Starting phenix.real_space_refine on Thu Feb 5 03:12:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvy_47226/02_2026/9dvy_47226.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvy_47226/02_2026/9dvy_47226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dvy_47226/02_2026/9dvy_47226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvy_47226/02_2026/9dvy_47226.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dvy_47226/02_2026/9dvy_47226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvy_47226/02_2026/9dvy_47226.map" } resolution = 3.2 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= -0.002 sd= 0.062 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 14 5.49 5 Mg 4 5.21 5 S 41 5.16 5 C 9208 2.51 5 N 2493 2.21 5 O 2672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14432 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2314 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 16, 'TRANS': 304} Chain breaks: 4 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 8, 'ARG:plan': 7, 'ASN:plan1': 4, 'GLN:plan1': 3, 'GLU:plan': 12, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 135 Chain: "B" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2676 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 17, 'TRANS': 333} Chain breaks: 4 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 2660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2660 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 16, 'TRANS': 335} Chain breaks: 4 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2584 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 17, 'TRANS': 325} Chain breaks: 4 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'HIS:plan': 2, 'ASP:plan': 7, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 70 Chain: "E" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2528 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 19, 'TRANS': 323} Chain breaks: 5 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'GLU:plan': 10, 'ARG:plan': 4, 'HIS:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 101 Chain: "F" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1454 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 12, 'TRANS': 225} Chain breaks: 11 Unresolved non-hydrogen bonds: 430 Unresolved non-hydrogen angles: 544 Unresolved non-hydrogen dihedrals: 339 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'TYR:plan': 5, 'ASN:plan1': 7, 'ASP:plan': 10, 'GLN:plan1': 8, 'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 221 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 61 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "A" 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: "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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.81, per 1000 atoms: 0.26 Number of scatterers: 14432 At special positions: 0 Unit cell: (146.51, 140.14, 92.82, 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 41 16.00 P 14 15.00 Mg 4 11.99 O 2672 8.00 N 2493 7.00 C 9208 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: 1.26 Conformation dependent library (CDL) restraints added in 582.3 milliseconds 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3638 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 18 sheets defined 54.4% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 168 through 177 removed outlier: 3.597A pdb=" N ASN A 174 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 200 removed outlier: 3.765A pdb=" N LYS A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 333 through 342 Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 376 through 389 removed outlier: 3.738A pdb=" N GLY A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 387 " --> pdb=" O GLY A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 469 through 480 removed outlier: 3.815A pdb=" N LYS A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 491 removed outlier: 3.608A pdb=" N GLU A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 499 Processing helix chain 'A' and resid 510 through 520 removed outlier: 3.680A pdb=" N GLN A 516 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A 519 " --> pdb=" O VAL A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 543 through 557 removed outlier: 3.516A pdb=" N ARG A 552 " --> pdb=" O LYS A 548 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 561 No H-bonds generated for 'chain 'A' and resid 559 through 561' Processing helix chain 'A' and resid 562 through 572 removed outlier: 3.501A pdb=" N SER A 566 " --> pdb=" O ARG A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 590 through 595 Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 183 through 205 Processing helix chain 'B' and resid 298 through 310 removed outlier: 4.118A pdb=" N LYS B 308 " --> pdb=" O GLN B 304 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 343 Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 359 through 364 removed outlier: 3.522A pdb=" N ILE B 363 " --> pdb=" O VAL B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 389 removed outlier: 4.808A pdb=" N LYS B 386 " --> pdb=" O GLN B 382 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 426 through 434 removed outlier: 3.700A pdb=" N ARG B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 480 removed outlier: 3.614A pdb=" N ASP B 471 " --> pdb=" O ASN B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 491 removed outlier: 3.593A pdb=" N LEU B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 498 Processing helix chain 'B' and resid 510 through 520 removed outlier: 3.831A pdb=" N GLN B 516 " --> pdb=" O LYS B 512 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR B 519 " --> pdb=" O VAL B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 536 removed outlier: 3.719A pdb=" N LEU B 532 " --> pdb=" O GLN B 528 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET B 535 " --> pdb=" O ALA B 531 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 556 removed outlier: 3.893A pdb=" N LYS B 548 " --> pdb=" O GLU B 544 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 558 No H-bonds generated for 'chain 'B' and resid 557 through 558' Processing helix chain 'B' and resid 559 through 562 removed outlier: 3.864A pdb=" N ARG B 562 " --> pdb=" O THR B 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 559 through 562' Processing helix chain 'B' and resid 563 through 572 removed outlier: 3.533A pdb=" N LYS B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 579 Processing helix chain 'B' and resid 590 through 595 Processing helix chain 'C' and resid 168 through 177 Processing helix chain 'C' and resid 183 through 205 Processing helix chain 'C' and resid 298 through 308 Processing helix chain 'C' and resid 320 through 322 No H-bonds generated for 'chain 'C' and resid 320 through 322' Processing helix chain 'C' and resid 333 through 343 removed outlier: 3.510A pdb=" N LEU C 339 " --> pdb=" O VAL C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 359 through 364 Processing helix chain 'C' and resid 377 through 389 removed outlier: 3.593A pdb=" N GLY C 383 " --> pdb=" O GLY C 379 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 385 " --> pdb=" O GLN C 381 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LYS C 386 " --> pdb=" O GLN C 382 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU C 387 " --> pdb=" O GLY C 383 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU C 389 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 434 removed outlier: 3.789A pdb=" N ARG C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 480 removed outlier: 3.706A pdb=" N ARG C 480 " --> pdb=" O ASP C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 491 Processing helix chain 'C' and resid 493 through 499 removed outlier: 3.678A pdb=" N ARG C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 520 removed outlier: 3.606A pdb=" N GLN C 516 " --> pdb=" O LYS C 512 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR C 519 " --> pdb=" O VAL C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 536 removed outlier: 3.692A pdb=" N MET C 535 " --> pdb=" O ALA C 531 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 556 removed outlier: 3.814A pdb=" N LYS C 548 " --> pdb=" O GLU C 544 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU C 556 " --> pdb=" O ARG C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 558 No H-bonds generated for 'chain 'C' and resid 557 through 558' Processing helix chain 'C' and resid 559 through 560 No H-bonds generated for 'chain 'C' and resid 559 through 560' Processing helix chain 'C' and resid 561 through 572 removed outlier: 4.209A pdb=" N ARG C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 566 " --> pdb=" O ARG C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 579 Processing helix chain 