Starting phenix.real_space_refine on Tue Mar 19 06:31:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffk_29045/03_2024/8ffk_29045.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffk_29045/03_2024/8ffk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffk_29045/03_2024/8ffk_29045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffk_29045/03_2024/8ffk_29045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffk_29045/03_2024/8ffk_29045.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffk_29045/03_2024/8ffk_29045.pdb" } 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 Residue "C PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 12.61, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 9.35 Conformation dependent library (CDL) restraints added in 4.9 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: 3.16 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: 10.10 Time building geometry restraints manager: 10.04 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: 99.33 - 106.26: 694 106.26 - 113.19: 13129 113.19 - 120.13: 8057 120.13 - 127.06: 10433 127.06 - 133.99: 219 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 2.440 nonbonded pdb=" O ILE A 974 " pdb=" OG SER A 978 " model vdw 2.200 2.440 nonbonded pdb=" O LYS C 631 " pdb=" NH1 ARG C 636 " model vdw 2.200 2.520 nonbonded pdb=" OH TYR A 757 " pdb=" OD1 ASP A 760 " model vdw 2.207 2.440 nonbonded pdb=" OH TYR A 467 " pdb=" OE1 GLN A 927 " model vdw 2.213 2.440 ... (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 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: 2.120 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: 0.030 Extract box with map and model: 10.420 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 65.280 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.590 ------------------------------------------------------------------------------- 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= 0.274 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 *********************** 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 fitting. rotamer outliers: 55 poor density : 475 time to evaluate : 2.271 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: 1.3187 time to fit residues: 777.7202 Evaluate side-chains 352 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 327 time to evaluate : 2.728 ------------------------------------------------------------------------------- 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: 3.9990 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 242 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 180 optimal weight: 0.5980 chunk 280 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 210 GLN A 415 ASN 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 C 58 GLN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN C 415 ASN C 576 GLN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 GLN C 686 GLN C 736 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23946 Z= 0.202 Angle : 0.529 8.151 32532 Z= 0.276 Chirality : 0.041 0.187 3811 Planarity : 0.004 0.035 4170 Dihedral : 5.295 59.684 3325 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.47 % Allowed : 11.41 % Favored : 85.12 % 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: 1.94 (0.15), residues: 3092 helix: 2.37 (0.12), residues: 1724 sheet: -0.20 (0.25), residues: 406 loop : 0.01 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 788 HIS 0.007 0.001 HIS A 525 PHE 0.018 0.001 PHE A 571 TYR 0.017 0.001 TYR A 540 ARG 0.005 0.000 ARG B 557 *********************** 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 fitting. rotamer outliers: 87 poor density : 357 time to evaluate : 2.482 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7256 (mp) REVERT: A 69 MET cc_start: 0.9027 (mmt) cc_final: 0.8739 (mmt) REVERT: A 101 ASP cc_start: 0.8130 (m-30) cc_final: 0.7815 (m-30) REVERT: A 124 GLN cc_start: 0.8161 (tt0) cc_final: 0.7671 (tt0) REVERT: A 184 MET cc_start: 0.9183 (tpp) cc_final: 0.8982 (tpp) REVERT: A 225 VAL cc_start: 0.8148 (t) cc_final: 0.7890 (m) REVERT: A 321 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8433 (mtt) REVERT: A 339 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7145 (mp0) REVERT: A 518 MET cc_start: 0.6223 (OUTLIER) cc_final: 0.5624 (tpt) REVERT: A 602 LYS cc_start: 0.7590 (ptmt) cc_final: 0.7199 (ptmm) REVERT: A 619 ARG cc_start: 0.7737 (mtm-85) cc_final: 0.7356 (mtm-85) REVERT: A 632 ASP cc_start: 0.7718 (t0) cc_final: 0.7424 (t70) REVERT: A 661 MET cc_start: 0.6981 (ttp) cc_final: 0.6690 (ttp) REVERT: A 856 TYR cc_start: 0.8622 (p90) cc_final: 0.8279 (p90) REVERT: A 866 ARG cc_start: 0.7072 (tpp-160) cc_final: 0.6783 (ttp-170) REVERT: A 918 ARG cc_start: 0.7569 (mmm160) cc_final: 0.5584 (mpt90) REVERT: A 992 SER cc_start: 0.8513 (p) cc_final: 0.8226 (t) REVERT: B 8 ARG cc_start: 0.6533 (mtt180) cc_final: 0.6102 (mtt90) REVERT: B 29 LYS cc_start: 0.7682 (mmtt) cc_final: 0.7136 (tttt) REVERT: B 137 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8367 (tp) REVERT: B 152 ASP cc_start: 0.7544 (m-30) cc_final: 0.7208 (m-30) REVERT: B 162 MET cc_start: 0.8603 (mtp) cc_final: 0.8258 (mtp) REVERT: B 184 MET cc_start: 0.8917 (tpp) cc_final: 0.8214 (tpp) REVERT: B 244 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6826 (mp0) REVERT: B 307 ARG cc_start: 0.6794 (mtt-85) cc_final: 0.6504 (mtm-85) REVERT: B 386 PHE cc_start: 0.7847 (m-80) cc_final: 0.7564 (m-80) REVERT: B 498 LYS cc_start: 0.8273 (mmtp) cc_final: 0.8012 (mptt) REVERT: B 517 ARG cc_start: 0.7403 (mtm110) cc_final: 0.7198 (mtm110) REVERT: B 518 MET cc_start: 0.5532 (mmm) cc_final: 0.4864 (ttp) REVERT: B 565 ASP cc_start: 0.8199 (m-30) cc_final: 0.7646 (m-30) REVERT: B 614 PHE cc_start: 0.8497 (t80) cc_final: 0.8260 (t80) REVERT: B 656 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7657 (mm-40) REVERT: B 661 MET cc_start: 0.6896 (mmt) cc_final: 0.6495 (mtt) REVERT: B 810 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.6641 (t80) REVERT: B 825 GLU cc_start: 0.8187 (tt0) cc_final: 0.7967 (tt0) REVERT: B 891 TYR cc_start: 0.8012 (m-80) cc_final: 0.6928 (m-80) REVERT: B 895 SER cc_start: 0.7557 (m) cc_final: 0.7225 (p) REVERT: B 954 LYS cc_start: 0.7679 (mttt) cc_final: 0.7410 (mptm) REVERT: B 961 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6593 (pt0) REVERT: B 969 MET cc_start: 0.7651 (mtp) cc_final: 0.7310 (mmm) REVERT: C 29 LYS cc_start: 0.7751 (mtpp) cc_final: 0.7446 (ttpt) REVERT: C 69 MET cc_start: 0.8942 (mmt) cc_final: 0.8612 (mmp) REVERT: C 76 MET cc_start: 0.8183 (mtt) cc_final: 0.7912 (mtm) REVERT: C 96 SER cc_start: 0.8710 (m) cc_final: 0.8451 (p) REVERT: C 162 MET cc_start: 0.8259 (mtp) cc_final: 0.7928 (mtp) REVERT: C 176 GLN cc_start: 0.8096 (mt0) cc_final: 0.7835 (tt0) REVERT: C 188 MET cc_start: 0.8834 (mtm) cc_final: 0.8495 (mtm) REVERT: C 226 LYS cc_start: 0.8496 (tptt) cc_final: 0.7583 (mppt) REVERT: C 274 SER cc_start: 0.8753 (t) cc_final: 