Starting phenix.real_space_refine on Fri Jun 20 10:15:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ffk_29045/06_2025/8ffk_29045.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ffk_29045/06_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_29045/06_2025/8ffk_29045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ffk_29045/06_2025/8ffk_29045.map" model { file = "/net/cci-nas-00/data/ceres_data/8ffk_29045/06_2025/8ffk_29045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ffk_29045/06_2025/8ffk_29045.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'HIS: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: 13.34, per 1000 atoms: 0.57 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: 5.43 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 3.48 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: 12.81 Time building geometry restraints manager: 6.51 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: 2.930 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: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 57.310 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.110 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:13.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.070 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP C 553 HIS 0.002 0.001 HIS C 708 PHE 0.013 0.001 PHE A 571 TYR 0.018 0.001 TYR A 540 ARG 0.004 0.000 ARG A 185 Details of bonding type rmsd hydrogen bonds : bond 0.14681 ( 1606) hydrogen bonds : angle 6.71433 ( 4890) covalent geometry : bond 0.00420 (23946) covalent geometry : angle 0.55625 (32532) *********************** 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 : 2.603 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: 1.5138 time to fit residues: 890.4216 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 : 2.377 ------------------------------------------------------------------------------- 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 260 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 242 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 280 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 104 GLN B 108 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 C 635 GLN C 686 GLN C 736 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.113212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.096036 restraints weight = 32216.120| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.78 r_work: 0.3028 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23946 Z= 0.187 Angle : 0.569 8.594 32532 Z= 0.298 Chirality : 0.043 0.185 3811 Planarity : 0.004 0.036 4170 Dihedral : 5.382 59.006 3325 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.43 % Allowed : 11.37 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.15), residues: 3092 helix: 2.31 (0.12), residues: 1719 sheet: -0.20 (0.25), residues: 399 loop : -0.01 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 788 HIS 0.003 0.001 HIS C 708 PHE 0.017 0.001 PHE B 681 TYR 0.019 0.001 TYR A 540 ARG 0.005 0.001 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.05000 ( 1606) hydrogen bonds : angle 5.16953 ( 4890) covalent geometry : bond 0.00432 (23946) covalent geometry : angle 0.56856 (32532) *********************** 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: 86 poor density : 358 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8088 (mp) REVERT: A 69 MET cc_start: 0.9513 (mmt) cc_final: 0.9305 (mmt) REVERT: A 124 GLN cc_start: 0.8844 (tt0) cc_final: 0.8607 (tt0) REVERT: A 184 MET cc_start: 0.9452 (tpp) cc_final: 0.9207 (tpp) REVERT: A 298 ASN cc_start: 0.8308 (t0) cc_final: 0.8025 (t0) REVERT: A 301 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8323 (m-30) REVERT: A 314 GLU cc_start: 0.8048 (tp30) cc_final: 0.7626 (tp30) REVERT: A 321 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8589 (mtt) REVERT: A 480 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8663 (mp) REVERT: A 602 LYS cc_start: 0.8432 (ptmt) cc_final: 0.8098 (ptmm) REVERT: A 661 MET cc_start: 0.7754 (ttp) cc_final: 0.7548 (ttp) REVERT: A 918 ARG cc_start: 0.8410 (mmm160) cc_final: 0.6927 (mpt90) REVERT: A 1000 ASN cc_start: 0.8962 (m-40) cc_final: 0.8580 (m-40) REVERT: B 8 ARG cc_start: 0.7880 (mtt180) cc_final: 0.7478 (mtt90) REVERT: B 29 LYS cc_start: 0.8432 (mmtt) cc_final: 0.7964 (tttt) REVERT: B 184 MET cc_start: 0.9323 (tpp) cc_final: 0.8954 (tpt) REVERT: B 244 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7883 (mp0) REVERT: B 307 ARG cc_start: 0.7853 (mtt-85) cc_final: 0.7633 (mtm-85) REVERT: B 355 MET cc_start: 0.9004 (mtm) cc_final: 0.8672 (mtp) REVERT: B 518 MET cc_start: 0.7351 (mmm) cc_final: 0.6597 (ttp) REVERT: B 527 THR cc_start: 0.8361 (m) cc_final: 0.8136 (p) REVERT: B 656 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8079 (mm-40) REVERT: B 661 MET cc_start: 0.8471 (mmt) cc_final: 0.8109 (mtt) REVERT: B 729 ASP cc_start: 0.8533 (m-30) cc_final: 0.8308 (m-30) REVERT: B 810 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.7236 (t80) REVERT: B 891 TYR cc_start: 0.8511 (m-80) cc_final: 0.7687 (m-80) REVERT: B 969 MET cc_start: 0.8847 (mtp) cc_final: 0.8551 (mmm) REVERT: C 69 MET cc_start: 0.9354 (mmt) cc_final: 0.9064 (mmp) REVERT: C 188 MET cc_start: 0.9398 (mtm) cc_final: 0.9090 (mtm) REVERT: C 226 LYS cc_start: 0.8863 (tptt) cc_final: 0.8129 (mppt) REVERT: C 276 ASP cc_start: 0.8479 (m-30) cc_final: 0.8262 (m-30) REVERT: C 346 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7843 (mt-10) REVERT: C 356 TYR cc_start: 0.8183 (t80) cc_final: 0.7932 (t80) REVERT: C 432 ARG cc_start: 0.7968 (ttm-80) cc_final: 0.7543 (mtt-85) REVERT: C 435 MET cc_start: 0.8665 (mmm) cc_final: 0.8068 (mmm) REVERT: C 496 MET cc_start: 0.5913 (tpt) cc_final: 0.5628 (tpt) REVERT: C 518 MET cc_start: 0.6586 (tpp) cc_final: 0.6116 (tmt) REVERT: C 525 HIS cc_start: 0.6871 (t70) cc_final: 0.6538 (m90) REVERT: C 636 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8297 (ptt180) REVERT: C 680 ASP cc_start: 0.7746 (m-30) cc_final: 0.7517 (m-30) REVERT: C 861 MET cc_start: 0.6999 (pmm) cc_final: 0.6734 (pmt) REVERT: C 917 PHE cc_start: 0.7082 (m-10) cc_final: 0.6360 (t80) REVERT: C 961 GLU cc_start: 0.8437 (tt0) cc_final: 0.8213 (mp0) REVERT: C 1015 ILE cc_start: 0.8412 (mm) cc_final: 0.8211 (tp) outliers start: 86 outliers final: 38 residues processed: 417 average time/residue: 1.4082 time to fit residues: 675.6221 Evaluate side-chains 360 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 314 time to evaluate : 2.793 ------------------------------------------------------------------------------- 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 301 ASP Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 480 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 