Starting phenix.real_space_refine on Sat Sep 12 06:42:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bwr_30234/09_2026/7bwr_30234.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bwr_30234/09_2026/7bwr_30234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bwr_30234/09_2026/7bwr_30234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bwr_30234/09_2026/7bwr_30234.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7bwr_30234/09_2026/7bwr_30234.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bwr_30234/09_2026/7bwr_30234.cif" model { file = "/net/cci-nas-00/data/ceres_data/7bwr_30234/09_2026/7bwr_30234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bwr_30234/09_2026/7bwr_30234.cif" } resolution = 3.5 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= 0.006 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 1 5.49 5 S 54 5.16 5 C 9253 2.51 5 N 2539 2.21 5 O 2602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14450 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 7948 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 77, 'TRANS': 980} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 7, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "B" Number of atoms: 5400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 850, 5400 Classifications: {'peptide': 850} Incomplete info: {'truncation_to_alanine': 306} Link IDs: {'PTRANS': 63, 'TRANS': 786} Chain breaks: 13 Unresolved chain link angles: 31 Unresolved non-hydrogen bonds: 1142 Unresolved non-hydrogen angles: 1486 Unresolved non-hydrogen dihedrals: 956 Unresolved non-hydrogen chiralities: 101 Planarities with less than four sites: {'TRP:plan': 7, 'GLN:plan1': 15, 'ARG:plan': 26, 'GLU:plan': 22, 'ASP:plan': 29, 'PHE:plan': 18, 'HIS:plan': 3, 'TYR:plan': 12, 'ASN:plan1': 7} Unresolved non-hydrogen planarities: 656 Chain: "C" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 520 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 3, 'TRANS': 74} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 51 Chain: "D" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 517 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 3, 'TRANS': 74} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {' CA': 1, 'F8L': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.08, per 1000 atoms: 0.21 Number of scatterers: 14450 At special positions: 0 Unit cell: (133.66, 121.36, 136.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 54 16.00 P 1 15.00 O 2602 8.00 N 2539 7.00 C 9253 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 806.7 milliseconds 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3796 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 18 sheets defined 38.7% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 removed outlier: 3.538A pdb=" N THR A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 44 Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.645A pdb=" N ALA A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 142 removed outlier: 3.677A pdb=" N VAL A 140 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 244 Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 274 through 280 Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.769A pdb=" N THR A 295 " --> pdb=" O GLN A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 319 through 325 removed outlier: 3.618A pdb=" N LEU A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 345 removed outlier: 4.703A pdb=" N ILE A 342 " --> pdb=" O PRO A 339 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N CYS A 343 " --> pdb=" O ASP A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 356 through 359 Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.681A pdb=" N ALA A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 382 Processing helix chain 'A' and resid 391 through 412 removed outlier: 3.951A pdb=" N ALA A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 427 Processing helix chain 'A' and resid 434 through 444 removed outlier: 4.261A pdb=" N VAL A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 455 Processing helix chain 'A' and resid 461 through 471 removed outlier: 3.642A pdb=" N ALA A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'A' and resid 484 through 499 removed outlier: 3.837A pdb=" N ILE A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG A 495 " --> pdb=" O ALA A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.604A pdb=" N ASN A 508 " --> pdb=" O TRP A 505 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU A 509 " --> pdb=" O THR A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 509' Processing helix chain 'A' and resid 521 through 528 removed outlier: 3.893A pdb=" N ARG A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 546 removed outlier: 3.708A pdb=" N ARG A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 571 removed outlier: 3.696A pdb=" N LEU A 560 " --> pdb=" O PRO A 556 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE A 569 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 586 removed outlier: 3.808A pdb=" N ALA A 586 " --> pdb=" O GLY A 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 583 through 586' Processing helix chain 'A' and resid 587 through 600 removed outlier: 3.644A pdb=" N ALA A 591 " --> pdb=" O ALA A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 626 removed outlier: 3.720A pdb=" N PHE A 614 " --> pdb=" O ASN A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 676 removed outlier: 3.916A pdb=" N LEU A 674 " --> pdb=" O PHE A 670 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 675 " --> pdb=" O TRP A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 687 Processing helix chain 'A' and resid 689 through 713 removed outlier: 3.996A pdb=" N VAL A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 726 removed outlier: 3.681A pdb=" N ASN A 723 " --> pdb=" O ASN A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 735 No H-bonds generated for 'chain 'A' and resid 733 through 735' Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 958 through 962 Processing helix