through 455 \ or (resid 460 and (name N or name CA or name C or name O or name CB )) or resid \ 461 through 466 or (resid 467 and (name N or name CA or name C or name O or nam \ e CB or name OG1)) or resid 468 through 526 or (resid 527 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name NE or name CZ )) o \ r resid 528 through 556 or (resid 557 and (name N or name CA or name C or name O \ or name CB )) or resid 558 through 589)) selection = (chain 'F' and (resid 223 through 262 or (resid 263 and (name N or name CA or na \ me C or name O or name CB or name CG or name SD )) or resid 264 through 276 or r \ esid 288 through 306 or (resid 307 through 308 and (name N or name CA or name C \ or name O or name CB )) or resid 309 through 330 or (resid 331 and (name N or na \ me CA or name C or name O or name CB )) or resid 332 through 360 or (resid 361 a \ nd (name N or name CA or name C or name O or name CB or name OG1)) or resid 362 \ through 423 or (resid 424 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ )) or resid 425 through 466 or (resi \ d 467 and (name N or name CA or name C or name O or name CB or name OG1)) or res \ id 468 through 481 or (resid 482 and (name N or name CA or name C or name O or n \ ame CB or name CG1 or name CG2)) or resid 483 through 556 or (resid 557 and (nam \ e N or name CA or name C or name O or name CB )) or resid 558 through 589)) } 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.310 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 : 0.004 0.139 17076 Z= 0.159 Angle : 0.621 9.361 23159 Z= 0.322 Chirality : 0.044 0.232 2709 Planarity : 0.005 0.084 3003 Dihedral : 13.628 89.914 6491 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.49 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.19), residues: 2143 helix: 1.44 (0.18), residues: 844 sheet: -1.01 (0.28), residues: 350 loop : -1.10 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 372 TYR 0.018 0.001 TYR E 318 PHE 0.012 0.001 PHE F 475 HIS 0.007 0.001 HIS B 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (17076) covalent geometry : angle 0.62066 / 0.32 (23159) hydrogen bonds : bond 0.17921 / 11.88 ( 694) hydrogen bonds : angle 6.68776 / 4.89 ( 2034) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 TYR cc_start: 0.4436 (t80) cc_final: 0.4171 (t80) REVERT: A 260 LYS cc_start: 0.7544 (mptt) cc_final: 0.7017 (mmtt) REVERT: A 330 GLU cc_start: 0.6032 (mm-30) cc_final: 0.5828 (mm-30) REVERT: A 341 MET cc_start: 0.8107 (ttt) cc_final: 0.7819 (ttt) REVERT: A 577 GLN cc_start: 0.6792 (tm-30) cc_final: 0.6577 (tm-30) REVERT: B 257 MET cc_start: 0.6348 (ttt) cc_final: 0.5798 (ttt) REVERT: B 394 MET cc_start: 0.8981 (tpt) cc_final: 0.8671 (tpp) REVERT: B 575 MET cc_start: 0.7565 (mmm) cc_final: 0.7089 (tpp) REVERT: D 263 MET cc_start: 0.7456 (mmm) cc_final: 0.6765 (mtt) REVERT: D 444 ARG cc_start: 0.7935 (mmt-90) cc_final: 0.7643 (mmm-85) REVERT: D 556 HIS cc_start: 0.7670 (t70) cc_final: 0.7387 (t70) REVERT: D 580 LYS cc_start: 0.6598 (mmtt) cc_final: 0.5386 (tptt) REVERT: E 263 MET cc_start: 0.7631 (tpp) cc_final: 0.7399 (tpp) REVERT: E 264 ARG cc_start: 0.6597 (mmt-90) cc_final: 0.5981 (mmt-90) REVERT: E 394 MET cc_start: 0.8761 (tpt) cc_final: 0.8408 (tpt) REVERT: E 556 HIS cc_start: 0.8065 (t70) cc_final: 0.7838 (t70) REVERT: F 321 GLN cc_start: 0.7473 (mt0) cc_final: 0.7257 (mt0) REVERT: F 364 GLN cc_start: 0.7866 (mt0) cc_final: 0.7635 (mt0) REVERT: F 449 TYR cc_start: 0.8378 (m-80) cc_final: 0.8072 (m-10) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.1299 time to fit residues: 59.1064 Evaluate side-chains 225 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 10.0000 chunk 77 optimal weight: 0.1980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN E 249 HIS ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.164906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132702 restraints weight = 20995.295| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.05 r_work: 0.3408 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17076 Z= 0.160 Angle : 0.624 8.742 23159 Z= 0.319 Chirality : 