'C' and resid 590 through 595 Processing helix chain 'D' and resid 168 through 177 Processing helix chain 'D' and resid 183 through 205 Processing helix chain 'D' and resid 298 through 308 removed outlier: 3.815A pdb=" N LYS D 308 " --> pdb=" O GLN D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 343 Processing helix chain 'D' and resid 346 through 351 Processing helix chain 'D' and resid 359 through 364 removed outlier: 3.606A pdb=" N ILE D 363 " --> pdb=" O VAL D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 390 removed outlier: 3.553A pdb=" N GLY D 383 " --> pdb=" O GLY D 379 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 385 " --> pdb=" O GLN D 381 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LYS D 386 " --> pdb=" O GLN D 382 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU D 387 " --> pdb=" O GLY D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 436 removed outlier: 3.525A pdb=" N ILE D 429 " --> pdb=" O GLY D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 483 through 491 Processing helix chain 'D' and resid 493 through 498 Processing helix chain 'D' and resid 510 through 520 removed outlier: 3.577A pdb=" N GLN D 516 " --> pdb=" O LYS D 512 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR D 519 " --> pdb=" O VAL D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 535 removed outlier: 3.574A pdb=" N TYR D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 556 removed outlier: 3.680A pdb=" N LYS D 548 " --> pdb=" O GLU D 544 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA D 549 " --> pdb=" O ASP D 545 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU D 556 " --> pdb=" O ARG D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 558 No H-bonds generated for 'chain 'D' and resid 557 through 558' Processing helix chain 'D' and resid 559 through 561 No H-bonds generated for 'chain 'D' and resid 559 through 561' Processing helix chain 'D' and resid 562 through 572 removed outlier: 3.666A pdb=" N SER D 566 " --> pdb=" O ARG D 562 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS D 570 " --> pdb=" O SER D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 579 Processing helix chain 'D' and resid 590 through 595 Processing helix chain 'E' and resid 168 through 177 Processing helix chain 'E' and resid 183 through 202 Processing helix chain 'E' and resid 271 through 277 Processing helix chain 'E' and resid 298 through 309 Processing helix chain 'E' and resid 333 through 343 removed outlier: 3.655A pdb=" N ALA E 337 " --> pdb=" O GLU E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 376 through 389 removed outlier: 3.715A pdb=" N LEU E 385 " --> pdb=" O GLN E 381 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N LYS E 386 " --> pdb=" O GLN E 382 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU E 387 " --> pdb=" O GLY E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 415 No H-bonds generated for 'chain 'E' and resid 413 through 415' Processing helix chain 'E' and resid 425 through 434 removed outlier: 3.605A pdb=" N ILE E 429 " --> pdb=" O GLY E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 480 Processing helix chain 'E' and resid 483 through 491 removed outlier: 3.937A pdb=" N GLU E 489 " --> pdb=" O ARG E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 493 through 498 Processing helix chain 'E' and resid 510 through 520 removed outlier: 3.678A pdb=" N THR E 519 " --> pdb=" O VAL E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 531 removed outlier: 3.939A pdb=" N GLN E 528 " --> pdb=" O ALA E 524 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR E 529 " --> pdb=" O VAL E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 558 Processing helix chain 'E' and resid 560 through 562 No H-bonds generated for 'chain 'E' and resid 560 through 562' Processing helix chain 'E' and resid 563 through 572 Processing helix chain 'E' and resid 572 through 579 Processing helix chain 'E' and resid 590 through 595 Processing helix chain 'F' and resid 168 through 177 Processing helix chain 'F' and resid 183 through 205 removed outlier: 3.601A pdb=" N ASN F 196 " --> pdb=" O VAL F 192 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG F 200 " --> pdb=" O ASN F 196 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE F 201 " --> pdb=" O HIS F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 307 Processing helix chain 'F' and resid 378 through 389 removed outlier: 3.730A pdb=" N LEU F 387 " --> pdb=" O GLY F 383 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU F 389 " --> pdb=" O LEU F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 480 Processing helix chain 'F' and resid 483 through 490 Processing helix chain 'F' and resid 493 through 498 Processing helix chain 'F' and resid 513 through 518 Processing helix chain 'F' and resid 529 through 536 removed outlier: 3.537A pdb=" N PHE F 533 " --> pdb=" O TYR F 529 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 558 removed outlier: 3.782A pdb=" N LYS F 548 " --> pdb=" O GLU F 544 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ALA F 549 " --> pdb=" O ASP F 545 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA F 554 " --> pdb=" O ILE F 550 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU F 555 " --> pdb=" O ALA F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 561 No H-bonds generated for 'chain 'F' and resid 559 through 561' Processing helix chain 'F' and resid 562 through 572 removed outlier: 4.511A pdb=" N SER F 566 " --> pdb=" O ARG F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 579 Processing sheet with id=AA1, first strand: chain 'A' and resid 314 through 318 removed outlier: 6.578A pdb=" N ALA A 315 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ASP A 358 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N CYS A 317 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N SER A 420 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 357 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU A 290 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA3, first strand: chain 'A' and resid 392 through 395 Processing sheet with id=AA4, first strand: chain 'A' and resid 539 through 542 removed outlier: 6.616A pdb=" N ILE A 603 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL A 587 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY A 601 " --> pdb=" O VAL A 587 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 314 through 318 removed outlier: 6.571A pdb=" N ALA B 315 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ASP B 358 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N CYS B 317 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL B 355 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N SER B 420 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU B 357 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE B 289 " --> pdb=" O ALA B 419 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU B 290 " --> pdb=" O VAL B 504 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 392 through 396 Processing sheet with id=AA7, first strand: chain 'B' and resid 539 through 542 removed outlier: 6.187A pdb=" N GLU B 539 " --> pdb=" O VAL B 587 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL B 589 " --> pdb=" O GLU B 539 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN B 541 " --> pdb=" O VAL B 589 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE B 603 " --> pdb=" O VAL B 585 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL B 587 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY B 601 " --> pdb=" O VAL B 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 314 through 318 removed outlier: 6.636A pdb=" N ALA C 315 " --> pdb=" O PHE C 356 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP C 358 " --> pdb=" O ALA C 315 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N CYS C 317 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL C 355 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N SER C 420 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU C 357 " --> pdb=" O SER C 420 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 392 through 396 Processing sheet with id=AB1, first strand: chain 'C' and resid 539 through 542 removed outlier: 6.370A pdb=" N GLU C 539 " --> pdb=" O VAL C 587 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL C 589 " --> pdb=" O GLU C 539 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN C 541 " --> pdb=" O VAL C 589 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE C 603 " --> pdb=" O VAL C 585 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL C 587 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY C 601 " --> pdb=" O VAL C 587 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 314 through 318 removed outlier: 6.644A pdb=" N ALA D 315 " --> pdb=" O PHE D 356 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ASP D 358 " --> pdb=" O ALA D 315 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS D 317 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL D 355 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N SER D 420 " --> pdb=" O VAL D 355 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU D 357 " --> pdb=" O SER D 420 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE D 289 " --> pdb=" O ALA D 419 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY D 421 " --> pdb=" O ILE D 289 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU D 291 " --> pdb=" O GLY D 421 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 392 through 395 Processing sheet with id=AB4, first strand: chain 'D' and resid 539 through 542 removed outlier: 6.151A pdb=" N GLU D 539 " --> pdb=" O VAL D 587 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL D 589 " --> pdb=" O GLU D 539 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASN D 541 " --> pdb=" O VAL D 589 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE D 603 " --> pdb=" O VAL D 585 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL D 587 " --> pdb=" O GLY D 601 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY D 601 " --> pdb=" O VAL D 587 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 314 through 318 removed outlier: 6.317A pdb=" N ALA E 315 " --> pdb=" O PHE E 356 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASP E 358 " --> pdb=" O ALA E 315 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N CYS E 317 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE E 289 " --> pdb=" O ALA E 419 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N GLY E 421 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU E 291 " --> pdb=" O GLY E 421 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 392 through 396 Processing sheet with id=AB7, first strand: chain 'E' and resid 541 through 542 removed outlier: 6.291A pdb=" N ASN E 541 " --> pdb=" O VAL E 589 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 418 through 420 removed outlier: 6.364A pdb=" N LEU F 290 " --> pdb=" O VAL F 504 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 588 through 589 615 hydrogen bonds defined for protein. 1770 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: 2.39 Time building geometry restraints manager: 1.64 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: 4588 1.34 - 1.45: 1395 1.45 - 1.57: 8576 1.57 - 1.69: 15 1.69 - 1.81: 62 Bond restraints: 14636 Sorted by residual: bond pdb=" CG1 ILE C 567 " pdb=" CD1 ILE C 567 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.83e+00 bond pdb=" CB ILE C 363 " pdb=" CG2 ILE C 363 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.36e+00 bond pdb=" CG GLN C 183 " pdb=" CD GLN C 183 " ideal model delta sigma weight residual 1.516 1.481 0.035 2.50e-02 1.60e+03 1.95e+00 bond pdb=" CB PRO F 165 " pdb=" CG PRO F 165 " ideal model delta sigma weight residual 1.492 1.561 -0.069 5.00e-02 4.00e+02 1.91e+00 bond pdb=" CG GLN E 183 " pdb=" CD GLN E 183 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.89e+00 ... (remaining 14631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 19371 2.02 - 4.04: 451 4.04 - 6.06: 64 6.06 - 8.08: 13 8.08 - 10.10: 2 Bond angle restraints: 19901 Sorted by residual: angle pdb=" N GLU D 520 " pdb=" CA GLU D 520 " pdb=" C GLU D 520 " ideal model delta sigma weight residual 109.81 117.33 -7.52 2.21e+00 2.05e-01 1.16e+01 angle pdb=" N VAL C 579 " pdb=" CA VAL C 579 " pdb=" C VAL C 579 " ideal model delta sigma weight residual 108.88 116.13 -7.25 2.16e+00 2.14e-01 1.13e+01 angle pdb=" N GLY E 182 " pdb=" CA GLY E 182 " pdb=" C GLY E 182 " ideal model delta sigma weight residual 113.18 121.12 -7.94 2.37e+00 1.78e-01 1.12e+01 angle pdb=" N VAL A 579 " pdb=" CA VAL A 579 " pdb=" C VAL A 579 " ideal model delta sigma weight residual 108.88 115.97 -7.09 2.16e+00 2.14e-01 1.08e+01 angle pdb=" C2' ADP E 701 " pdb=" C3' ADP E 701 " pdb=" C4' ADP E 701 " ideal model delta sigma weight residual 111.00 101.51 9.49 3.00e+00 1.11e-01 1.00e+01 ... (remaining 19896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.71: 8557 21.71 - 43.43: 316 43.43 - 65.14: 64 65.14 - 86.85: 23 86.85 - 108.57: 3 Dihedral angle restraints: 8963 sinusoidal: 3345 harmonic: 5618 Sorted by residual: dihedral pdb=" CA THR C 519 " pdb=" C THR C 519 " pdb=" N GLU C 520 " pdb=" CA GLU C 520 " ideal model delta harmonic sigma weight residual -180.00 -150.86 -29.14 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA THR D 519 " pdb=" C THR D 519 " pdb=" N GLU D 520 " pdb=" CA GLU D 520 " ideal model delta harmonic sigma weight residual -180.00 -151.06 -28.94 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA THR A 519 " pdb=" C THR A 519 " pdb=" N GLU A 520 " pdb=" CA GLU A 520 " ideal model delta harmonic sigma weight residual -180.00 -151.20 -28.80 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 8960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1320 0.038 - 0.077: 718 0.077 - 0.115: 271 0.115 - 0.153: 84 0.153 - 0.192: 14 Chirality restraints: 2407 Sorted by residual: chirality pdb=" CB VAL C 312 " pdb=" CA VAL C 312 " pdb=" CG1 VAL C 312 " pdb=" CG2 VAL C 312 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CA VAL B 312 " pdb=" N VAL B 312 " pdb=" C VAL B 312 " pdb=" CB VAL B 312 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CA PRO C 580 " pdb=" N PRO C 580 " pdb=" C PRO C 580 " pdb=" CB PRO C 580 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.69e-01 ... (remaining 2404 not shown) Planarity restraints: 2534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP C 702 " -0.033 2.00e-02 2.50e+03 2.31e-02 1.47e+01 pdb=" C2 ATP C 702 " 0.002 2.00e-02 2.50e+03 pdb=" C4 ATP C 702 " -0.016 2.00e-02 2.50e+03 pdb=" C5 ATP C 702 " 0.001 2.00e-02 2.50e+03 pdb=" C6 ATP C 702 " -0.002 2.00e-02 2.50e+03 pdb=" C8 ATP C 702 " -0.014 2.00e-02 2.50e+03 pdb=" N1 ATP C 702 " -0.001 2.00e-02 2.50e+03 pdb=" N3 ATP C 702 " 0.002 2.00e-02 2.50e+03 pdb=" N6 ATP C 702 " -0.004 2.00e-02 2.50e+03 pdb=" N7 ATP C 702 " -0.001 2.00e-02 2.50e+03 pdb=" N9 ATP C 702 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP B 702 " -0.032 2.00e-02 2.50e+03 2.21e-02 1.34e+01 pdb=" C2 ATP B 702 " 0.002 2.00e-02 2.50e+03 pdb=" C4 ATP B 702 " -0.017 2.00e-02 2.50e+03 pdb=" C5 ATP B 702 " -0.000 2.00e-02 2.50e+03 pdb=" C6 ATP B 702 " -0.002 2.00e-02 2.50e+03 pdb=" C8 ATP B 702 " -0.011 2.00e-02 2.50e+03 pdb=" N1 ATP B 702 " -0.001 2.00e-02 2.50e+03 pdb=" N3 ATP B 702 " 0.003 2.00e-02 2.50e+03 pdb=" N6 ATP B 702 " -0.004 2.00e-02 2.50e+03 pdb=" N7 ATP B 702 " -0.001 2.00e-02 2.50e+03 pdb=" N9 ATP B 702 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP D 702 " -0.028 2.00e-02 2.50e+03 2.04e-02 1.15e+01 pdb=" C2 ATP D 702 " 0.004 2.00e-02 2.50e+03 pdb=" C4 ATP D 702 " -0.022 2.00e-02 2.50e+03 pdb=" C5 ATP D 702 " -0.000 2.00e-02 2.50e+03 pdb=" C6 ATP D 702 " -0.003 2.00e-02 2.50e+03 pdb=" C8 ATP D 702 " -0.009 2.00e-02 2.50e+03 pdb=" N1 ATP D 702 " -0.000 2.00e-02 2.50e+03 pdb=" N3 ATP D 702 " 0.004 2.00e-02 2.50e+03 pdb=" N6 ATP D 702 " -0.002 2.00e-02 2.50e+03 pdb=" N7 ATP D 702 " -0.001 2.00e-02 2.50e+03 pdb=" N9 ATP D 702 " 0.057 2.00e-02 2.50e+03 ... (remaining 2531 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 16 2.35 - 2.98: 6943 2.98 - 3.62: 20012 3.62 - 4.26: 31534 4.26 - 4.90: 51719 Nonbonded interactions: 110224 Sorted by model distance: nonbonded pdb="MG MG A 701 " pdb=" O1B ATP A 702 " model vdw 1.707 2.170 nonbonded pdb="MG MG C 701 " pdb=" O1B ATP C 702 " model vdw 1.715 2.170 nonbonded pdb="MG MG D 701 " pdb=" O1B ATP D 702 " model vdw 1.838 2.170 nonbonded pdb="MG MG A 701 " pdb=" O2G ATP A 702 " model vdw 1.846 2.170 nonbonded pdb="MG MG C 701 " pdb=" O3G ATP C 702 " model vdw 1.857 2.170 ... (remaining 110219 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 165 through 171 or (resid 172 and (name N or name CA or na \ me C or name O or name CB )) or resid 173 through 191 or (resid 192 through 193 \ and (name N or name CA or name C or name O or name CB )) or resid 194 through 20 \ 4 or (resid 285 and (name N or name CA or name C or name O or name CB )) or resi \ d 286 through 296 or (resid 297 and (name N or name CA or name C or name O or na \ me CB )) or resid 298 through 308 or (resid 309 through 312 and (name N or name \ CA or name C or name O or name CB )) or resid 313 through 329 or (resid 330 and \ (name N or name CA or name C or name O or name CB )) or resid 331 through 357 or \ (resid 358 and (name N or name CA or name C or name O or name CB )) or resid 35 \ 9 through 366 or (resid 373 through 374 and (name N or name CA or name C or name \ O or name CB )) or resid 375 through 394 or (resid 395 and (name N or name CA o \ r name C or name O or name CB )) or resid 396 through 442 or (resid 468 through \ 477 and (name N or name CA or name C or name O or name CB )) or resid 478 throug \ h 488 or (resid 489 and (name N or name CA or name C or name O or name CB )) or \ resid 490 through 532 or (resid 533 through 535 and (name N or name CA or name C \ or name O or name CB )) or resid 540 through 542 or (resid 543 through 544 and \ (name N or name CA or name C or name O or name CB )) or resid 545 through 564 or \ (resid 565 through 566 and (name N or name CA or name C or name O or name CB )) \ or resid 567 through 568 or (resid 569 through 570 and (name N or name CA or na \ me C or name O or name CB )) or resid 571 through 573 or (resid 574 and (name N \ or name CA or name C or name O or name CB )) or resid 575 or (resid 576 through \ 577 and (name N or name CA or name C or name O or name CB )) or (resid 578 and ( \ name N or name CA or name C or name O or name CB or name CG )) or resid 579 thro \ ugh 580 or (resid 581 through 583 and (name N or name CA or name C or name O or \ name CB )) or resid 584 or (resid 585 through 586 and (name N or name CA or name \ C or name O or name CB )) or resid 587 or (resid 588 and (name N or name CA or \ name C or name O or name CB )) or resid 589 through 603)) selection = (chain 'B' and (resid 165 through 176 or (resid 177 through 178 and (name N or n \ ame CA or name C or name O or name CB )) or resid 179 through 187 or (resid 188 \ and (name N or name CA or name C or name O or name CB )) or resid 189 through 19 \ 0 or (resid 191 through 193 and (name N or name CA or name C or name O or name C \ B )) or resid 194 through 199 or (resid 200 through 201 and (name N or name CA o \ r name C or name O or name CB )) or resid 202 or (resid 203 and (name N or name \ CA or name C or name O or name CB )) or (resid 204 and (name N or name CA or nam \ e C or name O or name CB or name CG )) or (resid 285 and (name N or name CA or n \ ame C or name O or name CB )) or resid 286 through 296 or (resid 297 and (name N \ or name CA or name C or name O or name CB )) or resid 298 through 304 or (resid \ 305 and (name N or name CA or name C or name O or name CB )) or resid 306 throu \ gh 308 or (resid 309 through 312 and (name N or name CA or name C or name O or n \ ame CB )) or resid 313 through 316 or (resid 317 and (name N or name CA or name \ C or name O or name CB )) or resid 318 through 329 or (resid 330 and (name N or \ name CA or name C or name O or name CB )) or resid 331 through 337 or (resid 338 \ and (name N or name CA or name C or name O or name CB )) or resid 339 through 3 \ 40 or (resid 341 and (name N or name CA or name C or name O or name CB )) or res \ id 342 through 347 or (resid 348 and (name N or name CA or name C or name O or n \ ame CB )) or resid 349 through 351 or (resid 352 and (name N or name CA or name \ C or name O or name CB )) or resid 353 through 364 or (resid 365 and (name N or \ name CA or name C or name O or name CB )) or resid 366 or (resid 373 through 374 \ and (name N or name CA or name C or name O or name CB )) or resid 375 through 3 \ 77 or (resid 378 and (name N or name CA or name C or name O or name CB )) or res \ id 379 through 385 or (resid 386 and (name N or name CA or name C or name O or n \ ame CB )) or resid 387 through 388 or (resid 389 and (name N or name CA or name \ C or name O or name CB )) or resid 390 or (resid 391 through 392 and (name N or \ name CA or name C or name O or name CB )) or resid 393 through 394 or (resid 395 \ and (name N or name CA or name C or name O or name CB )) or resid 396 or resid \ 407 through 410 or (resid 411 and (name N or name CA or name C or name O or name \ CB )) or resid 412 or (resid 413 and (name N or name CA or name C or name O or \ name CB )) or resid 414 through 419 or (resid 420 and (name N or name CA or name \ C or name O or name CB )) or resid 421 through 423 or (resid 424 and (name N or \ name CA or name C or name O or name CB )) or resid 425 through 427 or (resid 42 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 429 through \ 430 or (resid 431 and (name N or name CA or name C or name O or name CB )) or re \ sid 432 through 434 or (resid 435 through 437 and (name N or name CA or name C o \ r name O or name CB )) or resid 438 through 442 or (resid 443 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 469 through 477 and (name N or \ name CA or name C or name O or name CB )) or resid 478 through 479 or (resid 480 \ and (name N or name CA or name C or name O or name CB )) or resid 481 through 4 \ 85 or (resid 486 and (name N or name CA or name C or name O or name CB )) or res \ id 487 through 498 or (resid 499 and (name N or name CA or name C or name O or n \ ame CB )) or resid 500 through 509 or (resid 510 through 511 and (name N or name \ CA or name C or name O or name CB )) or resid 512 or (resid 513 and (name N or \ name CA or name C or name O or name CB )) or resid 514 through 521 or (resid 522 \ and (name N or name CA or name C or name O or name CB )) or resid 523 through 5 \ 32 or (resid 533 through 535 and (name N or name CA or name C or name O or name \ CB )) or resid 540 through 542 or (resid 543 through 544 and (name N or name CA \ or name C or name O or name CB )) or resid 545 through 564 or (resid 565 through \ 566 and (name N or name CA or name C or name O or name CB )) or resid 567 throu \ gh 568 or (resid 569 through 570 and (name N or name CA or name C or name O or n \ ame CB )) or resid 571 through 575 or (resid 576 through 577 and (name N or name \ CA or name C or name O or name CB )) or (resid 578 and (name N or name CA or na \ me C or name O or name CB or name CG )) or resid 579 through 580 or (resid 581 t \ hrough 583 and (name N or name CA or name C or name O or name CB )) or resid 584 \ or (resid 585 through 586 and (name N or name CA or name C or name O or name CB \ )) or resid 587 or (resid 588 and (name N or name CA or name C or name O or nam \ e CB )) or resid 589 or (resid 590 through 592 and (name N or name CA or name C \ or name O or name CB )) or resid 593 through 596 or (resid 597 and (name N or na \ me CA or name C or name O or name CB )) or resid 598 through 603)) selection = (chain 'C' and (resid 165 through 171 or (resid 172 and (name N or name CA or na \ me C or name O or name CB )) or resid 173 through 176 or (resid 177 through 178 \ and (name N or name CA or name C or name O or name CB )) or resid 179 through 18 \ 7 or (resid 188 and (name N or name CA or name C or name O or name CB )) or resi \ d 189 through 199 or (resid 200 through 201 and (name N or name CA or name C or \ name O or name CB )) or resid 202 or (resid 203 and (name N or name CA or name C \ or name O or name CB )) or (resid 204 and (name N or name CA or name C or name \ O or name CB or name CG )) or (resid 285 and (name N or name CA or name C or nam \ e O or name CB )) or resid 286 through 296 or (resid 297 and (name N or name CA \ or name C or name O or name CB )) or resid 298 through 304 or (resid 305 and (na \ me N or name CA or name C or name O or name CB )) or resid 306 through 308 or (r \ esid 309 through 312 and (name N or name CA or name C or name O or name CB )) or \ resid 313 through 316 or (resid 317 and (name N or name CA or name C or name O \ or name CB )) or resid 318 through 329 or (resid 330 and (name N or name CA or n \ ame C or name O or name CB )) or resid 331 through 337 or (resid 338 and (name N \ or name CA or name C or name O or name CB )) or resid 339 through 340 or (resid \ 341 and (name N or name CA or name C or name O or name CB )) or resid 342 throu \ gh 347 or (resid 348 and (name N or name CA or name C or name O or name CB )) or \ resid 349 through 351 or (resid 352 and (name N or name CA or name C or name O \ or name CB )) or resid 353 through 357 or (resid 358 and (name N or name CA or n \ ame C or name O or name CB )) or resid 359 through 364 or (resid 365 and (name N \ or name CA or name C or name O or name CB )) or resid 366 or (resid 373 through \ 374 and (name N or name CA or name C or name O or name CB )) or resid 375 throu \ gh 377 or (resid 378 and (name N or name CA or name C or name O or name CB )) or \ resid 379 through 385 or (resid 386 and (name N or name CA or name C or name O \ or name CB )) or resid 387 through 388 or (resid 389 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 390 through 392 and (name N or name CA o \ r name C or name O or name CB )) or resid 393 through 396 or resid 407 through 4 \ 10 or (resid 411 and (name N or name CA or name C or name O or name CB )) or res \ id 412 or (resid 413 and (name N or name CA or name C or name O or name CB )) or \ resid 414 through 419 or (resid 420 and (name N or name CA or name C or name O \ or name CB )) or resid 421 through 423 or (resid 424 and (name N or name CA or n \ ame C or name O or