chain 'A' and resid 1001 through 1009 removed outlier: 3.526A pdb=" N THR A1009 " --> pdb=" O LYS A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1024 Processing helix chain 'B' and resid 27 through 43 removed outlier: 3.923A pdb=" N THR B 31 " --> pdb=" O ARG B 27 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU B 36 " --> pdb=" O ILE B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 112 removed outlier: 3.699A pdb=" N LEU B 111 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 244 removed outlier: 3.896A pdb=" N ALA B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE B 230 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 340 through 355 removed outlier: 3.695A pdb=" N ARG B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 381 Processing helix chain 'B' and resid 391 through 411 Processing helix chain 'B' and resid 414 through 429 Processing helix chain 'B' and resid 435 through 444 Processing helix chain 'B' and resid 444 through 455 Processing helix chain 'B' and resid 460 through 473 removed outlier: 4.239A pdb=" N ALA B 466 " --> pdb=" O TRP B 462 " (cutoff:3.500A) Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 473 through 481 Processing helix chain 'B' and resid 484 through 489 removed outlier: 3.571A pdb=" N LEU B 489 " --> pdb=" O ILE B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 547 Proline residue: B 538 - end of helix removed outlier: 3.656A pdb=" N PHE B 541 " --> pdb=" O PHE B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 567 Processing helix chain 'B' and resid 587 through 600 Processing helix chain 'B' and resid 608 through 626 removed outlier: 4.310A pdb=" N MET B 612 " --> pdb=" O ALA B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 676 removed outlier: 3.734A pdb=" N ILE B 664 " --> pdb=" O ALA B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 687 Processing helix chain 'B' and resid 692 through 703 removed outlier: 3.501A pdb=" N PHE B 697 " --> pdb=" O VAL B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 797 Processing helix chain 'B' and resid 919 through 923 removed outlier: 3.835A pdb=" N GLU B 922 " --> pdb=" O PRO B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 962 Processing helix chain 'B' and resid 1020 through 1027 removed outlier: 4.043A pdb=" N LEU B1027 " --> pdb=" O ILE B1023 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 20 Processing helix chain 'C' and resid 42 through 55 removed outlier: 3.936A pdb=" N GLU C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 67 removed outlier: 4.180A pdb=" N ALA C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 78 removed outlier: 3.934A pdb=" N VAL C 74 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE C 77 " --> pdb=" O VAL C 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 20 Processing helix chain 'D' and resid 42 through 55 removed outlier: 3.936A pdb=" N GLU D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 67 removed outlier: 3.925A pdb=" N ALA D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 78 removed outlier: 3.934A pdb=" N VAL D 74 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE D 77 " --> pdb=" O VAL D 73 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 147 through 150 removed outlier: 3.869A pdb=" N GLU A 78 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ALA A 54 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 49 " --> pdb=" O HIS A1069 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N HIS A1069 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLN A 51 " --> pdb=" O GLN A1067 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 192 removed outlier: 3.839A pdb=" N VAL A 67 " --> pdb=" O VAL A 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 117 removed outlier: 3.763A pdb=" N VAL A 125 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ALA A 133 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL A 127 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 956 through 957 Processing sheet with id=AA5, first strand: chain 'A' and resid 749 through 750 removed outlier: 4.500A pdb=" N THR A 749 " --> pdb=" O GLU A 845 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER A 837 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 749 through 750 removed outlier: 4.500A pdb=" N THR A 749 " --> pdb=" O GLU A 845 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 882 " --> pdb=" O GLU A 935 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU A 885 " --> pdb=" O ARG A 901 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG A 901 " --> pdb=" O LEU A 885 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYR A 887 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR A 889 " --> pdb=" O VAL A 897 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 897 " --> pdb=" O THR A 889 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.745A pdb=" N ALA A 826 " --> pdb=" O VAL A 947 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 862 " --> pdb=" O LEU A 916 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 986 through 987 removed outlier: 3.627A pdb=" N VAL A 990 " --> pdb=" O ALA A 987 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1028 through 1033 removed outlier: 4.558A pdb=" N LEU A1048 " --> pdb=" O MET A1033 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AB2, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AB3, first strand: chain 'B' and resid 99 through 100 removed outlier: 4.247A pdb=" N PHE B 99 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 116 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL B 125 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ALA B 133 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 738 through 739 Processing sheet with id=AB5, first strand: chain 'B' and resid 826 through 827 removed outlier: 3.784A pdb=" N ALA B 865 " --> pdb=" O ALA B 946 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 837 through 840 removed outlier: 3.932A pdb=" N SER B 837 " --> pdb=" O ASP B 936 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 839 " --> pdb=" O ALA B 934 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 934 " --> pdb=" O LEU B 839 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 967 through 968 Processing sheet with id=AB8, first strand: chain 'B' and resid 986 through 987 removed outlier: 3.710A pdb=" N VAL B 990 " --> pdb=" O ALA B 987 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1028 through 1029 554 hydrogen bonds defined for protein. 