0.045 0.259 2709 Planarity : 0.005 0.059 3003 Dihedral : 4.841 46.380 2388 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.20 % Allowed : 7.33 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.18), residues: 2143 helix: 1.31 (0.18), residues: 875 sheet: -0.92 (0.28), residues: 342 loop : -1.32 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 240 TYR 0.014 0.002 TYR E 318 PHE 0.011 0.001 PHE B 407 HIS 0.007 0.001 HIS D 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (17076) covalent geometry : angle 0.62434 / 0.32 (23159) hydrogen bonds : bond 0.04621 / 3.09 ( 694) hydrogen bonds : angle 5.12303 / 3.76 ( 2034) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 248 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 TYR cc_start: 0.6724 (m-80) cc_final: 0.6504 (m-80) REVERT: A 260 LYS cc_start: 0.6852 (mptt) cc_final: 0.6311 (mmtp) REVERT: A 341 MET cc_start: 0.8133 (ttt) cc_final: 0.7901 (ttt) REVERT: A 395 GLN cc_start: 0.7833 (mt0) cc_final: 0.7375 (mp10) REVERT: A 577 GLN cc_start: 0.7479 (tm-30) cc_final: 0.7189 (tm-30) REVERT: B 257 MET cc_start: 0.6837 (ttt) cc_final: 0.6441 (ttt) REVERT: B 394 MET cc_start: 0.9064 (tpt) cc_final: 0.8787 (tpp) REVERT: B 575 MET cc_start: 0.8375 (mmm) cc_final: 0.7985 (tpp) REVERT: C 429 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8398 (t) REVERT: C 444 ARG cc_start: 0.8084 (mmm-85) cc_final: 0.7689 (mpt-90) REVERT: D 263 MET cc_start: 0.7908 (mmm) cc_final: 0.7372 (mtt) REVERT: D 444 ARG cc_start: 0.8546 (mmt-90) cc_final: 0.8048 (mmm-85) REVERT: D 580 LYS cc_start: 0.6642 (mmtt) cc_final: 0.4854 (tptt) REVERT: E 236 TYR cc_start: 0.6189 (m-80) cc_final: 0.5978 (m-80) REVERT: E 394 MET cc_start: 0.8847 (tpt) cc_final: 0.8451 (tpt) REVERT: F 267 ASP cc_start: 0.7251 (m-30) cc_final: 0.7014 (m-30) REVERT: F 364 GLN cc_start: 0.8307 (mt0) cc_final: 0.7979 (mt0) outliers start: 22 outliers final: 17 residues processed: 260 average time/residue: 0.1184 time to fit residues: 46.6271 Evaluate side-chains 254 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 236 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 441 SER Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 544 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 182 optimal weight: 3.9990 chunk 195 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 79 optimal weight: 0.0060 chunk 39 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 321 GLN ** 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 = 0.3933 r_free = 0.3933 target = 0.165032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.132595 restraints weight = 21330.301| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.12 r_work: 0.3413 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17076 Z= 0.135 Angle : 0.578 8.915 23159 Z= 0.293 Chirality : 0.044 0.251 2709 Planarity : 0.005 0.048 3003 Dihedral : 4.739 41.047 2388 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.59 % Allowed : 9.63 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.19), residues: 2143 helix: 1.32 (0.18), residues: 877 sheet: -0.91 (0.29), residues: 330 loop : -1.29 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 527 TYR 0.016 0.001 TYR B 244 PHE 0.011 0.001 PHE B 407 HIS 0.005 0.001 HIS D 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (17076) covalent geometry : angle 0.57844 / 0.29 (23159) hydrogen bonds : bond 0.03991 / 2.67 ( 694) hydrogen bonds : angle 4.81242 / 3.50 ( 2034) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 248 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 LYS cc_start: 0.6754 (mptt) cc_final: 0.6192 (mmtp) REVERT: A 341 MET cc_start: 0.7964 (ttt) cc_final: 0.7643 (ttt) REVERT: A 395 GLN cc_start: 0.7741 (mt0) cc_final: 0.7256 (mp10) REVERT: A 577 GLN cc_start: 0.7611 (tm-30) cc_final: 0.7224 (tm-30) REVERT: B 257 MET cc_start: 0.6986 (ttt) cc_final: 0.6579 (ttt) REVERT: B 394 MET cc_start: 0.8996 (tpt) cc_final: 0.8743 (tpp) REVERT: B 469 LEU cc_start: 0.8091 (tt) cc_final: 0.7664 (tt) REVERT: B 575 MET cc_start: 0.8386 (mmm) cc_final: 0.7926 (mpp) REVERT: C 429 