0.8282 (p) REVERT: C 346 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6816 (mt-10) REVERT: C 356 TYR cc_start: 0.7150 (t80) cc_final: 0.6884 (t80) REVERT: C 432 ARG cc_start: 0.7543 (ttm-80) cc_final: 0.7089 (mtt-85) REVERT: C 435 MET cc_start: 0.8401 (mmm) cc_final: 0.7798 (mmm) REVERT: C 447 MET cc_start: 0.7882 (mmm) cc_final: 0.7672 (tpp) REVERT: C 496 MET cc_start: 0.5649 (tpt) cc_final: 0.5448 (tpt) REVERT: C 518 MET cc_start: 0.5472 (tpp) cc_final: 0.5149 (tmt) REVERT: C 521 LYS cc_start: 0.7257 (ttpp) cc_final: 0.6899 (ptmm) REVERT: C 525 HIS cc_start: 0.5992 (t70) cc_final: 0.5740 (m90) REVERT: C 592 GLU cc_start: 0.7116 (tp30) cc_final: 0.6914 (tp30) REVERT: C 606 GLU cc_start: 0.8186 (tp30) cc_final: 0.7873 (tp30) REVERT: C 636 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.5775 (ptm-80) REVERT: C 680 ASP cc_start: 0.6568 (m-30) cc_final: 0.6363 (m-30) REVERT: C 917 PHE cc_start: 0.6229 (m-10) cc_final: 0.5504 (t80) REVERT: C 918 ARG cc_start: 0.7535 (mmm-85) cc_final: 0.5828 (mpt180) REVERT: C 961 GLU cc_start: 0.7573 (tt0) cc_final: 0.7181 (mp0) REVERT: C 1015 ILE cc_start: 0.7532 (mm) cc_final: 0.7261 (tp) outliers start: 87 outliers final: 32 residues processed: 416 average time/residue: 1.3043 time to fit residues: 623.3942 Evaluate side-chains 357 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 316 time to evaluate : 2.657 ------------------------------------------------------------------------------- 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 463 THR Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 137 LEU 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 794 ASP Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 810 TYR Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain B residue 967 VAL 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 471 SER Chi-restraints excluded: chain C residue 478 MET 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 921 THR 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 155 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 233 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 281 optimal weight: 5.9990 chunk 303 optimal weight: 4.9990 chunk 250 optimal weight: 3.9990 chunk 278 optimal weight: 0.0670 chunk 95 optimal weight: 0.6980 chunk 225 optimal weight: 0.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23946 Z= 0.179 Angle : 0.505 8.037 32532 Z= 0.262 Chirality : 0.041 0.173 3811 Planarity : 0.004 0.042 4170 Dihedral : 5.050 59.859 3319 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.31 % Allowed : 13.33 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.97 (0.15), residues: 3092 helix: 2.40 (0.12), residues: 1733 sheet: -0.13 (0.25), residues: 404 loop : -0.04 (0.20), residues: 955 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 0.027 0.001 PHE A 362 TYR 0.017 0.001 TYR A 540 ARG 0.005 0.000 ARG B 557 *********************** 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 438 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 355 time to evaluate : 2.607 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7250 (mp) REVERT: A 69 MET cc_start: 0.9034 (mmt) cc_final: 0.8753 (mmt) REVERT: A 101 ASP cc_start: 0.8112 (m-30) cc_final: 0.7787 (m-30) REVERT: A 124 GLN cc_start: 0.8307 (tt0) cc_final: 0.7997 (tt0) REVERT: A 184 MET cc_start: 0.9187 (tpp) cc_final: 0.8961 (tpp) REVERT: A 225 VAL cc_start: 0.8121 (t) cc_final: 0.7854 (m) REVERT: A 314 GLU cc_start: 0.7530 (tp30) cc_final: 0.7188 (tp30) REVERT: A 321 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8420 (mtt) REVERT: A 339 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7129 (mp0) REVERT: A 407 ASP cc_start: 0.7698 (t0) cc_final: 0.7322 (t0) REVERT: A 439 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6711 (pt0) REVERT: A 518 MET cc_start: 0.6242 (OUTLIER) cc_final: 0.5645 (tpt) REVERT: A 602 LYS cc_start: 0.7588 (ptmt) cc_final: 0.7218 (ptmm) REVERT: A 632 ASP cc_start: 0.7870 (t0) cc_final: 0.7533 (t70) REVERT: A 661 MET cc_start: 0.6999 (ttp) cc_final: 0.6576 (ttp) REVERT: A 790 VAL cc_start: 0.8809 (OUTLIER) cc_final: 0.8597 (p) REVERT: A 866 ARG cc_start: 0.7007 (tpp-160) cc_final: 0.6776 (ttp-170) REVERT: A 918 ARG cc_start: 0.7525 (mmm160) cc_final: 0.5591 (mpt90) REVERT: A 939 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.7069 (ttpp) REVERT: A 992 SER cc_start: 0.8506 (p) cc_final: 0.8242 (t) REVERT: B 8 ARG cc_start: 0.6640 (mtt180) cc_final: 0.6241 (mtt90) REVERT: B 29 LYS cc_start: 0.7678 (mmtt) cc_final: 0.7134 (tttt) REVERT: B 152 ASP cc_start: 0.7623 (m-30) cc_final: 0.7308 (m-30) REVERT: B 184 MET cc_start: 0.8947 (tpp) cc_final: 0.8181 (tpp) REVERT: B 244 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6814 (mp0) REVERT: B 307 ARG cc_start: 0.6798 (mtt-85) cc_final: 0.6505 (mtm-85) REVERT: B 386 PHE cc_start: 0.7908 (m-80) cc_final: 0.7582 (m-80) REVERT: B 498 LYS cc_start: 0.8291 (mmtp) cc_final: 0.8030 (mptt) REVERT: B 517 ARG cc_start: 0.7319 (mtm110) cc_final: 0.7118 (mtm110) REVERT: B 518 MET cc_start: 0.5544 (mmm) cc_final: 0.4934 (ttp) REVERT: B 565 ASP cc_start: 0.8198 (m-30) cc_final: 0.7654 (m-30) REVERT: B 614 PHE cc_start: 0.8458 (t80) cc_final: 0.8223 (t80) REVERT: B 656 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7601 (mm-40) REVERT: B 661 MET cc_start: 0.6929 (mmt) cc_final: 0.6528 (mtt) REVERT: B 729 ASP cc_start: 0.8002 (m-30) cc_final: 0.7712 (m-30) REVERT: B 810 TYR cc_start: 0.7598 (OUTLIER) cc_final: 0.6610 (t80) REVERT: B 825 GLU cc_start: 0.8142 (tt0) cc_final: 0.7819 (tt0) REVERT: B 891 TYR cc_start: 0.8056 (m-80) cc_final: 0.6926 (m-80) REVERT: B 895 SER cc_start: 0.7594 (m) cc_final: 0.7280 (p) REVERT: B 942 ILE cc_start: 0.7957 (mt) cc_final: 0.7725 (mt) REVERT: B 969 MET cc_start: 0.7586 (mtp) cc_final: 0.7271 (mmm) REVERT: C 29 LYS cc_start: 0.7741 (mtpp) cc_final: 0.7425 (ttpt) REVERT: C 48 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8039 (ttt) REVERT: C 73 ASP cc_start: 0.8492 (m-30) cc_final: 0.8259 (m-30) REVERT: C 76 MET cc_start: 0.8111 (mtt) cc_final: 0.7880 (mtm) REVERT: C 96 SER cc_start: 0.8689 (m) cc_final: 0.8443 (p) REVERT: C 162 MET cc_start: 0.8236 (mtp) cc_final: 0.7879 (mtp) REVERT: C 176 GLN cc_start: 0.8124 (mt0) cc_final: 0.7854 (tt0) REVERT: C 188 MET cc_start: 0.8828 (mtm) cc_final: 0.8490 (mtm) REVERT: C 274 SER cc_start: 0.8742 (t) cc_final: 0.8259 (p) REVERT: C 346 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6844 (mt-10) REVERT: C 356 TYR cc_start: 0.7180 (t80) cc_final: 0.6878 (t80) REVERT: C 398 MET cc_start: 0.7397 (mtp) cc_final: 0.7181 (mtm) REVERT: C 432 ARG cc_start: 0.7538 (ttm-80) cc_final: 0.7093 (mtt-85) REVERT: C 435 MET cc_start: 0.8409 (mmm) cc_final: 0.7769 (mmm) REVERT: C 447 MET cc_start: 0.7937 (mmm) cc_final: 0.7702 (tpp) REVERT: C 518 MET cc_start: 0.5401 (tpp) cc_final: 0.5193 (tmm) REVERT: C 521 LYS cc_start: 0.7137 (ttpp) cc_final: 0.6846 (ptmm) REVERT: C 525 HIS cc_start: 