name CB )) or resid 425 through 427 or (resid 428 and (name N \ or name CA or name C or name O or name CB )) or resid 429 through 430 or (resid \ 431 and (name N or name CA or name C or name O or name CB )) or resid 432 throu \ gh 434 or (resid 435 through 437 and (name N or name CA or name C or name O or n \ ame CB )) or resid 438 through 442 or (resid 443 and (name N or name CA or name \ C or name O or name CB )) or (resid 469 through 477 and (name N or name CA or na \ me C or name O or name CB )) or resid 478 through 479 or (resid 480 and (name N \ or name CA or name C or name O or name CB )) or resid 481 through 485 or (resid \ 486 and (name N or name CA or name C or name O or name CB )) or resid 487 throug \ h 488 or (resid 489 and (name N or name CA or name C or name O or name CB )) or \ resid 490 through 498 or (resid 499 and (name N or name CA or name C or name O o \ r name CB )) or resid 500 through 510 or (resid 511 and (name N or name CA or na \ me C or name O or name CB )) or resid 512 or (resid 513 and (name N or name CA o \ r name C or name O or name CB )) or resid 514 through 519 or (resid 520 and (nam \ e N or name CA or name C or name O or name CB )) or resid 521 or (resid 522 and \ (name N or name CA or name C or name O or name CB )) or resid 523 through 532 or \ (resid 533 through 535 and (name N or name CA or name C or name O or name CB )) \ or resid 540 through 542 or (resid 543 through 544 and (name N or name CA or na \ me C or name O or name CB )) or resid 545 through 564 or (resid 565 through 566 \ and (name N or name CA or name C or name O or name CB )) or resid 567 through 56 \ 8 or (resid 569 through 570 and (name N or name CA or name C or name O or name C \ B )) or resid 571 through 573 or (resid 574 and (name N or name CA or name C or \ name O or name CB )) or resid 575 or (resid 576 through 577 and (name N or name \ CA or name C or name O or name CB )) or (resid 578 and (name N or name CA or nam \ e C or name O or name CB or name CG )) or resid 579 through 580 or (resid 581 th \ rough 583 and (name N or name CA or name C or name O or name CB )) or resid 584 \ through 590 or (resid 591 through 592 and (name N or name CA or name C or name O \ or name CB )) or resid 593 through 596 or (resid 597 and (name N or name CA or \ name C or name O or name CB )) or resid 598 or (resid 599 and (name N or name CA \ or name C or name O or name CB )) or resid 600 through 603)) selection = (chain 'D' and (resid 165 through 171 or (resid 172 and (name N or name CA or na \ me C or name O or name CB )) or resid 173 through 176 or (resid 177 through 178 \ and (name N or name CA or name C or name O or name CB )) or resid 179 through 18 \ 7 or (resid 188 and (name N or name CA or name C or name O or name CB )) or resi \ d 189 through 191 or (resid 192 through 193 and (name N or name CA or name C or \ name O or name CB )) or resid 194 through 199 or (resid 200 through 201 and (nam \ e N or name CA or name C or name O or name CB )) or resid 202 or (resid 203 and \ (name N or name CA or name C or name O or name CB )) or (resid 204 and (name N o \ r name CA or name C or name O or name CB or name CG )) or resid 285 through 304 \ or (resid 305 and (name N or name CA or name C or name O or name CB )) or resid \ 306 through 308 or (resid 309 through 312 and (name N or name CA or name C or na \ me O or name CB )) or resid 313 through 316 or (resid 317 and (name N or name CA \ or name C or name O or name CB )) or resid 318 through 333 or (resid 334 and (n \ ame N or name CA or name C or name O or name CB )) or resid 335 through 337 or ( \ resid 338 and (name N or name CA or name C or name O or name CB )) or resid 339 \ through 340 or (resid 341 and (name N or name CA or name C or name O or name CB \ )) or resid 342 through 347 or (resid 348 and (name N or name CA or name C or na \ me O or name CB )) or resid 349 through 351 or (resid 352 and (name N or name CA \ or name C or name O or name CB )) or resid 353 through 357 or (resid 358 and (n \ ame N or name CA or name C or name O or name CB )) or resid 359 through 366 or ( \ resid 373 through 374 and (name N or name CA or name C or name O or name CB )) o \ r resid 375 through 377 or (resid 378 and (name N or name CA or name C or name O \ or name CB )) or resid 379 through 385 or (resid 386 and (name N or name CA or \ name C or name O or name CB )) or resid 387 through 390 or (resid 391 through 39 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 393 through \ 394 or (resid 395 and (name N or name CA or name C or name O or name CB )) or re \ sid 396 or resid 407 through 410 or (resid 411 and (name N or name CA or name C \ or name O or name CB )) or resid 412 or (resid 413 and (name N or name CA or nam \ e C or name O or name CB )) or resid 414 through 423 or (resid 424 and (name N o \ r name CA or name C or name O or name CB )) or resid 425 through 427 or (resid 4 \ 28 and (name N or name CA or name C or name O or name CB )) or resid 429 through \ 430 or (resid 431 and (name N or name CA or name C or name O or name CB )) or r \ esid 432 through 434 or (resid 435 through 437 and (name N or name CA or name C \ or name O or name CB )) or resid 438 through 443 or (resid 469 through 477 and ( \ name N or name CA or name C or name O or name CB )) or resid 478 through 479 or \ (resid 480 and (name N or name CA or name C or name O or name CB )) or resid 481 \ through 485 or (resid 486 and (name N or name CA or name C or name O or name CB \ )) or resid 487 through 488 or (resid 489 and (name N or name CA or name C or n \ ame O or name CB )) or resid 490 through 498 or (resid 499 and (name N or name C \ A or name C or name O or name CB )) or resid 500 through 509 or (resid 510 throu \ gh 511 and (name N or name CA or name C or name O or name CB )) or resid 512 or \ (resid 513 and (name N or name CA or name C or name O or name CB )) or resid 514 \ through 521 or (resid 522 and (name N or name CA or name C or name O or name CB \ )) or resid 523 through 532 or (resid 533 through 535 and (name N or name CA or \ name C or name O or name CB )) or resid 540 through 542 or (resid 543 through 5 \ 44 and (name N or name CA or name C or name O or name CB )) or resid 545 through \ 564 or (resid 565 through 566 and (name N or name CA or name C or name O or nam \ e CB )) or resid 567 through 569 or (resid 570 and (name N or name CA or name C \ or name O or name CB )) or resid 571 through 573 or (resid 574 and (name N or na \ me CA or name C or name O or name CB )) or resid 575 or (resid 576 through 577 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 578 and (name \ N or name CA or name C or name O or name CB or name CG )) or resid 579 through 5 \ 80 or (resid 581 through 583 and (name N or name CA or name C or name O or name \ CB )) or resid 584 through 587 or (resid 588 and (name N or name CA or name C or \ name O or name CB )) or resid 589 through 590 or (resid 591 through 592 and (na \ me N or name CA or name C or name O or name CB )) or resid 593 through 596 or (r \ esid 597 and (name N or name CA or name C or name O or name CB )) or resid 598 o \ r (resid 599 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 00 through 603)) selection = (chain 'E' and (resid 165 through 171 or (resid 172 and (name N or name CA or na \ me C or name O or name CB )) or resid 173 through 176 or (resid 177 through 178 \ and (name N or name CA or name C or name O or name CB )) or resid 179 through 18 \ 7 or (resid 188 and (name N or name CA or name C or name O or name CB )) or resi \ d 189 through 191 or (resid 192 through 193 and (name N or name CA or name C or \ name O or name CB )) or resid 194 through 199 or (resid 200 through 201 and (nam \ e N or name CA or name C or name O or name CB )) or resid 202 through 203 or (re \ sid 204 and (name N or name CA or name C or name O or name CB or name CG )) or ( \ resid 285 and (name N or name CA or name C or name O or name CB )) or resid 286 \ or (resid 287 and (name N or name CA or name C or name O or name CB )) or resid \ 288 through 329 or (resid 330 and (name N or name CA or name C or name O or name \ CB )) or resid 331 through 333 or (resid 334 and (name N or name CA or name C o \ r name O or name CB )) or resid 335 through 337 or (resid 338 and (name N or nam \ e CA or name C or name O or name CB )) or resid 339 through 340 or (resid 341 an \ d (name N or name CA or name C or name O or name CB )) or resid 342 through 347 \ or (resid 348 and (name N or name CA or name C or name O or name CB )) or resid \ 349 through 351 or (resid 352 and (name N or name CA or name C or name O or name \ CB )) or resid 353 through 357 or (resid 358 and (name N or name CA or name C o \ r name O or name CB )) or resid 359 through 364 or (resid 365 and (name N or nam \ e CA or name C or name O or name CB )) or resid 366 