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 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 B residue 1018 ILE 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 456 MET 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 880 LEU 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 225 optimal weight: 0.9990 chunk 208 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 293 optimal weight: 2.9990 chunk 186 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.112921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.095817 restraints weight = 32292.801| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.79 r_work: 0.3027 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1565 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= 0.181 Angle : 0.556 8.624 32532 Z= 0.289 Chirality : 0.043 0.177 3811 Planarity : 0.004 0.047 4170 Dihedral : 5.257 58.019 3317 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.91 % Allowed : 12.77 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.15), residues: 3092 helix: 2.28 (0.12), residues: 1719 sheet: -0.24 (0.25), residues: 391 loop : -0.09 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 553 HIS 0.003 0.001 HIS C 708 PHE 0.028 0.001 PHE A 362 TYR 0.019 0.001 TYR A 540 ARG 0.007 0.000 ARG B 557 Details of bonding type rmsd hydrogen bonds : bond 0.04665 ( 1606) hydrogen bonds : angle 4.93451 ( 4890) covalent geometry : bond 0.00422 (23946) covalent geometry : angle 0.55597 (32532) *********************** 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 423 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 325 time to evaluate : 2.733 Fit side-chains REVERT: A 18 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8853 (mp) REVERT: A 28 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8142 (mp) REVERT: A 124 GLN cc_start: 0.8905 (tt0) cc_final: 0.8588 (tt0) REVERT: A 184 MET cc_start: 0.9467 (tpp) cc_final: 0.9204 (tpp) REVERT: A 245 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8367 (mt-10) REVERT: A 298 ASN cc_start: 0.8379 (t0) cc_final: 0.8106 (t0) REVERT: A 314 GLU cc_start: 0.8069 (tp30) cc_final: 0.7630 (tp30) REVERT: A 321 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8663 (mtt) REVERT: A 339 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7966 (mp0) REVERT: A 439 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8206 (pt0) REVERT: A 480 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8597 (mp) REVERT: A 518 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.6604 (tpt) REVERT: A 602 LYS cc_start: 0.8426 (ptmt) cc_final: 0.8125 (ptmm) REVERT: A 744 ASP cc_start: 0.8069 (m-30) cc_final: 0.7681 (m-30) REVERT: A 918 ARG cc_start: 0.8382 (mmm160) cc_final: 0.6894 (mpt90) REVERT: A 1000 ASN cc_start: 0.8944 (m-40) cc_final: 0.8597 (m-40) REVERT: B 8 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7661 (mtt90) REVERT: B 29 LYS cc_start: 0.8408 (mmtt) cc_final: 0.7947 (tttt) REVERT: B 184 MET cc_start: 0.9309 (tpp) cc_final: 0.8854 (tpt) REVERT: B 244 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7850 (mp0) REVERT: B 307 ARG cc_start: 0.7874 (mtt-85) cc_final: 0.7628 (mtm-85) REVERT: B 355 MET cc_start: 0.9003 (mtm) cc_final: 0.8667 (mtp) REVERT: B 498 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8370 (mptt) REVERT: B 518 MET cc_start: 0.7356 (mmm) cc_final: 0.6619 (ttp) REVERT: B 527 THR cc_start: 0.8304 (m) cc_final: 0.8036 (p) REVERT: B 656 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8100 (mm-40) REVERT: B 661 MET cc_start: 0.8470 (mmt) cc_final: 0.8122 (mtt) REVERT: B 810 TYR cc_start: 0.7953 (OUTLIER) cc_final: 0.7142 (t80) REVERT: B 891 TYR cc_start: 0.8520 (m-80) cc_final: 0.7600 (m-80) REVERT: B 969 MET cc_start: 0.8849 (mtp) cc_final: 0.8538 (mmm) REVERT: C 48 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8979 (ttt) REVERT: C 188 MET cc_start: 0.9391 (mtm) cc_final: 0.9120 (mtm) REVERT: C 226 LYS cc_start: 0.8888 (tptt) cc_final: 0.8101 (mppt) REVERT: C 276 ASP cc_start: 0.8538 (m-30) cc_final: 0.8315 (m-30) REVERT: C 346 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: C 356 TYR cc_start: 0.8208 (t80) cc_final: 0.7920 (t80) REVERT: C 432 ARG cc_start: 0.7966 (ttm-80) cc_final: 0.7509 (mtt-85) REVERT: C 435 MET cc_start: 0.8641 (mmm) cc_final: 0.8036 (mmm) REVERT: C 496 MET cc_start: 0.5871 (tpt) cc_final: 0.5570 (tpt) REVERT: C 518 MET cc_start: 0.6505 (tpp) cc_final: 0.6150 (tmt) REVERT: C 525 HIS cc_start: 0.6832 (t70) cc_final: 0.6597 (m90) REVERT: C 636 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8124 (ptt180) REVERT: C 640 GLU cc_start: 0.7222 (pm20) cc_final: 0.7019 (pm20) REVERT: C 667 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7732 (mt) REVERT: C 917 PHE cc_start: 0.7111 (m-10) cc_final: 0.6357 (t80) REVERT: C 918 ARG cc_start: 0.8349 (mmm-85) cc_final: 0.6868 (mpt180) REVERT: C 961 GLU cc_start: 0.8493 (tt0) cc_final: 0.8230 (mp0) outliers start: 98 outliers final: 44 residues processed: 390 average time/residue: 1.4038 time to fit residues: 634.8636 Evaluate side-chains 363 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 305 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE 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 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 439 GLN Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 480 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 713 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 978 SER 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 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 498 LYS Chi-restraints excluded: chain B residue 500 ILE 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 B residue 976 MET 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 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 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 106 optimal weight: 0.1980 chunk 265 optimal weight: 0.9980 chunk 89 optimal weight: 0.0270 chunk 166 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 chunk 245 optimal weight: 0.