1575 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2350 1.30 - 1.43: 3604 1.43 - 1.56: 8652 1.56 - 1.69: 27 1.69 - 1.81: 95 Bond restraints: 14728 Sorted by residual: bond pdb=" C55 F8L A2002 " pdb=" C57 F8L A2002 " ideal model delta sigma weight residual 1.545 1.329 0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C55 F8L A2002 " pdb=" O56 F8L A2002 " ideal model delta sigma weight residual 1.401 1.599 -0.198 2.00e-02 2.50e+03 9.85e+01 bond pdb=" C59 F8L A2002 " pdb=" C61 F8L A2002 " ideal model delta sigma weight residual 1.528 1.369 0.159 2.00e-02 2.50e+03 6.29e+01 bond pdb=" C61 F8L A2002 " pdb=" O56 F8L A2002 " ideal model delta sigma weight residual 1.421 1.540 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" C ILE A 523 " pdb=" O ILE A 523 " ideal model delta sigma weight residual 1.237 1.175 0.063 1.23e-02 6.61e+03 2.59e+01 ... (remaining 14723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.37: 20152 7.37 - 14.75: 57 14.75 - 22.12: 9 22.12 - 29.49: 0 29.49 - 36.86: 1 Bond angle restraints: 20219 Sorted by residual: angle pdb=" N PHE B 569 " pdb=" CA PHE B 569 " pdb=" C PHE B 569 " ideal model delta sigma weight residual 112.13 148.99 -36.86 1.37e+00 5.33e-01 7.24e+02 angle pdb=" N PRO A 575 " pdb=" CA PRO A 575 " pdb=" C PRO A 575 " ideal model delta sigma weight residual 113.84 131.69 -17.85 1.30e+00 5.92e-01 1.88e+02 angle pdb=" N PHE A 529 " pdb=" CA PHE A 529 " pdb=" C PHE A 529 " ideal model delta sigma weight residual 113.12 96.99 16.13 1.25e+00 6.40e-01 1.66e+02 angle pdb=" N PHE B 570 " pdb=" CA PHE B 570 " pdb=" CB PHE B 570 " ideal model delta sigma weight residual 110.01 92.09 17.92 1.45e+00 4.76e-01 1.53e+02 angle pdb=" C VAL A 527 " pdb=" CA VAL A 527 " pdb=" CB VAL A 527 " ideal model delta sigma weight residual 111.55 125.42 -13.87 1.15e+00 7.56e-01 1.45e+02 ... (remaining 20214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.82: 8464 32.82 - 65.65: 189 65.65 - 98.47: 20 98.47 - 131.29: 3 131.29 - 164.11: 2 Dihedral angle restraints: 8678 sinusoidal: 2802 harmonic: 5876 Sorted by residual: dihedral pdb=" N PHE B 570 " pdb=" C PHE B 570 " pdb=" CA PHE B 570 " pdb=" CB PHE B 570 " ideal model delta harmonic sigma weight residual 122.80 99.76 23.04 0 2.50e+00 1.60e-01 8.49e+01 dihedral pdb=" C VAL A 527 " pdb=" N VAL A 527 " pdb=" CA VAL A 527 " pdb=" CB VAL A 527 " ideal model delta harmonic sigma weight residual -122.00 -141.26 19.26 0 2.50e+00 1.60e-01 5.94e+01 dihedral pdb=" CA GLN B 60 " pdb=" C GLN B 60 " pdb=" N GLN B 61 " pdb=" CA GLN B 61 " ideal model delta harmonic sigma weight residual 180.00 150.66 29.34 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 8675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.254: 2482 0.254 - 0.508: 10 0.508 - 0.762: 4 0.762 - 1.017: 0 1.017 - 1.271: 1 Chirality restraints: 2497 Sorted by residual: chirality pdb=" CA PHE B 569 " pdb=" N PHE B 569 " pdb=" C PHE B 569 " pdb=" CB PHE B 569 " both_signs ideal model delta sigma weight residual False 2.51 1.24 1.27 2.00e-01 2.50e+01 4.04e+01 chirality pdb=" CA PRO A 575 " pdb=" N PRO A 575 " pdb=" C PRO A 575 " pdb=" CB PRO A 575 " both_signs ideal model delta sigma weight residual False 2.72 2.15 0.57 2.00e-01 2.50e+01 7.99e+00 chirality pdb=" CB ILE B 44 " pdb=" CA ILE B 44 " pdb=" CG1 ILE B 44 " pdb=" CG2 ILE B 44 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.56 2.00e-01 2.50e+01 7.79e+00 ... (remaining 2494 not shown) Planarity restraints: 2595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 695 " 0.021 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C ALA B 695 " -0.075 2.00e-02 2.50e+03 pdb=" O ALA B 695 " 0.028 2.00e-02 2.50e+03 pdb=" N GLY B 696 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 476 " -0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C LEU A 476 " 0.065 2.00e-02 2.50e+03 pdb=" O LEU A 476 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA A 477 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 28 " -0.060 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO D 29 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO D 29 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO D 29 " -0.050 5.00e-02 4.00e+02 ... (remaining 2592 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 5 2.13 - 2.82: 4583 2.82 - 3.52: 19192 3.52 - 4.21: 31425 4.21 - 4.90: 53422 Nonbonded interactions: 108627 Sorted by model distance: nonbonded pdb=" OG SER A 524 " pdb=" O HIS A 580 " model vdw 1.442 3.040 nonbonded pdb=" OD2 ASP A 936 " pdb="CA CA A2001 " model vdw 1.632 2.510 nonbonded pdb=" OG1 THR A 518 " pdb=" O60 F8L A2002 " model vdw 1.679 3.040 nonbonded pdb=" O PHE B 570 " pdb=" OG1 THR B 574 " model vdw 1.984 3.040 nonbonded pdb=" CB SER A 524 " pdb=" O HIS A 580 " model vdw 2.108 3.440 ... (remaining 108622 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 'C' and (resid 3 through 60 or (resid 61 through 63 and (name N or name C \ A or name C or name O or name CB )) or resid 64 through 80)) selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.220 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.008 0.216 14728 Z= 0.396 Angle : 1.343 36.863 20219 Z= 0.763 Chirality : 0.075 1.271 2497 Planarity : 0.010 0.091 2595 Dihedral : 15.425 164.114 4882 Min Nonbonded Distance : 1.442 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 14.17 % Favored : 85.64 % Rotamer: Outliers : 1.55 % Allowed : 15.93 % Favored : 82.52 % Cbeta Deviations : 0.21 % 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: -5.25 (0.14), residues: 2026 helix: -3.43 (0.13), residues: 713 sheet: -2.12 (0.42), residues: 133 loop : -3.88 (0.14), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 