0.5989 (t70) cc_final: 0.5661 (m90) REVERT: C 592 GLU cc_start: 0.7113 (tp30) cc_final: 0.6896 (tp30) REVERT: C 606 GLU cc_start: 0.8164 (tp30) cc_final: 0.7897 (tp30) REVERT: C 636 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6031 (ptm-80) REVERT: C 685 ASP cc_start: 0.7614 (t0) cc_final: 0.7404 (t0) REVERT: C 791 ARG cc_start: 0.8269 (ttp80) cc_final: 0.8060 (ttp-110) REVERT: C 906 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6226 (mt) REVERT: C 917 PHE cc_start: 0.6254 (m-10) cc_final: 0.5512 (t80) REVERT: C 961 GLU cc_start: 0.7655 (tt0) cc_final: 0.7209 (mp0) outliers start: 83 outliers final: 37 residues processed: 410 average time/residue: 1.2638 time to fit residues: 597.8851 Evaluate side-chains 373 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 324 time to evaluate : 2.689 ------------------------------------------------------------------------------- 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 439 GLN Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 939 LYS Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 794 ASP 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 C residue 48 MET Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 471 SER Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 545 LEU 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 921 THR 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 277 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 145 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 chunk 134 optimal weight: 0.0070 chunk 188 optimal weight: 0.0030 chunk 282 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 267 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.3810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 195 ASN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23946 Z= 0.146 Angle : 0.486 9.545 32532 Z= 0.250 Chirality : 0.040 0.164 3811 Planarity : 0.004 0.048 4170 Dihedral : 4.862 60.331 3313 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.07 % Allowed : 14.53 % Favored : 82.40 % 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: 2.02 (0.15), residues: 3092 helix: 2.44 (0.12), residues: 1734 sheet: -0.12 (0.24), residues: 423 loop : -0.02 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 788 HIS 0.001 0.000 HIS A 708 PHE 0.019 0.001 PHE A 614 TYR 0.018 0.001 TYR C 856 ARG 0.004 0.000 ARG B 557 *********************** 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 435 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 358 time to evaluate : 2.642 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7121 (mp) REVERT: A 69 MET cc_start: 0.9054 (mmt) cc_final: 0.8757 (mmt) REVERT: A 101 ASP cc_start: 0.8102 (m-30) cc_final: 0.7776 (m-30) REVERT: A 124 GLN cc_start: 0.8326 (tt0) cc_final: 0.8070 (tt0) REVERT: A 184 MET cc_start: 0.9165 (tpp) cc_final: 0.8959 (tpp) REVERT: A 245 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7001 (mt-10) REVERT: A 321 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8386 (mtt) REVERT: A 339 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7097 (mp0) REVERT: A 407 ASP cc_start: 0.7759 (t0) cc_final: 0.7273 (t0) REVERT: A 439 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6807 (pt0) REVERT: A 518 MET cc_start: 0.6136 (OUTLIER) cc_final: 0.5509 (tpt) REVERT: A 562 PHE cc_start: 0.8446 (m-80) cc_final: 0.8173 (m-80) REVERT: A 602 LYS cc_start: 0.7596 (ptmt) cc_final: 0.7313 (ptmm) REVERT: A 632 ASP cc_start: 0.7880 (t0) cc_final: 0.7533 (t70) REVERT: A 661 MET cc_start: 0.6902 (ttp) cc_final: 0.6528 (ttp) REVERT: A 918 ARG cc_start: 0.7395 (mmm160) cc_final: 0.5526 (mpt90) REVERT: A 939 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.7016 (ttpp) REVERT: A 992 SER cc_start: 0.8419 (p) cc_final: 0.8201 (t) REVERT: B 8 ARG cc_start: 0.6582 (mtt180) cc_final: 0.5965 (mtt90) REVERT: B 29 LYS cc_start: 0.7645 (mmtt) cc_final: 0.7101 (tttt) REVERT: B 152 ASP cc_start: 0.7601 (m-30) cc_final: 0.7343 (m-30) REVERT: B 162 MET cc_start: 0.8636 (mtp) cc_final: 0.8293 (mtp) REVERT: B 184 MET cc_start: 0.8963 (tpp) cc_final: 0.8124 (tpp) REVERT: B 244 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6818 (mp0) REVERT: B 307 ARG cc_start: 0.6760 (mtt-85) cc_final: 0.6388 (mtm-85) REVERT: B 386 PHE cc_start: 0.7953 (m-80) cc_final: 0.7616 (m-80) REVERT: B 498 LYS cc_start: 0.8308 (mmtp) cc_final: 0.8029 (mptt) REVERT: B 517 ARG cc_start: 0.7473 (mtm110) cc_final: 0.7272 (mtm110) REVERT: B 518 MET cc_start: 0.5592 (mmm) cc_final: 0.4954 (ttp) REVERT: B 565 ASP cc_start: 0.8204 (m-30) cc_final: 0.7678 (m-30) REVERT: B 656 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7711 (mm-40) REVERT: B 661 MET cc_start: 0.6915 (mmt) cc_final: 0.6504 (mtt) REVERT: B 729 ASP cc_start: 0.7911 (m-30) cc_final: 0.7660 (m-30) REVERT: B 809 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7217 (mt-10) REVERT: B 810 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.6628 (t80) REVERT: B 825 GLU cc_start: 0.7953 (tt0) cc_final: 0.7592 (tt0) REVERT: B 891 TYR cc_start: 0.8016 (m-80) cc_final: 0.6890 (m-80) REVERT: B 969 MET cc_start: 0.7592 (mtp) cc_final: 0.7258 (mmm) REVERT: C 29 LYS cc_start: 0.7566 (mtpp) cc_final: 0.7227 (ttpt) REVERT: C 48 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8114 (tpt) REVERT: C 73 ASP cc_start: 0.8505 (m-30) cc_final: 0.8271 (m-30) REVERT: C 76 MET cc_start: 0.7952 (mtt) cc_final: 0.7727 (mtm) REVERT: C 96 SER cc_start: 0.8650 (m) cc_final: 0.8392 (p) REVERT: C 162 MET cc_start: 0.8224 (mtp) cc_final: 0.7923 (mtp) REVERT: C 176 GLN cc_start: 0.8100 (mt0) cc_final: 0.7846 (tt0) REVERT: C 188 MET cc_start: 0.8819 (mtm) cc_final: 0.8559 (mtm) REVERT: C 274 SER cc_start: 0.8596 (t) cc_final: 0.8239 (p) REVERT: C 284 GLN cc_start: 0.7323 (tt0) cc_final: 0.6582 (mt0) REVERT: C 346 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6782 (mt-10) REVERT: C 356 TYR cc_start: 0.7046 (t80) cc_final: 0.6676 (t80) REVERT: C 398 MET cc_start: 0.7475 (mtp) cc_final: 0.7232 (mtm) REVERT: C 417 GLU cc_start: 0.6955 (tm-30) cc_final: 0.6694 (tm-30) REVERT: C 432 ARG cc_start: 0.7524 (ttm-80) cc_final: 0.7083 (mtt-85) REVERT: C 435 MET cc_start: 0.8407 (mmm) cc_final: 0.7804 (mmm) REVERT: C 447 MET cc_start: 0.7990 (mmm) cc_final: 0.7738 (tpp) REVERT: C 521 LYS cc_start: 0.7209 (ttpp) cc_final: 0.6907 (ptmm) REVERT: C 525 HIS cc_start: 0.5949 (t70) cc_final: 0.5634 (m90) REVERT: C 592 GLU cc_start: 0.7096 (tp30) cc_final: 0.6583 (tp30) REVERT: C 606 GLU cc_start: 0.8135 (tp30) cc_final: 0.7916 (tp30) REVERT: C 636 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6038 (ptm-80) REVERT: C 658 LYS cc_start: 0.6047 (mmmt) cc_final: 0.5716 (mptp) REVERT: C 667 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7002 (mt) REVERT: C 906 LEU cc_start: 0.6384 (OUTLIER) cc_final: 0.5966 (mt) REVERT: C 917 PHE cc_start: 0.6257 (m-10) cc_final: 0.5496 (t80) REVERT: C 918 ARG cc_start: 0.7563 (mmm-85) cc_final: 0.5857 (mpt180) REVERT: C 961 