Starting phenix.real_space_refine on Sat Jul 4 23:12:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k7v_36944/07_2026/8k7v_36944_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k7v_36944/07_2026/8k7v_36944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k7v_36944/07_2026/8k7v_36944_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k7v_36944/07_2026/8k7v_36944_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k7v_36944/07_2026/8k7v_36944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k7v_36944/07_2026/8k7v_36944.map" } resolution = 3.17 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= 0.001 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 15640 2.51 5 N 4108 2.21 5 O 4674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24546 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 6116 Classifications: {'peptide': 754} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 727} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 6128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6128 Classifications: {'peptide': 755} Link IDs: {'PTRANS': 26, 'TRANS': 728} Chain breaks: 1 Chain: "C" Number of atoms: 6119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 6119 Classifications: {'peptide': 754} Link IDs: {'PTRANS': 26, 'TRANS': 727} Chain breaks: 1 Chain: "D" Number of atoms: 6107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6107 Classifications: {'peptide': 752} Link IDs: {'PTRANS': 26, 'TRANS': 725} Chain breaks: 1 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'VQX': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'VQX:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'VQX': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'VQX:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'VQX': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'VQX:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'VQX': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'VQX:plan-2': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.22, per 1000 atoms: 0.21 Number of scatterers: 24546 At special positions: 0 Unit cell: (115.92, 144.44, 138.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 4674 8.00 N 4108 7.00 C 15640 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 777.3 milliseconds 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5640 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 31 sheets defined 22.5% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 305 through 320 removed outlier: 4.202A pdb=" N MET A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.501A pdb=" N LYS A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 394 through 407 removed outlier: 3.542A pdb=" N GLY A 398 " --> pdb=" O ASP A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 429 removed outlier: 3.587A pdb=" N ARG A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 433 removed outlier: 3.996A pdb=" N LEU A 433 " --> pdb=" O PRO A 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 430 through 433' Processing helix chain 'A' and resid 454 through 472 removed outlier: 4.055A pdb=" N VAL A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL A 468 " --> pdb=" O MET A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 520 removed outlier: 4.371A pdb=" N ILE A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 removed outlier: 3.638A pdb=" N LEU A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 565 removed outlier: 3.641A pdb=" N THR A 558 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 563 " --> pdb=" O LYS A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 599 removed outlier: 3.561A pdb=" N ARG A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 636 removed outlier: 3.702A pdb=" N LYS A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N GLU A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 742 through 747 removed outlier: 3.797A pdb=" N LYS A 746 " --> pdb=" O GLU A 742 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 742 through 747' Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 306 through 321 removed outlier: 3.659A pdb=" N LEU B 321 " --> pdb=" O TYR B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.665A pdb=" N THR B 341 " --> pdb=" O ASN B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 357 removed outlier: 3.510A pdb=" N ILE B 350 " --> pdb=" O ASN B 346 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 407 Processing helix chain 'B' and resid 423 through 429 removed outlier: 3.635A pdb=" N ARG B 427 " --> pdb=" O SER B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 433 removed outlier: 3.986A pdb=" N LEU B 433 " --> pdb=" O PRO B 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 430 through 433' Processing helix chain 'B' and resid 454 through 472 removed outlier: 3.926A pdb=" N VAL B 458 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 463 " --> pdb=" O ASP B 459 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE B 465 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B 467 " --> pdb=" O LYS B 463 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL B 468 " --> pdb=" O MET B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 499 removed outlier: 4.351A pdb=" N GLY B 499 " --> pdb=" O SER B 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 496 through 499' Processing helix chain 'B' and resid 500 through 520 removed outlier: 3.536A pdb=" N ILE B 506 " --> pdb=" O MET B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 553 through 565 removed outlier: 3.758A pdb=" N THR B 558 " --> pdb=" O ALA B 554 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 599 Processing helix chain 'B' and resid 613 through 636 removed outlier: 3.677A pdb=" N GLU B 618 " --> pdb=" O GLU B 614 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER B 619 " --> pdb=" O ALA B 615 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS B 621 " --> pdb=" O LEU B 617 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS B 622 " --> pdb=" O GLU B 618 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN B 623 " --> pdb=" O SER B 619 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 625 " --> pdb=" O LYS B 621 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 626 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLU B 632 " --> pdb=" O LYS B 628 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU B 633 " --> pdb=" O GLU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 712 removed outlier: 3.584A pdb=" N ALA B 710 " --> pdb=" O ASP B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 734 Processing helix chain 'C' and resid 46 through 50 Processing helix chain 'C' and resid 69 through 73 removed outlier: 3.501A pdb=" N TYR C 72 " --> pdb=" O SER C 69 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR C 73 " --> pdb=" O MET C 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 69 through 73' Processing helix chain 'C' and resid 305 through 320 removed outlier: 3.834A pdb=" N MET C 309 " --> pdb=" O GLY C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 327 removed outlier: 3.512A pdb=" N ARG C 327 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 357 removed outlier: 3.738A pdb=" N ILE C 350 " --> pdb=" O ASN C 346 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 351 " --> pdb=" O GLU C 347 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA C 357 " --> pdb=" O ILE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 407 removed outlier: 3.819A pdb=" N GLY C 398 " --> pdb=" O ASP C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 429 removed