Starting phenix.real_space_refine on Sun Aug 24 23:15:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ffk_29045/08_2025/8ffk_29045.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ffk_29045/08_2025/8ffk_29045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ffk_29045/08_2025/8ffk_29045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ffk_29045/08_2025/8ffk_29045.map" model { file = "/net/cci-nas-00/data/ceres_data/8ffk_29045/08_2025/8ffk_29045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ffk_29045/08_2025/8ffk_29045.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 131 5.16 5 C 15120 2.51 5 N 3873 2.21 5 O 4358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23482 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7819 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 985} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 7840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 7840 Classifications: {'peptide': 1033} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 985} Chain: "C" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 7823 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 985} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 4.82, per 1000 atoms: 0.21 Number of scatterers: 23482 At special positions: 0 Unit cell: (112.35, 121.98, 145.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 131 16.00 O 4358 8.00 N 3873 7.00 C 15120 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: 1.63 Conformation dependent library (CDL) restraints added in 825.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5632 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 24 sheets defined 60.9% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 removed outlier: 3.859A pdb=" N ASP A 7 " --> pdb=" O ASN A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 29 Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.509A pdb=" N ASN A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 298 through 313 Processing helix chain 'A' and resid 329 through 360 Processing helix chain 'A' and resid 361 through 370 Proline residue: A 368 - end of helix Processing helix chain 'A' and resid 371 through 386 Processing helix chain 'A' and resid 391 through 401 Processing helix chain 'A' and resid 401 through 423 Processing helix chain 'A' and resid 426 through 454 removed outlier: 5.279A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 460 through 497 removed outlier: 4.752A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix removed outlier: 3.610A pdb=" N LEU A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 536 removed outlier: 3.709A pdb=" N GLY A 513 " --> pdb=" O THR A 509 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER A 536 " --> pdb=" O ASN A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 558 removed outlier: 4.395A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 600 Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 638 through 641 Processing helix chain 'A' and resid 642 through 655 Processing helix chain 'A' and resid 690 through 707 removed outlier: 3.574A pdb=" N GLN A 707 " --> pdb=" O GLY A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 738 Processing helix chain 'A' and resid 741 through 754 Processing helix chain 'A' and resid 776 through 779 Processing helix chain 'A' and resid 781 through 787 Processing helix chain 'A' and resid 800 through 803 No H-bonds generated for 'chain 'A' and resid 800 through 803' Processing helix chain 'A' and resid 835 through 849 Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.594A pdb=" N GLN A 864 " --> pdb=" O GLY A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 892 removed outlier: 3.623A pdb=" N ALA A 874 " --> pdb=" O ASN A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 902 removed outlier: 3.864A pdb=" N VAL A 900 " --> pdb=" O ILE A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 918 removed outlier: 3.618A pdb=" N GLY A 907 " --> pdb=" O VAL A 903 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 955 Processing helix chain 'A' and resid 958 through 991 removed outlier: 4.726A pdb=" N ARG A 972 " --> pdb=" O ARG A 968 " (cutoff:3.500A) Proline residue: A 973 - end of helix Proline residue: A 987 - end of helix Processing helix chain 'A' and resid 995 through 1032 removed outlier: 4.163A pdb=" N GLY A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A1006 " --> pdb=" O VAL A1002 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Proline residue: A1022 - end of helix Processing helix chain 'B' and resid 2 through 8 Processing helix chain 'B' and resid 8 through 30 removed outlier: 3.703A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 69 Processing helix chain 'B' and resid 99 through 115 removed outlier: 3.933A pdb=" N LEU B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 298 through 314 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 329 through 360 removed outlier: 3.554A pdb=" N VAL B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 370 Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 370 through 386 removed outlier: 3.695A pdb=" N VAL B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 424 removed outlier: 4.219A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 452 removed outlier: 5.776A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 459 Processing helix chain 'B' and resid 461 through 496 removed outlier: 4.519A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 509 through 536 Processing helix chain 'B' and resid 536 through 558 removed outlier: 3.963A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 600 Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 638 through 641 Processing helix chain 'B' and resid 642 through 655 Processing helix chain 'B' and resid 690 through 707 Processing helix chain 'B' and resid 731 through 738 Processing helix chain 'B' and resid 741 through 754 Processing helix chain 'B' and resid 781 through 787 removed outlier: 3.689A pdb=" N GLY B 786 " --> pdb=" O GLU B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 803 No H-bonds generated for 'chain 'B' and resid 800 through 803' Processing helix chain 'B' and resid 835 through 849 Processing helix chain 'B' and resid 860 through 892 removed outlier: 3.501A pdb=" N GLN B 864 " --> pdb=" O GLY B 860 " (cutoff:3.500A) Proline residue: B 873 - end of helix Processing helix chain 'B' and resid 894 through 902 removed outlier: 3.506A pdb=" N LEU B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 918 removed outlier: 3.630A pdb=" N GLY B 907 " --> pdb=" O VAL B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 956 removed outlier: 4.256A pdb=" N PHE B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 970 Processing helix chain 'B' and resid 970 through 991 Proline residue: B 987 - end of helix Processing helix chain 'B' and resid 995 through 1016 removed outlier: 4.581A pdb=" N GLY B1005 " --> pdb=" O ALA B1001 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL B1006 " --> pdb=" O VAL B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1032 Proline residue: B1022 - end of helix Processing helix chain 'C' and resid 2 through 7 removed outlier: 4.068A pdb=" N ASP C 7 " --> pdb=" O ASN C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 30 Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 61 through 67 Processing helix chain 'C' and resid 99 through 113 removed outlier: 3.960A pdb=" N LEU C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 162 through 169 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 298 through 314 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 329 through 359 removed outlier: 3.618A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 387 Proline residue: C 368 - end of helix Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 391 through 424 removed outlier: 4.500A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 454 removed outlier: 5.258A pdb=" N GLY C 440 " --> pdb=" O GLY C 436 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ALA C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 459 removed outlier: 3.648A pdb=" N PHE C 459 " --> pdb=" O MET C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 497 removed outlier: 3.618A pdb=" N TYR C 467 " --> pdb=" O THR C 463 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 510 through 537 Processing helix chain 'C' and resid 538 through 558 Processing helix chain 'C' and resid 582 through 600 Processing helix chain 'C' and resid 632 through 636 Processing helix chain 'C' and resid 638 through 641 Processing helix chain 'C' and resid 642 through 658 Processing helix chain 'C' and resid 690 through 707 Processing helix chain 'C' and resid 731 through 739 Processing helix chain 'C' and resid 741 through 755 Processing helix chain 'C' and resid 776 through 779 Processing helix chain 'C' and resid 781 through 787 removed outlier: 3.524A pdb=" N GLY C 786 " --> pdb=" O GLU C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 848 Processing helix chain 'C' and resid 860 through 868 Processing helix chain 'C' and resid 871 through 892 Processing helix chain 'C' and resid 896 through 902 removed outlier: 4.001A pdb=" N VAL C 900 " --> pdb=" O ILE C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 919 removed outlier: 3.944A pdb=" N GLY C 907 " --> pdb=" O VAL C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 955 Processing helix chain 'C' and resid 958 through 990 removed outlier: 4.726A