GLU cc_start: 0.7595 (tt0) cc_final: 0.7123 (pm20) outliers start: 77 outliers final: 30 residues processed: 406 average time/residue: 1.3037 time to fit residues: 610.9348 Evaluate side-chains 369 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 327 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 321 MET 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 572 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 662 VAL 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 402 ILE Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 656 GLN 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 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 454 ILE Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 545 LEU 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 921 THR Chi-restraints excluded: chain C residue 985 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 0.0970 chunk 169 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 254 optimal weight: 4.9990 chunk 206 optimal weight: 0.0070 chunk 0 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 268 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN C 439 GLN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23946 Z= 0.165 Angle : 0.493 9.089 32532 Z= 0.251 Chirality : 0.040 0.167 3811 Planarity : 0.004 0.049 4170 Dihedral : 4.755 60.572 3312 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.11 % Allowed : 15.40 % Favored : 81.48 % 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: 2.05 (0.15), residues: 3092 helix: 2.45 (0.12), residues: 1733 sheet: -0.07 (0.24), residues: 439 loop : 0.01 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 788 HIS 0.002 0.000 HIS C 708 PHE 0.029 0.001 PHE A 362 TYR 0.016 0.001 TYR B 540 ARG 0.007 0.000 ARG A 535 *********************** 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 422 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 344 time to evaluate : 2.611 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7104 (mp) REVERT: A 69 MET cc_start: 0.9041 (mmt) cc_final: 0.8744 (mmt) REVERT: A 101 ASP cc_start: 0.8107 (m-30) cc_final: 0.7774 (m-30) REVERT: A 124 GLN cc_start: 0.8325 (tt0) cc_final: 0.8078 (tt0) REVERT: A 184 MET cc_start: 0.9171 (tpp) cc_final: 0.8962 (tpp) REVERT: A 245 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7042 (mt-10) REVERT: A 321 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8360 (mtt) REVERT: A 339 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7081 (mp0) REVERT: A 407 ASP cc_start: 0.7681 (t0) cc_final: 0.7407 (t0) REVERT: A 439 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6781 (pt0) REVERT: A 518 MET cc_start: 0.6170 (OUTLIER) cc_final: 0.5549 (tpt) REVERT: A 602 LYS cc_start: 0.7583 (ptmt) cc_final: 0.7226 (ptmm) REVERT: A 632 ASP cc_start: 0.7884 (t0) cc_final: 0.7520 (t70) REVERT: A 661 MET cc_start: 0.6969 (ttp) cc_final: 0.6637 (ttp) REVERT: A 865 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7329 (tt0) REVERT: A 918 ARG cc_start: 0.7400 (mmm160) cc_final: 0.5527 (mpt90) REVERT: A 992 SER cc_start: 0.8411 (p) cc_final: 0.8209 (t) REVERT: A 1010 MET cc_start: 0.7374 (mmp) cc_final: 0.7063 (mmm) REVERT: B 8 ARG cc_start: 0.6593 (mtt180) cc_final: 0.5988 (mtt90) REVERT: B 29 LYS cc_start: 0.7700 (mmtt) cc_final: 0.7143 (tttt) REVERT: B 152 ASP cc_start: 0.7651 (m-30) cc_final: 0.7362 (m-30) REVERT: B 184 MET cc_start: 0.8991 (tpp) cc_final: 0.8443 (mmm) REVERT: B 307 ARG cc_start: 0.6768 (mtt-85) cc_final: 0.6391 (mtm-85) REVERT: B 386 PHE cc_start: 0.7941 (m-80) cc_final: 0.7607 (m-80) REVERT: B 498 LYS cc_start: 0.8312 (mmtp) cc_final: 0.8019 (mptt) REVERT: B 518 MET cc_start: 0.5552 (mmm) cc_final: 0.4875 (ttp) REVERT: B 557 ARG cc_start: 0.7411 (mtp-110) cc_final: 0.7135 (ptm160) REVERT: B 614 PHE cc_start: 0.8247 (t80) cc_final: 0.7936 (t80) REVERT: B 656 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7727 (mm-40) REVERT: B 661 MET cc_start: 0.6933 (mmt) cc_final: 0.6530 (mtt) REVERT: B 729 ASP cc_start: 0.7897 (m-30) cc_final: 0.7658 (m-30) REVERT: B 809 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7224 (mt-10) REVERT: B 810 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.6593 (t80) REVERT: B 825 GLU cc_start: 0.7960 (tt0) cc_final: 0.7583 (tt0) REVERT: B 891 TYR cc_start: 0.8008 (m-80) cc_final: 0.6814 (m-80) REVERT: B 942 ILE cc_start: 0.7889 (mt) cc_final: 0.7686 (mt) REVERT: B 969 MET cc_start: 0.7601 (mtp) cc_final: 0.7267 (mmm) REVERT: C 29 LYS cc_start: 0.7602 (mtpp) cc_final: 0.7250 (ttpt) REVERT: C 48 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8066 (mmm) REVERT: C 73 ASP cc_start: 0.8514 (m-30) cc_final: 0.8275 (m-30) REVERT: C 76 MET cc_start: 0.7963 (mtt) cc_final: 0.7721 (mtm) REVERT: C 96 SER cc_start: 0.8648 (m) cc_final: 0.8382 (p) REVERT: C 176 GLN cc_start: 0.8086 (mt0) cc_final: 0.7823 (tt0) REVERT: C 188 MET cc_start: 0.8820 (mtm) cc_final: 0.8595 (mtm) REVERT: C 226 LYS cc_start: 0.8436 (tptt) cc_final: 0.7447 (mppt) REVERT: C 274 SER cc_start: 0.8599 (t) cc_final: 0.8257 (p) REVERT: C 284 GLN cc_start: 0.7404 (tt0) cc_final: 0.6696 (mt0) REVERT: C 346 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6786 (mt-10) REVERT: C 356 TYR cc_start: 0.7066 (t80) cc_final: 0.6688 (t80) REVERT: C 417 GLU cc_start: 0.6883 (tm-30) cc_final: 0.6624 (tm-30) REVERT: C 432 ARG cc_start: 0.7496 (ttm-80) cc_final: 0.7047 (mtt-85) REVERT: C 435 MET cc_start: 0.8412 (mmm) cc_final: 0.7783 (mmm) REVERT: C 447 MET cc_start: 0.8002 (mmm) cc_final: 0.7716 (tpp) REVERT: C 496 MET cc_start: 0.5717 (tpt) cc_final: 0.5371 (tpt) REVERT: C 521 LYS cc_start: 0.7250 (ttpp) cc_final: 0.6914 (ptmm) REVERT: C 525 HIS cc_start: 0.5949 (t70) cc_final: 0.5638 (m90) REVERT: C 592 GLU cc_start: 0.7111 (tp30) cc_final: 0.6601 (tp30) REVERT: C 636 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6218 (ptm-80) REVERT: C 658 LYS cc_start: 0.5825 (mmmt) cc_final: 0.5457 (mptp) REVERT: C 667 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7012 (mt) REVERT: C 680 ASP cc_start: 0.7130 (m-30) cc_final: 0.6755 (m-30) REVERT: C 906 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.5893 (mt) REVERT: C 917 PHE cc_start: 0.6287 (m-10) cc_final: 0.5503 (t80) REVERT: C 918 ARG cc_start: 0.7562 (mmm-85) cc_final: 0.5868 (mpt180) REVERT: C 961 GLU cc_start: 0.7601 (tt0) cc_final: 0.7123 (pm20) outliers start: 78 outliers final: 38 residues processed: 395 average time/residue: 1.2672 time to fit residues: 580.2415 Evaluate side-chains 380 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 330 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 321 MET 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 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 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 537 THR 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 C residue 48 MET Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 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 921 