outlier: 3.516A pdb=" N ARG C 427 " --> pdb=" O SER C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 433 removed outlier: 3.892A pdb=" N LEU C 433 " --> pdb=" O PRO C 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 430 through 433' Processing helix chain 'C' and resid 454 through 463 removed outlier: 3.529A pdb=" N VAL C 458 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 472 Processing helix chain 'C' and resid 500 through 520 Processing helix chain 'C' and resid 536 through 541 Processing helix chain 'C' and resid 556 through 565 removed outlier: 3.796A pdb=" N TYR C 562 " --> pdb=" O THR C 558 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY C 563 " --> pdb=" O LYS C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 599 Processing helix chain 'C' and resid 608 through 612 removed outlier: 3.823A pdb=" N LEU C 612 " --> pdb=" O LEU C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 636 removed outlier: 4.228A pdb=" N SER C 619 " --> pdb=" O ALA C 615 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLU C 632 " --> pdb=" O LYS C 628 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU C 633 " --> pdb=" O GLU C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 735 Processing helix chain 'D' and resid 46 through 50 Processing helix chain 'D' and resid 305 through 320 removed outlier: 3.915A pdb=" N MET D 309 " --> pdb=" O GLY D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 327 removed outlier: 3.631A pdb=" N ARG D 327 " --> pdb=" O VAL D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 357 removed outlier: 3.531A pdb=" N LYS D 352 " --> pdb=" O GLU D 348 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA D 357 " --> pdb=" O ILE D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 407 removed outlier: 3.869A pdb=" N GLY D 398 " --> pdb=" O ASP D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 429 Processing helix chain 'D' and resid 454 through 472 removed outlier: 3.812A pdb=" N VAL D 458 " --> pdb=" O ARG D 454 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS D 467 " --> pdb=" O LYS D 463 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL D 468 " --> pdb=" O MET D 464 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D 469 " --> pdb=" O ILE D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 499 removed outlier: 3.702A pdb=" N GLN D 498 " --> pdb=" O ALA D 495 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY D 499 " --> pdb=" O SER D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 520 Processing helix chain 'D' and resid 536 through 543 Processing helix chain 'D' and resid 556 through 565 removed outlier: 3.664A pdb=" N GLY D 563 " --> pdb=" O LYS D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 571 No H-bonds generated for 'chain 'D' and resid 569 through 571' Processing helix chain 'D' and resid 590 through 600 removed outlier: 4.409A pdb=" N PHE D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 612 removed outlier: 3.708A pdb=" N LEU D 612 " --> pdb=" O LEU D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.899A pdb=" N GLU D 618 " --> pdb=" O GLU D 614 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLU D 632 " --> pdb=" O LYS D 628 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU D 633 " --> pdb=" O GLU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 735 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 removed outlier: 3.841A pdb=" N TYR A 35 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG A 24 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ASN A 33 " --> pdb=" O ARG A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 93 removed outlier: 6.317A pdb=" N THR A 91 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N MET A 180 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 277 " --> pdb=" O MET A 180 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 182 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 275 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 259 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 217 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C 275 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA C 182 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE C 277 " --> pdb=" O MET C 180 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N MET C 180 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR C 91 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 284 through 286 removed outlier: 5.796A pdb=" N MET A 180 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 277 " --> pdb=" O MET A 180 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 182 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 275 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 259 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 217 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C 275 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA C 182 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE C 277 " --> pdb=" O MET C 180 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N MET C 180 " --> pdb=" O ILE C 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 112 removed outlier: 5.809A pdb=" N TYR A 105 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS A 139 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 107 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL A 159 " --> pdb=" O TYR A 154 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU A 296 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N PHE A 233 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU A 196 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU A 193 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ASN A 208 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN A 195 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL A 206 " --> pdb=" O GLN A 195 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N SER A 197 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A 204 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 104 through 112 removed outlier: 5.809A pdb=" N TYR A 105 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS A 139 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 107 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL A 159 " --> pdb=" O TYR A 154 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU A 290 " --> pdb=" O GLN A 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 545 through 546 removed outlier: 4.242A pdb=" N GLN A 545 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A 476 " --> pdb=" O PHE A 410 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N PHE A 365 " --> pdb=" O GLY A 411 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N TRP A 413 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 335 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AA8, first strand: chain 'A' and resid 639 through 644 removed outlier: 6.211A pdb=" N ALA A 653 " --> pdb=" O LEU A 643 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 664 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 752 " --> pdb=" O GLN A 670 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 3 through 4 removed outlier: 3.752A pdb=" N TYR B 35 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG B 24 " --> pdb=" O ASN B 33 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ASN B 33 " --> pdb=" O ARG B 24 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 93 removed outlier: 6.157A pdb=" N THR B 91 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 182 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 