pdb=" N ARG C 972 " --> pdb=" O ARG C 968 " (cutoff:3.500A) Proline residue: C 973 - end of helix Proline residue: C 987 - end of helix Processing helix chain 'C' and resid 995 through 1032 removed outlier: 4.084A pdb=" N PHE C1019 " --> pdb=" O ILE C1015 " (cutoff:3.500A) Proline residue: C1022 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 131 removed outlier: 3.926A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 77 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 12.452A pdb=" N ARG A 814 " --> pdb=" O GLU A 825 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N GLU A 825 " --> pdb=" O ARG A 814 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU A 816 " --> pdb=" O SER A 823 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 131 removed outlier: 3.926A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 77 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 12.452A pdb=" N ARG A 814 " --> pdb=" O GLU A 825 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N GLU A 825 " --> pdb=" O ARG A 814 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU A 816 " --> pdb=" O SER A 823 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N GLU A 825 " --> pdb=" O PRO A 717 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU A 827 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL A 715 " --> pdb=" O LEU A 827 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.054A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN A 144 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET A 138 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL A 139 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.054A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 272 removed outlier: 7.743A pdb=" N TYR A 182 " --> pdb=" O VAL A 767 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS A 769 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN A 759 " --> pdb=" O VAL A 770 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE A 772 " --> pdb=" O TYR A 757 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N TYR A 757 " --> pdb=" O ILE A 772 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 234 through 235 removed outlier: 6.380A pdb=" N ILE A 235 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE B 730 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 250 through 253 Processing sheet with id=AA8, first strand: chain 'A' and resid 804 through 811 removed outlier: 8.472A pdb=" N ILE C 235 " --> pdb=" O PRO A 724 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE A 726 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLY C 217 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 789 through 791 Processing sheet with id=AB1, first strand: chain 'B' and resid 127 through 131 removed outlier: 4.018A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 12.013A pdb=" N ARG B 814 " --> pdb=" O GLU B 825 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLU B 825 " --> pdb=" O ARG B 814 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 816 " --> pdb=" O SER B 823 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN B 829 " --> pdb=" O GLY B 714 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLY B 714 " --> pdb=" O GLN B 829 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 127 through 131 removed outlier: 4.018A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 12.013A pdb=" N ARG B 814 " --> pdb=" O GLU B 825 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLU B 825 " --> pdb=" O ARG B 814 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 816 " --> pdb=" O SER B 823 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 828 " --> pdb=" O PHE B 679 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.558A pdb=" N ASP B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN B 144 " --> pdb=" O PRO B 285 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 139 " --> pdb=" O PRO B 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.558A pdb=" N ASP B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER B 629 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL B 608 " --> pdb=" O PHE B 627 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N PHE B 627 " --> pdb=" O VAL B 608 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA B 610 " --> pdb=" O ILE B 625 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 625 " --> pdb=" O ALA B 610 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 266 through 272 removed outlier: 8.374A pdb=" N TYR B 182 " --> pdb=" O VAL B 767 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS B 769 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN B 759 " --> pdb=" O VAL B 770 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE B 772 " --> pdb=" O TYR B 757 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N TYR B 757 " --> pdb=" O ILE B 772 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 218 through 219 removed outlier: 4.707A pdb=" N SER B 233 " --> pdb=" O PRO C 724 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 250 through 253 removed outlier: 6.937A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 789 through 791 Processing sheet with id=AB9, first strand: chain 'C' and resid 128 through 130 removed outlier: 4.157A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 12.366A pdb=" N ARG C 814 " --> pdb=" O GLU C 825 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N GLU C 825 " --> pdb=" O ARG C 814 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU C 816 " --> pdb=" O SER C 823 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU C 825 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN C 829 " --> pdb=" O GLY C 714 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLY C 714 " --> pdb=" O GLN C 829 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 128 through 130 removed outlier: 4.157A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 12.366A pdb=" N ARG C 814 " --> pdb=" O GLU C 825 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N GLU C 825 " --> pdb=" O ARG C 814 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU C 816 " --> pdb=" O SER C 823 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP C 680 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.946A pdb=" N ASN C 144 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.258A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER C 629 " --> pdb=" O GLU C 606 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL C 608 " --> pdb=" O PHE C 627 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE C 627 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA C 610 " --> pdb=" O ILE C 625 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE C 625 " --> pdb=" O ALA C 610 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ASN C 612 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N THR C 623 " --> pdb=" O ASN C 612 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 266 through 272 removed outlier: 8.457A pdb=" N TYR C 182 " --> pdb=" O VAL C 767 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS C 769 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN C 759 " --> pdb=" O VAL C 770 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE C 772 " --> pdb=" O TYR C 757 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N TYR C 757 " --> pdb=" O ILE C 772 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 250 through 253 Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 791 1687 hydrogen bonds defined for protein. 4890 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: 4.65 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7563 1.34 - 1.45: 3091 1.45 - 1.57: 13036 1.57 - 1.69: 0 1.69 - 1.81: 256 Bond restraints: 23946 Sorted by residual: bond pdb=" CA ASP B 923 " pdb=" C ASP B 923 " ideal model delta sigma weight residual 1.530 1.505 0.026 1.12e-02 7.97e+03 5.29e+00 bond pdb=" CA TYR C 182 " pdb=" C TYR C 182 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.30e-02 5.92e+03 3.96e+00 bond pdb=" C ARG A 972 " pdb=" O ARG A 972 " ideal model delta sigma weight residual 1.244 1.225 0.019 1.00e-02 1.00e+04 3.48e+00 bond pdb=" CA ARG A 968 " pdb=" C ARG A 968 " ideal model delta sigma weight residual 1.524 1.502 0.021 1.27e-02 6.20e+03 2.85e+00 bond pdb=" CA SER B 561 " pdb=" CB SER B 561 " ideal model delta sigma weight residual 1.538 1.518 0.020 1.22e-02 6.72e+03 2.62e+00 ... (remaining 23941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 32001 1.73 - 3.46: 428 3.46 - 5.19: 85 5.19 - 6.91: 17 6.91 - 8.64: 1 Bond angle restraints: 32532 Sorted by residual: angle pdb=" C GLY B 221 " pdb=" N THR B 222 " pdb=" CA THR B 222 " ideal model delta sigma weight residual 120.49 127.05 -6.56 1.42e+00 4.96e-01 2.13e+01 angle pdb=" C ARG A 972 " pdb=" N PRO A 973 " pdb=" CA PRO A 973 " ideal model delta sigma weight residual 119.05 114.65 4.40 1.11e+00 8.12e-01 1.57e+01 angle pdb=" C THR B 60 " pdb=" N VAL B 61 " pdb=" CA VAL B 61 " ideal model delta sigma weight residual 123.16 118.98 4.18 1.06e+00 8.90e-01 1.55e+01 angle pdb=" N ARG A 968 " pdb=" CA ARG A 968 " pdb=" C ARG A 968 " ideal model delta sigma weight residual 111.07 107.03 4.04 1.07e+00 8.73e-01 1.43e+01 angle pdb=" N GLY A 531 " pdb=" CA GLY A 531 " pdb=" C GLY A 531 " ideal model delta sigma weight residual 112.50 108.55 3.95 1.16e+00 7.43e-01 1.16e+01 ... (remaining 32527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 13429 17.16 - 34.33: 672 34.33 - 51.49: 134 51.49 - 