27 TYR 0.042 0.003 TYR B 180 PHE 0.038 0.003 PHE B 214 TRP 0.017 0.002 TRP B1041 HIS 0.012 0.002 HIS A 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00826 / 0.40 (14728) covalent geometry : angle 1.34326 / 0.76 (20219) hydrogen bonds : bond 0.17748 / 11.73 ( 551) hydrogen bonds : angle 8.40516 / 5.82 ( 1575) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 311 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.6690 (mpp) cc_final: 0.6091 (mmm) REVERT: A 490 GLU cc_start: 0.8077 (tt0) cc_final: 0.7793 (tt0) REVERT: A 526 ARG cc_start: 0.7047 (mmt-90) cc_final: 0.6833 (mtp180) REVERT: A 534 MET cc_start: 0.8708 (ppp) cc_final: 0.7925 (ptt) REVERT: A 592 MET cc_start: 0.8506 (tpt) cc_final: 0.8121 (tpp) REVERT: A 736 ASP cc_start: 0.8852 (p0) cc_final: 0.8202 (p0) REVERT: A 1041 TRP cc_start: 0.7944 (m-90) cc_final: 0.7417 (m-90) REVERT: B 90 ASP cc_start: 0.8139 (p0) cc_final: 0.7786 (p0) REVERT: B 146 GLN cc_start: 0.8505 (pt0) cc_final: 0.8211 (mt0) REVERT: B 349 LEU cc_start: 0.9002 (tp) cc_final: 0.8665 (tp) REVERT: B 370 MET cc_start: 0.8553 (tmm) cc_final: 0.7900 (tpp) REVERT: B 459 VAL cc_start: 0.8269 (m) cc_final: 0.8051 (m) REVERT: B 565 PHE cc_start: 0.7589 (t80) cc_final: 0.7295 (t80) REVERT: C 5 GLN cc_start: 0.6149 (mm110) cc_final: 0.5934 (tp-100) REVERT: C 78 GLN cc_start: 0.7762 (pt0) cc_final: 0.7525 (pp30) outliers start: 20 outliers final: 10 residues processed: 327 average time/residue: 0.1104 time to fit residues: 53.5082 Evaluate side-chains 227 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 217 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain C residue 70 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 40.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN A 252 HIS A 298 HIS ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 ASN B 57 ASN B 129 ASN B 881 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.149708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115108 restraints weight = 26508.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.113894 restraints weight = 21620.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.114631 restraints weight = 20985.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.114996 restraints weight = 12212.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.115400 restraints weight = 11165.367| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14728 Z= 0.224 Angle : 0.778 10.548 20219 Z= 0.395 Chirality : 0.047 0.219 2497 Planarity : 0.006 0.068 2595 Dihedral : 10.626 173.813 2257 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.71 % Favored : 89.14 % Rotamer: Outliers : 5.05 % Allowed : 20.98 % Favored : 73.97 % 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: -3.75 (0.16), residues: 2026 helix: -1.61 (0.17), residues: 754 sheet: -1.56 (0.44), residues: 139 loop : -3.39 (0.16), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 122 TYR 0.018 0.002 TYR A 288 PHE 0.019 0.002 PHE B 565 TRP 0.024 0.002 TRP B 913 HIS 0.004 0.001 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (14728) covalent geometry : angle 0.77846 / 0.39 (20219) hydrogen bonds : bond 0.03936 / 2.68 ( 551) hydrogen bonds : angle 5.90897 / 4.15 ( 1575) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 231 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8490 (ppp) cc_final: 0.7767 (ptt) REVERT: A 592 MET cc_start: 0.8304 (tpt) cc_final: 0.8069 (tpt) REVERT: A 736 ASP cc_start: 0.8898 (p0) cc_final: 0.8233 (p0) REVERT: A 859 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8059 (pp) REVERT: A 1041 TRP cc_start: 0.8022 (m-90) cc_final: 0.7647 (m-90) REVERT: B 41 SER cc_start: 0.9288 (m) cc_final: 0.8676 (t) REVERT: B 90 ASP cc_start: 0.7895 (p0) cc_final: 0.7630 (p0) REVERT: B 129 ASN cc_start: 0.7604 (OUTLIER) cc_final: 0.7398 (m110) REVERT: B 349 LEU cc_start: 0.8913 (tp) cc_final: 0.8605 (tp) REVERT: B 370 MET cc_start: 0.8420 (tmm) cc_final: 0.7924 (tpp) REVERT: B 381 TRP cc_start: 0.7965 (OUTLIER) cc_final: 0.7517 (m-10) REVERT: B 473 THR cc_start: 0.8769 (p) cc_final: 0.8131 (p) REVERT: B 565 PHE cc_start: 0.7791 (t80) cc_final: 0.7430 (t80) REVERT: B 857 HIS cc_start: 0.5640 (m90) cc_final: 0.5333 (m90) REVERT: C 76 TYR cc_start: 0.8075 (m-80) cc_final: 0.7807 (m-80) REVERT: C 78 GLN cc_start: 0.7982 (pt0) cc_final: 0.7714 (pp30) outliers start: 65 outliers final: 39 residues processed: 276 average time/residue: 0.0977 time to fit residues: 42.1035 Evaluate side-chains 249 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 207 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 558 TRP Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 47 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 39 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 56 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 128 optimal weight: 0.0270 overall best weight: 2.2844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 HIS ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN C 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.150886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.115541 restraints weight = 26768.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.113113 restraints weight = 20235.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.113904 restraints weight = 20591.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.114681 restraints weight = 12776.