275 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER D 217 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 217 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU D 275 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA D 182 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N THR D 91 " --> pdb=" O GLU D 177 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 284 through 286 removed outlier: 3.715A pdb=" N ALA B 182 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 275 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER D 217 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 217 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU D 275 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA D 182 " --> pdb=" O LEU D 275 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 104 through 112 removed outlier: 7.029A pdb=" N THR B 137 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N HIS B 108 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU B 135 " --> pdb=" O HIS B 108 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE B 110 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR B 133 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS B 112 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ALA B 131 " --> pdb=" O LYS B 112 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL B 159 " --> pdb=" O TYR B 154 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU B 296 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE B 233 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU B 196 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU B 193 " --> pdb=" O ASN B 208 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN B 208 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLN B 195 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL B 206 " --> pdb=" O GLN B 195 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER B 197 " --> pdb=" O ARG B 204 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG B 204 " --> pdb=" O SER B 197 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 104 through 112 removed outlier: 7.029A pdb=" N THR B 137 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N HIS B 108 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU B 135 " --> pdb=" O HIS B 108 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE B 110 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR B 133 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS B 112 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ALA B 131 " --> pdb=" O LYS B 112 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL B 159 " --> pdb=" O TYR B 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 573 through 574 removed outlier: 7.358A pdb=" N THR B 546 " --> pdb=" O GLY B 574 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE B 525 " --> pdb=" O GLN B 545 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N TRP B 547 " --> pdb=" O PHE B 525 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N SER B 527 " --> pdb=" O TRP B 547 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 477 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N CYS B 528 " --> pdb=" O ILE B 477 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N TRP B 479 " --> pdb=" O CYS B 528 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE B 365 " --> pdb=" O GLY B 411 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N TRP B 413 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU B 335 " --> pdb=" O VAL B 366 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 418 through 419 Processing sheet with id=AB7, first strand: chain 'B' and resid 639 through 644 removed outlier: 5.636A pdb=" N PHE B 640 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL B 657 " --> pdb=" O PHE B 640 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ARG B 642 " --> pdb=" O MET B 655 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N MET B 655 " --> pdb=" O ARG B 642 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B 653 " --> pdb=" O LEU B 644 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 680 through 682 removed outlier: 4.195A pdb=" N ILE B 680 " --> pdb=" O ILE B 739 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 3 through 4 removed outlier: 3.713A pdb=" N TYR C 35 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG C 24 " --> pdb=" O ASN C 33 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASN C 33 " --> pdb=" O ARG C 24 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 104 through 111 removed outlier: 5.516A pdb=" N TYR C 105 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N HIS C 139 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER C 107 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR C 145 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL C 159 " --> pdb=" O TYR C 154 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU C 296 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N PHE C 233 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU C 196 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 235 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU C 193 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASN C 208 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN C 195 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL C 206 " --> pdb=" O GLN C 195 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N SER C 197 " --> pdb=" O ARG C 204 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG C 204 " --> pdb=" O SER C 197 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 104 through 111 removed outlier: 5.516A pdb=" N TYR C 105 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N HIS C 139 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER C 107 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR C 145 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL C 159 " --> pdb=" O TYR C 154 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 545 through 546 removed outlier: 4.311A pdb=" N GLN C 545 " --> pdb=" O PHE C 525 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C 527 " --> pdb=" O GLN C 545 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N PHE C 365 " --> pdb=" O GLY C 411 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N TRP C 413 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU C 335 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU C 334 " --> pdb=" O TYR C 605 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 418 through 419 Processing sheet with id=AC5, first strand: chain 'C' and resid 639 through 644 removed outlier: 6.240A pdb=" N ALA C 653 " --> pdb=" O LEU C 643 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP C 654 " --> pdb=" O ALA C 667 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 664 " --> pdb=" O LEU C 758 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 752 " --> pdb=" O GLN C 670 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 680 through 682 removed outlier: 4.233A pdb=" N ILE C 680 " --> pdb=" O ILE C 739 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 3 through 4 removed outlier: 3.787A pdb=" N TYR D 35 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG D 24 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASN D 33 " --> pdb=" O ARG D 24 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 104 through 112 removed outlier: 5.658A pdb=" N TYR D 105 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N HIS D 139 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR D 145 