68.65: 14 68.65 - 85.81: 5 Dihedral angle restraints: 14254 sinusoidal: 5446 harmonic: 8808 Sorted by residual: dihedral pdb=" CA SER C 536 " pdb=" C SER C 536 " pdb=" N THR C 537 " pdb=" CA THR C 537 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ALA A 706 " pdb=" C ALA A 706 " pdb=" N GLN A 707 " pdb=" CA GLN A 707 " ideal model delta harmonic sigma weight residual 180.00 163.58 16.42 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA SER A 774 " pdb=" C SER A 774 " pdb=" N GLU A 775 " pdb=" CA GLU A 775 " ideal model delta harmonic sigma weight residual 180.00 164.22 15.78 0 5.00e+00 4.00e-02 9.96e+00 ... (remaining 14251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2633 0.036 - 0.071: 832 0.071 - 0.107: 259 0.107 - 0.142: 84 0.142 - 0.177: 3 Chirality restraints: 3811 Sorted by residual: chirality pdb=" CB ILE C 367 " pdb=" CA ILE C 367 " pdb=" CG1 ILE C 367 " pdb=" CG2 ILE C 367 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB VAL C1021 " pdb=" CA VAL C1021 " pdb=" CG1 VAL C1021 " pdb=" CG2 VAL C1021 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA ILE B 90 " pdb=" N ILE B 90 " pdb=" C ILE B 90 " pdb=" CB ILE B 90 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 ... (remaining 3808 not shown) Planarity restraints: 4170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 965 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C GLU A 965 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU A 965 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA A 966 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 199 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO C 200 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 200 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 200 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 498 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO C 499 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 499 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 499 " -0.021 5.00e-02 4.00e+02 ... (remaining 4167 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1982 2.74 - 3.28: 24286 3.28 - 3.82: 40750 3.82 - 4.36: 48707 4.36 - 4.90: 85600 Nonbonded interactions: 201325 Sorted by model distance: nonbonded pdb=" OH TYR B 467 " pdb=" OE1 GLN B 927 " model vdw 2.195 3.040 nonbonded pdb=" O ILE A 974 " pdb=" OG SER A 978 " model vdw 2.200 3.040 nonbonded pdb=" O LYS C 631 " pdb=" NH1 ARG C 636 " model vdw 2.200 3.120 nonbonded pdb=" OH TYR A 757 " pdb=" OD1 ASP A 760 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR A 467 " pdb=" OE1 GLN A 927 " model vdw 2.213 3.040 ... (remaining 201320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 499 or (resid 500 through 502 and (name N or nam \ e CA or name C or name O or name CB )) or resid 503 through 1030 or (resid 1031 \ and (name N or name CA or name C or name O or name CB )) or resid 1032 through 1 \ 033)) selection = (chain 'B' and (resid 2 through 499 or (resid 500 through 502 and (name N or nam \ e CA or name C or name O or name CB )) or resid 503 through 504 or (resid 505 an \ d (name N or name CA or name C or name O or name CB )) or resid 506 through 671 \ or (resid 672 and (name N or name CA or name C or name O or name CB )) or resid \ 673 through 1030 or (resid 1031 and (name N or name CA or name C or name O or na \ me CB )) or resid 1032 through 1033)) selection = (chain 'C' and (resid 2 through 504 or (resid 505 and (name N or name CA or name \ C or name O or name CB )) or resid 506 through 671 or (resid 672 and (name N or \ name CA or name C or name O or name CB )) or resid 673 through 1033)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.680 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23946 Z= 0.196 Angle : 0.556 8.642 32532 Z= 0.311 Chirality : 0.041 0.177 3811 Planarity : 0.004 0.040 4170 Dihedral : 10.749 85.814 8622 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.19 % Allowed : 5.19 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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 aren not related in a simple way. whole: 1.77 (0.15), residues: 3092 helix: 2.20 (0.12), residues: 1704 sheet: -0.19 (0.25), residues: 411 loop : 0.01 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 185 TYR 0.018 0.001 TYR A 540 PHE 0.013 0.001 PHE A 571 TRP 0.009 0.001 TRP C 553 HIS 0.002 0.001 HIS C 708 Details of bonding type rmsd covalent geometry : bond 0.00420 (23946) covalent geometry : angle 0.55625 (32532) hydrogen bonds : bond 0.14681 ( 1606) hydrogen bonds : angle 6.71433 ( 4890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 475 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 69 MET cc_start: 0.9017 (mmt) cc_final: 0.8694 (mmt) REVERT: A 101 ASP cc_start: 0.8137 (m-30) cc_final: 0.7809 (m-30) REVERT: A 124 GLN cc_start: 0.8149 (tt0) cc_final: 0.7870 (tt0) REVERT: A 150 ASN cc_start: 0.7364 (p0) cc_final: 0.7020 (p0) REVERT: A 225 VAL cc_start: 0.8131 (t) cc_final: 0.7875 (m) REVERT: A 245 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7081 (mt-10) REVERT: A 267 LYS cc_start: 0.7912 (tttp) cc_final: 0.7686 (mtpp) REVERT: A 298 ASN cc_start: 0.6839 (t0) cc_final: 0.6632 (t0) REVERT: A 321 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8394 (mtt) REVERT: A 339 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7169 (mp0) REVERT: A 574 MET cc_start: 0.6592 (tmm) cc_final: 0.6377 (tmm) REVERT: A 602 LYS cc_start: 0.7548 (ptmt) cc_final: 0.7227 (ptmm) REVERT: A 619 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.7441 (mtm-85) REVERT: A 632 ASP cc_start: 0.7799 (t0) cc_final: 0.7559 (t70) REVERT: A 661 MET cc_start: 0.7409 (ttp) cc_final: 0.7097 (ttp) REVERT: A 856 TYR cc_start: 0.8685 (p90) cc_final: 0.8403 (p90) REVERT: A 866 ARG cc_start: 0.7265 (tpp-160) cc_final: 0.6841 (ttp-170) REVERT: A 918 ARG cc_start: 0.8092 (mmm160) cc_final: 0.6176 (mpt90) REVERT: A 992 SER cc_start: 0.8539 (p) cc_final: 0.8264 (t) REVERT: B 8 ARG cc_start: 0.6822 (mtt180) cc_final: 0.6212 (mtt90) REVERT: B 29 LYS cc_start: 0.7525 (mmtt) cc_final: 0.7010 (tttt) REVERT: B 44 SER cc_start: 0.8693 (t) cc_final: 0.8387 (p) REVERT: B 184 MET cc_start: 0.8982 (tpp) cc_final: 0.8281 (tpp) REVERT: B 244 GLU cc_start: 0.7602 (mm-30) cc_final: 0.6950 (mp0) REVERT: B 307 ARG cc_start: 0.6807 (mtt-85) cc_final: 0.6525 (mtm-85) REVERT: B 355 MET cc_start: 0.7886 (mtm) cc_final: 0.7529 (mtp) REVERT: B 386 PHE cc_start: 0.7850 (m-80) cc_final: 0.7582 (m-80) REVERT: B 498 LYS cc_start: 0.8300 (mmtp) cc_final: 0.7979 (mptt) REVERT: B 517 ARG cc_start: 0.7419 (mtm110) cc_final: 0.7195 (mtm110) REVERT: B 518 MET cc_start: 0.5436 (mmm) cc_final: 0.4923 (ttp) REVERT: B 614 PHE cc_start: 0.8507 (t80) cc_final: 0.8210 (t80) REVERT: B 661 MET cc_start: 0.6869 (mmt) cc_final: 0.6517 (mtt) REVERT: B 891 TYR cc_start: 0.8006 (m-80) cc_final: 0.6964 (m-80) REVERT: B 895 SER cc_start: 0.7612 (m) cc_final: 0.7278 (p) REVERT: B 954 LYS cc_start: 0.7932 (mttt) cc_final: 0.7581 (mptm) REVERT: B 961 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6565 (pt0) REVERT: B 969 MET cc_start: 0.7683 (mtp) cc_final: 0.7315 (mmm) REVERT: C 29 LYS cc_start: 0.7709 (mtpp) cc_final: 0.7429 (ttpt) REVERT: C 69 MET cc_start: 0.8943 (mmt) cc_final: 0.8296 (mmp) REVERT: C 76 MET cc_start: 0.8435 (mtt) cc_final: 0.8109 (mtm) REVERT: C 96 SER cc_start: 0.8683 (m) cc_final: 0.8373 (p) REVERT: C 176 GLN cc_start: 0.8065 (mt0) cc_final: 0.7773 (tt0) REVERT: C 188 MET cc_start: 0.8750 (mtm) cc_final: 0.8438 (mtm) REVERT: C 226 LYS cc_start: 0.8504 (tptt) cc_final: 0.7552 (mppt) REVERT: C 274 SER cc_start: 0.8796 (t) cc_final: 0.8409 (p) REVERT: C 346 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6824 (mt-10) REVERT: C 356 TYR cc_start: 0.7137 (t80) cc_final: 0.6901 (t80) REVERT: C 366 LEU cc_start: 0.6849 (tp) cc_final: 0.6580 (mt) REVERT: C 420 MET cc_start: 0.7053 (ttp) cc_final: 0.6695 (ttm) REVERT: C 435 MET cc_start: 0.8488 (mmm) cc_final: 0.7871 (mmm) REVERT: C 447 MET cc_start: 0.8073 (mmm) cc_final: 0.7779 (tpp) REVERT: C 518 MET cc_start: 0.5835 (tpp) cc_final: 0.5129 (tmt) REVERT: C 521 LYS cc_start: 0.7248 (ttpp) cc_final: 0.6900 (ptmm) REVERT: C 525 HIS cc_start: 0.5966 (t70) cc_final: 0.5674 (m90) REVERT: C 574 MET cc_start: 0.7392 (ttt) cc_final: 0.7101 (ttp) REVERT: C 606 GLU cc_start: 0.8164 (tp30) cc_final: 0.7887 (tp30) REVERT: C 636 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.6796 (ptt-90) REVERT: C 680 ASP cc_start: 0.6472 (m-30) cc_final: 0.6234 (m-30) REVERT: C 840 MET cc_start: 0.6604 (mtm) cc_final: 0.6121 (mtm) REVERT: C 845 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7127 (tt0) REVERT: C 861 MET cc_start: 0.5987 (pmm) cc_final: 0.5580 (pmt) REVERT: C 917 PHE cc_start: 0.6242 (m-10) cc_final: 0.5505 (t80) REVERT: C 918 ARG cc_start: 0.7522 (mmm-85) cc_final: 0.5850 (mpt180) REVERT: C 961 GLU cc_start: 0.7521 (tt0) cc_final: 0.7135 (mp0) REVERT: C 1015 ILE cc_start: 0.7538 (mm) cc_final: 0.7263 (tp) outliers start: 55 outliers final: 21 residues processed: 516 average time/residue: 0.5814 time to fit residues: 342.5101 Evaluate side-chains 352 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 327 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 636 ARG Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 921 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 210 GLN A 656 GLN B 109 ASN B 144 ASN B 360 GLN B 516 ASN B 583 GLN B 700 GLN B 708 HIS B 718 ASN B 871 GLN C 58 GLN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN C 576 GLN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 GLN C 686 GLN C 736 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.097703 restraints weight = 32387.530| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.80 r_work: 0.3053 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23946 Z= 0.140 Angle : 0.537 7.851 32532 Z= 0.281 Chirality : 0.042 0.179 3811 Planarity : 0.004 0.034 4170 Dihedral : 5.297 59.804 3325 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.19 % Allowed : 11.57 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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 aren not related in a simple way. whole: 1.98 (0.15), residues: 3092 helix: 2.39 (0.12), residues: 1719 sheet: -0.18 (0.25), residues: 403 loop : 0.08 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 8 TYR 0.017 0.001 TYR A 540 PHE 0.018 0.001 PHE A 571 TRP 0.010 0.001 TRP B 753 HIS 0.008 0.001 HIS A 525 Details of bonding type rmsd covalent geometry : bond 0.00304 (23946) covalent geometry : angle 0.53688 (32532) hydrogen bonds : bond 0.04704 ( 1606) hydrogen bonds : angle 5.09584 ( 4890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 364 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8095 (mp) REVERT: A 69 MET cc_start: 0.9500 (mmt) cc_final: 0.9279 (mmt) REVERT: A 124 GLN cc_start: 0.8835 (tt0) cc_final: 0.8534 (tt0) REVERT: A 298 ASN cc_start: 0.8305 (t0) cc_final: 0.8100 (t0) REVERT: A 321 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8652 (mtt) REVERT: A 407 ASP cc_start: 0.8426 (t0) cc_final: 0.8164 (t0) REVERT: A 423 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7828 (mm-30) REVERT: A 602 LYS cc_start: 0.8409 (ptmt) cc_final: 0.8029 (ptmm) REVERT: A 632 ASP cc_start: 0.8263 (t0) cc_final: 0.8054 (t70) REVERT: A 918 ARG cc_start: 0.8282 (mmm160) cc_final: 0.6718 (mpt90) REVERT: A 939 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8590 (ttpp) REVERT: A 1000 ASN cc_start: 0.8961 (m-40) cc_final: 0.8573 (m-40) REVERT: B 8 ARG cc_start: 0.7820 (mtt180) cc_final: 0.7505 (mtt90) REVERT: B 29 LYS cc_start: 0.8398 (mmtt) cc_final: 0.7971 (tttt) REVERT: B 162 MET cc_start: 0.9243 (mtp) cc_final: 0.8994 (mtp) REVERT: B 184 MET cc_start: 0.9324 (tpp) cc_final: 0.8705 (tpp) REVERT: B 307 ARG cc_start: 0.7845 (mtt-85) cc_final: 0.7629 (mtm-85) REVERT: B 518 MET cc_start: 0.7334 (mmm) cc_final: 0.6593 (ttp) REVERT: B 527 THR cc_start: 0.8315 (m) cc_final: 0.8085 (p) REVERT: B 656 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8057 (mm-40) REVERT: B 661 MET cc_start: 0.8459 (mmt) cc_final: 0.8090 (mtt) REVERT: B 810 TYR cc_start: 0.7859 (OUTLIER) cc_final: 0.7165 (t80) REVERT: B 891 TYR cc_start: 0.8490 (m-80) cc_final: 0.7667 (m-80) REVERT: B 969 MET cc_start: 0.8865 (mtp) cc_final: 0.8583 (mmm) REVERT: C 69 MET cc_start: 0.9346 (mmt) cc_final: 0.9048 (mmp) REVERT: C 188 MET cc_start: 0.9405 (mtm) cc_final: 0.9124 (mtm) REVERT: C 226 LYS cc_start: 0.8893 (tptt) cc_final: 0.8143 (mppt) REVERT: C 276 ASP cc_start: 0.8519 (m-30) cc_final: 0.8272 (m-30) REVERT: C 346 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7821 (mt-10) REVERT: C 356 TYR cc_start: 0.8139 (t80) cc_final: 0.7809 (t80) REVERT: C 432 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7524 (mtt-85) REVERT: C 435 MET cc_start: 0.8673 (mmm) cc_final: 0.8061 (mmm) REVERT: C 496 MET cc_start: 0.5794 (tpt) cc_final: 0.5576 (tpt) REVERT: C 518 MET cc_start: 0.6585 (tpp) cc_final: 0.6116 (tmt) REVERT: C 521 LYS cc_start: 0.8083 (ttpp) cc_final: 0.7875 (ptmm) REVERT: C 525 HIS cc_start: 0.6845 (t70) cc_final: 0.6629 (m90) REVERT: C 636 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8248 (ptt180) REVERT: C 791 ARG cc_start: 0.8769 (ttp80) cc_final: 0.8345 (ttp-170) REVERT: C 917 PHE cc_start: 0.7047 (m-10) cc_final: 0.6350 (t80) REVERT: C 918 ARG cc_start: 0.8212 (mmm-85) cc_final: 0.6789 (mpt180) REVERT: C 961 GLU cc_start: 0.8416 (tt0) cc_final: 0.8206 (mp0) outliers start: 80 outliers final: 31 residues processed: 418 average time/residue: 0.5852 time to fit residues: 279.1097 Evaluate side-chains 348 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 309 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 939 LYS Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 810 TYR Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 636 ARG Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 986 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 36 optimal weight: 3.9990 chunk 188 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 306 optimal weight: 0.7980 chunk 216 optimal weight: 3.9990 chunk 280 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN B 718 ASN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 GLN C 736 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.113845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.096706 restraints weight = 32437.836| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.80 r_work: 0.3040 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23946 Z= 0.167 Angle : 0.543 8.538 32532 Z= 0.282 Chirality : 0.042 0.176 3811 Planarity : 0.004 0.044 4170 Dihedral : 5.178 59.193 3317 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.75 % Allowed : 12.97 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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 aren not related in a simple way. whole: 1.90 (0.15), residues: 3092 helix: 2.35 (0.12), residues: 1721 sheet: -0.23 (0.25), residues: 393 loop : -0.02 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 557 TYR 0.018 0.001 TYR A 540 PHE 0.027 0.001 PHE A 362 TRP 0.008 0.001 TRP C 788 HIS 0.003 0.001 HIS C 708 Details of bonding type rmsd covalent geometry : bond 0.00387 (23946) covalent geometry : angle 0.54333 (32532) hydrogen bonds : bond 0.04517 ( 1606) hydrogen bonds : angle 4.88420 ( 4890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 330 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8122 (mp) REVERT: A 124 GLN cc_start: 0.8963 (tt0) cc_final: 0.8610 (tt0) REVERT: A 184 MET cc_start: 0.9447 (tpp) cc_final: 0.9221 (tpp) REVERT: A 245 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8359 (mt-10) REVERT: A 298 ASN cc_start: 0.8339 (t0) cc_final: 0.8083 (t0) REVERT: A 314 GLU cc_start: 0.8068 (tp30) cc_final: 0.7655 (tp30) REVERT: A 321 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8631 (mtt) REVERT: A 339 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7934 (mp0) REVERT: A 407 ASP cc_start: 0.8433 (t0) cc_final: 0.8144 (t0) REVERT: A 423 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7868 (mm-30) REVERT: A 518 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.6628 (tpt) REVERT: A 602 LYS cc_start: 0.8422 (ptmt) cc_final: 0.8082 (ptmm) REVERT: A 632 ASP cc_start: 0.8408 (t0) cc_final: 0.8188 (t70) REVERT: A 918 ARG cc_start: 0.8371 (mmm160) cc_final: 0.8020 (ttt-90) REVERT: A 939 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8582 (ttpp) REVERT: B 8 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7645 (mtt90) REVERT: B 29 LYS cc_start: 0.8458 (mmtt) cc_final: 0.7981 (tttt) REVERT: B 184 MET cc_start: 0.9309 (tpp) cc_final: 0.8773 (tpp) REVERT: B 307 ARG cc_start: 0.7837 (mtt-85) cc_final: 0.7610 (mtm-85) REVERT: B 518 MET cc_start: 0.7292 (mmm) cc_final: 0.6544 (ttp) REVERT: B 527 THR cc_start: 0.8314 (m) cc_final: 0.8026 (p) REVERT: B 656 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8108 (mm-40) REVERT: B 661 MET cc_start: 0.8450 (mmt) cc_final: 0.8091 (mtt) REVERT: B 729 ASP cc_start: 0.8525 (m-30) cc_final: 0.8319 (m-30) REVERT: B 810 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.7160 (t80) REVERT: B 891 TYR cc_start: 0.8516 (m-80) cc_final: 0.7588 (m-80) REVERT: B 969 MET cc_start: 0.8852 (mtp) cc_final: 0.8552 (mmm) REVERT: B 1029 ARG cc_start: 0.8362 (mmm160) cc_final: 0.8062 (mmm160) REVERT: C 48 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8935 (ttt) REVERT: C 69 MET cc_start: 0.9325 (mmt) cc_final: 0.8705 (mmp) REVERT: C 188 MET cc_start: 0.9398 (mtm) cc_final: 0.9070 (mtm) REVERT: C 226 LYS cc_start: 0.8886 (tptt) cc_final: 0.8101 (mppt) REVERT: C 276 ASP cc_start: 0.8492 (m-30) cc_final: 0.8256 (m-30) REVERT: C 346 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7826 (mt-10) REVERT: C 356 TYR cc_start: 0.8165 (t80) cc_final: 0.7850 (t80) REVERT: C 432 ARG cc_start: 0.7960 (ttm-80) cc_final: 0.7644 (mtp85) REVERT: C 435 MET cc_start: 0.8652 (mmm) cc_final: 0.8017 (mmm) REVERT: C 496 MET cc_start: 0.5855 (tpt) cc_final: 0.5557 (tpt) REVERT: C 518 MET cc_start: 0.6551 (tpp) cc_final: 0.6092 (tmt) REVERT: C 521 LYS cc_start: 0.8006 (ttpp) cc_final: 0.7780 (ptmm) REVERT: C 525 HIS cc_start: 0.6864 (t70) cc_final: 0.6640 (m90) REVERT: C 636 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8221 (ptt180) REVERT: C 680 ASP cc_start: 0.7830 (m-30) cc_final: 0.7538 (m-30) REVERT: C 906 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7635 (mt) REVERT: C 917 PHE cc_start: 0.7135 (m-10) cc_final: 0.6357 (t80) REVERT: C 961 GLU cc_start: 0.8497 (tt0) cc_final: 0.8238 (mp0) outliers start: 94 outliers final: 42 residues processed: 394 average time/residue: 0.5554 time to fit residues: 251.0942 Evaluate side-chains 362 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 308 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 939 LYS Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 810 TYR Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 636 