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.116284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.099076 restraints weight = 32547.350| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.83 r_work: 0.3071 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23946 Z= 0.122 Angle : 0.510 9.841 32532 Z= 0.265 Chirality : 0.041 0.169 3811 Planarity : 0.004 0.049 4170 Dihedral : 5.069 58.106 3316 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.35 % Allowed : 14.01 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.15), residues: 3092 helix: 2.40 (0.12), residues: 1721 sheet: -0.24 (0.26), residues: 385 loop : -0.05 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 553 HIS 0.002 0.000 HIS A 708 PHE 0.016 0.001 PHE A 571 TYR 0.018 0.001 TYR C 856 ARG 0.008 0.000 ARG B 557 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 1606) hydrogen bonds : angle 4.67057 ( 4890) covalent geometry : bond 0.00265 (23946) covalent geometry : angle 0.50971 (32532) *********************** 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 437 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 353 time to evaluate : 2.713 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8034 (mp) REVERT: A 124 GLN cc_start: 0.8938 (tt0) cc_final: 0.8722 (tt0) REVERT: A 245 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8414 (mt-10) REVERT: A 298 ASN cc_start: 0.8311 (t0) cc_final: 0.8095 (t0) REVERT: A 321 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8665 (mtt) REVERT: A 339 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: A 439 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8054 (pt0) REVERT: A 518 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.6621 (tpt) REVERT: A 602 LYS cc_start: 0.8411 (ptmt) cc_final: 0.8101 (ptmm) REVERT: A 865 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: A 918 ARG cc_start: 0.8293 (mmm160) cc_final: 0.6807 (mpt90) REVERT: A 996 SER cc_start: 0.8207 (p) cc_final: 0.7620 (t) REVERT: A 1000 ASN cc_start: 0.8969 (m-40) cc_final: 0.8575 (m-40) REVERT: B 8 ARG cc_start: 0.7813 (mtt180) cc_final: 0.7307 (mtt90) REVERT: B 29 LYS cc_start: 0.8357 (mmtt) cc_final: 0.7932 (tttt) REVERT: B 48 MET cc_start: 0.8483 (mmm) cc_final: 0.8222 (mmt) REVERT: B 184 MET cc_start: 0.9310 (tpp) cc_final: 0.8776 (tpp) REVERT: B 307 ARG cc_start: 0.7895 (mtt-85) cc_final: 0.7671 (mtm-85) REVERT: B 439 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: B 498 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8386 (mptt) REVERT: B 518 MET cc_start: 0.7294 (mmm) cc_final: 0.6551 (ttp) REVERT: B 527 THR cc_start: 0.8250 (m) cc_final: 0.7963 (p) REVERT: B 656 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8065 (mm-40) REVERT: B 661 MET cc_start: 0.8493 (mmt) cc_final: 0.8134 (mtt) REVERT: B 810 TYR cc_start: 0.8005 (OUTLIER) cc_final: 0.7171 (t80) REVERT: B 891 TYR cc_start: 0.8490 (m-80) cc_final: 0.7549 (m-80) REVERT: B 969 MET cc_start: 0.8853 (mtp) cc_final: 0.8542 (mmm) REVERT: B 1006 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8966 (m) REVERT: C 48 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.9005 (tpt) REVERT: C 68 ASN cc_start: 0.9110 (m-40) cc_final: 0.8892 (m110) REVERT: C 73 ASP cc_start: 0.8976 (m-30) cc_final: 0.8731 (m-30) REVERT: C 188 MET cc_start: 0.9398 (mtm) cc_final: 0.9126 (mtm) REVERT: C 226 LYS cc_start: 0.8844 (tptt) cc_final: 0.8073 (mppt) REVERT: C 276 ASP cc_start: 0.8490 (m-30) cc_final: 0.8265 (m-30) REVERT: C 284 GLN cc_start: 0.8286 (tt0) cc_final: 0.7860 (mt0) REVERT: C 346 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: C 355 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8104 (tpt) REVERT: C 356 TYR cc_start: 0.8171 (t80) cc_final: 0.7841 (t80) REVERT: C 432 ARG cc_start: 0.7946 (ttm-80) cc_final: 0.7507 (mtt-85) REVERT: C 435 MET cc_start: 0.8621 (mmm) cc_final: 0.8005 (mmm) REVERT: C 496 MET cc_start: 0.5813 (tpt) cc_final: 0.5576 (tpt) REVERT: C 518 MET cc_start: 0.6477 (tpp) cc_final: 0.6195 (tmm) REVERT: C 525 HIS cc_start: 0.6810 (t70) cc_final: 0.6525 (m90) REVERT: C 636 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8139 (ptt180) REVERT: C 658 LYS cc_start: 0.6303 (mmmt) cc_final: 0.5933 (mptp) REVERT: C 680 ASP cc_start: 0.7765 (m-30) cc_final: 0.7501 (m-30) REVERT: C 906 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7468 (mt) REVERT: C 917 PHE cc_start: 0.7050 (m-10) cc_final: 0.6319 (t80) REVERT: C 961 GLU cc_start: 0.8510 (tt0) cc_final: 0.8221 (mp0) outliers start: 84 outliers final: 30 residues processed: 410 average time/residue: 1.3148 time to fit residues: 623.5756 Evaluate side-chains 367 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 321 time to evaluate : 2.397 ------------------------------------------------------------------------------- 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 339 GLU Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 662 VAL 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 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 439 GLN 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 1006 VAL 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 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 904 VAL Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 979 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 103 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 270 optimal weight: 0.9980 chunk 185 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 chunk 183 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 277 optimal weight: 7.9990 chunk 186 optimal weight: 0.9990 chunk 159 optimal weight: 0.0770 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 ASN ** 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 = 0.3436 r_free = 0.3436 target = 0.116090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.098871 restraints weight = 32346.972| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.82 r_work: 0.3072 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23946 Z= 0.126 Angle : 0.514 9.106 32532 Z= 0.265 Chirality : 0.041 0.168 3811 Planarity : 0.004 0.050 4170 Dihedral : 4.960 58.330 3313 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.19 % Allowed : 15.20 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.15), residues: 3092 helix: 2.40 (0.12), residues: 1726 sheet: -0.20 (0.25), residues: 392 loop : -0.04 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 553 HIS 0.002 0.000 HIS A 708 PHE 0.029 0.001 PHE A 362 TYR 0.016 0.001 TYR A 540 ARG 0.009 0.000 ARG B 557 Details of bonding type rmsd hydrogen bonds : bond 0.03973 ( 1606) hydrogen bonds : angle 4.59876 ( 4890) covalent geometry : bond 0.00281 (23946) covalent geometry : angle 0.51449 (32532) *********************** 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 424 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 344 time to evaluate : 2.434 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8011 (mp) REVERT: A 124 GLN cc_start: 0.8934 (tt0) cc_final: 0.8723 (tt0) REVERT: A 245 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8461 (mt-10) REVERT: A 298 ASN cc_start: 0.8303 (t0) cc_final: 0.8075 (t0) REVERT: A 314 GLU cc_start: 0.8048 (tp30) cc_final: 0.7610 (tp30) REVERT: A 321 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8616 (mtt) REVERT: A 339 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: A 439 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8091 (pt0) REVERT: A 518 