THR Chi-restraints excluded: chain C residue 981 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 5.9990 chunk 268 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 298 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 156 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23946 Z= 0.188 Angle : 0.500 9.143 32532 Z= 0.255 Chirality : 0.040 0.163 3811 Planarity : 0.004 0.050 4170 Dihedral : 4.718 60.471 3312 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.19 % Allowed : 15.36 % Favored : 81.44 % 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: 2.04 (0.15), residues: 3092 helix: 2.44 (0.12), residues: 1735 sheet: -0.07 (0.24), residues: 436 loop : 0.02 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.003 0.000 HIS A 525 PHE 0.020 0.001 PHE C 614 TYR 0.016 0.001 TYR A 540 ARG 0.005 0.000 ARG A 535 *********************** 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 422 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 342 time to evaluate : 2.675 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7120 (mp) REVERT: A 69 MET cc_start: 0.9040 (mmt) cc_final: 0.8759 (mmt) REVERT: A 101 ASP cc_start: 0.8114 (m-30) cc_final: 0.7781 (m-30) REVERT: A 124 GLN cc_start: 0.8331 (tt0) cc_final: 0.8087 (tt0) REVERT: A 184 MET cc_start: 0.9172 (tpp) cc_final: 0.8956 (tpp) REVERT: A 245 GLU cc_start: 0.7502 (mt-10) cc_final: 0.6986 (mt-10) REVERT: A 321 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8370 (mtt) REVERT: A 339 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7074 (mp0) REVERT: A 407 ASP cc_start: 0.7685 (t0) cc_final: 0.7424 (t0) REVERT: A 439 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.6786 (pt0) REVERT: A 518 MET cc_start: 0.6165 (OUTLIER) cc_final: 0.5542 (tpt) REVERT: A 562 PHE cc_start: 0.8466 (m-80) cc_final: 0.8139 (m-80) REVERT: A 602 LYS cc_start: 0.7572 (ptmt) cc_final: 0.7196 (ptmm) REVERT: A 632 ASP cc_start: 0.7874 (t0) cc_final: 0.7502 (t70) REVERT: A 661 MET cc_start: 0.7013 (ttp) cc_final: 0.6695 (ttp) REVERT: A 713 THR cc_start: 0.7766 (OUTLIER) cc_final: 0.7492 (p) REVERT: A 865 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7350 (tt0) REVERT: A 918 ARG cc_start: 0.7404 (mmm160) cc_final: 0.5529 (mpt90) REVERT: A 992 SER cc_start: 0.8412 (p) cc_final: 0.8162 (t) REVERT: B 8 ARG cc_start: 0.6623 (mtt180) cc_final: 0.6016 (mtt90) REVERT: B 29 LYS cc_start: 0.7681 (mmtt) cc_final: 0.7132 (tttt) REVERT: B 152 ASP cc_start: 0.7717 (m-30) cc_final: 0.7426 (m-30) REVERT: B 162 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8327 (mtp) REVERT: B 184 MET cc_start: 0.8974 (tpp) cc_final: 0.8180 (tpp) REVERT: B 307 ARG cc_start: 0.6773 (mtt-85) cc_final: 0.6389 (mtm-85) REVERT: B 386 PHE cc_start: 0.8013 (m-80) cc_final: 0.7690 (m-80) REVERT: B 498 LYS cc_start: 0.8321 (mmtp) cc_final: 0.8021 (mptt) REVERT: B 512 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7763 (m-10) REVERT: B 518 MET cc_start: 0.5566 (mmm) cc_final: 0.4875 (ttp) REVERT: B 557 ARG cc_start: 0.7403 (mtp-110) cc_final: 0.7114 (ptm160) REVERT: B 614 PHE cc_start: 0.8268 (t80) cc_final: 0.7954 (t80) REVERT: B 643 VAL cc_start: 0.7781 (OUTLIER) cc_final: 0.7481 (t) REVERT: B 656 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7731 (mm-40) REVERT: B 661 MET cc_start: 0.6942 (mmt) cc_final: 0.6528 (mtt) REVERT: B 729 ASP cc_start: 0.7953 (m-30) cc_final: 0.7664 (m-30) REVERT: B 809 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7206 (mt-10) REVERT: B 810 TYR cc_start: 0.7652 (OUTLIER) cc_final: 0.6565 (t80) REVERT: B 825 GLU cc_start: 0.7967 (tt0) cc_final: 0.7608 (tt0) REVERT: B 891 TYR cc_start: 0.8031 (m-80) cc_final: 0.6867 (m-80) REVERT: B 942 ILE cc_start: 0.7906 (mt) cc_final: 0.7676 (mt) REVERT: B 969 MET cc_start: 0.7605 (mtp) cc_final: 0.7270 (mmm) REVERT: C 29 LYS cc_start: 0.7629 (mtpp) cc_final: 0.7258 (ttpt) REVERT: C 48 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8126 (tpt) REVERT: C 73 ASP cc_start: 0.8525 (m-30) cc_final: 0.8282 (m-30) REVERT: C 76 MET cc_start: 0.8021 (mtt) cc_final: 0.7740 (mtm) REVERT: C 96 SER cc_start: 0.8654 (m) cc_final: 0.8381 (p) REVERT: C 176 GLN cc_start: 0.8059 (mt0) cc_final: 0.7788 (tt0) REVERT: C 188 MET cc_start: 0.8819 (mtm) cc_final: 0.8599 (mtm) REVERT: C 226 LYS cc_start: 0.8441 (tptt) cc_final: 0.7457 (mppt) REVERT: C 274 SER cc_start: 0.8613 (t) cc_final: 0.8261 (p) REVERT: C 284 GLN cc_start: 0.7388 (tt0) cc_final: 0.6700 (mt0) REVERT: C 346 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6790 (mt-10) REVERT: C 356 TYR cc_start: 0.7137 (t80) cc_final: 0.6760 (t80) REVERT: C 417 GLU cc_start: 0.6931 (tm-30) cc_final: 0.6659 (tm-30) REVERT: C 432 ARG cc_start: 0.7499 (ttm-80) cc_final: 0.7057 (mtt-85) REVERT: C 435 MET cc_start: 0.8412 (mmm) cc_final: 0.7795 (mmm) REVERT: C 447 MET cc_start: 0.8012 (mmm) cc_final: 0.7714 (tpp) REVERT: C 496 MET cc_start: 0.5745 (tpt) cc_final: 0.5306 (tpt) REVERT: C 521 LYS cc_start: 0.7037 (ttpp) cc_final: 0.6694 (ptmm) REVERT: C 525 HIS cc_start: 0.5954 (t70) cc_final: 0.5645 (m90) REVERT: C 592 GLU cc_start: 0.7122 (tp30) cc_final: 0.6625 (tp30) REVERT: C 635 GLN cc_start: 0.7646 (mm-40) cc_final: 0.7228 (mt0) REVERT: C 640 GLU cc_start: 0.6798 (pm20) cc_final: 0.6578 (pm20) REVERT: C 658 LYS cc_start: 0.6064 (mmmt) cc_final: 0.5713 (mptp) REVERT: C 667 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.6646 (mt) REVERT: C 783 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7674 (pt0) REVERT: C 906 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.5936 (mt) REVERT: C 917 PHE cc_start: 0.6313 (m-10) cc_final: 0.5502 (t80) REVERT: C 918 ARG cc_start: 0.7536 (mmm-85) cc_final: 0.5860 (mpt180) REVERT: C 961 GLU cc_start: 0.7629 (tt0) cc_final: 0.7126 (pm20) outliers start: 80 outliers final: 42 residues processed: 394 average time/residue: 1.2432 time to fit residues: 568.5650 Evaluate side-chains 391 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 333 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 321 MET 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 713 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 865 GLU 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 162 MET Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 647 THR 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 C residue 48 MET Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 783 GLU Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 921 THR 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 288 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 170 optimal weight: 0.3980 chunk 218 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 251 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 297 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN C 587 GLN ** C 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23946 Z= 0.210 Angle : 0.513 9.474 32532 Z= 0.262 Chirality : 0.041 0.219 3811 Planarity : 0.004 0.050 4170 Dihedral : 4.701 59.961 