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8249 (t) REVERT: C 444 ARG cc_start: 0.8055 (mmm-85) cc_final: 0.7664 (mpt-90) REVERT: D 263 MET cc_start: 0.7913 (mmm) cc_final: 0.7491 (mtt) REVERT: D 580 LYS cc_start: 0.6615 (mmtt) cc_final: 0.4750 (tptt) REVERT: E 394 MET cc_start: 0.8833 (tpt) cc_final: 0.8428 (tpt) REVERT: F 364 GLN cc_start: 0.8338 (mt0) cc_final: 0.8015 (mt0) REVERT: F 508 GLU cc_start: 0.6630 (mt-10) cc_final: 0.6150 (mt-10) REVERT: F 521 ASP cc_start: 0.7188 (t0) cc_final: 0.6813 (t0) outliers start: 29 outliers final: 21 residues processed: 268 average time/residue: 0.1288 time to fit residues: 52.9809 Evaluate side-chains 258 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 236 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 545 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 76 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 144 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 161 optimal weight: 0.0970 chunk 145 optimal weight: 0.9980 chunk 198 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.166383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.134949 restraints weight = 21068.717| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.12 r_work: 0.3432 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17076 Z= 0.118 Angle : 0.556 8.877 23159 Z= 0.282 Chirality : 0.043 0.249 2709 Planarity : 0.005 0.048 3003 Dihedral : 4.598 38.930 2388 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.64 % Allowed : 11.49 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.19), residues: 2143 helix: 1.39 (0.18), residues: 879 sheet: -0.88 (0.29), residues: 332 loop : -1.27 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 240 TYR 0.015 0.001 TYR B 244 PHE 0.009 0.001 PHE F 475 HIS 0.005 0.001 HIS E 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (17076) covalent geometry : angle 0.55626 / 0.28 (23159) hydrogen bonds : bond 0.03553 / 2.38 ( 694) hydrogen bonds : angle 4.62995 / 3.36 ( 2034) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 251 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 LYS cc_start: 0.6723 (mptt) cc_final: 0.6138 (mmtp) REVERT: A 341 MET cc_start: 0.7955 (ttt) cc_final: 0.7633 (ttp) REVERT: A 395 GLN cc_start: 0.7746 (mt0) cc_final: 0.7051 (mp10) REVERT: A 509 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7442 (mt-10) REVERT: A 577 GLN cc_start: 0.7669 (tm-30) cc_final: 0.7227 (tm-30) REVERT: B 257 MET cc_start: 0.6974 (ttt) cc_final: 0.6356 (ttm) REVERT: B 394 MET cc_start: 0.8984 (tpt) cc_final: 0.8725 (tpp) REVERT: B 575 MET cc_start: 0.8357 (mmm) cc_final: 0.7935 (mpp) REVERT: C 429 VAL cc_start: 0.8715 (OUTLIER) cc_final: 0.8207 (t) REVERT: D 263 MET cc_start: 0.7974 (mmm) cc_final: 0.7614 (mtt) REVERT: D 422 ILE cc_start: 0.8222 (tp) cc_final: 0.7898 (tp) REVERT: D 556 HIS cc_start: 0.7818 (t70) cc_final: 0.7411 (t70) REVERT: D 580 LYS cc_start: 0.6579 (mmtt) cc_final: 0.4587 (tptt) REVERT: E 230 LEU cc_start: 0.7992 (tt) cc_final: 0.7635 (tt) REVERT: E 372 ARG cc_start: 0.8045 (ttt-90) cc_final: 0.7814 (ttt-90) REVERT: E 394 MET cc_start: 0.8789 (tpt) cc_final: 0.8352 (tpt) REVERT: F 364 GLN cc_start: 0.8304 (mt0) cc_final: 0.7991 (mt0) REVERT: F 508 GLU cc_start: 0.6616 (mt-10) cc_final: 0.6110 (mt-10) REVERT: F 521 ASP cc_start: 0.7288 (t0) cc_final: 0.6785 (t0) outliers start: 30 outliers final: 20 residues processed: 275 average time/residue: 0.1314 time to fit residues: 55.1636 Evaluate side-chains 263 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 242 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 545 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 185 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 7 optimal weight: 0.4980 chunk 91 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.166130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.135184 restraints weight = 21036.547| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.14 r_work: 0.3430 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17076 Z= 0.121 Angle : 0.562 11.083 23159 Z= 0.283 Chirality : 0.043 0.243 2709 Planarity : 0.005 