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL D 159 " --> pdb=" O TYR D 154 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU D 296 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N PHE D 233 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU D 196 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU D 193 " --> pdb=" O ASN D 208 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASN D 208 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLN D 195 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL D 206 " --> pdb=" O GLN D 195 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N SER D 197 " --> pdb=" O ARG D 204 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG D 204 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 104 through 112 removed outlier: 5.658A pdb=" N TYR D 105 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N HIS D 139 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR D 145 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL D 159 " --> pdb=" O TYR D 154 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 573 through 574 removed outlier: 7.510A pdb=" N THR D 546 " --> pdb=" O GLY D 574 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N PHE D 525 " --> pdb=" O GLN D 545 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N TRP D 547 " --> pdb=" O PHE D 525 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N SER D 527 " --> pdb=" O TRP D 547 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE D 365 " --> pdb=" O GLY D 411 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N TRP D 413 " --> pdb=" O PHE D 365 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU D 335 " --> pdb=" O VAL D 366 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 418 through 420 Processing sheet with id=AD3, first strand: chain 'D' and resid 639 through 644 removed outlier: 6.310A pdb=" N ALA D 653 " --> pdb=" O LEU D 643 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 680 through 682 removed outlier: 4.234A pdb=" N ILE D 680 " --> pdb=" O ILE D 739 " (cutoff:3.500A) 976 hydrogen bonds defined for protein. 2706 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: 5.14 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.45: 11471 1.45 - 1.70: 13419 1.70 - 1.95: 232 1.95 - 2.20: 0 2.20 - 2.46: 4 Bond restraints: 25126 Sorted by residual: bond pdb=" C4 VQX B 801 " pdb=" N1 VQX B 801 " ideal model delta sigma weight residual 1.485 2.455 -0.970 2.00e-02 2.50e+03 2.35e+03 bond pdb=" C4 VQX D 801 " pdb=" N1 VQX D 801 " ideal model delta sigma weight residual 1.485 2.446 -0.961 2.00e-02 2.50e+03 2.31e+03 bond pdb=" C4 VQX A 801 " pdb=" N1 VQX A 801 " ideal model delta sigma weight residual 1.485 2.432 -0.947 2.00e-02 2.50e+03 2.24e+03 bond pdb=" C4 VQX C 801 " pdb=" N1 VQX C 801 " ideal model delta sigma weight residual 1.485 2.418 -0.933 2.00e-02 2.50e+03 2.18e+03 bond pdb=" C8 VQX B 801 " pdb=" N1 VQX B 801 " ideal model delta sigma weight residual 1.423 1.332 0.091 2.00e-02 2.50e+03 2.09e+01 ... (remaining 25121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.40: 33963 10.40 - 20.79: 2 20.79 - 31.19: 15 31.19 - 41.59: 0 41.59 - 51.98: 4 Bond angle restraints: 33984 Sorted by residual: angle pdb=" C4 VQX B 801 " pdb=" C5 VQX B 801 " pdb=" N1 VQX B 801 " ideal model delta sigma weight residual 58.81 110.79 -51.98 3.00e+00 1.11e-01 3.00e+02 angle pdb=" C4 VQX D 801 " pdb=" C5 VQX D 801 " pdb=" N1 VQX D 801 " ideal model delta sigma weight residual 58.81 110.07 -51.26 3.00e+00 1.11e-01 2.92e+02 angle pdb=" C4 VQX A 801 " pdb=" C5 VQX A 801 " pdb=" N1 VQX A 801 " ideal model delta sigma weight residual 58.81 109.28 -50.47 3.00e+00 1.11e-01 2.83e+02 angle pdb=" C4 VQX C 801 " pdb=" C5 VQX C 801 " pdb=" N1 VQX C 801 " ideal model delta sigma weight residual 58.81 108.39 -49.58 3.00e+00 1.11e-01 2.73e+02 angle pdb=" C4 VQX C 801 " pdb=" N1 VQX C 801 " pdb=" C8 VQX C 801 " ideal model delta sigma weight residual 129.46 160.22 -30.76 3.00e+00 1.11e-01 1.05e+02 ... (remaining 33979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.70: 14578 31.70 - 63.40: 446 63.40 - 95.10: 36 95.10 - 126.80: 2 126.80 - 158.50: 4 Dihedral angle restraints: 15066 sinusoidal: 6227 harmonic: 8839 Sorted by residual: dihedral pdb=" CA ILE A 117 " pdb=" C ILE A 117 " pdb=" N PRO A 118 " pdb=" CA PRO A 118 " ideal model delta harmonic sigma weight residual -180.00 -155.63 -24.37 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" C6 VQX B 801 " pdb=" C5 VQX B 801 " pdb=" N1 VQX B 801 " pdb=" C8 VQX B 801 " ideal model delta sinusoidal sigma weight residual 8.87 167.37 -158.50 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C3 VQX D 801 " pdb=" C4 VQX D 801 " pdb=" N1 VQX D 801 " pdb=" C8 VQX D 801 " ideal model delta sinusoidal sigma weight residual -12.08 136.27 -148.35 1 3.00e+01 1.11e-03 1.97e+01 ... (remaining 15063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3189 0.087 - 0.174: 383 0.174 - 0.261: 23 0.261 - 0.348: 5 0.348 - 0.436: 3 Chirality restraints: 3603 Sorted by residual: chirality pdb=" C4 VQX C 801 " pdb=" C3 VQX C 801 " pdb=" C5 VQX C 801 " pdb=" N1 VQX C 801 " both_signs ideal model delta sigma weight residual True 2.37 2.80 -0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" C4 VQX A 801 " pdb=" C3 VQX A 801 " pdb=" C5 VQX A 801 " pdb=" N1 VQX A 801 " both_signs ideal model delta sigma weight residual True 2.37 2.79 -0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" C4 VQX D 801 " pdb=" C3 VQX D 801 " pdb=" C5 VQX D 801 " pdb=" N1 VQX D 801 " both_signs ideal model delta sigma weight residual True 2.37 2.77 -0.40 2.00e-01 2.50e+01 3.97e+00 ... (remaining 3600 not shown) Planarity restraints: 4383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4 VQX A 801 " -0.482 2.00e-02 2.50e+03 3.17e-01 1.50e+03 pdb=" C5 VQX A 801 " 0.462 2.00e-02 2.50e+03 pdb=" C8 VQX A 801 " 0.005 2.00e-02 2.50e+03 pdb=" C9 VQX A 801 " -0.125 2.00e-02 2.50e+03 pdb=" N1 VQX A 801 " 0.326 2.00e-02 2.50e+03 pdb=" O5 VQX A 801 " -0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 VQX B 801 " 0.458 2.00e-02 2.50e+03 2.97e-01 1.32e+03 pdb=" C5 VQX B 801 " -0.437 2.00e-02 2.50e+03 pdb=" C8 VQX B 801 " -0.019 2.00e-02 2.50e+03 pdb=" C9 VQX B 801 " 0.242 2.00e-02 2.50e+03 pdb=" N1 VQX B 801 " 0.018 2.00e-02 2.50e+03 pdb=" O5 VQX B 801 " -0.262 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 VQX D 801 " -0.117 2.00e-02 2.50e+03 1.32e-01 2.62e+02 pdb=" C5 VQX D 801 " 0.258 2.00e-02 2.50e+03 pdb=" C8 VQX D 801 " -0.036 2.00e-02 2.50e+03 pdb=" C9 VQX D 801 " 0.079 2.00e-02 2.50e+03 pdb=" N1 VQX D 801 " -0.101 2.00e-02 2.50e+03 pdb=" O5 VQX D 801 " -0.083 2.00e-02 2.50e+03 ... (remaining 4380 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2887 2.75 - 3.29: 21493 3.29 - 3.83: 36775 3.83 - 4.36: 47252 4.36 - 4.90: 84848 Nonbonded interactions: 193255 Sorted by model distance: nonbonded pdb=" NH1 ARG B 375 " pdb=" O ASP B 377 " model vdw 2.216 3.120 nonbonded pdb=" ND2 ASN B 420 " pdb=" O HIS B 446 " model vdw 2.216 3.120 nonbonded pdb=" OD1 ASP C 494 " pdb=" N ALA C 495 " model vdw 2.235 3.120 nonbonded pdb=" OG SER B 530 " pdb=" NE2 GLN D 57 " model vdw 2.252 3.120 nonbonded pdb=" OG SER B 256 " pdb=" OH TYR B 510 " model vdw 2.256 3.040 ... (remaining 193250 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 2 through 713 or resid 722 through 801)) selection = (chain 'B' and (resid 2 through 393 or (resid 394 and (name N or name CA or name \ C or name O or name CB )) or resid 395 through 713 or resid 722 through 801)) selection = (chain 'C' and (resid 2 