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.115899 restraints weight = 11214.814| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14728 Z= 0.151 Angle : 0.693 11.783 20219 Z= 0.348 Chirality : 0.045 0.185 2497 Planarity : 0.005 0.061 2595 Dihedral : 10.091 174.707 2254 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.32 % Favored : 89.54 % Rotamer: Outliers : 5.83 % Allowed : 22.07 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.00 (0.17), residues: 2026 helix: -0.74 (0.19), residues: 748 sheet: -1.59 (0.44), residues: 149 loop : -3.09 (0.17), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 122 TYR 0.016 0.001 TYR B 402 PHE 0.014 0.001 PHE B 569 TRP 0.013 0.001 TRP A 671 HIS 0.003 0.001 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (14728) covalent geometry : angle 0.69350 / 0.35 (20219) hydrogen bonds : bond 0.03445 / 2.35 ( 551) hydrogen bonds : angle 5.33701 / 3.75 ( 1575) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 222 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.7236 (mpp) cc_final: 0.5890 (mmm) REVERT: A 358 ARG cc_start: 0.8457 (tpt90) cc_final: 0.8205 (tpt90) REVERT: A 534 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7737 (ptt) REVERT: A 572 MET cc_start: 0.6115 (mmm) cc_final: 0.5388 (mmt) REVERT: A 581 HIS cc_start: 0.8454 (OUTLIER) cc_final: 0.8206 (p-80) REVERT: A 736 ASP cc_start: 0.8836 (p0) cc_final: 0.8331 (p0) REVERT: A 1041 TRP cc_start: 0.7959 (m-90) cc_final: 0.7626 (m-90) REVERT: B 57 ASN cc_start: 0.6893 (m-40) cc_final: 0.6668 (m-40) REVERT: B 90 ASP cc_start: 0.7800 (p0) cc_final: 0.7532 (p0) REVERT: B 251 MET cc_start: 0.6292 (mtm) cc_final: 0.6063 (mtm) REVERT: B 349 LEU cc_start: 0.8910 (tp) cc_final: 0.8617 (tp) REVERT: B 359 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7226 (pp) REVERT: B 381 TRP cc_start: 0.7973 (OUTLIER) cc_final: 0.7633 (m-10) REVERT: B 543 MET cc_start: 0.7214 (tmm) cc_final: 0.6606 (tmm) REVERT: B 565 PHE cc_start: 0.7724 (t80) cc_final: 0.7379 (t80) REVERT: B 857 HIS cc_start: 0.5727 (m90) cc_final: 0.5468 (m90) REVERT: D 16 ILE cc_start: 0.8709 (tp) cc_final: 0.8504 (tp) outliers start: 75 outliers final: 50 residues processed: 278 average time/residue: 0.0923 time to fit residues: 40.8957 Evaluate side-chains 259 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 205 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 462 TRP Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 47 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 111 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 chunk 200 optimal weight: 0.0870 chunk 60 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 overall best weight: 2.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 HIS C 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.150912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.116519 restraints weight = 26910.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.113204 restraints weight = 21516.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114302 restraints weight = 21750.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.114707 restraints weight = 12421.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.115178 restraints weight = 11065.116| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14728 Z= 0.143 Angle : 0.668 10.705 20219 Z= 0.334 Chirality : 0.044 0.182 2497 Planarity : 0.005 0.058 2595 Dihedral : 9.669 171.808 2253 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.22 % Favored : 89.63 % Rotamer: Outliers : 6.29 % Allowed : 23.47 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.18), residues: 2026 helix: -0.32 (0.19), residues: 746 sheet: -1.56 (0.44), residues: 151 loop : -2.91 (0.17), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 554 TYR 0.015 0.001 TYR B 402 PHE 0.012 0.001 PHE A 585 TRP 0.013 0.001 TRP A 671 HIS 0.013 0.002 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (14728) covalent geometry : angle 0.66849 / 0.33 (20219) hydrogen bonds : bond 0.03206 / 2.16 ( 551) hydrogen bonds : angle 5.06683 / 3.56 ( 1575) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 223 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.7159 (mpp) cc_final: 0.5728 (mmm) REVERT: A 534 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7778 (ptt) REVERT: A 736 ASP cc_start: 0.8849 (p0) cc_final: 0.8388 (p0) REVERT: A 859 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7906 (pp) REVERT: A 1041 TRP cc_start: 0.7950 (m-90) cc_final: 0.7601 (m-90) REVERT: B 66 ASN cc_start: 0.8852 (m-40) cc_final: 0.8376 (m110) REVERT: B 349 LEU cc_start: 0.8929 (tp) cc_final: 0.8650 (tp) REVERT: B 359 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7256 (pp) REVERT: B 543 MET cc_start: 0.7404 (tmm) cc_final: 0.6769 (tmm) REVERT: B 565 PHE cc_start: 0.7707 (t80) cc_final: 0.7435 (t80) REVERT: B 857 HIS cc_start: 0.5734 (m90) cc_final: 0.5500 (m90) outliers start: 81 outliers final: 54 residues processed: 283 average time/residue: 0.0906 time to fit residues: 40.8400 Evaluate side-chains 257 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 200 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 558 TRP Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain D residue 47 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 94 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 168 optimal weight: 30.0000 chunk 58 optimal weight: 20.0000 chunk 97 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.151139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.116914 restraints weight = 26681.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.114701 restraints weight = 22740.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115362 restraints weight = 23128.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.116108 restraints weight = 13279.