ARG Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 880 LEU Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 986 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 265 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 266 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 284 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN A1000 ASN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.114103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.096985 restraints weight = 32465.572| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.81 r_work: 0.3041 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23946 Z= 0.164 Angle : 0.542 9.800 32532 Z= 0.281 Chirality : 0.042 0.174 3811 Planarity : 0.004 0.049 4170 Dihedral : 5.165 58.417 3316 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.79 % Allowed : 13.53 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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 aren not related in a simple way. whole: 1.84 (0.15), residues: 3092 helix: 2.33 (0.12), residues: 1722 sheet: -0.23 (0.25), residues: 401 loop : -0.12 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 557 TYR 0.018 0.001 TYR A 540 PHE 0.019 0.001 PHE A 614 TRP 0.009 0.001 TRP A 788 HIS 0.003 0.001 HIS C 708 Details of bonding type rmsd covalent geometry : bond 0.00381 (23946) covalent geometry : angle 0.54176 (32532) hydrogen bonds : bond 0.04384 ( 1606) hydrogen bonds : angle 4.79624 ( 4890) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 331 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8033 (mp) REVERT: A 124 GLN cc_start: 0.8955 (tt0) cc_final: 0.8552 (tt0) REVERT: A 245 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8442 (mt-10) REVERT: A 298 ASN cc_start: 0.8362 (t0) cc_final: 0.8055 (t0) REVERT: A 301 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8336 (m-30) REVERT: A 314 GLU cc_start: 0.8052 (tp30) cc_final: 0.7636 (tp30) REVERT: A 339 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: A 407 ASP cc_start: 0.8437 (t0) cc_final: 0.8166 (t0) REVERT: A 423 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7896 (mm-30) REVERT: A 518 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.6646 (tpt) REVERT: A 602 LYS cc_start: 0.8431 (ptmt) cc_final: 0.8128 (ptmm) REVERT: A 632 ASP cc_start: 0.8489 (t0) cc_final: 0.8228 (t70) REVERT: A 865 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8134 (tt0) REVERT: A 939 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8604 (ttpp) REVERT: B 8 ARG cc_start: 0.7859 (mtt180) cc_final: 0.7562 (mtt90) REVERT: B 29 LYS cc_start: 0.8400 (mmtt) cc_final: 0.7952 (tttt) REVERT: B 184 MET cc_start: 0.9300 (tpp) cc_final: 0.8744 (tpp) REVERT: B 307 ARG cc_start: 0.7886 (mtt-85) cc_final: 0.7644 (mtm-85) REVERT: B 518 MET cc_start: 0.7371 (mmm) cc_final: 0.6618 (ttp) REVERT: B 527 THR cc_start: 0.8324 (m) cc_final: 0.8031 (p) REVERT: B 614 PHE cc_start: 0.8766 (t80) cc_final: 0.8546 (t80) REVERT: B 656 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8069 (mm-40) REVERT: B 661 MET cc_start: 0.8492 (mmt) cc_final: 0.8154 (mtt) REVERT: B 810 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7266 (t80) REVERT: B 891 TYR cc_start: 0.8513 (m-80) cc_final: 0.7564 (m-80) REVERT: B 969 MET cc_start: 0.8862 (mtp) cc_final: 0.8564 (mmm) REVERT: B 1006 VAL cc_start: 0.9234 (OUTLIER) cc_final: 0.9028 (m) REVERT: C 68 ASN cc_start: 0.9094 (m-40) cc_final: 0.8887 (m110) REVERT: C 188 MET cc_start: 0.9398 (mtm) cc_final: 0.9097 (mtm) REVERT: C 226 LYS cc_start: 0.8859 (tptt) cc_final: 0.8097 (mppt) REVERT: C 276 ASP cc_start: 0.8491 (m-30) cc_final: 0.8257 (m-30) REVERT: C 346 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: C 355 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8154 (tpt) REVERT: C 356 TYR cc_start: 0.8213 (t80) cc_final: 0.7916 (t80) REVERT: C 432 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7506 (mtt-85) REVERT: C 435 MET cc_start: 0.8626 (mmm) cc_final: 0.7985 (mmm) REVERT: C 496 MET cc_start: 0.5841 (tpt) cc_final: 0.5621 (tpt) REVERT: C 518 MET cc_start: 0.6491 (tpp) cc_final: 0.6160 (tmt) REVERT: C 521 LYS cc_start: 0.8032 (ttpp) cc_final: 0.7821 (ptmm) REVERT: C 592 GLU cc_start: 0.8286 (tp30) cc_final: 0.8058 (mt-10) REVERT: C 636 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8141 (ptt180) REVERT: C 667 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7758 (mt) REVERT: C 680 ASP cc_start: 0.7813 (m-30) cc_final: 0.7566 (m-30) REVERT: C 783 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8160 (pt0) REVERT: C 917 PHE cc_start: 0.7138 (m-10) cc_final: 0.6347 (t80) REVERT: C 918 ARG cc_start: 0.8331 (mmm-85) cc_final: 0.6844 (mpt180) REVERT: C 961 GLU cc_start: 0.8518 (tt0) cc_final: 0.8244 (mp0) outliers start: 95 outliers final: 47 residues processed: 391 average time/residue: 0.5488 time to fit residues: 248.1764 Evaluate side-chains 372 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 310 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 939 LYS Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 810 TYR Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 636 ARG Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 744 ASP Chi-restraints excluded: chain C residue 783 GLU Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 880 LEU Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 986 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 202 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 300 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN B 81 ASN B 195 ASN C 150 ASN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.097876 restraints weight = 32241.853| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.81 r_work: 0.3058 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23946 Z= 0.136 Angle : 0.522 9.134 32532 Z= 0.270 Chirality : 0.041 0.171 3811 Planarity : 0.004 0.050 4170 Dihedral : 5.061 57.968 3315 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.63 % Allowed : 14.33 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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 aren not related in a simple way. whole: 1.90 (0.15), residues: 3092 helix: 2.37 (0.12), residues: 1725 sheet: -0.21 (0.25), residues: 403 loop : -0.09 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 557 TYR 0.017 0.001 TYR A 540 PHE 0.028 0.001 PHE A 362 TRP 0.009 0.001 TRP A 788 HIS 0.002 0.000 HIS C 708 Details of bonding type rmsd covalent geometry : bond 0.00309 (23946) covalent geometry : angle 0.52172 (32532) hydrogen bonds : bond 0.04122 ( 1606) hydrogen bonds : angle 4.67874 ( 4890) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 328 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8034 (mp) REVERT: A 245 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8434 (mt-10) REVERT: A 298 ASN cc_start: 0.8342 (t0) cc_final: 0.8087 (t0) REVERT: A 314 GLU cc_start: 0.8059 (tp30) cc_final: 0.7636 (tp30) REVERT: A 321 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8599 (mtt) REVERT: A 339 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7873 (mp0) REVERT: A 407 ASP cc_start: 0.8478 (t0) cc_final: 0.8133 (t0) REVERT: A 518 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.6631 (tpt) REVERT: A 602 LYS cc_start: 0.8410 (ptmt) cc_final: 0.8096 (ptmm) REVERT: A 632 ASP cc_start: 0.8508 (t0) cc_final: 0.8240 (t70) REVERT: A 865 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: A 939 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8540 (ttpp) REVERT: B 8 ARG cc_start: 0.7838 (mtt180) cc_final: 0.7346 (mtt90) REVERT: B 29 LYS cc_start: 0.8386 (mmtt) cc_final: 0.7919 (tttt) REVERT: B 184 MET cc_start: 0.9304 (tpp) cc_final: 0.8764 (tpp) REVERT: B 307 ARG cc_start: 0.7927 (mtt-85) cc_final: 0.7680 (mtm-85) REVERT: B 498 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8244 (mppt) REVERT: B 518 MET cc_start: 0.7324 (mmm) cc_final: 0.6554 (ttp) REVERT: B 614 PHE cc_start: 0.8725 (t80) cc_final: 0.8505 (t80) REVERT: B 656 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8083 (mm-40) REVERT: B 661 MET cc_start: 0.8478 (mmt) cc_final: 0.8140 (mtt) REVERT: B 810 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.7227 (t80) REVERT: B 891 TYR cc_start: 0.8471 (m-80) cc_final: 0.7493 (m-80) REVERT: B 969 MET cc_start: 0.8845 (mtp) cc_final: 0.8540 (mmm) REVERT: C 68 ASN cc_start: 0.9110 (m-40) cc_final: 0.8894 (m110) REVERT: C 188 MET cc_start: 0.9400 (mtm) cc_final: 0.9150 (mtm) REVERT: C 226 LYS cc_start: 0.8864 (tptt) cc_final: 0.8099 (mppt) REVERT: C 276 ASP cc_start: 0.8467 (m-30) cc_final: 0.8238 (m-30) REVERT: C 284 GLN cc_start: 0.8199 (tt0) cc_final: 0.7858 (mt0) REVERT: C 346 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: C 355 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.8089 (tpt) REVERT: C 356 TYR cc_start: 0.8117 (t80) cc_final: 0.7744 (t80) REVERT: C 432 ARG cc_start: 0.7939 (ttm-80) cc_final: 0.7360 (mtt-85) REVERT: C 435 MET cc_start: 0.8643 (mmm) cc_final: 0.8032 (mmm) REVERT: C 518 MET cc_start: 0.6450 (tpp) cc_final: 0.6109 (tmt) REVERT: C 636 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8088 (ptt180) REVERT: C 667 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7747 (mt) REVERT: C 680 ASP cc_start: 0.7784 (m-30) cc_final: 0.7511 (m-30) REVERT: C 783 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8118 (pt0) REVERT: C 906 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7529 (mt) REVERT: C 917 PHE cc_start: 0.7118 (m-10) cc_final: 0.6329 (t80) REVERT: C 918 ARG cc_start: 0.8310 (mmm-85) cc_final: 0.6812 (mpt180) REVERT: C 961 GLU cc_start: 0.8471 (tt0) cc_final: 0.8221 (mp0) outliers start: 91 outliers final: 44 residues processed: 386 average time/residue: 0.5510 time to fit residues: 245.6401 Evaluate side-chains 370 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 311 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 939 LYS Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 810 TYR Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain B residue 1030 ARG Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 636 ARG Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 744 ASP Chi-restraints excluded: chain C residue 783 GLU Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 981 PHE Chi-restraints excluded: chain C residue 985 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 168 optimal weight: 1.9990 chunk 42 optimal weight: 0.0470 chunk 116 optimal weight: 0.8980 chunk 304 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 193 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 289 optimal weight: 10.0000 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN C 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.116100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.098976 restraints weight = 32555.170| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.82 r_work: 0.3073 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23946 Z= 0.122 Angle : 0.516 8.923 32532 Z= 0.265 Chirality : 0.041 0.181 3811 Planarity : 0.004 0.051 4170 Dihedral : 4.959 58.161 3313 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.27 % Allowed : 15.00 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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 aren not related in a simple way. whole: 1.93 (0.15), residues: 3092 helix: 2.39 (0.12), residues: 1732 sheet: -0.18 (0.25), residues: 391 loop : -0.08 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 557 TYR 0.016 0.001 TYR A 540 PHE 0.017 0.001 PHE A 571 TRP 0.009 0.001 TRP A 788 HIS 0.003 0.001 HIS A 525 Details of bonding type rmsd covalent geometry : bond 0.00272 (23946) covalent geometry : angle 0.51592 (32532) hydrogen bonds : bond 0.03922 ( 1606) hydrogen bonds : angle 4.58893 ( 4890) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 339 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8036 (mp) REVERT: A 124 GLN cc_start: 0.9002 (tt0) cc_final: 0.8798 (tt0) REVERT: A 245 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8477 (mt-10) REVERT: A 298 ASN cc_start: 0.8323 (t0) cc_final: 0.8079 (t0) REVERT: A 314 GLU cc_start: 0.8057 (tp30) cc_final: 0.7611 (tp30) REVERT: A 321 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8578 (mtt) REVERT: A 339 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: A 407 ASP cc_start: 0.8488 (t0) cc_final: 0.8143 (t0) REVERT: A 518 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.6652 (tpt) REVERT: A 602 LYS cc_start: 0.8385 (ptmt) cc_final: 0.8057 (ptmm) REVERT: A 632 ASP cc_start: 0.8496 (t0) cc_final: 0.8214 (t70) REVERT: A 865 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8046 (tt0) REVERT: A 939 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8570 (ttpp) REVERT: A 1010 MET cc_start: 0.8907 (tpp) cc_final: 0.8639 (mmp) REVERT: B 8 ARG cc_start: 0.7822 (mtt180) cc_final: 0.7341 (mtt90) REVERT: B 29 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7902 (tttt) REVERT: B 128 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8559 (p) REVERT: B 184 MET cc_start: 0.9297 (tpp) cc_final: 0.8753 (tpp) REVERT: B 307 ARG cc_start: 0.7927 (mtt-85) cc_final: 0.7678 (mtm-85) REVERT: B 518 MET cc_start: 0.7327 (mmm) cc_final: 0.6556 (ttp) REVERT: B 557 ARG cc_start: 0.8279 (mtp-110) cc_final: 0.7933 (ptm160) REVERT: B 656 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8077 (mm-40) REVERT: B 661 MET cc_start: 0.8475 (mmt) cc_final: 0.8104 (mtt) REVERT: B 810 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7260 (t80) REVERT: B 891 TYR cc_start: 0.8454 (m-80) cc_final: 0.7519 (m-80) REVERT: B 969 MET cc_start: 0.8832 (mtp) cc_final: 0.8511 (mmm) REVERT: C 73 ASP cc_start: 0.8995 (m-30) cc_final: 0.8754 (m-30) REVERT: C 188 MET cc_start: 0.9399 (mtm) cc_final: 0.9182 (mtm) REVERT: C 226 LYS cc_start: 0.8832 (tptt) cc_final: 0.8057 (mppt) REVERT: C 276 ASP cc_start: 0.8445 (m-30) cc_final: 0.8219 (m-30) REVERT: C 284 GLN cc_start: 0.8288 (tt0) cc_final: 0.7960 (mt0) REVERT: C 346 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: C 356 TYR cc_start: 0.8188 (t80) cc_final: 0.7859 (t80) REVERT: C 432 ARG cc_start: 0.7923 (ttm-80) cc_final: 0.7326 (mtt-85) REVERT: C 435 MET cc_start: 0.8628 (mmm) cc_final: 0.8038 (mmm) REVERT: C 518 MET cc_start: 0.6499 (tpp) cc_final: 0.6176 (tmt) REVERT: C 592 GLU cc_start: 0.8199 (tp30) cc_final: 0.7938 (mt-10) REVERT: C 636 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8120 (ptt180) REVERT: C 667 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7607 (mt) REVERT: C 680 ASP cc_start: 0.7742 (m-30) cc_final: 0.7521 (m-30) REVERT: C 734 LYS cc_start: 0.8790 (mttt) cc_final: 0.8501 (mtmt) REVERT: C 906 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7375 (mt) REVERT: C 917 PHE cc_start: 0.7122 (m-10) cc_final: 0.6336 (t80) REVERT: C 918 ARG cc_start: 0.8241 (mmm-85) cc_final: 0.6817 (mpt180) REVERT: C 961 GLU cc_start: 0.8446 (tt0) cc_final: 0.8157 (pm20) outliers start: 82 outliers final: 40 residues processed: 394 average time/residue: 0.5491 time to fit residues: 250.2549 Evaluate side-chains 379 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 326 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 939 LYS Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 810 TYR Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain B residue 1030 ARG Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 636 ARG Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 906 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 6 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 25 optimal weight: 0.2980 chunk 231 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN C 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.098288 restraints weight = 32291.257| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.81 r_work: 0.3063 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23946 Z= 0.141 Angle : 0.533 9.163 32532 Z= 0.272 Chirality : 0.041 0.208 3811 Planarity : 0.004 0.051 4170 Dihedral : 4.969 58.061 3313 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.11 % Allowed : 15.52 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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 aren not related in a simple way. whole: 1.91 (0.15), residues: 3092 helix: 2.36 (0.12), residues: 1731 sheet: -0.12 (0.25), residues: 400 loop : -0.10 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 557 TYR 0.017 0.001 TYR A 540 PHE 0.028 0.001 PHE A 362 TRP 0.008 0.001 TRP A 788 HIS 0.002 0.001 HIS C 525 Details of bonding type rmsd covalent geometry : bond 0.00323 (23946) covalent geometry : angle 0.53309 (32532) hydrogen bonds : bond 0.04033 ( 1606) hydrogen bonds : angle 4.59243 ( 4890) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 330 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8036 (mp) REVERT: A 124 GLN cc_start: 0.8991 (tt0) cc_final: 0.8779 (tt0) REVERT: A 245 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8461 (mt-10) REVERT: A 298 ASN cc_start: 0.8322 (t0) cc_final: 0.8049 (t0) REVERT: A 314 GLU cc_start: 0.8049 (tp30) cc_final: 0.7594 (tp30) REVERT: A 321 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8518 (mtt) REVERT: A 339 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: A 407 ASP cc_start: 0.8508 (t0) cc_final: 0.8175 (t0) REVERT: A 518 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.6634 (tpt) REVERT: A 602 LYS cc_start: 0.8369 (ptmt) cc_final: 0.8050 (ptmm) REVERT: A 632 ASP cc_start: 0.8518 (t0) cc_final: 0.8217 (t70) REVERT: A 865 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: A 939 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8580 (ttpp) REVERT: A 1010 MET cc_start: 0.8908 (tpp) cc_final: 0.8646 (mmm) REVERT: B 8 ARG cc_start: 0.7819 (mtt180) cc_final: 0.7350 (mtt90) REVERT: B 29 LYS cc_start: 0.8437 (mmtt) cc_final: 0.7979 (tttt) REVERT: B 128 SER cc_start: 0.8768 (OUTLIER) cc_final: 0.8547 (p) REVERT: B 184 MET cc_start: 0.9309 (tpp) cc_final: 0.8748 (mmm) REVERT: B 307 ARG cc_start: 0.7983 (mtt-85) cc_final: 0.7695 (mtm-85) REVERT: B 518 MET cc_start: 0.7243 (mmm) cc_final: 0.6434 (ttp) REVERT: B 557 ARG cc_start: 0.8168 (mtp-110) cc_final: 0.7745 (ptm160) REVERT: B 656 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8105 (mm-40) REVERT: B 661 MET cc_start: 0.8469 (mmt) cc_final: 0.8095 (mtt) REVERT: B 810 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.7160 (t80) REVERT: B 891 TYR cc_start: 0.8457 (m-80) cc_final: 0.7492 (m-80) REVERT: B 969 MET cc_start: 0.8808 (mtp) cc_final: 0.8465 (mmm) REVERT: B 976 MET cc_start: 0.9132 (mtm) cc_final: 0.8929 (mtp) REVERT: C 69 MET cc_start: 0.9315 (mmt) cc_final: 0.9032 (mmp) REVERT: C 73 ASP cc_start: 0.9003 (m-30) cc_final: 0.8756 (m-30) REVERT: C 188 MET cc_start: 0.9402 (mtm) cc_final: 0.9177 (mtm) REVERT: C 226 LYS cc_start: 0.8829 (tptt) cc_final: 0.8057 (mppt) REVERT: C 276 ASP cc_start: 0.8466 (m-30) cc_final: 0.8251 (m-30) REVERT: C 284 GLN cc_start: 0.8247 (tt0) cc_final: 0.7917 (mt0) REVERT: C 346 