through 393 or (resid 394 and (name N or name CA or name \ C or name O or name CB )) or resid 395 through 713 or resid 722 through 801)) selection = (chain 'D' and (resid 2 through 393 or (resid 394 and (name N or name CA or name \ C or name O or name CB )) or resid 395 through 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.390 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 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 : 0.013 0.970 25130 Z= 0.704 Angle : 1.121 51.984 33984 Z= 0.583 Chirality : 0.055 0.436 3603 Planarity : 0.008 0.317 4383 Dihedral : 15.146 158.496 9426 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: -1.78 (0.15), residues: 2999 helix: -0.79 (0.21), residues: 595 sheet: 0.59 (0.20), residues: 768 loop : -2.33 (0.13), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 557 TYR 0.024 0.001 TYR A 725 PHE 0.013 0.001 PHE A 452 TRP 0.073 0.003 TRP B 654 HIS 0.009 0.001 HIS D 314 Details of bonding type rmsd/Z covalent geometry : bond 0.01323 / 0.70 (25126) covalent geometry : angle 1.12109 / 0.58 (33984) hydrogen bonds : bond 0.17730 / 11.79 ( 817) hydrogen bonds : angle 6.18909 / 4.23 ( 2706) Misc. bond : bond 0.07107 / 3.27 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: C 347 GLU cc_start: 0.6665 (pt0) cc_final: 0.6209 (tt0) REVERT: D 422 ASP cc_start: 0.7561 (t0) cc_final: 0.7205 (t0) REVERT: D 517 THR cc_start: 0.8756 (m) cc_final: 0.8544 (m) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.1654 time to fit residues: 89.2696 Evaluate side-chains 280 residues out of total 2620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 8.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 ASN B 57 GLN B 545 GLN C 346 ASN C 482 ASN D 258 ASN D 337 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.124092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.098447 restraints weight = 29805.144| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.75 r_work: 0.2844 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25130 Z= 0.181 Angle : 0.745 36.174 33984 Z= 0.365 Chirality : 0.046 0.157 3603 Planarity : 0.005 0.061 4383 Dihedral : 6.658 104.271 3503 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.07 % Allowed : 7.45 % Favored : 91.49 % 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: -1.50 (0.15), residues: 2999 helix: -0.41 (0.21), residues: 605 sheet: 0.73 (0.20), residues: 766 loop : -2.20 (0.13), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 380 TYR 0.018 0.002 TYR D 313 PHE 0.016 0.002 PHE A 452 TRP 0.039 0.002 TRP B 654 HIS 0.009 0.001 HIS D 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (25126) covalent geometry : angle 0.74461 / 0.37 (33984) hydrogen bonds : bond 0.06450 / 4.27 ( 817) hydrogen bonds : angle 4.95859 / 3.38 ( 2706) Misc. bond : bond 0.00634 / 0.27 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 283 time to evaluate : 0.949 Fit side-chains REVERT: A 335 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8614 (tp) REVERT: A 427 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7552 (mtm-85) REVERT: C 550 ASP cc_start: 0.8473 (t0) cc_final: 0.8200 (t0) REVERT: D 126 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7271 (tm-30) outliers start: 28 outliers final: 19 residues processed: 300 average time/residue: 0.1729 time to fit residues: 81.3886 Evaluate side-chains 288 residues out of total 2620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 268 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 694 GLU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 513 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 78 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 73 optimal weight: 0.6980 chunk 251 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 chunk 75 optimal weight: 20.0000 chunk 205 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 overall best weight: 7.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 ASN B 57 GLN B 420 ASN C 346 ASN C 482 ASN D 337 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.120593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.095073 restraints weight = 29930.983| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.76 r_work: 0.2759 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 25130 Z= 0.266 Angle : 0.814 34.111 33984 Z= 0.408 Chirality : 0.050 0.194 3603 Planarity : 0.005 0.046 4383 Dihedral : 7.130 110.117 3503 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.95 % Allowed : 10.96 % Favored : 87.09 % 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: -1.63 (0.15), residues: 2999 helix: -0.48 (0.21), residues: 591 sheet: 0.56 (0.20), residues: 797 loop : -2.29 (0.13), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 534 TYR 0.042 0.002 TYR D 484 PHE 0.017 0.002 PHE A 535 TRP 0.026 0.002 TRP A 654 HIS 0.012 0.002 HIS D 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.27 (25126) covalent geometry : angle 0.81395 / 0.41 (33984) hydrogen bonds : bond 0.07710 / 5.11 ( 817) hydrogen bonds : angle 5.03956 / 3.44 ( 2706) Misc. bond : bond 0.00569 / 0.26 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 273 time to evaluate : 1.187 Fit side-chains REVERT: A 171 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7307 (mp0) REVERT: A 335 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8722 (tp) REVERT: A 378 ASP cc_start: 0.8409 (p0) cc_final: 0.8007 (p0) REVERT: A 418 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8189 (mtt) REVERT: A 427 ARG cc_start: 0.8094 (mtm-85) cc_final: 0.7418 (mtm-85) REVERT: A 494 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7296 (t0) REVERT: C 550 ASP cc_start: 0.8649 (t0) cc_final: 0.8325 (t0) REVERT: D 132 GLU cc_start: 0.8215 (tp30) cc_final: 0.7940 (tp30) outliers start: 51 outliers final: 33 residues processed: 305 average time/residue: 0.1717 time to fit residues: 82.8466 Evaluate side-chains 298 residues out of total 2620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 262 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 694 GLU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 513 TYR Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 757 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 262 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 271 optimal weight: 8.9990 chunk 125 optimal weight: 7.9990 chunk 176 optimal weight: 8.9990 chunk 182 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 299 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 64 optimal weight: 0.0170 overall best weight: 5.