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.116687 restraints weight = 11482.451| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14728 Z= 0.146 Angle : 0.672 10.104 20219 Z= 0.333 Chirality : 0.044 0.183 2497 Planarity : 0.005 0.057 2595 Dihedral : 9.406 173.269 2253 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.27 % Favored : 89.59 % Rotamer: Outliers : 5.83 % Allowed : 25.33 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.18), residues: 2026 helix: -0.12 (0.19), residues: 755 sheet: -1.55 (0.43), residues: 166 loop : -2.85 (0.17), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 122 TYR 0.022 0.001 TYR A 402 PHE 0.012 0.001 PHE B 565 TRP 0.015 0.001 TRP A 671 HIS 0.003 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (14728) covalent geometry : angle 0.67241 / 0.33 (20219) hydrogen bonds : bond 0.03151 / 2.13 ( 551) hydrogen bonds : angle 4.92429 / 3.45 ( 1575) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 219 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 534 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7862 (ptt) REVERT: A 572 MET cc_start: 0.6707 (mmt) cc_final: 0.5955 (mmt) REVERT: A 736 ASP cc_start: 0.8829 (p0) cc_final: 0.8436 (p0) REVERT: A 1041 TRP cc_start: 0.7947 (m-90) cc_final: 0.7595 (m-90) REVERT: B 41 SER cc_start: 0.9299 (m) cc_final: 0.8808 (t) REVERT: B 146 GLN cc_start: 0.8314 (mt0) cc_final: 0.8046 (mt0) REVERT: B 349 LEU cc_start: 0.8951 (tp) cc_final: 0.8691 (tp) REVERT: B 359 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7199 (pp) REVERT: B 370 MET cc_start: 0.8601 (tpt) cc_final: 0.8316 (tpt) REVERT: B 702 MET cc_start: 0.5998 (OUTLIER) cc_final: 0.5678 (mmt) outliers start: 75 outliers final: 58 residues processed: 273 average time/residue: 0.0879 time to fit residues: 39.0445 Evaluate side-chains 265 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 204 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 462 TRP Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 558 TRP Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 47 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 105 optimal weight: 30.0000 chunk 110 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 163 optimal weight: 0.0970 chunk 12 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 HIS A 789 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.151909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.116848 restraints weight = 26918.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115251 restraints weight = 20271.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115906 restraints weight = 20178.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116463 restraints weight = 11498.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.117055 restraints weight = 10111.966| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14728 Z= 0.133 Angle : 0.660 13.052 20219 Z= 0.326 Chirality : 0.044 0.183 2497 Planarity : 0.004 0.056 2595 Dihedral : 9.113 173.474 2253 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.41 % Favored : 89.44 % Rotamer: Outliers : 6.14 % Allowed : 25.64 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.19), residues: 2026 helix: 0.23 (0.20), residues: 739 sheet: -1.37 (0.43), residues: 170 loop : -2.76 (0.17), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 122 TYR 0.013 0.001 TYR A 288 PHE 0.008 0.001 PHE B 614 TRP 0.018 0.001 TRP A 671 HIS 0.003 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (14728) covalent geometry : angle 0.66017 / 0.33 (20219) hydrogen bonds : bond 0.02978 / 2.00 ( 551) hydrogen bonds : angle 4.76820 / 3.34 ( 1575) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 222 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 451 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9104 (tt) REVERT: A 534 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7821 (ptt) REVERT: A 572 MET cc_start: 0.6918 (mmt) cc_final: 0.6217 (mmm) REVERT: A 736 ASP cc_start: 0.8789 (p0) cc_final: 0.8442 (p0) REVERT: A 935 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6834 (mt-10) REVERT: A 1041 TRP cc_start: 0.7870 (m-90) cc_final: 0.7592 (m-90) REVERT: B 41 SER cc_start: 0.9314 (m) cc_final: 0.8791 (t) REVERT: B 146 GLN cc_start: 0.8269 (mt0) cc_final: 0.7277 (pm20) REVERT: B 349 LEU cc_start: 0.8900 (tp) cc_final: 0.8636 (tp) REVERT: B 359 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7209 (pp) REVERT: B 431 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8337 (pp30) outliers start: 79 outliers final: 54 residues processed: 281 average time/residue: 0.0895 time to fit residues: 40.5132 Evaluate side-chains 264 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 206 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 462 TRP Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 558 TRP Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain D residue 47 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 48 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 171 optimal weight: 40.0000 chunk 133 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.151633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.117478 restraints weight = 26640.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.114510 restraints weight = 22486.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.115729 restraints weight = 22718.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.116152 restraints weight = 13322.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117572 restraints weight = 11835.921| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14728 Z= 0.145 Angle : 0.670 11.242 20219 Z= 0.329 Chirality : 0.044 0.188 2497 Planarity : 0.004 0.055 2595 Dihedral : 8.906 174.331 2251 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.22 % Favored : 89.63 % Rotamer: Outliers : 5.98 % Allowed : 25.95 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.19), residues: 2026 helix: 0.34 (0.20), residues: 740 sheet: -1.21 (0.44), residues: 163 loop : -2.69 (0.17), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 122 TYR 0.016 0.001 TYR A 402 PHE 0.012 0.001 PHE A 624 TRP 0.018 0.001 TRP A 671 HIS 0.003 0.001 HIS A 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (14728) covalent geometry : angle 0.66977 / 0.33 (20219) hydrogen bonds : bond 0.02967 / 2.00 ( 551) hydrogen bonds : angle 4.71897 / 3.30 ( 1575) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 215 time to evaluate : 0.488 Fit side-chains REVERT: A 114 MET cc_start: 0.8662 (ttp) cc_final: 0.8210 (ttp) REVERT: A 451 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.9056 (tt) REVERT: A 534 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7892 (ptt) REVERT: A 572 MET cc_start: 0.6938 (mmt) cc_final: 0.6053 (mmt) REVERT: A 736 ASP cc_start: 0.8785 (p0) cc_final: 0.8465 (p0) REVERT: A 1041 TRP cc_start: 0.7919 (m-90) cc_final: 0.7602 (m-90) REVERT: B 41 SER cc_start: 0.9359 (m) cc_final: 0.8826 (t) REVERT: B 146 GLN cc_start: 