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.6616 (tpt) REVERT: A 602 LYS cc_start: 0.8404 (ptmt) cc_final: 0.8081 (ptmm) REVERT: A 619 ARG cc_start: 0.7979 (mtm-85) cc_final: 0.7691 (mtm-85) REVERT: A 865 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: A 918 ARG cc_start: 0.8284 (mmm160) cc_final: 0.6869 (mpt90) REVERT: A 939 LYS cc_start: 0.9017 (ttpt) cc_final: 0.8579 (tttt) REVERT: A 996 SER cc_start: 0.8204 (p) cc_final: 0.7621 (t) REVERT: A 1000 ASN cc_start: 0.8940 (m-40) cc_final: 0.8537 (m-40) REVERT: B 8 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7320 (mtt90) REVERT: B 29 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7940 (tttt) REVERT: B 48 MET cc_start: 0.8414 (mmm) cc_final: 0.8170 (mmt) REVERT: B 162 MET cc_start: 0.9255 (mtp) cc_final: 0.9028 (mtp) REVERT: B 184 MET cc_start: 0.9304 (tpp) cc_final: 0.8755 (tpp) REVERT: B 244 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7882 (mp0) REVERT: B 307 ARG cc_start: 0.7917 (mtt-85) cc_final: 0.7682 (mtm-85) REVERT: B 518 MET cc_start: 0.7267 (mmm) cc_final: 0.6478 (ttp) REVERT: B 557 ARG cc_start: 0.8322 (mtp-110) cc_final: 0.7960 (ptm160) REVERT: B 656 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8063 (mm-40) REVERT: B 661 MET cc_start: 0.8476 (mmt) cc_final: 0.8102 (mtt) REVERT: B 810 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.7169 (t80) REVERT: B 969 MET cc_start: 0.8835 (mtp) cc_final: 0.8527 (mmm) REVERT: B 1006 VAL cc_start: 0.9182 (OUTLIER) cc_final: 0.8978 (m) REVERT: C 73 ASP cc_start: 0.8991 (m-30) cc_final: 0.8742 (m-30) REVERT: C 188 MET cc_start: 0.9402 (mtm) cc_final: 0.9157 (mtm) REVERT: C 226 LYS cc_start: 0.8832 (tptt) cc_final: 0.8065 (mppt) REVERT: C 276 ASP cc_start: 0.8467 (m-30) cc_final: 0.8239 (m-30) REVERT: C 284 GLN cc_start: 0.8420 (tt0) cc_final: 0.7935 (mt0) REVERT: C 346 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7864 (mt-10) REVERT: C 349 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8512 (mp) REVERT: C 355 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8106 (tpt) REVERT: C 356 TYR cc_start: 0.8190 (t80) cc_final: 0.7809 (t80) REVERT: C 417 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: C 432 ARG cc_start: 0.7932 (ttm-80) cc_final: 0.7328 (mtt-85) REVERT: C 435 MET cc_start: 0.8617 (mmm) cc_final: 0.8007 (mmm) REVERT: C 496 MET cc_start: 0.5843 (tpt) cc_final: 0.5638 (tpt) REVERT: C 518 MET cc_start: 0.6441 (tpp) cc_final: 0.6180 (tmm) REVERT: C 525 HIS cc_start: 0.6807 (t70) cc_final: 0.6532 (m90) REVERT: C 636 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8086 (ptt180) REVERT: C 658 LYS cc_start: 0.6169 (mmmt) cc_final: 0.5800 (mptp) REVERT: C 667 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7579 (mt) REVERT: C 680 ASP cc_start: 0.7747 (m-30) cc_final: 0.7461 (m-30) REVERT: C 906 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7403 (mt) REVERT: C 917 PHE cc_start: 0.7118 (m-10) cc_final: 0.6318 (t80) REVERT: C 918 ARG cc_start: 0.8275 (mmm-85) cc_final: 0.6839 (mpt180) REVERT: C 961 GLU cc_start: 0.8438 (tt0) cc_final: 0.8166 (pm20) outliers start: 80 outliers final: 40 residues processed: 394 average time/residue: 1.3315 time to fit residues: 609.4143 Evaluate side-chains 380 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 324 time to evaluate : 2.568 ------------------------------------------------------------------------------- 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 439 GLN 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 816 GLU Chi-restraints excluded: chain A residue 865 GLU 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 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 1006 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 355 MET 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 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 920 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 985 VAL Chi-restraints excluded: chain C residue 1012 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 114 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 269 optimal weight: 1.9990 chunk 288 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 199 optimal weight: 4.9990 chunk 299 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 C 439 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 = 0.3401 r_free = 0.3401 target = 0.113578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.096261 restraints weight = 32387.399| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.81 r_work: 0.3027 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 23946 Z= 0.197 Angle : 0.565 10.189 32532 Z= 0.291 Chirality : 0.043 0.194 3811 Planarity : 0.004 0.048 4170 Dihedral : 5.110 57.623 3313 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.67 % Allowed : 15.36 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.15), residues: 3092 helix: 2.30 (0.12), residues: 1724 sheet: -0.14 (0.26), residues: 391 loop : -0.09 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 788 HIS 0.004 0.001 HIS C 708 PHE 0.021 0.001 PHE C 614 TYR 0.019 0.001 TYR A 540 ARG 0.006 0.000 ARG B 557 Details of bonding type rmsd hydrogen bonds : bond 0.04478 ( 1606) hydrogen bonds : angle 4.72239 ( 4890) covalent geometry : bond 0.00466 (23946) covalent geometry : angle 0.56519 (32532) *********************** 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 426 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 334 time to evaluate : 2.529 Fit side-chains revert: symmetry clash REVERT: A 18 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8841 (mp) REVERT: A 28 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8005 (mp) REVERT: A 245 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8446 (mt-10) REVERT: A 298 ASN cc_start: 0.8375 (t0) cc_final: 0.8059 (t0) REVERT: A 314 GLU cc_start: 0.8084 (tp30) cc_final: 0.7636 (tp30) REVERT: A 321 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8627 (mtt) REVERT: A 339 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: A 518 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.6631 (tpt) REVERT: A 602 LYS cc_start: 0.8391 (ptmt) cc_final: 0.8076 (ptmm) REVERT: A 865 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: A 918 ARG cc_start: 0.8302 (mmm160) cc_final: 0.6858 (mpt90) REVERT: A 996 SER cc_start: 0.8196 (p) cc_final: 0.7614 (t) REVERT: A 1000 ASN cc_start: 0.8932 (m-40) cc_final: 0.8539 (m-40) REVERT: B 8 ARG cc_start: 0.7950 (mtt180) cc_final: 0.7470 (mtt90) REVERT: B 29 LYS cc_start: 0.8447 (mmtt) cc_final: 0.7954 (tttt) REVERT: B 48 MET cc_start: 0.8418 (mmm) cc_final: 0.8168 (mmt) REVERT: B 184 MET cc_start: 0.9285 (tpp) cc_final: 0.8715 (mmm) REVERT: B 244 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7873 (mp0) REVERT: B 307 ARG cc_start: 