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 ASN C 337 ASN C 443 HIS C 482 ASN D 337 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.121788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.095613 restraints weight = 29734.460| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.79 r_work: 0.2782 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25130 Z= 0.193 Angle : 0.739 34.558 33984 Z= 0.367 Chirality : 0.047 0.172 3603 Planarity : 0.004 0.046 4383 Dihedral : 6.962 109.282 3503 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.33 % Allowed : 12.98 % Favored : 84.69 % 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: -1.52 (0.15), residues: 2999 helix: -0.31 (0.21), residues: 585 sheet: 0.61 (0.20), residues: 796 loop : -2.24 (0.13), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 534 TYR 0.029 0.002 TYR D 484 PHE 0.015 0.002 PHE B 668 TRP 0.015 0.002 TRP B 654 HIS 0.007 0.001 HIS D 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 (25126) covalent geometry : angle 0.73903 / 0.37 (33984) hydrogen bonds : bond 0.06549 / 4.34 ( 817) hydrogen bonds : angle 4.88196 / 3.33 ( 2706) Misc. bond : bond 0.00411 / 0.18 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 272 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8736 (pp20) cc_final: 0.8407 (pt0) REVERT: A 77 TYR cc_start: 0.8935 (OUTLIER) cc_final: 0.7241 (m-80) REVERT: A 171 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7348 (mp0) REVERT: A 335 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8640 (tp) REVERT: A 378 ASP cc_start: 0.8462 (p0) cc_final: 0.8166 (p0) REVERT: A 418 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8052 (mtt) REVERT: A 427 ARG cc_start: 0.8050 (mtm-85) cc_final: 0.7460 (mtm-85) REVERT: A 494 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7387 (t0) REVERT: A 616 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7357 (mt-10) REVERT: A 734 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.7838 (mt0) REVERT: C 418 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.7773 (mtt) REVERT: C 550 ASP cc_start: 0.8592 (t0) cc_final: 0.8238 (t0) REVERT: D 422 ASP cc_start: 0.7805 (t0) cc_final: 0.7389 (t0) REVERT: D 734 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8755 (mt0) outliers start: 61 outliers final: 38 residues processed: 313 average time/residue: 0.1723 time to fit residues: 85.2510 Evaluate side-chains 306 residues out of total 2620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 261 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 694 GLU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 513 TYR Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain D residue 734 GLN Chi-restraints excluded: chain D residue 750 ASP Chi-restraints excluded: chain D residue 757 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 12 optimal weight: 6.9990 chunk 290 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 273 optimal weight: 10.0000 chunk 113 optimal weight: 0.5980 chunk 180 optimal weight: 7.9990 chunk 81 optimal weight: 0.0970 chunk 299 optimal weight: 5.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 57 GLN C 482 ASN C 497 GLN D 337 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.123834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.098070 restraints weight = 29522.964| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.72 r_work: 0.2880 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25130 Z= 0.138 Angle : 0.678 35.091 33984 Z= 0.333 Chirality : 0.044 0.158 3603 Planarity : 0.004 0.045 4383 Dihedral : 6.664 110.826 3503 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.21 % Allowed : 14.66 % Favored : 83.12 % 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: -1.37 (0.15), residues: 2999 helix: -0.11 (0.22), residues: 590 sheet: 0.66 (0.20), residues: 798 loop : -2.16 (0.13), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 483 TYR 0.019 0.001 TYR D 484 PHE 0.013 0.001 PHE B 668 TRP 0.012 0.001 TRP B 654 HIS 0.004 0.001 HIS D 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (25126) covalent geometry : angle 0.67829 / 0.33 (33984) hydrogen bonds : bond 0.05476 / 3.62 ( 817) hydrogen bonds : angle 4.69470 / 3.20 ( 2706) Misc. bond : bond 0.00315 / 0.14 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 277 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8352 (pt0) REVERT: A 171 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7321 (mp0) REVERT: A 335 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8658 (tp) REVERT: A 427 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.7510 (mtm-85) REVERT: A 429 HIS cc_start: 0.7852 (OUTLIER) cc_final: 0.7593 (p-80) REVERT: A 494 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7469 (t0) REVERT: A 616 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7347 (mt-10) REVERT: A 723 LYS cc_start: 0.4549 (OUTLIER) cc_final: 0.3074 (tptt) REVERT: A 734 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.7701 (mt0) REVERT: C 27 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6814 (pt0) REVERT: C 550 ASP cc_start: 0.8496 (t0) cc_final: 0.8186 (t0) REVERT: D 422 ASP cc_start: 0.7831 (t0) cc_final: 0.7451 (t0) REVERT: D 734 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8726 (mt0) outliers start: 58 outliers final: 32 residues processed: 314 average time/residue: 0.1659 time to fit residues: 82.2529 Evaluate side-chains 307 residues out of total 2620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 266 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 513 TYR Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain D residue 734 GLN Chi-restraints excluded: chain D residue 750 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 10 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 246 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 154 optimal weight: 0.0050 chunk 1 optimal weight: 10.0000 chunk 157 optimal weight: 0.6980 chunk 185 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 overall best weight: 3.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 57 GLN C 337 ASN D 337 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.123621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.097943 restraints weight = 29564.910| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.72 r_work: 0.2842 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25130 Z= 0.151 Angle : 0.684 35.338 33984 Z= 0.335 Chirality : 0.044 0.158 3603 Planarity : 0.004 0.045 4383 Dihedral : 6.517 110.870 3503 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.63 % Allowed : 14.93 % Favored : 82.44 % 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: -1.32 (0.15), residues: 2999 helix: -0.04 (0.22), residues: 588 sheet: 0.68 (0.20), residues: 799 loop : -2.12 (0.13), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 483 TYR 0.020 0.001 TYR D 484 PHE 0.013 0.001 PHE B 668 TRP 0.011 0.001 TRP B 479 HIS 0.005 0.001 HIS D 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (25126) covalent geometry : angle 0.68395 / 0.34 (33984) hydrogen bonds : bond 0.05612 / 3.71 ( 817) hydrogen bonds : angle 4.65357 / 3.17 ( 2706) Misc. bond : bond 0.00323 / 0.14 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 267 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8359 (pt0) REVERT: A 77 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.7255 (m-80) REVERT: A 171 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7277 (mp0) REVERT: A 335 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8645 (tp) REVERT: A 427 ARG cc_start: 0.8056 (mtm-85) cc_final: 0.7465 (mtm-85) REVERT: A 429 HIS cc_start: 0.7856 (OUTLIER) cc_final: 0.7478 (p-80) REVERT: A 494 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7514 (t0) REVERT: A 723 LYS cc_start: 0.4652 (OUTLIER) cc_final: 0.3141 (tptt) REVERT: A 734 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.7725 (mt0) REVERT: B 355 GLU cc_start: 0.8145 (tp30) cc_final: 0.7742 (tt0) REVERT: B 672 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7943 (mmm) REVERT: C 27 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6728 (pt0) REVERT: C 418 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7702 (mtt) REVERT: C 526 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7160 (tp30) REVERT: C 550 ASP cc_start: 0.8516 (t0) cc_final: 0.8216 (t0) REVERT: D 422 ASP cc_start: 0.7847 (t0) cc_final: 0.7476 (t0) REVERT: D 734 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8741 (mt0) outliers start: 69 outliers final: 42 residues processed: 315 average time/residue: 0.1753 time to fit residues: 87.0196 Evaluate side-chains 316 residues out of total 2620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 262 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 694 GLU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 513 TYR Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 734 GLN Chi-restraints excluded: chain D residue 750 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 180 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 268 optimal weight: 0.3980 chunk 291 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 162 optimal weight: 0.0670 chunk 132 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 overall best weight: 2.