or (resid 373 through 374 an \ d (name N or name CA or name C or name O or name CB )) or resid 375 through 385 \ or (resid 386 and (name N or name CA or name C or name O or name CB )) or resid \ 387 through 391 or (resid 392 and (name N or name CA or name C or name O or name \ CB )) or resid 393 through 394 or (resid 395 and (name N or name CA or name C o \ r name O or name CB )) or resid 396 or resid 407 through 410 or (resid 411 and ( \ name N or name CA or name C or name O or name CB )) or resid 412 or (resid 413 a \ nd (name N or name CA or name C or name O or name CB )) or resid 414 through 423 \ or (resid 424 and (name N or name CA or name C or name O or name CB )) or resid \ 425 through 427 or (resid 428 and (name N or name CA or name C or name O or nam \ e CB )) or resid 429 through 434 or (resid 435 through 437 and (name N or name C \ A or name C or name O or name CB )) or resid 438 through 443 or (resid 469 throu \ gh 477 and (name N or name CA or name C or name O or name CB )) or resid 478 thr \ ough 479 or (resid 480 and (name N or name CA or name C or name O or name CB )) \ or resid 481 through 485 or (resid 486 and (name N or name CA or name C or name \ O or name CB )) or resid 487 through 498 or (resid 499 and (name N or name CA or \ name C or name O or name CB )) or resid 500 through 509 or (resid 510 through 5 \ 11 and (name N or name CA or name C or name O or name CB )) or resid 512 or (res \ id 513 and (name N or name CA or name C or name O or name CB )) or resid 514 thr \ ough 521 or (resid 522 and (name N or name CA or name C or name O or name CB )) \ or resid 523 through 543 or (resid 544 and (name N or name CA or name C or name \ O or name CB )) or resid 545 through 565 or (resid 566 and (name N or name CA or \ name C or name O or name CB )) or resid 567 through 569 or (resid 570 and (name \ N or name CA or name C or name O or name CB )) or resid 571 through 573 or (res \ id 574 and (name N or name CA or name C or name O or name CB )) or resid 575 thr \ ough 584 or (resid 585 through 586 and (name N or name CA or name C or name O or \ name CB )) or resid 587 or (resid 588 and (name N or name CA or name C or name \ O or name CB )) or resid 589 or (resid 590 through 592 and (name N or name CA or \ name C or name O or name CB )) or resid 593 through 596 or (resid 597 and (name \ N or name CA or name C or name O or name CB )) or resid 598 or (resid 599 and ( \ name N or name CA or name C or name O or name CB )) or resid 600 through 603)) } 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: 4.050 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: 0.030 Set scattering table: 0.030 Process input model: 15.120 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 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 : 0.006 0.069 14636 Z= 0.237 Angle : 0.788 10.104 19901 Z= 0.428 Chirality : 0.054 0.192 2407 Planarity : 0.007 0.089 2534 Dihedral : 13.021 108.567 5325 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.17), residues: 1872 helix: -2.16 (0.13), residues: 924 sheet: -0.01 (0.30), residues: 284 loop : -0.62 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.003 ARG E 200 TYR 0.028 0.004 TYR B 195 PHE 0.032 0.003 PHE E 496 HIS 0.014 0.002 HIS C 507 Details of bonding type rmsd covalent geometry : bond 0.00618 (14636) covalent geometry : angle 0.78822 (19901) hydrogen bonds : bond 0.24491 ( 615) hydrogen bonds : angle 8.23456 ( 1770) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.598 Fit side-chains REVERT: A 346 ASN cc_start: 0.7249 (t0) cc_final: 0.6544 (t0) REVERT: A 382 GLN cc_start: 0.8593 (tp40) cc_final: 0.8371 (mm-40) REVERT: A 432 ARG cc_start: 0.7745 (mtm-85) cc_final: 0.7447 (ptp-110) REVERT: B 534 SER cc_start: 0.8154 (t) cc_final: 0.7913 (m) REVERT: C 200 ARG cc_start: 0.7516 (mtt180) cc_final: 0.7053 (mtm110) REVERT: D 374 ASP cc_start: 0.8461 (t0) cc_final: 0.8240 (t70) REVERT: D 386 LYS cc_start: 0.8616 (mtpp) cc_final: 0.8361 (mtpt) REVERT: D 541 ASN cc_start: 0.8326 (m-40) cc_final: 0.8114 (m-40) REVERT: E 346 ASN cc_start: 0.7616 (t0) cc_final: 0.7383 (t0) REVERT: E 412 THR cc_start: 0.8573 (p) cc_final: 0.8350 (m) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.1575 time to fit residues: 82.6442 Evaluate side-chains 218 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 394 ASN A 516 GLN A 523 ASN A 541 ASN B 341 GLN B 344 ASN B 346 ASN B 351 GLN B 352 GLN B 469 HIS C 203 ASN C 507 HIS C 541 ASN D 435 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.173779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.152843 restraints weight = 14377.978| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 0.88 r_work: 0.3382 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14636 Z= 0.146 Angle : 0.619 7.019 19901 Z= 0.323 Chirality : 0.045 0.163 2407 Planarity : 0.005 0.056 2534 Dihedral : 10.752 95.921 2197 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.81 % Allowed : 7.80 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.19), residues: 1872 helix: -0.53 (0.16), residues: 953 sheet: 0.17 (0.30), residues: 299 loop : -0.16 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 552 TYR 0.013 0.001 TYR C 195 PHE 0.020 0.001 PHE A 185 HIS 0.008 0.001 HIS C 507 Details of bonding type rmsd covalent geometry : bond 0.00342 (14636) covalent geometry : angle 0.61862 (19901) hydrogen bonds : bond 0.05148 ( 615) hydrogen bonds : angle 5.07277 ( 1770) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 236 time to evaluate : 0.395 Fit side-chains REVERT: A 382 GLN cc_start: 0.8294 (tp40) cc_final: 0.8022 (mm-40) REVERT: A 557 ARG cc_start: 0.7948 (ptp-110) cc_final: 0.7451 (ptm160) REVERT: B 200 ARG cc_start: 0.8056 (tmm-80) cc_final: 0.7671 (ttp-170) REVERT: B 534 SER cc_start: 0.8002 (t) cc_final: 0.7770 (m) REVERT: C 200 ARG cc_start: 0.7544 (mtt180) cc_final: 0.7322 (mtm110) REVERT: C 555 LEU cc_start: 0.8915 (tp) cc_final: 0.8689 (tp) REVERT: D 374 ASP cc_start: 0.8275 (t0) cc_final: 0.8010 (t70) REVERT: E 346 ASN cc_start: 0.7624 (t0) cc_final: 0.7300 (t0) REVERT: F 171 LYS cc_start: 0.6834 (ptmm) cc_final: 0.6344 (mtmm) REVERT: F 188 LYS cc_start: 0.6085 (ttmm) cc_final: 0.5603 (ptmt) outliers start: 25 outliers final: 15 residues processed: 252 average time/residue: 0.1510 time to fit residues: 51.8161 Evaluate side-chains 213 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 566 SER Chi-restraints excluded: chain E residue 589 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 81 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 chunk 187 optimal weight: 30.0000 chunk 182 optimal weight: 8.9990 chunk 169 optimal weight: 0.7980 chunk 150 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 174 optimal weight: 20.0000 chunk 168 optimal weight: 5.9990 chunk 122 optimal weight: 0.0370 overall best weight: 1.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 ASN C 203 ASN D 203 ASN D 409 GLN D 481 HIS F 197 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.167614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.140639 restraints weight = 14624.898| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.09 r_work: 0.3182 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 14636 Z= 0.210 Angle : 0.658 7.448 19901 Z= 0.333 Chirality : 0.048 0.165 2407 Planarity : 0.005 0.061 2534 Dihedral : 10.691 88.830 2197 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.45 % Allowed : 9.68 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.19), residues: 1872 helix: -0.14 (0.16), residues: 946 sheet: 0.27 (0.31), residues: 302 loop : -0.40 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 552 TYR 0.017 0.002 TYR C 195 PHE 0.023 0.002 PHE E 496 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00543 (14636) covalent geometry : angle 0.65785 (19901) hydrogen bonds : bond 0.05114 ( 615) hydrogen bonds : angle 4.84668 ( 1770) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 0.550 Fit side-chains REVERT: A 333 GLU cc_start: 0.7269 (pp20) cc_final: 0.6788 (pm20) REVERT: A 349 LYS cc_start: 0.7573 (ptpt) cc_final: 0.7225 (pttt) REVERT: A 382 GLN cc_start: 0.8238 (tp40) cc_final: 0.8014 (mm-40) REVERT: A 557 ARG cc_start: 0.8085 (ptp-110) cc_final: 0.7605 (ptm160) REVERT: B 534 SER cc_start: 0.8137 (t) cc_final: 0.7904 (m) REVERT: C 200 ARG cc_start: 0.7719 (mtt180) cc_final: 0.7400 (mtm110) REVERT: C 555 LEU cc_start: 0.8971 (tp) cc_final: 0.8747 (tp) REVERT: E 346 ASN cc_start: 0.7961 (t0) cc_final: 0.7615 (t0) REVERT: F 171 LYS cc_start: 0.6771 (ptmm) cc_final: 0.6226 (mtmm) REVERT: F 188 LYS cc_start: 0.5934 (ttmm) cc_final: 0.5655 (ptmt) outliers start: 34 outliers final: 20 residues processed: 224 average time/residue: 0.1470 time to fit residues: 45.3772 Evaluate side-chains 200 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 542 