0.8010 (mtt-85) cc_final: 0.7711 (mtm-85) REVERT: B 498 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8450 (mptt) REVERT: B 518 MET cc_start: 0.7299 (mmm) cc_final: 0.6459 (ttp) REVERT: B 656 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8097 (mm-40) REVERT: B 661 MET cc_start: 0.8495 (mmt) cc_final: 0.8152 (mtt) REVERT: B 810 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7169 (t80) REVERT: B 969 MET cc_start: 0.8840 (mtp) cc_final: 0.8523 (mmm) REVERT: C 73 ASP cc_start: 0.8998 (m-30) cc_final: 0.8747 (m-30) REVERT: C 188 MET cc_start: 0.9408 (mtm) cc_final: 0.9140 (mtm) REVERT: C 226 LYS cc_start: 0.8863 (tptt) cc_final: 0.8072 (mppt) REVERT: C 276 ASP cc_start: 0.8435 (m-30) cc_final: 0.8216 (m-30) REVERT: C 284 GLN cc_start: 0.8382 (tt0) cc_final: 0.7920 (mt0) REVERT: C 346 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: C 355 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8019 (tpt) REVERT: C 356 TYR cc_start: 0.8214 (t80) cc_final: 0.7963 (t80) REVERT: C 417 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: C 432 ARG cc_start: 0.7956 (ttm-80) cc_final: 0.7369 (mtt-85) REVERT: C 435 MET cc_start: 0.8648 (mmm) cc_final: 0.8017 (mmm) REVERT: C 482 VAL cc_start: 0.8951 (p) cc_final: 0.8692 (m) REVERT: C 518 MET cc_start: 0.6530 (tpp) cc_final: 0.6186 (tmt) REVERT: C 525 HIS cc_start: 0.6821 (t70) cc_final: 0.6592 (m90) REVERT: C 636 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7854 (ptm-80) REVERT: C 658 LYS cc_start: 0.6269 (mmmt) cc_final: 0.5972 (mptp) REVERT: C 667 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7639 (mt) REVERT: C 680 ASP cc_start: 0.7790 (m-30) cc_final: 0.7510 (m-30) REVERT: C 734 LYS cc_start: 0.8784 (mttt) cc_final: 0.8501 (mtmt) REVERT: C 906 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7579 (mt) REVERT: C 917 PHE cc_start: 0.7128 (m-10) cc_final: 0.6279 (t80) REVERT: C 918 ARG cc_start: 0.8302 (mmm-85) cc_final: 0.6870 (mpt180) REVERT: C 961 GLU cc_start: 0.8500 (tt0) cc_final: 0.8234 (mp0) outliers start: 92 outliers final: 47 residues processed: 396 average time/residue: 1.4071 time to fit residues: 643.3787 Evaluate side-chains 387 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 325 time to evaluate : 5.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE 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 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 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 816 GLU Chi-restraints excluded: chain A residue 865 GLU 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 498 LYS 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 1018 ILE 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 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 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 920 LEU Chi-restraints excluded: chain C residue 981 PHE Chi-restraints excluded: chain C residue 985 VAL Chi-restraints excluded: chain C residue 986 MET Chi-restraints excluded: chain C residue 1012 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 150 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 208 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 251 optimal weight: 0.0980 chunk 69 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 192 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 204 optimal weight: 0.6980 chunk 255 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN C 150 ASN C 439 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 = 0.3442 r_free = 0.3442 target = 0.116518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.099338 restraints weight = 32371.208| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.82 r_work: 0.3081 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23946 Z= 0.120 Angle : 0.518 8.425 32532 Z= 0.267 Chirality : 0.041 0.184 3811 Planarity : 0.004 0.052 4170 Dihedral : 4.978 57.446 3313 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.07 % Allowed : 15.96 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.15), residues: 3092 helix: 2.37 (0.12), residues: 1726 sheet: -0.16 (0.26), residues: 389 loop : -0.04 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 753 HIS 0.002 0.000 HIS A 708 PHE 0.029 0.001 PHE A 362 TYR 0.021 0.001 TYR C 856 ARG 0.011 0.000 ARG B 557 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 1606) hydrogen bonds : angle 4.56382 ( 4890) covalent geometry : bond 0.00266 (23946) covalent geometry : angle 0.51771 (32532) *********************** 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 424 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 347 time to evaluate : 2.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8863 (mp) REVERT: A 28 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8064 (mp) REVERT: A 124 GLN cc_start: 0.8984 (tt0) cc_final: 0.8722 (tt0) REVERT: A 245 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8449 (mt-10) REVERT: A 298 ASN cc_start: 0.8299 (t0) cc_final: 0.8065 (t0) REVERT: A 314 GLU cc_start: 0.8068 (tp30) cc_final: 0.7614 (tp30) REVERT: A 321 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8566 (mtt) REVERT: A 339 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: A 518 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.6597 (tpt) REVERT: A 602 LYS cc_start: 0.8347 (ptmt) cc_final: 0.8023 (ptmm) REVERT: A 865 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: A 918 ARG cc_start: 0.8226 (mmm160) cc_final: 0.6765 (mpt90) REVERT: A 939 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8511 (tttt) REVERT: A 996 SER cc_start: 0.8168 (p) cc_final: 0.7714 (t) REVERT: A 1000 ASN cc_start: 0.8934 (m-40) cc_final: 0.8544 (m-40) REVERT: B 8 ARG cc_start: 0.7801 (mtt180) cc_final: 0.7329 (mtt90) REVERT: B 29 LYS cc_start: 0.8262 (mmtt) cc_final: 0.7860 (tttt) REVERT: B 48 MET cc_start: 0.8428 (mmm) cc_final: 0.8191 (mmt) REVERT: B 184 MET cc_start: 0.9306 (tpp) cc_final: 0.8743 (tpp) REVERT: B 244 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7873 (mp0) REVERT: B 307 ARG cc_start: 0.7975 (mtt-85) cc_final: 0.7695 (mtm-85) REVERT: B 518 MET cc_start: 0.7337 (mmm) cc_final: 0.6563 (ttp) REVERT: B 527 THR cc_start: 0.8301 (m) cc_final: 0.8095 (p) REVERT: B 557 ARG cc_start: 0.8211 (mtp-110) cc_final: 0.7846 (ptm160) REVERT: B 656 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8076 (mm-40) REVERT: B 661 MET cc_start: 0.8482 (mmt) cc_final: 0.8141 (mtt) REVERT: B 810 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7089 (t80) REVERT: B 969 MET cc_start: 0.8812 (mtp) cc_final: 0.8494 (mmm) REVERT: B 1029 ARG cc_start: 0.8191 (mmm160) cc_final: 0.7290 (mmt90) REVERT: C 73 ASP cc_start: 0.8976 (m-30) cc_final: 0.8723 (m-30) REVERT: C 188 MET cc_start: 0.9403 (mtm) cc_final: 0.9184 (mtm) REVERT: C 226 LYS cc_start: 