0.048 3003 Dihedral : 4.565 39.161 2388 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.64 % Allowed : 12.58 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.19), residues: 2143 helix: 1.40 (0.18), residues: 882 sheet: -0.87 (0.29), residues: 333 loop : -1.29 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 240 TYR 0.013 0.001 TYR E 318 PHE 0.009 0.001 PHE F 475 HIS 0.005 0.001 HIS E 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (17076) covalent geometry : angle 0.56206 / 0.28 (23159) hydrogen bonds : bond 0.03507 / 2.35 ( 694) hydrogen bonds : angle 4.56564 / 3.30 ( 2034) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 TYR cc_start: 0.6551 (m-80) cc_final: 0.6346 (m-80) REVERT: A 260 LYS cc_start: 0.6694 (mptt) cc_final: 0.6109 (mmtp) REVERT: A 341 MET cc_start: 0.7959 (ttt) cc_final: 0.7733 (ttt) REVERT: A 395 GLN cc_start: 0.8179 (mt0) cc_final: 0.7299 (mp10) REVERT: A 577 GLN cc_start: 0.7516 (tm-30) cc_final: 0.7039 (tm-30) REVERT: B 257 MET cc_start: 0.6966 (ttt) cc_final: 0.6574 (ttt) REVERT: B 394 MET cc_start: 0.8968 (tpt) cc_final: 0.8715 (tpp) REVERT: B 575 MET cc_start: 0.8380 (mmm) cc_final: 0.7908 (mpp) REVERT: C 429 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8194 (t) REVERT: D 263 MET cc_start: 0.8030 (mmm) cc_final: 0.7737 (mtt) REVERT: D 422 ILE cc_start: 0.8200 (tp) cc_final: 0.7890 (tp) REVERT: D 556 HIS cc_start: 0.7814 (t70) cc_final: 0.7384 (t70) REVERT: D 580 LYS cc_start: 0.6449 (mmtt) cc_final: 0.4438 (tptt) REVERT: E 230 LEU cc_start: 0.7971 (tt) cc_final: 0.7611 (tt) REVERT: E 372 ARG cc_start: 0.8036 (ttt-90) cc_final: 0.7803 (ttt-90) REVERT: E 394 MET cc_start: 0.8779 (tpt) cc_final: 0.8316 (tpt) REVERT: E 569 GLN cc_start: 0.8727 (mt0) cc_final: 0.8466 (mp10) REVERT: F 364 GLN cc_start: 0.8315 (mt0) cc_final: 0.7995 (mt0) REVERT: F 508 GLU cc_start: 0.6623 (mt-10) cc_final: 0.6102 (mt-10) REVERT: F 521 ASP cc_start: 0.7324 (t0) cc_final: 0.6991 (t0) outliers start: 30 outliers final: 24 residues processed: 272 average time/residue: 0.1099 time to fit residues: 46.1744 Evaluate side-chains 269 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 244 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 441 SER Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 521 ASP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 545 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 82 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 95 optimal weight: 0.3980 chunk 202 optimal weight: 20.0000 chunk 133 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 146 optimal weight: 0.0170 chunk 179 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 23 optimal weight: 0.0030 overall best weight: 0.3428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.168735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.137633 restraints weight = 20862.807| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.08 r_work: 0.3475 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 17076 Z= 0.101 Angle : 0.543 9.172 23159 Z= 0.273 Chirality : 0.043 0.239 2709 Planarity : 0.005 0.049 3003 Dihedral : 4.417 38.959 2388 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.70 % Allowed : 12.96 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.19), residues: 2143 helix: 1.55 (0.18), residues: 882 sheet: -0.94 (0.28), residues: 355 loop : -1.18 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 240 TYR 0.011 0.001 TYR E 318 PHE 0.008 0.001 PHE F 475 HIS 0.006 0.001 HIS E 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (17076) covalent geometry : angle 0.54297 / 0.27 (23159) hydrogen bonds : bond 0.03129 / 2.09 ( 694) hydrogen bonds : angle 4.42591 / 3.19 ( 2034) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 259 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LYS cc_start: 0.6802 (mptt) cc_final: 0.6193 (mmtp) REVERT: A 341 MET cc_start: 0.7981 (ttt) cc_final: 0.7710 (ttp) REVERT: A 577 GLN cc_start: 0.7397 (tm-30) cc_final: 0.6927 (tm-30) REVERT: B 257 MET cc_start: 0.6949 (ttt) cc_final: 0.6382 (ttm) REVERT: B 394 MET cc_start: 0.9005 (tpt) cc_final: 