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 75 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 80 optimal weight: 0.3980 chunk 192 optimal weight: 30.0000 chunk 63 optimal weight: 0.5980 chunk 117 optimal weight: 0.0670 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 ASN F 197 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.172174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.147189 restraints weight = 14429.606| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.06 r_work: 0.3279 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14636 Z= 0.112 Angle : 0.531 6.434 19901 Z= 0.271 Chirality : 0.043 0.149 2407 Planarity : 0.005 0.057 2534 Dihedral : 10.123 86.458 2197 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.66 % Allowed : 11.55 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.19), residues: 1872 helix: 0.35 (0.17), residues: 958 sheet: 0.30 (0.31), residues: 302 loop : -0.25 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 552 TYR 0.012 0.001 TYR E 198 PHE 0.021 0.001 PHE A 185 HIS 0.004 0.001 HIS E 507 Details of bonding type rmsd covalent geometry : bond 0.00262 (14636) covalent geometry : angle 0.53087 (19901) hydrogen bonds : bond 0.03633 ( 615) hydrogen bonds : angle 4.42250 ( 1770) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.555 Fit side-chains REVERT: A 185 PHE cc_start: 0.8056 (t80) cc_final: 0.7699 (t80) REVERT: A 333 GLU cc_start: 0.7277 (pp20) cc_final: 0.6831 (pm20) REVERT: A 346 ASN cc_start: 0.7807 (t0) cc_final: 0.7530 (t0) REVERT: A 349 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7232 (pttt) REVERT: A 557 ARG cc_start: 0.7995 (ptp-110) cc_final: 0.7644 (ptm160) REVERT: B 292 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8655 (mt) REVERT: B 534 SER cc_start: 0.7997 (t) cc_final: 0.7777 (m) REVERT: C 200 ARG cc_start: 0.7687 (mtt180) cc_final: 0.7360 (mtm110) REVERT: C 555 LEU cc_start: 0.8933 (tp) cc_final: 0.8720 (tp) REVERT: C 583 ASP cc_start: 0.6196 (p0) cc_final: 0.5858 (p0) REVERT: D 409 GLN cc_start: 0.7655 (mt0) cc_final: 0.7319 (mp10) REVERT: D 510 ASP cc_start: 0.6741 (t0) cc_final: 0.6442 (m-30) REVERT: F 171 LYS cc_start: 0.6778 (ptmm) cc_final: 0.6260 (mtmm) REVERT: F 188 LYS cc_start: 0.5789 (ttmm) cc_final: 0.5564 (ptmt) outliers start: 23 outliers final: 14 residues processed: 216 average time/residue: 0.1344 time to fit residues: 40.0594 Evaluate side-chains 210 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 487 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 110 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 101 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 161 optimal weight: 0.7980 chunk 170 optimal weight: 0.1980 chunk 96 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A 523 ASN D 203 ASN E 341 GLN E 507 HIS E 516 GLN F 197 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.173134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.147867 restraints weight = 14461.231| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.12 r_work: 0.3274 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14636 Z= 0.105 Angle : 0.518 6.590 19901 Z= 0.262 Chirality : 0.043 0.143 2407 Planarity : 0.004 0.055 2534 Dihedral : 9.575 86.756 2197 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.59 % Allowed : 12.06 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.20), residues: 1872 helix: 0.67 (0.17), residues: 962 sheet: 0.36 (0.31), residues: 306 loop : -0.09 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 200 TYR 0.015 0.001 TYR B 175 PHE 0.012 0.001 PHE A 185 HIS 0.003 0.000 HIS E 507 Details of bonding type rmsd covalent geometry : bond 0.00247 (14636) covalent geometry : angle 0.51845 (19901) hydrogen bonds : bond 0.03362 ( 615) hydrogen bonds : angle 4.25032 ( 1770) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 0.560 Fit side-chains REVERT: A 333 GLU cc_start: 0.7210 (pp20) cc_final: 0.6973 (pm20) REVERT: A 349 LYS cc_start: 0.7257 (ptpt) cc_final: 0.7013 (pttt) REVERT: A 557 ARG cc_start: 0.7720 (ptp-110) cc_final: 0.7462 (ptm160) REVERT: B 292 LEU cc_start: 0.8837 (mt) cc_final: 0.8617 (mt) REVERT: B 304 GLN cc_start: 0.8346 (mt0) cc_final: 0.8133 (mt0) REVERT: C 200 ARG cc_start: 0.7576 (mtt180) cc_final: 0.7343 (mtm110) REVERT: F 171 LYS cc_start: 0.6729 (ptmm) cc_final: 0.6398 (mtmm) outliers start: 22 outliers final: 17 residues processed: 216 average time/residue: 0.1434 time to fit residues: 43.2768 Evaluate side-chains 204 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 487 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 61 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 91 optimal weight: 0.3980 chunk 121 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 68 optimal weight: 0.0370 chunk 145 optimal weight: 4.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A 523 ASN D 203 ASN D 435 ASN E 341 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.170724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.132436 restraints weight = 14507.331| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.53 r_work: 0.3062 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14636 Z= 0.136 Angle : 0.552 6.639 19901 Z= 0.278 Chirality : 0.044 0.147 2407 Planarity : 0.005 0.053 2534 Dihedral : 9.676 87.532 2197 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.60 % Allowed : 11.62 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.20), residues: 1872 helix: 0.70 (0.17), residues: 963 sheet: 0.35 (0.31), residues: 306 loop : -0.07 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 200 TYR 0.018 0.001 TYR D 175 PHE 0.012 0.001 PHE E 496 HIS 0.003 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00340 (14636) covalent geometry : angle 0.55221 (19901) hydrogen bonds : bond 0.03662 ( 615) hydrogen bonds : angle 4.31601 ( 1770) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.546 Fit side-chains REVERT: A 333 GLU cc_start: 0.7268 (pp20) cc_final: 0.6860 (pm20) REVERT: A 557 ARG cc_start: 0.7896 (ptp-110) cc_final: 0.7531 (ptm160) REVERT: B 292 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8716 (mt) REVERT: B 304 GLN cc_start: 0.8580 (mt0) cc_final: 0.8357 (mt0) REVERT: B 591 LYS cc_start: 0.8807 (tmtt) cc_final: 0.8564 (tptt) REVERT: C 200 ARG cc_start: 0.7756 (mtt180) cc_final: 0.7332 (mtm110) REVERT: E 335 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8100 (m) REVERT: E 413 THR cc_start: 0.8691 (t) cc_final: 0.8433 (m) REVERT: E 528 GLN cc_start: 0.7066 (mt0) cc_final: 0.6788 (mm-40) REVERT: F 171 LYS cc_start: 0.6769 (ptmm) cc_final: 0.6218 (mtmm) outliers start: 36 outliers final: 30 residues processed: 213 average time/residue: 0.1446 time to fit residues: 42.5529 Evaluate side-chains 225 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 487 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 181 optimal weight: 30.0000 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 51 optimal weight: 0.0770 chunk 118 optimal weight: 0.0770 chunk 49 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 169 optimal weight: 0.0870 overall best weight: 0.3874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A 523 ASN E 341 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.172655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.145072 restraints weight = 14294.518| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.14 r_work: 0.3249 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14636 Z= 0.100 Angle : 0.514 6.609 19901 Z= 0.259 Chirality : 0.042 0.143 2407 Planarity : 0.004 0.050 2534 Dihedral : 9.329 85.746 2197 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.09 % Allowed : 11.91 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.20), residues: 1872 helix: 0.92 (0.18), residues: 956 sheet: 0.40 (0.31), residues: 306 loop : 0.02 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 200 TYR 0.016 0.001 TYR D 175 PHE 0.006 0.001 PHE E 314 HIS 0.001 0.000 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00229 (14636) covalent geometry : angle 0.51445 (19901) hydrogen bonds : bond 0.03142 ( 615) hydrogen bonds : angle 4.16851 ( 1770) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 0.501 Fit side-chains REVERT: A 333 GLU cc_start: 0.7210 (pp20) cc_final: 0.6841 (pm20) REVERT: B 292 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8646 (mt) REVERT: B 591 LYS cc_start: 0.8736 (tmtt) cc_final: 0.8456 (tttp) REVERT: C 183 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.6581 (mt0) REVERT: C 200 ARG cc_start: 0.7657 (mtt180) cc_final: 0.7339 (mtm110) REVERT: C 205 ILE cc_start: 0.7331 (OUTLIER) cc_final: 0.6305 (tp) REVERT: C 597 LYS cc_start: 0.7376 (mmtp) cc_final: 0.7169 (mttt) REVERT: E 413 THR cc_start: 0.8584 (t) cc_final: 0.8353 (m) REVERT: E 552 ARG cc_start: 0.6877 (ttm110) cc_final: 0.6353 (ttm-80) REVERT: E 570 LYS cc_start: 0.7739 (tmmt) cc_final: 0.7100 (ttmt) REVERT: F 171 LYS cc_start: 0.6751 (ptmm) cc_final: 0.6258 (mtmm) outliers start: 29 outliers final: 21 residues processed: 213 average time/residue: 0.1293 time to fit residues: 38.2184 Evaluate side-chains 213 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 487 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 10 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 179 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN E 341 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.171850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.144450 restraints weight = 14449.525| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.12 r_work: 0.3227 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14636 Z= 0.118 Angle : 0.536 6.652 19901 Z= 0.270 Chirality : 0.043 0.143 2407 Planarity : 0.004 0.050 2534 Dihedral : 9.327 86.614 2197 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.74 % Allowed : 12.27 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.68 (0.20), residues: 1872 helix: 0.92 (0.18), residues: 963 sheet: 0.40 (0.31), residues: 306 loop : -0.09 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 200 TYR 0.016 0.001 TYR E 202 PHE 0.016 0.001 PHE A 185 HIS 0.002 0.000 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00291 (14636) covalent geometry : angle 0.53624 (19901) hydrogen bonds : bond 0.03348 ( 615) hydrogen bonds : angle 4.18759 ( 1770) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.558 Fit side-chains REVERT: A 333 GLU cc_start: 0.7330 (pp20) cc_final: 0.6907 (pm20) REVERT: B 292 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8708 (mt) REVERT: B 591 LYS cc_start: 0.8825 (tmtt) cc_final: 0.8526 (tttp) REVERT: C 183 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.6628 (mt0) REVERT: C 200 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7413 (mtm110) REVERT: C 205 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.6250 (tp) REVERT: E 335 VAL cc_start: 0.8461 (OUTLIER) cc_final: 0.8151 (m) REVERT: E 349 LYS cc_start: 0.7982 (mmtm) cc_final: 0.7318 (mmmt) REVERT: E 413 THR cc_start: 0.8690 (t) cc_final: 0.8452 (m) REVERT: E 528 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7617 (mm-40) REVERT: E 552 ARG cc_start: 0.7037 (ttm110) cc_final: 0.6398 (ttm-80) REVERT: F 171 LYS cc_start: 0.6881 (ptmm) cc_final: 0.6257 (mtmm) outliers start: 38 outliers final: 27 residues processed: 220 average time/residue: 0.1442 time to fit residues: 43.8398 Evaluate side-chains 217 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 487 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 172 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 157 optimal weight: 0.0970 chunk 138 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 181 optimal weight: 20.0000 chunk 5 optimal weight: 0.0670 chunk 32 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 186 optimal weight: 0.0970 overall best weight: 0.3114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN B 528 GLN C 481 HIS D 203 ASN E 341 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.174927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.146259 restraints weight = 14441.525| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.17 r_work: 0.3259 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14636 Z= 0.095 Angle : 0.504 6.872 19901 Z= 0.254 Chirality : 0.042 0.151 2407 Planarity : 0.004 0.049 2534 Dihedral : 8.480 84.431 2197 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.81 % Allowed : 13.43 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.20), residues: 1872 helix: 1.13 (0.18), residues: 962 sheet: 0.50 (0.31), residues: 306 loop : 0.06 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 200 TYR 0.016 0.001 TYR E 202 PHE 0.008 0.001 PHE A 185 HIS 0.001 0.000 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00213 (14636) covalent geometry : angle 0.50361 (19901) hydrogen bonds : bond 0.02821 ( 615) hydrogen bonds : angle 4.03313 ( 1770) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.561 Fit side-chains REVERT: A 333 GLU cc_start: 0.7150 (pp20) cc_final: 0.6904 (pm20) REVERT: B 292 LEU cc_start: 0.8823 (mt) cc_final: 0.8621 (mt) REVERT: B 591 LYS cc_start: 0.8723 (tmtt) cc_final: 0.8463 (tttp) REVERT: C 200 ARG cc_start: 0.7555 (mtt180) cc_final: 0.7306 (mtm110) REVERT: C 205 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.6451 (tp) REVERT: D 597 LYS cc_start: 0.7511 (ptpt) cc_final: 0.7239 (pttt) REVERT: E 349 LYS cc_start: 0.8127 (mmtm) cc_final: 0.7601 (mmmt) REVERT: E 413 THR cc_start: 0.8561 (t) cc_final: 0.8341 (m) REVERT: E 528 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7448 (mm-40) REVERT: E 552 ARG cc_start: 0.6903 (ttm110) cc_final: 0.6398 (ttm-80) REVERT: E 570 LYS cc_start: 0.7643 (tmmt) cc_final: 0.7067 (ttmt) REVERT: F 171 LYS cc_start: 0.6832 (ptmm) cc_final: 0.6250 (mtmm) outliers start: 25 outliers final: 20 residues processed: 219 average time/residue: 0.1584 time to fit residues: 47.1463 Evaluate side-chains 207 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 487 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 175 optimal weight: 0.5980 chunk 65 optimal weight: 0.0670 chunk 149 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN B 304 GLN ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 341 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.171778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.144086 restraints weight = 14419.963| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.12 r_work: 0.3240 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14636 Z= 0.126 Angle : 0.548 8.095 19901 Z= 0.274 Chirality : 0.043 0.176 2407 Planarity : 0.004 0.050 2534 Dihedral : 8.845 86.592 2197 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.02 % Allowed : 13.65 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.20), residues: 1872 helix: 1.07 (0.18), residues: 963 sheet: 0.52 (0.31), residues: 306 loop : -0.03 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 433 TYR 0.014 0.001 TYR A 529 PHE 0.018 0.001 PHE A 185 HIS 0.003 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00311 (14636) covalent geometry : angle 0.54841 (19901) hydrogen bonds : bond 0.03346 ( 615) hydrogen bonds : angle 4.14634 ( 1770) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 0.526 Fit side-chains REVERT: A 333 GLU cc_start: 0.7226 (pp20) cc_final: 0.6931 (pm20) REVERT: A 342 ASP cc_start: 0.7369 (t0) cc_final: 0.7120 (t0) REVERT: B 292 LEU cc_start: 0.8939 (mt) cc_final: 0.8709 (mt) REVERT: B 591 LYS cc_start: 0.8770 (tmtt) cc_final: 0.8508 (tttp) REVERT: C 200 ARG cc_start: 0.7668 (mtt180) cc_final: 0.7263 (mtm110) REVERT: C 205 ILE cc_start: 0.7311 (OUTLIER) cc_final: 0.6345 (tp) REVERT: D 597 LYS cc_start: 0.7697 (ptpt) cc_final: 0.7317 (pttt) REVERT: E 335 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8148 (m) REVERT: E 349 LYS cc_start: 0.8065 (mmtm) cc_final: 0.7490 (mmmt) REVERT: E 413 THR cc_start: 0.8650 (t) cc_final: 0.8382 (m) REVERT: E 528 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7521 (mm-40) REVERT: E 552 ARG cc_start: 0.7012 (ttm110) cc_final: 0.6408 (ttm-80) REVERT: E 570 LYS cc_start: 0.7660 (tmmt) cc_final: 0.7052 (ttmt) REVERT: F 171 LYS cc_start: 0.6862 (ptmm) cc_final: 0.6215 (mtmm) outliers start: 28 outliers final: 24 residues processed: 207 average time/residue: 0.1415 time to fit residues: 40.3719 Evaluate side-chains 215 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 487 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 181 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 188 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN B 304 GLN B 528 GLN ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 341 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.170558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.147849 restraints weight = 14547.586| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 0.99 r_work: 0.3299 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14636 Z= 0.140 Angle : 0.564 7.566 19901 Z= 0.282 Chirality : 0.044 0.220 2407 Planarity : 0.005 0.050 2534 Dihedral : 9.124 86.747 2197 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.45 % Allowed : 13.36 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.20), residues: 1872 helix: 1.01 (0.18), residues: 962 sheet: 0.53 (0.31), residues: 306 loop : -0.11 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 433 TYR 0.018 0.001 TYR A 529 PHE 0.011 0.001 PHE E 496 HIS 0.003 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00353 (14636) covalent geometry : angle 0.56365 (19901) hydrogen bonds : bond 0.03544 ( 615) hydrogen bonds : angle 4.21480 ( 1770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3604.86 seconds wall clock time: 62 minutes 15.08 seconds (3735.08 seconds total)