0.8822 (tptt) cc_final: 0.7965 (mppt) REVERT: C 276 ASP cc_start: 0.8455 (m-30) cc_final: 0.8205 (m-30) REVERT: C 284 GLN cc_start: 0.8393 (tt0) cc_final: 0.7971 (mt0) REVERT: C 307 ARG cc_start: 0.8674 (mtt-85) cc_final: 0.8388 (mtt180) REVERT: C 346 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7834 (mt-10) REVERT: C 355 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8123 (tpt) REVERT: C 356 TYR cc_start: 0.8204 (t80) cc_final: 0.7829 (t80) REVERT: C 417 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7711 (tm-30) REVERT: C 432 ARG cc_start: 0.7929 (ttm-80) cc_final: 0.7342 (mtt-85) REVERT: C 435 MET cc_start: 0.8607 (mmm) cc_final: 0.7994 (mmm) REVERT: C 518 MET cc_start: 0.6453 (tpp) cc_final: 0.6199 (tmm) REVERT: C 525 HIS cc_start: 0.6802 (t70) cc_final: 0.6574 (m90) REVERT: C 658 LYS cc_start: 0.6192 (mmmt) cc_final: 0.5932 (mptp) REVERT: C 680 ASP cc_start: 0.7707 (m-30) cc_final: 0.7434 (m-30) REVERT: C 734 LYS cc_start: 0.8774 (mttt) cc_final: 0.8481 (mtmt) REVERT: C 906 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7396 (mt) REVERT: C 917 PHE cc_start: 0.7078 (m-10) cc_final: 0.6266 (t80) REVERT: C 918 ARG cc_start: 0.8248 (mmm-85) cc_final: 0.6841 (mpt180) REVERT: C 961 GLU cc_start: 0.8521 (tt0) cc_final: 0.8183 (pm20) outliers start: 77 outliers final: 39 residues processed: 397 average time/residue: 1.3307 time to fit residues: 611.1250 Evaluate side-chains 385 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 333 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE 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 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 574 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 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 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 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 351 VAL Chi-restraints excluded: chain C residue 355 MET 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 733 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 60 optimal weight: 0.4980 chunk 302 optimal weight: 3.9990 chunk 258 optimal weight: 0.9980 chunk 267 optimal weight: 0.0770 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 295 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN 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 = 0.3433 r_free = 0.3433 target = 0.115823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.098586 restraints weight = 32339.988| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.81 r_work: 0.3066 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23946 Z= 0.139 Angle : 0.539 9.553 32532 Z= 0.275 Chirality : 0.041 0.207 3811 Planarity : 0.004 0.050 4170 Dihedral : 4.959 57.704 3309 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.43 % Allowed : 16.96 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.15), residues: 3092 helix: 2.37 (0.12), residues: 1725 sheet: -0.11 (0.26), residues: 398 loop : -0.05 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 753 HIS 0.002 0.001 HIS A 525 PHE 0.018 0.001 PHE C 614 TYR 0.017 0.001 TYR A 540 ARG 0.009 0.000 ARG B 557 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 1606) hydrogen bonds : angle 4.57422 ( 4890) covalent geometry : bond 0.00318 (23946) covalent geometry : angle 0.53869 (32532) *********************** 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 402 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 341 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8883 (mp) REVERT: A 28 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8063 (mp) REVERT: A 245 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8457 (mt-10) REVERT: A 298 ASN cc_start: 0.8351 (t0) cc_final: 0.8073 (t0) REVERT: A 314 GLU cc_start: 0.8055 (tp30) cc_final: 0.7596 (tp30) REVERT: A 321 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8546 (mtt) REVERT: A 339 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: A 518 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.6635 (tpt) REVERT: A 602 LYS cc_start: 0.8375 (ptmt) cc_final: 0.8049 (ptmm) REVERT: A 918 ARG cc_start: 0.8222 (mmm160) cc_final: 0.6750 (mpt90) REVERT: A 996 SER cc_start: 0.8159 (p) cc_final: 0.7653 (t) REVERT: A 1000 ASN cc_start: 0.8913 (m-40) cc_final: 0.8542 (m-40) REVERT: B 8 ARG cc_start: 0.7829 (mtt180) cc_final: 0.7372 (mtt90) REVERT: B 29 LYS cc_start: 0.8374 (mmtt) cc_final: 0.7963 (tttt) REVERT: B 48 MET cc_start: 0.8403 (mmm) cc_final: 0.8170 (mmt) REVERT: B 184 MET cc_start: 0.9300 (tpp) cc_final: 0.8727 (mmm) REVERT: B 244 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7880 (mp0) REVERT: B 307 ARG cc_start: 0.8000 (mtt-85) cc_final: 0.7713 (mtm-85) REVERT: B 518 MET cc_start: 0.7283 (mmm) cc_final: 0.6473 (ttp) REVERT: B 527 THR cc_start: 0.8310 (m) cc_final: 0.8103 (p) REVERT: B 557 ARG cc_start: 0.8159 (mtp-110) cc_final: 0.7758 (ptm160) REVERT: B 656 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8060 (mm-40) REVERT: B 661 MET cc_start: 0.8515 (mmt) cc_final: 0.8158 (mtt) REVERT: B 810 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.7006 (t80) REVERT: B 969 MET cc_start: 0.8804 (mtp) cc_final: 0.8492 (mmm) REVERT: B 1029 ARG cc_start: 0.8203 (mmm160) cc_final: 0.7293 (mmt90) REVERT: C 73 ASP cc_start: 0.8994 (m-30) cc_final: 0.8742 (m-30) REVERT: C 188 MET cc_start: 0.9407 (mtm) cc_final: 0.9107 (mtm) REVERT: C 226 LYS cc_start: 0.8813 (tptt) cc_final: 0.8074 (mppt) REVERT: C 284 GLN cc_start: 0.8389 (tt0) cc_final: 0.7988 (mt0) REVERT: C 307 ARG cc_start: 0.8695 (mtt-85) cc_final: 0.8396 (mtt180) REVERT: C 346 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: C 355 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8086 (tpt) REVERT: C 356 TYR cc_start: 0.8260 (t80) cc_final: 0.7919 (t80) REVERT: C 417 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7702 (tm-30) REVERT: C 432 ARG cc_start: 0.7934 (ttm-80) cc_final: 0.7344 (mtt-85) REVERT: C 435 MET cc_start: 0.8622 (mmm) cc_final: 0.8011 (mmm) REVERT: C 518 MET cc_start: 0.6463 (tpp) cc_final: 0.6180 (tmm) REVERT: C 525 HIS cc_start: 0.6828 (t70) cc_final: 0.6605 (m90) REVERT: C 542 VAL cc_start: 0.8536 (t) cc_final: 0.8310 (p) REVERT: C 658 LYS cc_start: 0.6220 (mmmt) cc_final: 0.5946 (mptp) REVERT: C 680 ASP cc_start: 0.7756 (m-30) cc_final: 0.7476 (m-30) REVERT: C 734 LYS cc_start: 0.8776 (mttt) cc_final: 0.8483 (mtmt) REVERT: C 906 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7477 (mt) REVERT: C 917 PHE cc_start: 0.7110 (m-10) cc_final: 0.6281 (t80) REVERT: C 918 ARG cc_start: 0.8277 (mmm-85) cc_final: 0.6887 (mpt180) REVERT: C 961 GLU cc_start: 0.8495 (tt0) cc_final: 0.8146 (pm20) outliers start: 61 outliers final: 38 residues processed: 379 average time/residue: 1.3103 time to fit residues: 573.2756 Evaluate