0.8336 (mt0) cc_final: 0.7233 (pm20) REVERT: B 227 LEU cc_start: 0.9145 (mt) cc_final: 0.8673 (tp) REVERT: B 349 LEU cc_start: 0.8872 (tp) cc_final: 0.8632 (tp) REVERT: B 359 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7260 (pp) REVERT: B 431 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8308 (pp30) REVERT: B 543 MET cc_start: 0.6950 (tmm) cc_final: 0.6698 (tmm) outliers start: 77 outliers final: 62 residues processed: 273 average time/residue: 0.0886 time to fit residues: 39.3927 Evaluate side-chains 268 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 202 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 462 TRP Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 558 TRP Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain D residue 47 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 25 optimal weight: 0.9980 chunk 156 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 93 optimal weight: 0.2980 chunk 99 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 190 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 19 optimal weight: 0.0970 chunk 149 optimal weight: 8.9990 chunk 177 optimal weight: 0.0020 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.155154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.120483 restraints weight = 26677.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.118361 restraints weight = 18827.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.118826 restraints weight = 19822.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120011 restraints weight = 12067.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.120391 restraints weight = 10186.536| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14728 Z= 0.110 Angle : 0.651 12.029 20219 Z= 0.317 Chirality : 0.043 0.176 2497 Planarity : 0.004 0.054 2595 Dihedral : 8.475 170.231 2251 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.48 % Favored : 90.38 % Rotamer: Outliers : 4.82 % Allowed : 27.58 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.89 (0.19), residues: 2026 helix: 0.36 (0.20), residues: 757 sheet: -0.87 (0.46), residues: 154 loop : -2.62 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 122 TYR 0.011 0.001 TYR A 319 PHE 0.011 0.001 PHE A 624 TRP 0.020 0.001 TRP A 671 HIS 0.003 0.000 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (14728) covalent geometry : angle 0.65106 / 0.32 (20219) hydrogen bonds : bond 0.02813 / 1.88 ( 551) hydrogen bonds : angle 4.55972 / 3.18 ( 1575) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 233 time to evaluate : 0.354 Fit side-chains REVERT: A 114 MET cc_start: 0.8540 (ttp) cc_final: 0.8322 (ttp) REVERT: A 451 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.9036 (tt) REVERT: A 529 PHE cc_start: 0.7850 (t80) cc_final: 0.7542 (t80) REVERT: A 534 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7672 (ptt) REVERT: A 572 MET cc_start: 0.6829 (mmt) cc_final: 0.6140 (mmm) REVERT: A 736 ASP cc_start: 0.8608 (p0) cc_final: 0.8342 (p0) REVERT: A 935 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6771 (mt-10) REVERT: A 1041 TRP cc_start: 0.7744 (m-90) cc_final: 0.7521 (m-90) REVERT: B 41 SER cc_start: 0.9329 (m) cc_final: 0.8789 (t) REVERT: B 146 GLN cc_start: 0.8324 (mt0) cc_final: 0.7162 (pm20) REVERT: B 227 LEU cc_start: 0.8992 (mt) cc_final: 0.8569 (tp) REVERT: B 349 LEU cc_start: 0.8841 (tp) cc_final: 0.8628 (tp) REVERT: B 359 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7178 (pp) REVERT: B 431 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8269 (pp30) REVERT: B 543 MET cc_start: 0.6703 (tmm) cc_final: 0.6385 (tmm) outliers start: 62 outliers final: 45 residues processed: 281 average time/residue: 0.0938 time to fit residues: 41.6174 Evaluate side-chains 257 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 208 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 462 TRP Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1073 TYR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 558 TRP Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain C residue 68 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 92 optimal weight: 4.9990 chunk 105 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 153 optimal weight: 0.0270 chunk 37 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 chunk 139 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 overall best weight: 2.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 386 ASN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.153002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.118010 restraints weight = 26896.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.116760 restraints weight = 21970.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.117410 restraints weight = 20981.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118245 restraints weight = 12735.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.119338 restraints weight = 10979.876| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14728 Z= 0.138 Angle : 0.679 11.083 20219 Z= 0.330 Chirality : 0.044 0.178 2497 Planarity : 0.004 0.053 2595 Dihedral : 8.374 173.494 2250 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.67 % Favored : 90.18 % Rotamer: Outliers : 4.97 % Allowed : 27.82 % Favored : 67.21 % 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: -1.85 (0.19), residues: 2026 helix: 0.41 (0.19), residues: 758 sheet: -1.18 (0.43), residues: 170 loop : -2.56 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 137 TYR 0.018 0.001 TYR B 158 PHE 0.009 0.001 PHE B 480 TRP 0.021 0.001 TRP A 671 HIS 0.002 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (14728) covalent geometry : angle 0.67905 / 0.33 (20219) hydrogen bonds : bond 0.02839 / 1.90 ( 551) hydrogen bonds : angle 4.55410 / 3.18 ( 1575) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 206 time to evaluate : 0.499 Fit side-chains REVERT: A 114 MET cc_start: 0.8658 (ttp) cc_final: 0.8386 (ttp) REVERT: A 451 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9045 (tt) REVERT: A 534 