0.8759 (tpp) REVERT: B 430 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7608 (mt-10) REVERT: B 575 MET cc_start: 0.8340 (mmm) cc_final: 0.7932 (mpp) REVERT: C 429 VAL cc_start: 0.8600 (OUTLIER) cc_final: 0.8107 (t) REVERT: D 263 MET cc_start: 0.7986 (mmm) cc_final: 0.7642 (mtt) REVERT: D 556 HIS cc_start: 0.7852 (t70) cc_final: 0.7466 (t70) REVERT: D 580 LYS cc_start: 0.6443 (mmtt) cc_final: 0.4723 (tptt) REVERT: E 230 LEU cc_start: 0.7953 (tt) cc_final: 0.7599 (tt) REVERT: E 236 TYR cc_start: 0.6086 (m-80) cc_final: 0.5769 (m-80) REVERT: E 257 MET cc_start: 0.6716 (mtt) cc_final: 0.6353 (mtm) REVERT: E 372 ARG cc_start: 0.8033 (ttt-90) cc_final: 0.7813 (ttt-90) REVERT: E 394 MET cc_start: 0.8736 (tpt) cc_final: 0.8298 (tpt) REVERT: E 526 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: E 569 GLN cc_start: 0.8747 (mt0) cc_final: 0.8542 (mp10) REVERT: F 364 GLN cc_start: 0.8316 (mt0) cc_final: 0.8023 (mt0) REVERT: F 489 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7710 (t) REVERT: F 508 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6965 (mt-10) REVERT: F 521 ASP cc_start: 0.7327 (t0) cc_final: 0.6982 (t0) outliers start: 31 outliers final: 21 residues processed: 282 average time/residue: 0.1164 time to fit residues: 50.0959 Evaluate side-chains 272 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 248 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 441 SER Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 521 ASP Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 489 THR Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 545 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 205 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 168 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 195 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 298 ASN D 568 HIS E 261 ASN F 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.167129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.134881 restraints weight = 20928.105| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.20 r_work: 0.3440 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17076 Z= 0.121 Angle : 0.555 8.608 23159 Z= 0.280 Chirality : 0.043 0.248 2709 Planarity : 0.005 0.049 3003 Dihedral : 4.459 39.410 2388 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.91 % Allowed : 13.40 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.19), residues: 2143 helix: 1.50 (0.18), residues: 882 sheet: -0.84 (0.29), residues: 329 loop : -1.28 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 444 TYR 0.013 0.001 TYR C 244 PHE 0.024 0.001 PHE F 552 HIS 0.004 0.001 HIS E 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (17076) covalent geometry : angle 0.55461 / 0.28 (23159) hydrogen bonds : bond 0.03389 / 2.26 ( 694) hydrogen bonds : angle 4.41616 / 3.18 ( 2034) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 255 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LYS cc_start: 0.6720 (mptt) cc_final: 0.6292 (mmtt) REVERT: A 395 GLN cc_start: 0.8141 (mt0) cc_final: 0.7238 (mp10) REVERT: A 577 GLN cc_start: 0.7460 (tm-30) cc_final: 0.6961 (tm-30) REVERT: B 257 MET cc_start: 0.6970 (ttt) cc_final: 0.6398 (ttm) REVERT: B 321 GLN cc_start: 0.6842 (mp10) cc_final: 0.6548 (mp10) REVERT: B 394 MET cc_start: 0.8984 (tpt) cc_final: 0.8705 (tpp) REVERT: B 430 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7625 (mt-10) REVERT: B 575 MET cc_start: 0.8381 (mmm) cc_final: 0.7879 (mpp) REVERT: C 429 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8160 (t) REVERT: D 263 MET cc_start: 0.8082 (mmm) cc_final: 0.7818 (mtt) REVERT: D 422 ILE cc_start: 0.8171 (tp) cc_final: 0.7912 (tp) REVERT: D 495 MET cc_start: 0.9069 (mmm) cc_final: 0.8785 (mmm) REVERT: D 521 ASP cc_start: 0.7738 (t0) cc_final: 0.7370 (m-30) REVERT: D 580 LYS cc_start: 0.6396 (mmtt) cc_final: 0.4632 (tptt) REVERT: E 230 LEU cc_start: 0.8002 (tt) cc_final: 0.7647 (tt) REVERT: E 236 TYR cc_start: 0.6029 (m-80) cc_final: 0.5699 (m-80) REVERT: E 257 MET cc_start: 0.6794 (mtt) cc_final: 0.6404 (mtm) REVERT: E 372 ARG cc_start: 0.8047 (ttt-90) cc_final: 0.7814 (ttt-90) REVERT: E 394 MET cc_start: 0.8845 (tpt) cc_final: 0.8404 (tpt) REVERT: E 526 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7933 (mp0) REVERT: E 569 GLN cc_start: 0.8786 (mt0) cc_final: 0.8554 (mp10) REVERT: E 575 MET cc_start: 0.9006 (mmt) cc_final: 0.8687 (mmm) REVERT: F 364 GLN cc_start: 0.8412 (mt0) cc_final: 0.8108 (mt0) REVERT: F 489 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7695 (t) REVERT: F 508 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6899 (mt-10) REVERT: F 521 ASP cc_start: 0.7338 (t0) cc_final: 0.6994 (t0) outliers start: 35 outliers final: 24 residues processed: 282 average time/residue: 0.1138 time to fit residues: 49.5159 Evaluate side-chains 273 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 246 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 441 SER Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 489 THR Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 545 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 160 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 169 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 368 ASN E 261 ASN F 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.163473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.131107 restraints weight = 21260.569| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.19 r_work: 0.3394 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17076 Z= 0.180 Angle : 0.608 8.404 23159 Z= 0.308 Chirality : 0.046 0.244 2709 Planarity : 0.005 0.053 3003 Dihedral : 4.741 41.435 2388 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.86 % Allowed : 14.44 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.19), residues: 2143 helix: 1.27 (0.17), residues: 880 sheet: -1.07 (0.28), residues: 341 loop : -1.24 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 348 TYR 0.014 0.002 TYR E 318 PHE 0.019 0.002 PHE F 552 HIS 0.004 0.001 HIS D 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.18 (17076) covalent geometry : angle 0.60782 / 0.31 (23159) hydrogen bonds : bond 0.03994 / 2.69 ( 694) hydrogen bonds : angle 4.53951 / 3.28 ( 2034) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 250 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LYS cc_start: 0.6779 (mptt) cc_final: 0.6155 (mmtp) REVERT: A 395 GLN cc_start: 0.8135 (mt0) cc_final: 0.7186 (mp10) REVERT: B 257 MET cc_start: 0.7012 (ttt) cc_final: 0.6430 (ttm) REVERT: B 321 GLN cc_start: 0.6838 (mp10) cc_final: 0.6635 (mp10) REVERT: B 394 MET cc_start: 0.9031 (tpt) cc_final: 0.8764 (tpp) REVERT: B 575 MET cc_start: 0.8419 (mmm) cc_final: 0.7888 (mpp) REVERT: C 294 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8376 (tt) REVERT: C 429 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8110 (t) REVERT: C 447 ARG cc_start: 0.8486 (mtm110) cc_final: 0.8170 (mtp180) REVERT: D 263 MET cc_start: 0.8122 (mmm) cc_final: 0.7912 (mtt) REVERT: D 329 THR cc_start: 0.8939 (m) cc_final: 0.8386 (p) REVERT: D 495 MET cc_start: 0.9056 (mmm) cc_final: 0.8842 (mmm) REVERT: D 580 LYS cc_start: 0.6420 (mmtt) cc_final: 0.4621 (tptt) REVERT: E 236 TYR cc_start: 0.6029 (m-80) cc_final: 0.5740 (m-80) REVERT: E 372 ARG cc_start: 0.8032 (ttt-90) cc_final: 0.7660 (ttt-90) REVERT: E 394 MET cc_start: 0.8891 (tpt) cc_final: 0.8452 (tpt) REVERT: E 526 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: E 569 GLN cc_start: 0.8753 (mt0) cc_final: 0.8505 (mp10) REVERT: E 575 MET cc_start: 0.8891 (mmt) cc_final: 0.8546 (mmm) REVERT: F 364 GLN cc_start: 0.8364 (mt0) cc_final: 0.8090 (mt0) REVERT: F 489 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7761 (t) REVERT: F 508 GLU cc_start: 0.6612 (mt-10) cc_final: 0.6194 (mt-10) REVERT: F 521 ASP cc_start: 0.7351 (t0) cc_final: 0.7001 (t0) outliers start: 34 outliers final: 26 residues processed: 275 average time/residue: 0.1372 time to fit residues: 56.7079 Evaluate side-chains 276 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 441 SER Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 489 THR Chi-restraints excluded: chain F residue 545 