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7857 (mt-10) REVERT: C 356 TYR cc_start: 0.8163 (t80) cc_final: 0.7820 (t80) REVERT: C 417 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: C 432 ARG cc_start: 0.7924 (ttm-80) cc_final: 0.7327 (mtt-85) REVERT: C 435 MET cc_start: 0.8631 (mmm) cc_final: 0.8029 (mmm) REVERT: C 518 MET cc_start: 0.6557 (tpp) cc_final: 0.6131 (tmt) REVERT: C 592 GLU cc_start: 0.8197 (tp30) cc_final: 0.7994 (tp30) REVERT: C 636 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8483 (ptt90) REVERT: C 667 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7587 (mt) REVERT: C 680 ASP cc_start: 0.7753 (m-30) cc_final: 0.7527 (m-30) REVERT: C 734 LYS cc_start: 0.8775 (mttt) cc_final: 0.8483 (mtmt) REVERT: C 783 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8161 (pt0) REVERT: C 906 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7377 (mt) REVERT: C 917 PHE cc_start: 0.7101 (m-10) cc_final: 0.6273 (t80) REVERT: C 918 ARG cc_start: 0.8274 (mmm-85) cc_final: 0.6844 (mpt180) REVERT: C 961 GLU cc_start: 0.8452 (tt0) cc_final: 0.8179 (pm20) outliers start: 78 outliers final: 46 residues processed: 384 average time/residue: 0.5591 time to fit residues: 248.3695 Evaluate side-chains 384 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 323 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 939 LYS Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 810 TYR Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain B residue 1030 ARG Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 636 ARG Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 733 GLU Chi-restraints excluded: chain C residue 783 GLU Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 985 VAL Chi-restraints excluded: chain C residue 1012 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 203 optimal weight: 0.7980 chunk 237 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 281 optimal weight: 0.9990 chunk 264 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 286 optimal weight: 0.8980 chunk 208 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN C 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.115757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.098632 restraints weight = 32340.452| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.82 r_work: 0.3065 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23946 Z= 0.139 Angle : 0.536 7.987 32532 Z= 0.274 Chirality : 0.041 0.184 3811 Planarity : 0.004 0.051 4170 Dihedral : 4.968 57.778 3313 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.83 % Allowed : 16.16 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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 aren not related in a simple way. whole: 1.89 (0.15), residues: 3092 helix: 2.34 (0.12), residues: 1731 sheet: -0.10 (0.25), residues: 401 loop : -0.10 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 557 TYR 0.016 0.001 TYR A 540 PHE 0.026 0.001 PHE C 614 TRP 0.007 0.001 TRP A 788 HIS 0.003 0.001 HIS C 525 Details of bonding type rmsd covalent geometry : bond 0.00318 (23946) covalent geometry : angle 0.53603 (32532) hydrogen bonds : bond 0.04024 ( 1606) hydrogen bonds : angle 4.58783 ( 4890) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 332 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ILE cc_start: 0.9011 (mp) cc_final: 0.8607 (mp) REVERT: A 28 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8038 (mp) REVERT: A 245 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8465 (mt-10) REVERT: A 298 ASN cc_start: 0.8334 (t0) cc_final: 0.8068 (t0) REVERT: A 314 GLU cc_start: 0.8052 (tp30) cc_final: 0.7588 (tp30) REVERT: A 321 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8539 (mtt) REVERT: A 339 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: A 407 ASP cc_start: 0.8492 (t0) cc_final: 0.8162 (t0) REVERT: A 518 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.6646 (tpt) REVERT: A 602 LYS cc_start: 0.8374 (ptmt) cc_final: 0.8054 (ptmm) REVERT: A 632 ASP cc_start: 0.8519 (t0) cc_final: 0.8217 (t70) REVERT: A 865 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8048 (tt0) REVERT: A 939 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8554 (ttpp) REVERT: B 8 ARG cc_start: 0.7833 (mtt180) cc_final: 0.7368 (mtt90) REVERT: B 29 LYS cc_start: 0.8350 (mmtt) cc_final: 0.7950 (tttt) REVERT: B 128 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8558 (p) REVERT: B 184 MET cc_start: 0.9299 (tpp) cc_final: 0.8733 (mmm) REVERT: B 307 ARG cc_start: 0.7981 (mtt-85) cc_final: 0.7695 (mtm-85) REVERT: B 512 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8377 (m-10) REVERT: B 518 MET cc_start: 0.7273 (mmm) cc_final: 0.6463 (ttp) REVERT: B 557 ARG cc_start: 0.8159 (mtp-110) cc_final: 0.7753 (ptm160) REVERT: B 656 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8099 (mm-40) REVERT: B 661 MET cc_start: 0.8483 (mmt) cc_final: 0.8115 (mtt) REVERT: B 810 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7116 (t80) REVERT: B 891 TYR cc_start: 0.8449 (m-80) cc_final: 0.7504 (m-80) REVERT: B 969 MET cc_start: 0.8815 (mtp) cc_final: 0.8495 (mmm) REVERT: C 73 ASP cc_start: 0.8998 (m-30) cc_final: 0.8753 (m-30) REVERT: C 188 MET cc_start: 0.9407 (mtm) cc_final: 0.9115 (mtm) REVERT: C 226 LYS cc_start: 0.8819 (tptt) cc_final: 0.8085 (mppt) REVERT: C 276 ASP cc_start: 0.8445 (m-30) cc_final: 0.8223 (m-30) REVERT: C 284 GLN cc_start: 0.8236 (tt0) cc_final: 0.7955 (mt0) REVERT: C 307 ARG cc_start: 0.8667 (mtt-85) cc_final: 0.8374 (mtt180) REVERT: C 346 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: C 356 TYR cc_start: 0.8187 (t80) cc_final: 0.7825 (t80) REVERT: C 417 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: C 432 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7337 (mtt-85) REVERT: C 435 MET cc_start: 0.8623 (mmm) cc_final: 0.8023 (mmm) REVERT: C 518 MET cc_start: 0.6575 (tpp) cc_final: 0.6151 (tmt) REVERT: C 542 VAL cc_start: 0.8543 (t) cc_final: 0.8328 (p) REVERT: C 592 GLU cc_start: 0.8225 (tp30) cc_final: 0.7951 (mt-10) REVERT: C 636 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8478 (ptt90) REVERT: C 667 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7611 (mt) REVERT: C 680 ASP cc_start: 0.7734 (m-30) cc_final: 0.7516 (m-30) REVERT: C 734 LYS cc_start: 0.8786 (mttt) cc_final: 0.8491 (mtmt) REVERT: C 783 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8161 (pt0) REVERT: C 906 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7409 (mt) REVERT: C 917 PHE cc_start: 0.7109 (m-10) cc_final: 0.6282 (t80) REVERT: C 918 ARG cc_start: 0.8296 (mmm-85) cc_final: 0.6881 (mpt180) REVERT: C 961 GLU cc_start: 0.8476 (tt0) cc_final: 0.8181 (pm20) outliers start: 71 outliers final: 43 residues processed: 382 average time/residue: 0.5474 time to fit residues: 240.6427 Evaluate side-chains 385 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 326 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 939 LYS Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 810 TYR Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain B residue 1030 ARG Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 636 ARG Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 733 GLU Chi-restraints excluded: chain C residue 783 GLU Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 985 VAL Chi-restraints excluded: chain C residue 1012 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 282 optimal weight: 2.9990 chunk 199 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 258 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 293 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN C 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.098830 restraints weight = 32548.229| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.83 r_work: 0.3070 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23946 Z= 0.133 Angle : 0.533 8.144 32532 Z= 0.272 Chirality : 0.041 0.173 3811 Planarity : 0.004 0.051 4170 Dihedral : 4.935 57.762 3312 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.67 % Allowed : 16.68 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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 aren not related in a simple way. whole: 1.91 (0.15), residues: 3092 helix: 2.36 (0.12), residues: 1729 sheet: -0.10 (0.25), residues: 403 loop : -0.09 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 557 TYR 0.020 0.001 TYR C 856 PHE 0.028 0.001 PHE A 362 TRP 0.007 0.001 TRP C 788 HIS 0.003 0.001 HIS C 525 Details of bonding type rmsd covalent geometry : bond 0.00303 (23946) covalent geometry : angle 0.53330 (32532) hydrogen bonds : bond 0.03968 ( 1606) hydrogen bonds : angle 4.57225 ( 4890) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 338 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8035 (mp) REVERT: A 245 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8471 (mt-10) REVERT: A 298 ASN cc_start: 0.8353 (t0) cc_final: 0.8082 (t0) REVERT: A 321 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8540 (mtt) REVERT: A 339 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: A 407 ASP cc_start: 0.8477 (t0) cc_final: 0.8099 (t0) REVERT: A 518 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.6649 (tpt) REVERT: A 602 LYS cc_start: 0.8371 (ptmt) cc_final: 0.8045 (ptmm) REVERT: A 632 ASP cc_start: 0.8505 (t0) cc_final: 0.8207 (t70) REVERT: A 939 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8545 (ttpp) REVERT: B 8 ARG cc_start: 0.7847 (mtt180) cc_final: 0.7390 (mtt90) REVERT: B 29 LYS cc_start: 0.8326 (mmtt) cc_final: 0.7958 (tttt) REVERT: B 69 MET cc_start: 0.8733 (mmt) cc_final: 0.8506 (mmt) REVERT: B 184 MET cc_start: 0.9297 (tpp) cc_final: 0.8733 (mmm) REVERT: B 307 ARG cc_start: 0.7964 (mtt-85) cc_final: 0.7690 (mtm-85) REVERT: B 512 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8377 (m-10) REVERT: B 518 MET cc_start: 0.7233 (mmm) cc_final: 0.6504 (ttp) REVERT: B 557 ARG cc_start: 0.8147 (mtp-110) cc_final: 0.7756 (ptm160) REVERT: B 656 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8114 (mm-40) REVERT: B 661 MET cc_start: 0.8487 (mmt) cc_final: 0.8121 (mtt) REVERT: B 810 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.7023 (t80) REVERT: B 891 TYR cc_start: 0.8435 (m-80) cc_final: 0.7490 (m-80) REVERT: B 969 MET cc_start: 0.8756 (mtp) cc_final: 0.8426 (mmm) REVERT: C 8 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7565 (mmt90) REVERT: C 73 ASP cc_start: 0.8998 (m-30) cc_final: 0.8750 (m-30) REVERT: C 188 MET cc_start: 0.9401 (mtm) cc_final: 0.9119 (mtm) REVERT: C 226 LYS cc_start: 0.8809 (tptt) cc_final: 0.7981 (mppt) REVERT: C 284 GLN cc_start: 0.8234 (tt0) cc_final: 0.7953 (mt0) REVERT: C 307 ARG cc_start: 0.8684 (mtt-85) cc_final: 0.8385 (mtt180) REVERT: C 346 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7870 (mt-10) REVERT: C 356 TYR cc_start: 0.8230 (t80) cc_final: 0.7867 (t80) REVERT: C 417 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7703 (tm-30) REVERT: C 432 ARG cc_start: 0.7926 (ttm-80) cc_final: 0.7338 (mtt-85) REVERT: C 435 MET cc_start: 0.8636 (mmm) cc_final: 0.8046 (mmm) REVERT: C 518 MET cc_start: 0.6586 (tpp) cc_final: 0.6160 (tmt) REVERT: C 542 VAL cc_start: 0.8533 (t) cc_final: 0.8307 (p) REVERT: C 592 GLU cc_start: 0.8210 (tp30) cc_final: 0.7977 (mt-10) REVERT: C 636 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8523 (ptt90) REVERT: C 667 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7602 (mt) REVERT: C 680 ASP cc_start: 0.7718 (m-30) cc_final: 0.7506 (m-30) REVERT: C 783 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8167 (pt0) REVERT: C 906 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7454 (mt) REVERT: C 917 PHE cc_start: 0.7112 (m-10) cc_final: 0.6273 (t80) REVERT: C 918 ARG cc_start: 0.8300 (mmm-85) cc_final: 0.6897 (mpt180) REVERT: C 961 GLU cc_start: 0.8508 (tt0) cc_final: 0.8186 (pm20) outliers start: 67 outliers final: 42 residues processed: 386 average time/residue: 0.5485 time to fit residues: 245.5284 Evaluate side-chains 387 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 330 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 939 LYS Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 810 TYR Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain B residue 1030 ARG Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 636 ARG Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 733 GLU Chi-restraints excluded: chain C residue 783 GLU Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 985 VAL Chi-restraints excluded: chain C residue 1012 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 219 optimal weight: 3.9990 chunk 36 optimal weight: 0.0040 chunk 37 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 196 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN C 736 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.116767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.099604 restraints weight = 32426.790| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.83 r_work: 0.3076 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23946 Z= 0.129 Angle : 0.534 8.678 32532 Z= 0.273 Chirality : 0.041 0.177 3811 Planarity : 0.004 0.052 4170 Dihedral : 4.923 57.799 3312 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.35 % Allowed : 16.96 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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 aren not related in a simple way. whole: 1.92 (0.15), residues: 3092 helix: 2.35 (0.12), residues: 1729 sheet: -0.07 (0.26), residues: 391 loop : -0.08 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 557 TYR 0.016 0.001 TYR A 540 PHE 0.022 0.001 PHE C 614 TRP 0.010 0.001 TRP C 753 HIS 0.002 0.001 HIS B 691 Details of bonding type rmsd covalent geometry : bond 0.00293 (23946) covalent geometry : angle 0.53388 (32532) hydrogen bonds : bond 0.03942 ( 1606) hydrogen bonds : angle 4.55107 ( 4890) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 329 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8035 (mp) REVERT: A 245 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8433 (mt-10) REVERT: A 298 ASN cc_start: 0.8350 (t0) cc_final: 0.8083 (t0) REVERT: A 339 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: A 518 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.6644 (tpt) REVERT: A 602 LYS cc_start: 0.8366 (ptmt) cc_final: 0.8043 (ptmm) REVERT: A 632 ASP cc_start: 0.8494 (t0) cc_final: 0.8188 (t70) REVERT: A 939 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8662 (tttm) REVERT: A 1010 MET cc_start: 0.8905 (tpp) cc_final: 0.8509 (mmp) REVERT: B 8 ARG cc_start: 0.7842 (mtt180) cc_final: 0.7367 (mtt90) REVERT: B 29 LYS cc_start: 0.8340 (mmtt) cc_final: 0.7960 (tttt) REVERT: B 69 MET cc_start: 0.8791 (mmt) cc_final: 0.8499 (mmt) REVERT: B 184 MET cc_start: 0.9290 (tpp) cc_final: 0.8720 (tpp) REVERT: B 307 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7704 (mtm-85) REVERT: B 512 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8407 (m-10) REVERT: B 518 MET cc_start: 0.7222 (mmm) cc_final: 0.6497 (ttp) REVERT: B 557 ARG cc_start: 0.8059 (mtp-110) cc_final: 0.7712 (ptm160) REVERT: B 656 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8137 (mm-40) REVERT: B 661 MET cc_start: 0.8503 (mmt) cc_final: 0.8142 (mtt) REVERT: B 810 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.7020 (t80) REVERT: B 969 MET cc_start: 0.8756 (mtp) cc_final: 0.8419 (mmm) REVERT: C 8 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7550 (mmt90) REVERT: C 73 ASP cc_start: 0.9004 (m-30) cc_final: 0.8758 (m-30) REVERT: C 188 MET cc_start: 0.9399 (mtm) cc_final: 0.9125 (mtm) REVERT: C 226 LYS cc_start: 0.8793 (tptt) cc_final: 0.7973 (mppt) REVERT: C 284 GLN cc_start: 0.8214 (tt0) cc_final: 0.7951 (mt0) REVERT: C 307 ARG cc_start: 0.8679 (mtt-85) cc_final: 0.8373 (mtt180) REVERT: C 346 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: C 356 TYR cc_start: 0.8219 (t80) cc_final: 0.7876 (t80) REVERT: C 417 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: C 432 ARG cc_start: 0.7889 (ttm-80) cc_final: 0.7298 (mtt-85) REVERT: C 435 MET cc_start: 0.8631 (mmm) cc_final: 0.8052 (mmm) REVERT: C 518 MET cc_start: 0.6601 (tpp) cc_final: 0.6159 (tmt) REVERT: C 542 VAL cc_start: 0.8513 (t) cc_final: 0.8285 (p) REVERT: C 592 GLU cc_start: 0.8020 (tp30) cc_final: 0.7773 (tp30) REVERT: C 667 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7549 (mt) REVERT: C 680 ASP cc_start: 0.7712 (m-30) cc_final: 0.7461 (m-30) REVERT: C 783 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8157 (pt0) REVERT: C 906 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7380 (mt) REVERT: C 917 PHE cc_start: 0.7154 (m-10) cc_final: 0.6285 (t80) REVERT: C 918 ARG cc_start: 0.8291 (mmm-85) cc_final: 0.6885 (mpt180) REVERT: C 961 GLU cc_start: 0.8494 (tt0) cc_final: 0.8138 (pm20) outliers start: 59 outliers final: 39 residues processed: 377 average time/residue: 0.5618 time to fit residues: 244.1460 Evaluate side-chains 370 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 318 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 939 LYS Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 810 TYR Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain B residue 1030 ARG Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 733 GLU Chi-restraints excluded: chain C residue 783 GLU Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 985 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 220 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 230 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 257 optimal weight: 3.9990 chunk 267 optimal weight: 0.7980 chunk 279 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 241 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN C 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.116691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.099477 restraints weight = 32304.888| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.83 r_work: 0.3077 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23946 Z= 0.132 Angle : 0.541 10.590 32532 Z= 0.275 Chirality : 0.041 0.170 3811 Planarity : 0.004 0.052 4170 Dihedral : 4.731 57.671 3305 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.08 % Allowed : 17.52 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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 aren not related in a simple way. whole: 1.91 (0.15), residues: 3092 helix: 2.34 (0.12), residues: 1729 sheet: -0.10 (0.25), residues: 404 loop : -0.06 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 918 TYR 0.016 0.001 TYR A 540 PHE 0.030 0.001 PHE A 362 TRP 0.007 0.001 TRP C 753 HIS 0.002 0.001 HIS A 708 Details of bonding type rmsd covalent geometry : bond 0.00301 (23946) covalent geometry : angle 0.54103 (32532) hydrogen bonds : bond 0.03946 ( 1606) hydrogen bonds : angle 4.55107 ( 4890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7011.43 seconds wall clock time: 120 minutes 7.08 seconds (7207.08 seconds total)