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7647 (ptt) REVERT: A 572 MET cc_start: 0.6876 (mmt) cc_final: 0.6051 (mmt) REVERT: A 736 ASP cc_start: 0.8660 (p0) cc_final: 0.8377 (p0) REVERT: A 935 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6785 (mt-10) REVERT: A 1041 TRP cc_start: 0.7763 (m-90) cc_final: 0.7407 (m-90) REVERT: B 146 GLN cc_start: 0.8297 (mt0) cc_final: 0.7119 (pm20) REVERT: B 227 LEU cc_start: 0.8957 (mt) cc_final: 0.8417 (tp) REVERT: B 349 LEU cc_start: 0.8814 (tp) cc_final: 0.8595 (tp) REVERT: B 359 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7093 (pp) REVERT: B 431 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8270 (pp30) REVERT: B 543 MET cc_start: 0.6745 (tmm) cc_final: 0.6434 (tmm) REVERT: B 573 PHE cc_start: 0.6818 (OUTLIER) cc_final: 0.6368 (t80) outliers start: 64 outliers final: 52 residues processed: 256 average time/residue: 0.0859 time to fit residues: 35.8759 Evaluate side-chains 260 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 203 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 462 TRP Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 558 TRP Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain D residue 47 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.0270 chunk 127 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 176 optimal weight: 30.0000 chunk 87 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 128 optimal weight: 0.0970 chunk 99 optimal weight: 1.9990 chunk 122 optimal weight: 50.0000 chunk 157 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 overall best weight: 1.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.153754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.118638 restraints weight = 26907.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.118258 restraints weight = 20448.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.118869 restraints weight = 18494.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.119405 restraints weight = 11732.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.120560 restraints weight = 10374.333| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14728 Z= 0.123 Angle : 0.667 12.999 20219 Z= 0.324 Chirality : 0.044 0.176 2497 Planarity : 0.004 0.052 2595 Dihedral : 8.211 172.650 2250 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.67 % Favored : 90.18 % Rotamer: Outliers : 4.51 % Allowed : 28.05 % Favored : 67.44 % 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: -1.74 (0.19), residues: 2026 helix: 0.44 (0.19), residues: 764 sheet: -1.02 (0.43), residues: 167 loop : -2.48 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1079 TYR 0.018 0.001 TYR A 402 PHE 0.008 0.001 PHE B 480 TRP 0.023 0.001 TRP A 671 HIS 0.002 0.000 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (14728) covalent geometry : angle 0.66731 / 0.32 (20219) hydrogen bonds : bond 0.02787 / 1.86 ( 551) hydrogen bonds : angle 4.51987 / 3.15 ( 1575) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 209 time to evaluate : 0.543 Fit side-chains REVERT: A 114 MET cc_start: 0.8642 (ttp) cc_final: 0.8383 (ttp) REVERT: A 451 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.9048 (tt) REVERT: A 534 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7633 (ptt) REVERT: A 572 MET cc_start: 0.6854 (mmt) cc_final: 0.6055 (mmt) REVERT: A 736 ASP cc_start: 0.8646 (p0) cc_final: 0.8407 (p0) REVERT: A 935 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6760 (mt-10) REVERT: A 1041 TRP cc_start: 0.7721 (m-90) cc_final: 0.7334 (m-90) REVERT: B 41 SER cc_start: 0.9258 (m) cc_final: 0.8699 (t) REVERT: B 146 GLN cc_start: 0.8308 (mt0) cc_final: 0.7123 (pm20) REVERT: B 227 LEU cc_start: 0.8947 (mt) cc_final: 0.8552 (tp) REVERT: B 231 VAL cc_start: 0.9028 (m) cc_final: 0.8806 (t) REVERT: B 349 LEU cc_start: 0.8827 (tp) cc_final: 0.8620 (tp) REVERT: B 359 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7090 (pp) REVERT: B 431 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8227 (pp30) REVERT: B 543 MET cc_start: 0.6741 (tmm) cc_final: 0.6398 (tmm) outliers start: 58 outliers final: 51 residues processed: 251 average time/residue: 0.0875 time to fit residues: 35.9278 Evaluate side-chains 255 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 200 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 462 TRP Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 558 TRP Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain D residue 47 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 129 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 177 optimal weight: 50.0000 chunk 83 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.149093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114228 restraints weight = 26759.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.112605 restraints weight = 22259.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.112633 restraints weight = 24506.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.113090 restraints weight = 13309.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.114303 restraints weight = 11329.912| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14728 Z= 0.224 Angle : 0.742 15.428 20219 Z= 0.362 Chirality : 0.046 0.221 2497 Planarity : 0.005 0.052 2595 Dihedral : 8.469 179.800 2248 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.06 % Favored : 88.80 % Rotamer: Outliers : 4.90 % Allowed : 27.97 % Favored : 67.13 % 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: -1.87 (0.19), residues: 2026 helix: 0.26 (0.19), residues: 769 sheet: -1.02 (0.43), residues: 167 loop : -2.52 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1079 TYR 0.024 0.002 TYR A 288 PHE 0.011 0.001 PHE A 769 TRP 0.023 0.002 TRP A 671 HIS 0.002 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (14728) covalent geometry : angle 0.74232 / 0.36 (20219) hydrogen bonds : bond 0.03097 / 2.07 ( 551) hydrogen bonds : angle 4.74429 / 3.32 ( 1575) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2449.68 seconds wall clock time: 42 minutes 56.40 seconds (2576.40 seconds total)