side-chains 384 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 335 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE 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 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 574 MET 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 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 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 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 351 VAL Chi-restraints excluded: chain C residue 355 MET 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 733 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 38 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 202 optimal weight: 7.9990 chunk 141 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 172 optimal weight: 0.9980 chunk 274 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 271 optimal weight: 0.9980 chunk 286 optimal weight: 0.2980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN 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 = 0.3440 r_free = 0.3440 target = 0.116433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.099252 restraints weight = 32337.975| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.82 r_work: 0.3075 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23946 Z= 0.133 Angle : 0.539 8.065 32532 Z= 0.274 Chirality : 0.041 0.201 3811 Planarity : 0.004 0.051 4170 Dihedral : 4.935 57.426 3309 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.35 % Allowed : 17.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.15), residues: 3092 helix: 2.35 (0.12), residues: 1726 sheet: -0.07 (0.26), residues: 376 loop : -0.06 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 753 HIS 0.002 0.000 HIS A 708 PHE 0.029 0.001 PHE A 362 TYR 0.016 0.001 TYR A 540 ARG 0.009 0.000 ARG B 557 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 1606) hydrogen bonds : angle 4.56249 ( 4890) covalent geometry : bond 0.00304 (23946) covalent geometry : angle 0.53879 (32532) *********************** 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 392 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 333 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8880 (mp) REVERT: A 28 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8060 (mp) REVERT: A 245 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8425 (mt-10) REVERT: A 298 ASN cc_start: 0.8339 (t0) cc_final: 0.8074 (t0) REVERT: A 321 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8537 (mtt) REVERT: A 339 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: A 518 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.6643 (tpt) REVERT: A 602 LYS cc_start: 0.8374 (ptmt) cc_final: 0.8045 (ptmm) REVERT: A 918 ARG cc_start: 0.8218 (mmm160) cc_final: 0.6753 (mpt90) REVERT: A 996 SER cc_start: 0.8122 (p) cc_final: 0.7645 (t) REVERT: A 1000 ASN cc_start: 0.8920 (m-40) cc_final: 0.8556 (m-40) REVERT: B 8 ARG cc_start: 0.7821 (mtt180) cc_final: 0.7363 (mtt90) REVERT: B 29 LYS cc_start: 0.8343 (mmtt) cc_final: 0.7947 (tttt) REVERT: B 48 MET cc_start: 0.8419 (mmm) cc_final: 0.8189 (mmt) REVERT: B 184 MET cc_start: 0.9299 (tpp) cc_final: 0.8729 (mmm) REVERT: B 244 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7878 (mp0) REVERT: B 307 ARG cc_start: 0.8012 (mtt-85) cc_final: 0.7726 (mtm-85) REVERT: B 518 MET cc_start: 0.7304 (mmm) cc_final: 0.6490 (ttp) REVERT: B 527 THR cc_start: 0.8313 (m) cc_final: 0.8103 (p) REVERT: B 557 ARG cc_start: 0.8110 (mtp-110) cc_final: 0.7744 (ptm160) REVERT: B 656 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8141 (mm-40) REVERT: B 661 MET cc_start: 0.8506 (mmt) cc_final: 0.8142 (mtt) REVERT: B 810 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.6993 (t80) REVERT: B 969 MET cc_start: 0.8800 (mtp) cc_final: 0.8488 (mmm) REVERT: B 1029 ARG cc_start: 0.8197 (mmm160) cc_final: 0.7196 (mmt90) REVERT: C 8 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7536 (mmt90) REVERT: C 73 ASP cc_start: 0.9016 (m-30) cc_final: 0.8766 (m-30) REVERT: C 188 MET cc_start: 0.9404 (mtm) cc_final: 0.9123 (mtm) REVERT: C 226 LYS cc_start: 0.8799 (tptt) cc_final: 0.8055 (mppt) REVERT: C 284 GLN cc_start: 0.8381 (tt0) cc_final: 0.8008 (mt0) REVERT: C 307 ARG cc_start: 0.8695 (mtt-85) cc_final: 0.8398 (mtt180) REVERT: C 346 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: C 355 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8059 (tpt) REVERT: C 356 TYR cc_start: 0.8264 (t80) cc_final: 0.7908 (t80) REVERT: C 417 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: C 432 ARG cc_start: 0.7901 (ttm-80) cc_final: 0.7312 (mtt-85) REVERT: C 435 MET cc_start: 0.8621 (mmm) cc_final: 0.8022 (mmm) REVERT: C 518 MET cc_start: 0.6499 (tpp) cc_final: 0.6202 (tmm) REVERT: C 525 HIS cc_start: 0.6828 (t70) cc_final: 0.6597 (m90) REVERT: C 542 VAL cc_start: 0.8522 (t) cc_final: 0.8290 (p) REVERT: C 658 LYS cc_start: 0.5978 (mmmt) cc_final: 0.5760 (mptp) REVERT: C 680 ASP cc_start: 0.7722 (m-30) cc_final: 0.7440 (m-30) REVERT: C 906 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7418 (mt) REVERT: C 917 PHE cc_start: 0.7151 (m-10) cc_final: 0.6300 (t80) REVERT: C 918 ARG cc_start: 0.8274 (mmm-85) cc_final: 0.6899 (mpt180) REVERT: C 961 GLU cc_start: 0.8493 (tt0) cc_final: 0.8148 (pm20) outliers start: 59 outliers final: 41 residues processed: 372 average time/residue: 1.3714 time to fit residues: 588.7323 Evaluate side-chains 383 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 330 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE 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 463 THR Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 574 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 723 THR 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 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 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 351 VAL Chi-restraints excluded: chain C residue 355 MET 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 733 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 920 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 50 optimal weight: 0.7980 chunk 276 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 209 optimal weight: 0.2980 chunk 164 optimal weight: 5.9990 chunk 244 optimal weight: 0.7980 chunk 270 optimal weight: 0.9990 chunk 282 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN B 68 ASN C 439 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 = 0.3445 r_free = 0.3445 target = 0.116757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.099558 restraints weight = 32509.066| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.82 r_work: 0.3081 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 23946 Z= 0.129 Angle : 0.540 8.208 32532 Z= 0.275 