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 57 GLN D 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.124681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.099342 restraints weight = 29505.813| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.71 r_work: 0.2869 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25130 Z= 0.126 Angle : 0.642 34.152 33984 Z= 0.317 Chirality : 0.043 0.220 3603 Planarity : 0.004 0.045 4383 Dihedral : 6.199 111.480 3503 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.33 % Allowed : 15.54 % Favored : 82.13 % 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: -1.23 (0.15), residues: 2999 helix: 0.06 (0.22), residues: 590 sheet: 0.73 (0.20), residues: 799 loop : -2.08 (0.13), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 483 TYR 0.014 0.001 TYR D 484 PHE 0.012 0.001 PHE A 345 TRP 0.010 0.001 TRP B 413 HIS 0.003 0.001 HIS D 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (25126) covalent geometry : angle 0.64239 / 0.32 (33984) hydrogen bonds : bond 0.05094 / 3.37 ( 817) hydrogen bonds : angle 4.56033 / 3.11 ( 2706) Misc. bond : bond 0.00367 / 0.17 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 269 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8339 (pt0) REVERT: A 77 TYR cc_start: 0.8910 (OUTLIER) cc_final: 0.7189 (m-80) REVERT: A 171 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7249 (mp0) REVERT: A 335 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8629 (tp) REVERT: A 427 ARG cc_start: 0.8066 (mtm-85) cc_final: 0.7545 (mtm-85) REVERT: A 429 HIS cc_start: 0.7838 (OUTLIER) cc_final: 0.7397 (p-80) REVERT: A 723 LYS cc_start: 0.4542 (OUTLIER) cc_final: 0.3019 (tptt) REVERT: A 734 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.7738 (mt0) REVERT: B 355 GLU cc_start: 0.8162 (tp30) cc_final: 0.7732 (tt0) REVERT: B 464 MET cc_start: 0.7308 (tpp) cc_final: 0.7082 (ttm) REVERT: B 672 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7968 (mmm) REVERT: C 27 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6736 (pt0) REVERT: C 418 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7681 (mtt) REVERT: C 526 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7141 (tp30) REVERT: C 550 ASP cc_start: 0.8488 (t0) cc_final: 0.8230 (t0) REVERT: D 126 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7271 (tm-30) REVERT: D 422 ASP cc_start: 0.7837 (t0) cc_final: 0.7486 (t0) REVERT: D 734 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8724 (mt0) outliers start: 61 outliers final: 38 residues processed: 312 average time/residue: 0.1712 time to fit residues: 84.2385 Evaluate side-chains 309 residues out of total 2620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 260 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 694 GLU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 513 TYR Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 734 GLN Chi-restraints excluded: chain D residue 757 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 260 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 240 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 257 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 ASN D 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.122205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.096442 restraints weight = 29624.031| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.72 r_work: 0.2816 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25130 Z= 0.195 Angle : 0.704 34.067 33984 Z= 0.353 Chirality : 0.046 0.160 3603 Planarity : 0.004 0.045 4383 Dihedral : 6.323 110.714 3503 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.67 % Allowed : 15.58 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.31 (0.15), residues: 2999 helix: -0.02 (0.22), residues: 584 sheet: 0.69 (0.20), residues: 799 loop : -2.12 (0.13), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 454 TYR 0.023 0.002 TYR D 484 PHE 0.014 0.002 PHE B 668 TRP 0.014 0.002 TRP B 479 HIS 0.005 0.001 HIS D 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 (25126) covalent geometry : angle 0.70402 / 0.35 (33984) hydrogen bonds : bond 0.06286 / 4.16 ( 817) hydrogen bonds : angle 4.71146 / 3.22 ( 2706) Misc. bond : bond 0.00408 / 0.19 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 260 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8377 (pt0) REVERT: A 77 TYR cc_start: 0.8940 (OUTLIER) cc_final: 0.7341 (m-80) REVERT: A 171 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7378 (mp0) REVERT: A 335 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8650 (tp) REVERT: A 427 ARG cc_start: 0.8053 (mtm-85) cc_final: 0.7467 (mtm-85) REVERT: A 429 HIS cc_start: 0.7886 (OUTLIER) cc_final: 0.7458 (p-80) REVERT: A 723 LYS cc_start: 0.4670 (OUTLIER) cc_final: 0.3248 (tptt) REVERT: A 734 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.7798 (mt0) REVERT: B 355 GLU cc_start: 0.8164 (tp30) cc_final: 0.7877 (tp30) REVERT: B 429 HIS cc_start: 0.7483 (OUTLIER) cc_final: 0.7043 (p-80) REVERT: B 464 MET cc_start: 0.7416 (tpp) cc_final: 0.7110 (ttm) REVERT: B 672 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.8000 (mmm) REVERT: C 27 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6694 (pt0) REVERT: C 77 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7789 (t80) REVERT: C 418 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.7775 (mtt) REVERT: C 526 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7212 (tp30) REVERT: C 550 ASP cc_start: 0.8543 (t0) cc_final: 0.8263 (t0) REVERT: D 422 ASP cc_start: 0.7901 (t0) cc_final: 0.7520 (t0) REVERT: D 734 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8744 (mt0) outliers start: 70 outliers final: 49 residues processed: 312 average time/residue: 0.1746 time to fit residues: 85.9950 Evaluate side-chains 320 residues out of total 2620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 258 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 77 TYR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 429 HIS Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 694 GLU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 513 TYR Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 734 GLN Chi-restraints excluded: chain D residue 750 ASP Chi-restraints excluded: chain D residue 757 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 105 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 262 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 251 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 273 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 57 GLN ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.120522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.094421 restraints weight = 29808.760| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.75 r_work: 0.2804 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 25130 Z= 0.259 Angle : 0.775 33.902 33984 Z= 0.393 Chirality : 0.049 0.201 3603 