3308 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.99 % Allowed : 15.96 % Favored : 81.05 % 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: 1.96 (0.15), residues: 3092 helix: 2.39 (0.12), residues: 1738 sheet: -0.07 (0.24), residues: 430 loop : -0.07 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 788 HIS 0.002 0.000 HIS C 708 PHE 0.029 0.001 PHE A 362 TYR 0.018 0.001 TYR C 540 ARG 0.004 0.000 ARG A 535 *********************** 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 414 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 339 time to evaluate : 2.466 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7099 (mp) REVERT: A 69 MET cc_start: 0.9033 (mmt) cc_final: 0.8769 (mmt) REVERT: A 101 ASP cc_start: 0.8120 (m-30) cc_final: 0.7788 (m-30) REVERT: A 124 GLN cc_start: 0.8331 (tt0) cc_final: 0.8092 (tt0) REVERT: A 184 MET cc_start: 0.9171 (tpp) cc_final: 0.8952 (tpp) REVERT: A 245 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6964 (mt-10) REVERT: A 301 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7924 (m-30) REVERT: A 321 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8332 (mtt) REVERT: A 339 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7056 (mp0) REVERT: A 407 ASP cc_start: 0.7727 (t0) cc_final: 0.7368 (t0) REVERT: A 420 MET cc_start: 0.7089 (ttp) cc_final: 0.6859 (ttm) REVERT: A 439 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6880 (pt0) REVERT: A 518 MET cc_start: 0.6166 (OUTLIER) cc_final: 0.5546 (tpt) REVERT: A 602 LYS cc_start: 0.7570 (ptmt) cc_final: 0.7222 (ptmm) REVERT: A 632 ASP cc_start: 0.7917 (t0) cc_final: 0.7526 (t70) REVERT: A 661 MET cc_start: 0.7024 (ttp) cc_final: 0.6723 (ttp) REVERT: A 713 THR cc_start: 0.7739 (OUTLIER) cc_final: 0.7484 (p) REVERT: A 865 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: A 918 ARG cc_start: 0.7409 (mmm160) cc_final: 0.5533 (mpt90) REVERT: A 939 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.7091 (ttpp) REVERT: A 992 SER cc_start: 0.8373 (p) cc_final: 0.8170 (t) REVERT: B 8 ARG cc_start: 0.6650 (mtt180) cc_final: 0.6034 (mtt90) REVERT: B 29 LYS cc_start: 0.7596 (mmtt) cc_final: 0.7084 (tttt) REVERT: B 128 SER cc_start: 0.7755 (OUTLIER) cc_final: 0.7284 (p) REVERT: B 152 ASP cc_start: 0.7472 (m-30) cc_final: 0.7169 (m-30) REVERT: B 184 MET cc_start: 0.8958 (tpp) cc_final: 0.8694 (tpt) REVERT: B 307 ARG cc_start: 0.6808 (mtt-85) cc_final: 0.6395 (mtm-85) REVERT: B 386 PHE cc_start: 0.8098 (m-80) cc_final: 0.7805 (m-80) REVERT: B 498 LYS cc_start: 0.8331 (mmtp) cc_final: 0.8010 (mptt) REVERT: B 512 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7762 (m-10) REVERT: B 518 MET cc_start: 0.5568 (mmm) cc_final: 0.4873 (ttp) REVERT: B 565 ASP cc_start: 0.8219 (m-30) cc_final: 0.7680 (m-30) REVERT: B 614 PHE cc_start: 0.8310 (t80) cc_final: 0.7963 (t80) REVERT: B 643 VAL cc_start: 0.7787 (OUTLIER) cc_final: 0.7481 (t) REVERT: B 656 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7758 (mm-40) REVERT: B 661 MET cc_start: 0.6956 (mmt) cc_final: 0.6528 (mtt) REVERT: B 729 ASP cc_start: 0.7936 (m-30) cc_final: 0.7650 (m-30) REVERT: B 810 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.6617 (t80) REVERT: B 825 GLU cc_start: 0.7978 (tt0) cc_final: 0.7616 (tt0) REVERT: B 891 TYR cc_start: 0.8021 (m-80) cc_final: 0.6846 (m-80) REVERT: B 969 MET cc_start: 0.7619 (mtp) cc_final: 0.7271 (mmm) REVERT: C 29 LYS cc_start: 0.7634 (mtpp) cc_final: 0.7256 (ttpt) REVERT: C 48 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8143 (tpt) REVERT: C 73 ASP cc_start: 0.8523 (m-30) cc_final: 0.8278 (m-30) REVERT: C 76 MET cc_start: 0.8035 (mtt) cc_final: 0.7742 (mtm) REVERT: C 96 SER cc_start: 0.8679 (m) cc_final: 0.8411 (p) REVERT: C 176 GLN cc_start: 0.8078 (mt0) cc_final: 0.7767 (tt0) REVERT: C 188 MET cc_start: 0.8822 (mtm) cc_final: 0.8586 (mtm) REVERT: C 226 LYS cc_start: 0.8466 (tptt) cc_final: 0.7480 (mppt) REVERT: C 274 SER cc_start: 0.8599 (t) cc_final: 0.8233 (p) REVERT: C 284 GLN cc_start: 0.7375 (tt0) cc_final: 0.6690 (mt0) REVERT: C 346 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6800 (mt-10) REVERT: C 356 TYR cc_start: 0.7173 (t80) cc_final: 0.6822 (t80) REVERT: C 417 GLU cc_start: 0.6859 (tm-30) cc_final: 0.6569 (tm-30) REVERT: C 432 ARG cc_start: 0.7489 (ttm-80) cc_final: 0.7049 (mtt-85) REVERT: C 435 MET cc_start: 0.8411 (mmm) cc_final: 0.7780 (mmm) REVERT: C 447 MET cc_start: 0.8023 (mmm) cc_final: 0.7723 (tpp) REVERT: C 496 MET cc_start: 0.5802 (tpt) cc_final: 0.5411 (tpt) REVERT: C 521 LYS cc_start: 0.7135 (ttpp) cc_final: 0.6733 (ptmm) REVERT: C 525 HIS cc_start: 0.5965 (t70) cc_final: 0.5648 (m90) REVERT: C 592 GLU cc_start: 0.7152 (tp30) cc_final: 0.6641 (tp30) REVERT: C 635 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7284 (mt0) REVERT: C 640 GLU cc_start: 0.6829 (pm20) cc_final: 0.6595 (pm20) REVERT: C 658 LYS cc_start: 0.6064 (mmmt) cc_final: 0.5737 (mptp) REVERT: C 667 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6996 (mt) REVERT: C 680 ASP cc_start: 0.7034 (m-30) cc_final: 0.6534 (m-30) REVERT: C 783 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7650 (pt0) REVERT: C 906 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.5950 (mt) REVERT: C 917 PHE cc_start: 0.6293 (m-10) cc_final: 0.5468 (t80) REVERT: C 918 ARG cc_start: 0.7518 (mmm-85) cc_final: 0.5856 (mpt180) REVERT: C 961 GLU cc_start: 0.7661 (tt0) cc_final: 0.7139 (pm20) outliers start: 75 outliers final: 48 residues processed: 391 average time/residue: 1.2856 time to fit residues: 581.3723 Evaluate side-chains 396 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 330 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 336 SER 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 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 827 LEU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 939 LYS Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 647 THR 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 937 SER Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 666 ASN Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 783 GLU Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 921 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 177 optimal weight: 0.7980 chunk 89 optimal weight: 0.0060 chunk 58 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 202 optimal weight: 0.4980 chunk 147 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 234 optimal weight: 0.8980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN ** C 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23946 Z= 0.153 Angle : 0.496 8.316 32532 Z= 0.253 Chirality : 0.040 0.206 3811 Planarity : 0.004 0.055 4170 Dihedral : 4.694 60.063 3308 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.63 % Allowed : 16.52 % Favored : 80.85 % 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: 2.01 (0.15), residues: 3092 helix: 2.41 (0.12), residues: 1735 sheet: -0.06 (0.24), residues: 424 loop : 0.01 