Chirality : 0.041 0.186 3811 Planarity : 0.004 0.051 4170 Dihedral : 4.921 57.433 3309 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.15 % Allowed : 17.88 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.15), residues: 3092 helix: 2.34 (0.12), residues: 1733 sheet: -0.06 (0.26), residues: 388 loop : -0.09 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 753 HIS 0.002 0.000 HIS A 708 PHE 0.022 0.001 PHE C 614 TYR 0.020 0.001 TYR C 856 ARG 0.009 0.000 ARG C 363 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 1606) hydrogen bonds : angle 4.55532 ( 4890) covalent geometry : bond 0.00295 (23946) covalent geometry : angle 0.53972 (32532) ********************** 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 390 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 336 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8868 (mp) REVERT: A 28 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8056 (mp) REVERT: A 245 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8445 (mt-10) REVERT: A 298 ASN cc_start: 0.8341 (t0) cc_final: 0.8075 (t0) REVERT: A 321 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8542 (mtt) REVERT: A 339 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: A 518 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.6655 (tpt) REVERT: A 602 LYS cc_start: 0.8383 (ptmt) cc_final: 0.8045 (ptmm) REVERT: A 918 ARG cc_start: 0.8228 (mmm160) cc_final: 0.6761 (mpt90) REVERT: A 939 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8497 (tttt) REVERT: A 986 MET cc_start: 0.8115 (mmm) cc_final: 0.7832 (mmm) REVERT: A 996 SER cc_start: 0.8118 (p) cc_final: 0.7670 (t) REVERT: A 1000 ASN cc_start: 0.8942 (m-40) cc_final: 0.8546 (m-40) REVERT: B 8 ARG cc_start: 0.7822 (mtt180) cc_final: 0.7364 (mtt90) REVERT: B 29 LYS cc_start: 0.8316 (mmtt) cc_final: 0.7925 (tttt) REVERT: B 48 MET cc_start: 0.8504 (mmm) cc_final: 0.8271 (mmt) REVERT: B 78 MET cc_start: 0.8941 (ttp) cc_final: 0.8653 (ttp) REVERT: B 149 MET cc_start: 0.7777 (ptp) cc_final: 0.7537 (ptt) REVERT: B 184 MET cc_start: 0.9293 (tpp) cc_final: 0.8720 (mmm) REVERT: B 244 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7883 (mp0) REVERT: B 307 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7709 (mtm-85) REVERT: B 512 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8408 (m-10) REVERT: B 518 MET cc_start: 0.7300 (mmm) cc_final: 0.6487 (ttp) REVERT: B 527 THR cc_start: 0.8306 (m) cc_final: 0.8095 (p) REVERT: B 557 ARG cc_start: 0.8100 (mtp-110) cc_final: 0.7757 (ptm160) REVERT: B 656 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8120 (mm-40) REVERT: B 661 MET cc_start: 0.8512 (mmt) cc_final: 0.8151 (mtt) REVERT: B 810 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.6984 (t80) REVERT: B 969 MET cc_start: 0.8789 (mtp) cc_final: 0.8477 (mmm) REVERT: B 1029 ARG cc_start: 0.8206 (mmm160) cc_final: 0.7231 (mmt90) REVERT: C 8 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7562 (mmt90) REVERT: C 73 ASP cc_start: 0.8991 (m-30) cc_final: 0.8732 (m-30) REVERT: C 188 MET cc_start: 0.9399 (mtm) cc_final: 0.9130 (mtm) REVERT: C 226 LYS cc_start: 0.8808 (tptt) cc_final: 0.7973 (mppt) REVERT: C 284 GLN cc_start: 0.8392 (tt0) cc_final: 0.8009 (mt0) REVERT: C 307 ARG cc_start: 0.8692 (mtt-85) cc_final: 0.8401 (mtt180) REVERT: C 346 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7809 (mt-10) REVERT: C 355 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8077 (tpt) REVERT: C 356 TYR cc_start: 0.8215 (t80) cc_final: 0.7908 (t80) REVERT: C 417 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7688 (tm-30) REVERT: C 432 ARG cc_start: 0.7905 (ttm-80) cc_final: 0.7317 (mtt-85) REVERT: C 435 MET cc_start: 0.8604 (mmm) cc_final: 0.8035 (mmm) REVERT: C 518 MET cc_start: 0.6477 (tpp) cc_final: 0.6197 (tmm) REVERT: C 525 HIS cc_start: 0.6830 (t70) cc_final: 0.6594 (m90) REVERT: C 539 ARG cc_start: 0.7565 (mtt90) cc_final: 0.7331 (mtt90) REVERT: C 542 VAL cc_start: 0.8504 (t) cc_final: 0.8289 (p) REVERT: C 658 LYS cc_start: 0.6069 (mmmt) cc_final: 0.5868 (mptp) REVERT: C 667 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7600 (mt) REVERT: C 680 ASP cc_start: 0.7709 (m-30) cc_final: 0.7411 (m-30) REVERT: C 906 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7394 (mt) REVERT: C 917 PHE cc_start: 0.7154 (m-10) cc_final: 0.6297 (t80) REVERT: C 918 ARG cc_start: 0.8270 (mmm-85) cc_final: 0.6896 (mpt180) REVERT: C 961 GLU cc_start: 0.8516 (tt0) cc_final: 0.8154 (pm20) outliers start: 54 outliers final: 36 residues processed: 371 average time/residue: 1.3254 time to fit residues: 566.0909 Evaluate side-chains 381 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 330 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE 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 339 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 574 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 723 THR 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 985 VAL 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 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 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 351 VAL Chi-restraints excluded: chain C residue 355 MET 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 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 920 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 293 optimal weight: 0.9990 chunk 242 optimal weight: 0.5980 chunk 303 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 235 optimal weight: 5.9990 chunk 173 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 195 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN 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 = 0.115574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.098335 restraints weight = 32427.789| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.82 r_work: 0.3064 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23946 Z= 0.149 Angle : 0.552 8.788 32532 Z= 0.281 Chirality : 0.042 0.182 3811 Planarity : 0.004 0.050 4170 Dihedral : 4.957 57.161 3309 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.35 % Allowed : 17.84 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.15), residues: 3092 helix: 2.32 (0.12), residues: 1730 sheet: -0.10 (0.26), residues: 402 loop : -0.12 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 788 HIS 0.002 0.001 HIS C 708 PHE 0.030 0.001 PHE A 362 TYR 0.017 0.001 TYR A 540 ARG 0.007 0.000 ARG B 557 Details of bonding type rmsd hydrogen bonds : bond 0.04068 ( 1606) hydrogen bonds : angle 4.59355 ( 4890) covalent geometry : bond 0.00346 (23946) covalent geometry : angle 0.55187 (32532) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17176.00 seconds wall clock time: 298 minutes 1.08 seconds (17881.08 seconds total)