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 96 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 chunk 191 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 135 optimal weight: 0.0170 chunk 110 optimal weight: 0.8980 chunk 108 optimal weight: 0.0040 chunk 10 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 overall best weight: 0.4030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 556 HIS C 368 ASN E 261 ASN F 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.168531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.137438 restraints weight = 20950.647| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.12 r_work: 0.3464 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 17076 Z= 0.105 Angle : 0.555 8.656 23159 Z= 0.279 Chirality : 0.043 0.246 2709 Planarity : 0.005 0.054 3003 Dihedral : 4.483 39.653 2388 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.70 % Allowed : 14.88 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.19), residues: 2143 helix: 1.57 (0.18), residues: 878 sheet: -1.02 (0.29), residues: 326 loop : -1.26 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.011 0.001 TYR E 318 PHE 0.019 0.001 PHE F 552 HIS 0.006 0.001 HIS E 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 (17076) covalent geometry : angle 0.55526 / 0.28 (23159) hydrogen bonds : bond 0.03185 / 2.12 ( 694) hydrogen bonds : angle 4.34442 / 3.12 ( 2034) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 255 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 260 LYS cc_start: 0.6670 (mptt) cc_final: 0.6230 (mmtt) REVERT: A 395 GLN cc_start: 0.8079 (mt0) cc_final: 0.7121 (mp10) REVERT: B 257 MET cc_start: 0.6937 (ttt) cc_final: 0.6390 (ttm) REVERT: B 318 TYR cc_start: 0.4826 (m-10) cc_final: 0.4417 (m-10) REVERT: B 321 GLN cc_start: 0.6868 (mp10) cc_final: 0.6604 (mp10) REVERT: B 394 MET cc_start: 0.8993 (tpt) cc_final: 0.8721 (tpp) REVERT: B 575 MET cc_start: 0.8427 (mmm) cc_final: 0.7982 (mpp) REVERT: C 252 TYR cc_start: 0.7091 (t80) cc_final: 0.6687 (t80) REVERT: C 294 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8485 (tt) REVERT: C 429 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8140 (t) REVERT: D 263 MET cc_start: 0.8052 (mmm) cc_final: 0.7730 (mtt) REVERT: D 329 THR cc_start: 0.8874 (m) cc_final: 0.8387 (p) REVERT: D 580 LYS cc_start: 0.7004 (mmtt) cc_final: 0.5065 (tptt) REVERT: E 236 TYR cc_start: 0.6093 (m-80) cc_final: 0.5810 (m-80) REVERT: E 394 MET cc_start: 0.8733 (tpt) cc_final: 0.8268 (tpt) REVERT: E 521 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7996 (m-30) REVERT: E 526 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: E 551 GLU cc_start: 0.7793 (tt0) cc_final: 0.7332 (tt0) REVERT: E 575 MET cc_start: 0.8615 (mmt) cc_final: 0.8336 (mmm) REVERT: F 321 GLN cc_start: 0.8025 (mt0) cc_final: 0.7586 (mp10) REVERT: F 364 GLN cc_start: 0.8408 (mt0) cc_final: 0.8073 (mt0) REVERT: F 489 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7632 (t) REVERT: F 508 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6906 (mt-10) REVERT: F 521 ASP cc_start: 0.7294 (t0) cc_final: 0.6936 (t0) outliers start: 31 outliers final: 21 residues processed: 278 average time/residue: 0.1321 time to fit residues: 55.8878 Evaluate side-chains 270 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 521 ASP Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 489 THR Chi-restraints excluded: chain F residue 545 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 176 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 150 optimal weight: 0.0970 chunk 97 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 188 optimal weight: 0.2980 chunk 104 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 131 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 556 HIS E 568 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.166930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.134530 restraints weight = 21009.508| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.12 r_work: 0.3443 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17076 Z= 0.123 Angle : 0.574 8.479 