Planarity : 0.005 0.045 4383 Dihedral : 6.572 110.847 3503 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.52 % Allowed : 16.04 % Favored : 81.44 % 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: -1.50 (0.15), residues: 2999 helix: -0.24 (0.21), residues: 584 sheet: 0.59 (0.20), residues: 799 loop : -2.22 (0.13), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 454 TYR 0.028 0.002 TYR D 484 PHE 0.016 0.002 PHE B 668 TRP 0.018 0.002 TRP B 479 HIS 0.007 0.001 HIS D 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.26 (25126) covalent geometry : angle 0.77517 / 0.39 (33984) hydrogen bonds : bond 0.07290 / 4.83 ( 817) hydrogen bonds : angle 4.89949 / 3.34 ( 2706) Misc. bond : bond 0.00486 / 0.22 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 263 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8363 (pt0) REVERT: A 77 TYR cc_start: 0.8997 (OUTLIER) cc_final: 0.7379 (m-80) REVERT: A 171 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7381 (mp0) REVERT: A 335 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8676 (tp) REVERT: A 427 ARG cc_start: 0.8083 (mtm-85) cc_final: 0.7419 (mtm-85) REVERT: A 429 HIS cc_start: 0.7873 (OUTLIER) cc_final: 0.7570 (p-80) REVERT: A 723 LYS cc_start: 0.4734 (OUTLIER) cc_final: 0.3363 (tptt) REVERT: A 734 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.7826 (mt0) REVERT: B 429 HIS cc_start: 0.7628 (OUTLIER) cc_final: 0.7150 (p-80) REVERT: B 672 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7945 (mmt) REVERT: C 27 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6831 (pt0) REVERT: C 77 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7880 (t80) REVERT: C 418 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.7877 (mtt) REVERT: C 526 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7314 (tp30) REVERT: D 132 GLU cc_start: 0.8181 (tp30) cc_final: 0.7928 (tp30) REVERT: D 422 ASP cc_start: 0.7973 (t0) cc_final: 0.7533 (t0) REVERT: D 588 MET cc_start: 0.7928 (tpp) cc_final: 0.7720 (tpp) REVERT: D 734 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8708 (mt0) outliers start: 66 outliers final: 49 residues processed: 312 average time/residue: 0.1748 time to fit residues: 85.4353 Evaluate side-chains 320 residues out of total 2620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 258 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 77 TYR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 429 HIS Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 694 GLU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 77 TYR Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 513 TYR Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 734 GLN Chi-restraints excluded: chain D residue 750 ASP Chi-restraints excluded: chain D residue 757 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 20 optimal weight: 8.9990 chunk 180 optimal weight: 6.9990 chunk 252 optimal weight: 2.9990 chunk 234 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 222 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 GLN D 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.121879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.095962 restraints weight = 29614.693| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.77 r_work: 0.2796 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25130 Z= 0.180 Angle : 0.704 33.883 33984 Z= 0.354 Chirality : 0.046 0.163 3603 Planarity : 0.004 0.045 4383 Dihedral : 6.452 111.885 3503 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.44 % Allowed : 16.34 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.43 (0.15), residues: 2999 helix: -0.13 (0.22), residues: 584 sheet: 0.61 (0.20), residues: 799 loop : -2.20 (0.13), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 445 TYR 0.020 0.002 TYR D 484 PHE 0.014 0.002 PHE B 668 TRP 0.013 0.002 TRP B 479 HIS 0.005 0.001 HIS D 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (25126) covalent geometry : angle 0.70366 / 0.35 (33984) hydrogen bonds : bond 0.06220 / 4.12 ( 817) hydrogen bonds : angle 4.77563 / 3.26 ( 2706) Misc. bond : bond 0.00386 / 0.17 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 260 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8364 (pt0) REVERT: A 77 TYR cc_start: 0.8928 (OUTLIER) cc_final: 0.7354 (m-80) REVERT: A 171 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7407 (mp0) REVERT: A 335 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8654 (tp) REVERT: A 427 ARG cc_start: 0.8054 (mtm-85) cc_final: 0.7415 (mtm-85) REVERT: A 429 HIS cc_start: 0.7813 (OUTLIER) cc_final: 0.7528 (p-80) REVERT: A 723 LYS cc_start: 0.4734 (OUTLIER) cc_final: 0.3375 (tptt) REVERT: A 734 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.7809 (mt0) REVERT: B 429 HIS cc_start: 0.7513 (OUTLIER) cc_final: 0.7065 (p-80) REVERT: B 672 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.8021 (mmm) REVERT: C 27 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6747 (pt0) REVERT: C 77 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.7835 (t80) REVERT: C 418 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.7802 (mtt) REVERT: C 526 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7273 (tp30) REVERT: D 422 ASP cc_start: 0.7945 (t0) cc_final: 0.7520 (t0) REVERT: D 734 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8731 (mt0) outliers start: 64 outliers final: 48 residues processed: 308 average time/residue: 0.1675 time to fit residues: 81.7080 Evaluate side-chains 320 residues out of total 2620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 259 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 77 TYR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 429 HIS Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 694 GLU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 513 TYR Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 734 GLN Chi-restraints excluded: chain D residue 750 ASP Chi-restraints excluded: chain D residue 757 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 42 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 286 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 243 optimal weight: 8.9990 chunk 58 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 chunk 277 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 204 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 GLN D 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.120478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.094843 restraints weight = 29800.176| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.78 r_work: 0.2777 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 25130 Z= 0.241 Angle : 0.760 33.792 33984 Z= 0.385 Chirality : 0.049 0.194 3603 Planarity : 0.005 0.045 4383 Dihedral : 6.629 111.915 3503 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.71 % Allowed : 16.00 % Favored : 81.29 % 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: -1.54 (0.15), residues: 2999 helix: -0.26 (0.21), residues: 584 sheet: 0.55 (0.20), residues: 798 loop : -2.25 (0.13), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 445 TYR 0.025 0.002 TYR D 484 PHE 0.016 0.002 PHE B 668 TRP 0.017 0.002 TRP B 479 HIS 0.006 0.001 HIS D 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.24 (25126) covalent geometry : angle 0.75999 / 0.38 (33984) hydrogen bonds : bond 0.07093 / 4.70 ( 817) hydrogen bonds : angle 4.89867 / 3.35 ( 2706) Misc. bond : bond 0.00452 / 0.21 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5777.99 seconds wall clock time: 99 minutes 45.86 seconds (5985.86 seconds total)