23159 Z= 0.288 Chirality : 0.044 0.240 2709 Planarity : 0.005 0.051 3003 Dihedral : 4.530 39.995 2388 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.42 % Allowed : 15.32 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.19), residues: 2143 helix: 1.52 (0.18), residues: 879 sheet: -1.04 (0.28), residues: 341 loop : -1.21 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 444 TYR 0.012 0.001 TYR E 318 PHE 0.016 0.001 PHE F 552 HIS 0.005 0.001 HIS E 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 (17076) covalent geometry : angle 0.57400 / 0.29 (23159) hydrogen bonds : bond 0.03387 / 2.28 ( 694) hydrogen bonds : angle 4.36494 / 3.13 ( 2034) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 251 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 260 LYS cc_start: 0.6658 (mptt) cc_final: 0.6220 (mmtt) REVERT: A 395 GLN cc_start: 0.8107 (mt0) cc_final: 0.7159 (mp10) REVERT: B 257 MET cc_start: 0.6944 (ttt) cc_final: 0.6397 (ttm) REVERT: B 321 GLN cc_start: 0.6793 (mp10) cc_final: 0.6522 (mp10) REVERT: B 394 MET cc_start: 0.9009 (tpt) cc_final: 0.8740 (tpp) REVERT: B 575 MET cc_start: 0.8433 (mmm) cc_final: 0.7944 (mpp) REVERT: B 578 LEU cc_start: 0.6723 (mt) cc_final: 0.6219 (mt) REVERT: C 252 TYR cc_start: 0.7118 (t80) cc_final: 0.6765 (t80) REVERT: C 263 MET cc_start: 0.9088 (mtm) cc_final: 0.8769 (ptp) REVERT: C 294 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8282 (tt) REVERT: C 429 VAL cc_start: 0.8645 (OUTLIER) cc_final: 0.8103 (t) REVERT: C 447 ARG cc_start: 0.8401 (mtm110) cc_final: 0.8054 (mtp180) REVERT: D 263 MET cc_start: 0.8085 (mmm) cc_final: 0.7799 (mtt) REVERT: D 329 THR cc_start: 0.8760 (m) cc_final: 0.8302 (p) REVERT: D 521 ASP cc_start: 0.7438 (t0) cc_final: 0.6998 (m-30) REVERT: D 580 LYS cc_start: 0.6978 (mmtt) cc_final: 0.5063 (tptt) REVERT: E 236 TYR cc_start: 0.6077 (m-80) cc_final: 0.5799 (m-80) REVERT: E 394 MET cc_start: 0.8835 (tpt) cc_final: 0.8391 (tpt) REVERT: E 526 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: E 569 GLN cc_start: 0.8736 (mt0) cc_final: 0.8487 (mp10) REVERT: E 575 MET cc_start: 0.8638 (mmt) cc_final: 0.8361 (mmm) REVERT: F 321 GLN cc_start: 0.8026 (mt0) cc_final: 0.7562 (mp10) REVERT: F 364 GLN cc_start: 0.8381 (mt0) cc_final: 0.8063 (mt0) REVERT: F 489 THR cc_start: 0.8093 (OUTLIER) cc_final: 0.7640 (t) REVERT: F 508 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6888 (mt-10) REVERT: F 521 ASP cc_start: 0.7281 (t0) cc_final: 0.6937 (t0) outliers start: 26 outliers final: 22 residues processed: 271 average time/residue: 0.1336 time to fit residues: 54.9816 Evaluate side-chains 273 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 247 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 489 THR Chi-restraints excluded: chain F residue 545 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 130 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 22 optimal weight: 0.0470 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 556 HIS F 289 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.167286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.136160 restraints weight = 21040.212| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.09 r_work: 0.3451 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17076 Z= 0.118 Angle : 0.568 8.320 23159 Z= 0.285 Chirality : 0.043 0.242 2709 Planarity : 0.005 0.049 3003 Dihedral : 4.502 40.424 2388 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.53 % Allowed : 15.37 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.19), residues: 2143 helix: 1.54 (0.18), residues: 880 sheet: -1.04 (0.28), residues: 343 loop : -1.20 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 444 TYR 0.012 0.001 TYR E 318 PHE 0.020 0.001 PHE B 587 HIS 0.005 0.001 HIS E 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (17076) covalent geometry : angle 0.56838 / 0.29 (23159) hydrogen bonds : bond 0.03323 / 2.24 ( 694) hydrogen bonds : angle 4.33929 / 3.11 ( 2034) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4316.94 seconds wall clock time: 74 minutes 37.22 seconds (4477.22 seconds total)