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 553 HIS 0.002 0.000 HIS A 708 PHE 0.019 0.001 PHE C 614 TYR 0.024 0.001 TYR C 856 ARG 0.013 0.000 ARG B 557 *********************** 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 411 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 345 time to evaluate : 2.707 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7132 (mp) REVERT: A 101 ASP cc_start: 0.8105 (m-30) cc_final: 0.7773 (m-30) REVERT: A 124 GLN cc_start: 0.8317 (tt0) cc_final: 0.8082 (tt0) REVERT: A 184 MET cc_start: 0.9173 (tpp) cc_final: 0.8952 (tpp) REVERT: A 245 GLU cc_start: 0.7527 (mt-10) cc_final: 0.6981 (mt-10) REVERT: A 339 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7008 (mp0) REVERT: A 407 ASP cc_start: 0.7729 (t0) cc_final: 0.7332 (t0) REVERT: A 439 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6745 (pt0) REVERT: A 518 MET cc_start: 0.6138 (OUTLIER) cc_final: 0.5526 (tpt) REVERT: A 562 PHE cc_start: 0.8458 (m-80) cc_final: 0.8096 (m-80) REVERT: A 602 LYS cc_start: 0.7540 (ptmt) cc_final: 0.7199 (ptmm) REVERT: A 632 ASP cc_start: 0.7918 (t0) cc_final: 0.7543 (t70) REVERT: A 661 MET cc_start: 0.7006 (ttp) cc_final: 0.6712 (ttp) REVERT: A 918 ARG cc_start: 0.7399 (mmm160) cc_final: 0.5543 (mpt90) REVERT: A 939 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7069 (ttpp) REVERT: A 1000 ASN cc_start: 0.7519 (m-40) cc_final: 0.6985 (m-40) REVERT: A 1007 MET cc_start: 0.6430 (ttt) cc_final: 0.6230 (ttt) REVERT: B 8 ARG cc_start: 0.6623 (mtt180) cc_final: 0.6022 (mtt90) REVERT: B 29 LYS cc_start: 0.7538 (mmtt) cc_final: 0.7070 (tttt) REVERT: B 62 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.7972 (t) REVERT: B 128 SER cc_start: 0.7749 (OUTLIER) cc_final: 0.7317 (p) REVERT: B 152 ASP cc_start: 0.7461 (m-30) cc_final: 0.7173 (m-30) REVERT: B 184 MET cc_start: 0.8991 (tpp) cc_final: 0.8452 (mmm) REVERT: B 230 LEU cc_start: 0.7941 (tp) cc_final: 0.7739 (tm) REVERT: B 307 ARG cc_start: 0.6798 (mtt-85) cc_final: 0.6394 (mtm-85) REVERT: B 498 LYS cc_start: 0.8335 (mmtp) cc_final: 0.8014 (mptt) REVERT: B 518 MET cc_start: 0.5619 (mmm) cc_final: 0.4947 (ttp) REVERT: B 557 ARG cc_start: 0.7391 (mtp-110) cc_final: 0.7103 (ptm160) REVERT: B 614 PHE cc_start: 0.8165 (t80) cc_final: 0.7876 (t80) REVERT: B 643 VAL cc_start: 0.7740 (OUTLIER) cc_final: 0.7537 (t) REVERT: B 656 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7786 (mm-40) REVERT: B 661 MET cc_start: 0.6945 (mmt) cc_final: 0.6533 (mtt) REVERT: B 809 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7225 (mt-10) REVERT: B 825 GLU cc_start: 0.7999 (tt0) cc_final: 0.7529 (tt0) REVERT: B 969 MET cc_start: 0.7674 (mtp) cc_final: 0.7316 (mmm) REVERT: C 29 LYS cc_start: 0.7616 (mtpp) cc_final: 0.7231 (ttpt) REVERT: C 48 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8068 (mmm) REVERT: C 73 ASP cc_start: 0.8525 (m-30) cc_final: 0.8290 (m-30) REVERT: C 76 MET cc_start: 0.7944 (mtt) cc_final: 0.7706 (mtm) REVERT: C 96 SER cc_start: 0.8649 (m) cc_final: 0.8375 (p) REVERT: C 176 GLN cc_start: 0.8051 (mt0) cc_final: 0.7793 (tt0) REVERT: C 188 MET cc_start: 0.8824 (mtm) cc_final: 0.8599 (mtm) REVERT: C 226 LYS cc_start: 0.8397 (tptt) cc_final: 0.7435 (mppt) REVERT: C 274 SER cc_start: 0.8581 (t) cc_final: 0.8223 (p) REVERT: C 284 GLN cc_start: 0.7358 (tt0) cc_final: 0.6717 (mt0) REVERT: C 346 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6784 (mt-10) REVERT: C 356 TYR cc_start: 0.7171 (t80) cc_final: 0.6831 (t80) REVERT: C 417 GLU cc_start: 0.6842 (tm-30) cc_final: 0.6555 (tm-30) REVERT: C 432 ARG cc_start: 0.7515 (ttm-80) cc_final: 0.7142 (mtt-85) REVERT: C 435 MET cc_start: 0.8388 (mmm) cc_final: 0.7771 (mmm) REVERT: C 447 MET cc_start: 0.8012 (mmm) cc_final: 0.7731 (tpp) REVERT: C 496 MET cc_start: 0.5844 (tpt) cc_final: 0.5469 (tpt) REVERT: C 521 LYS cc_start: 0.7183 (ttpp) cc_final: 0.6779 (ptmm) REVERT: C 525 HIS cc_start: 0.5944 (t70) cc_final: 0.5642 (m90) REVERT: C 592 GLU cc_start: 0.7165 (tp30) cc_final: 0.6696 (tp30) REVERT: C 635 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7289 (mt0) REVERT: C 640 GLU cc_start: 0.6803 (pm20) cc_final: 0.6579 (pm20) REVERT: C 658 LYS cc_start: 0.5972 (mmmt) cc_final: 0.5654 (mptp) REVERT: C 680 ASP cc_start: 0.6982 (m-30) cc_final: 0.6592 (m-30) REVERT: C 829 GLN cc_start: 0.5641 (mt0) cc_final: 0.5065 (mp10) REVERT: C 917 PHE cc_start: 0.6310 (m-10) cc_final: 0.5499 (t80) REVERT: C 918 ARG cc_start: 0.7500 (mmm-85) cc_final: 0.5866 (mpt180) REVERT: C 961 GLU cc_start: 0.7632 (tt0) cc_final: 0.7104 (pm20) outliers start: 66 outliers final: 37 residues processed: 392 average time/residue: 1.2808 time to fit residues: 578.4408 Evaluate side-chains 374 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 327 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 293 LEU 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 628 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 921 THR 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 62 THR 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 452 VAL Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 643 VAL 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 967 VAL Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 921 THR Chi-restraints excluded: chain C residue 985 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 1.9990 chunk 285 optimal weight: 0.0570 chunk 260 optimal weight: 0.7980 chunk 277 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 217 optimal weight: 0.0470 chunk 85 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23946 Z= 0.184 Angle : 0.512 8.689 32532 Z= 0.261 Chirality : 0.041 0.222 3811 Planarity : 0.004 0.051 4170 Dihedral : 4.578 60.173 3304 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.31 % Allowed : 17.16 % Favored : 80.53 % 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: 2.02 (0.15), residues: 3092 helix: 2.41 (0.12), residues: 1737 sheet: -0.02 (0.24), residues: 421 loop : -0.01 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.002 0.000 HIS A 708 PHE 0.030 0.001 PHE A 362 TYR 0.017 0.001 TYR C 540 ARG 0.011 0.000 ARG B 557 *********************** 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 390 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 332 time to evaluate : 2.614 Fit side-chains revert: symmetry clash REVERT: A 18 ILE cc_start: 0.7815 (mp) cc_final: 0.7456 (mp) REVERT: A 28 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7106 (mp) REVERT: A 101 ASP cc_start: 0.8113 (m-30) cc_final: 0.7779 (m-30) REVERT: A 124 GLN cc_start: 0.8328 (tt0) cc_final: 0.8088 (tt0) REVERT: A 184 MET cc_start: 0.9174 (tpp) cc_final: 0.8951 (tpp) REVERT: A 245 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7108 (mt-10) REVERT: A 339 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6981 (mp0) REVERT: A 407 ASP cc_start: 0.7730 (t0) cc_final: 0.7332 (t0) REVERT: A 439 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6750 (pt0) REVERT: A 518 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.5564 (tpt) REVERT: A 562 PHE cc_start: 0.8419 (m-80) cc_final: 0.8073 (m-80) REVERT: A 602 LYS cc_start: 0.7515 (ptmt) cc_final: 0.7167 (ptmm) REVERT: A 632 ASP cc_start: 0.7898 (t0) cc_final: 0.7500 (t70) REVERT: A 661 MET cc_start: 0.6991 (ttp) cc_final: 0.6715 (ttp) REVERT: A 918 ARG cc_start: 0.7403 (mmm160) cc_final: 0.5547 (mpt90) REVERT: A 939 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.7075 (ttpp) REVERT: A 1000 ASN cc_start: 0.7578 (m-40) cc_final: 0.7062 (m-40) REVERT: B 8 ARG cc_start: 0.6621 (mtt180) cc_final: 0.6015 (mtt90) REVERT: B 29 LYS cc_start: 0.7656 (mmtt) cc_final: 0.7177 (tttt) REVERT: B 128 SER cc_start: 0.7747 (OUTLIER) cc_final: 0.7320 (p) REVERT: B 152 ASP cc_start: 0.7472 (m-30) cc_final: 0.7184 (m-30) REVERT: B 184 MET cc_start: 0.8974 (tpp) cc_final: 0.8452 (mmm) REVERT: B 307 ARG cc_start: 0.6810 (mtt-85) cc_final: 0.6404 (mtm-85) REVERT: B 498 LYS cc_start: 0.8344 (mmtp) cc_final: 0.8014 (mptt) REVERT: B 518 MET cc_start: 0.5573 (mmm) cc_final: 0.4869 (ttp) REVERT: B 557 ARG cc_start: 0.7362 (mtp-110) cc_final: 0.6973 (ptm160) REVERT: B 614 PHE cc_start: 0.8188 (t80) cc_final: 0.7880 (t80) REVERT: B 643 VAL cc_start: 0.7747 (OUTLIER) cc_final: 0.7431 (t) REVERT: B 656 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7794 (mm-40) REVERT: B 661 MET cc_start: 0.6999 (mmt) cc_final: 0.6574 (mtt) REVERT: B 729 ASP cc_start: 0.7933 (m-30) cc_final: 0.7690 (m-30) REVERT: B 825 GLU cc_start: 0.8016 (tt0) cc_final: 0.7609 (tt0) REVERT: B 969 MET cc_start: 0.7683 (mtp) cc_final: 0.7279 (mmm) REVERT: C 29 LYS cc_start: 0.7590 (mtpp) cc_final: 0.7268 (ttpt) REVERT: C 48 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8071 (tpt) REVERT: C 73 ASP cc_start: 0.8523 (m-30) cc_final: 0.8289 (m-30) REVERT: C 76 MET cc_start: 0.8010 (mtt) cc_final: 0.7721 (mtm) REVERT: C 96 SER cc_start: 0.8656 (m) cc_final: 0.8360 (p) REVERT: C 149 MET cc_start: 0.7529 (mtp) cc_final: 0.7091 (ptp) REVERT: C 176 GLN cc_start: 0.8062 (mt0) cc_final: 0.7773 (tt0) REVERT: C 188 MET cc_start: 0.8815 (mtm) cc_final: 0.8497 (mtm) REVERT: C 226 LYS cc_start: 0.8409 (tptt) cc_final: 0.7452 (mppt) REVERT: C 274 SER cc_start: 0.8606 (t) cc_final: 0.8244 (p) REVERT: C 284 GLN cc_start: 0.7359 (tt0) cc_final: 0.6702 (mt0) REVERT: C 346 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6775 (mt-10) REVERT: C 356 TYR cc_start: 0.7123 (t80) cc_final: 0.6793 (t80) REVERT: C 417 GLU cc_start: 0.6815 (tm-30) cc_final: 0.6560 (tm-30) REVERT: C 432 ARG cc_start: 0.7499 (ttm-80) cc_final: 0.7076 (mtt-85) REVERT: C 435 MET cc_start: 0.8393 (mmm) cc_final: 0.7770 (mmm) REVERT: C 447 MET cc_start: 0.8033 (mmm) cc_final: 0.7797 (tpp) REVERT: C 496 MET cc_start: 0.5844 (tpt) cc_final: 0.5455 (tpt) REVERT: C 521 LYS cc_start: 0.7133 (ttpp) cc_final: 0.6734 (ptmm) REVERT: C 525 HIS cc_start: 0.6005 (t70) cc_final: 0.5694 (m90) REVERT: C 592 GLU cc_start: 0.7181 (tp30) cc_final: 0.6717 (tp30) REVERT: C 635 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7292 (mt0) REVERT: C 640 GLU cc_start: 0.6789 (pm20) cc_final: 0.6575 (pm20) REVERT: C 658 LYS cc_start: 0.6019 (mmmt) cc_final: 0.5743 (mptp) REVERT: C 680 ASP cc_start: 0.6969 (m-30) cc_final: 0.6537 (m-30) REVERT: C 829 GLN cc_start: 0.5624 (mt0) cc_final: 0.5070 (mp10) REVERT: C 917 PHE cc_start: 0.6293 (m-10) cc_final: 0.5474 (t80) REVERT: C 918 ARG cc_start: 0.7548 (mmm-85) cc_final: 0.5935 (mpt180) REVERT: C 961 GLU cc_start: 0.7629 (tt0) cc_final: 0.7098 (pm20) outliers start: 58 outliers final: 38 residues processed: 373 average time/residue: 1.3258 time to fit residues: 572.0608 Evaluate side-chains 373 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 326 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 439 GLN 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 723 THR Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 921 THR 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 79 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 481 SER Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 647 THR 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 967 VAL Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 545 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 920 LEU Chi-restraints excluded: chain C residue 921 THR 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 182 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 139 optimal weight: 0.0060 chunk 204 optimal weight: 0.9990 chunk 307 optimal weight: 0.9980 chunk 283 optimal weight: 0.9990 chunk 245 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 189 optimal weight: 0.6980 chunk 150 optimal weight: 0.5980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23946 Z= 0.168 Angle : 0.505 8.689 32532 Z= 0.258 Chirality : 0.040 0.206 3811 Planarity : 0.004 0.054 4170 Dihedral : 4.543 59.962 3303 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.11 % Allowed : 17.52 % Favored : 80.37 % 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: 2.06 (0.15), residues: 3092 helix: 2.43 (0.12), residues: 1737 sheet: -0.00 (0.24), residues: 424 loop : 0.02 (0.21), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.002 0.000 HIS A 708 PHE 0.024 0.001 PHE C 614 TYR 0.021 0.001 TYR C 856 ARG 0.011 0.000 ARG B 557 ********************** 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 fitting. rotamer outliers: 53 poor density : 337 time to evaluate : 3.279 Fit side-chains revert: symmetry clash REVERT: A 18 ILE cc_start: 0.7830 (mp) cc_final: 0.7466 (mp) REVERT: A 28 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7139 (mp) REVERT: A 101 ASP cc_start: 0.8107 (m-30) cc_final: 0.7773 (m-30) REVERT: A 124 GLN cc_start: 0.8326 (tt0) cc_final: 0.8094 (tt0) REVERT: A 184 MET cc_start: 0.9173 (tpp) cc_final: 0.8952 (tpp) REVERT: A 245 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7109 (mt-10) REVERT: A 339 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6976 (mp0) REVERT: A 407 ASP cc_start: 0.7728 (t0) cc_final: 0.7303 (t0) REVERT: A 417 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5892 (tm-30) REVERT: A 420 MET cc_start: 0.7053 (ttp) cc_final: 0.6847 (ttm) REVERT: A 439 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6734 (pt0) REVERT: A 518 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.5556 (tpt) REVERT: A 562 PHE cc_start: 0.8448 (m-80) cc_final: 0.8090 (m-80) REVERT: A 602 LYS cc_start: 0.7486 (ptmt) cc_final: 0.7132 (ptmm) REVERT: A 632 ASP cc_start: 0.7892 (t0) cc_final: 0.7491 (t70) REVERT: A 661 MET cc_start: 0.6970 (ttp) cc_final: 0.6730 (ttp) REVERT: A 856 TYR cc_start: 0.8078 (p90) cc_final: 0.7773 (p90) REVERT: A 918 ARG cc_start: 0.7397 (mmm160) cc_final: 0.5542 (mpt90) REVERT: A 939 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7067 (ttpp) REVERT: A 1000 ASN cc_start: 0.7587 (m-40) cc_final: 0.7063 (m-40) REVERT: B 8 ARG cc_start: 0.6611 (mtt180) cc_final: 0.6008 (mtt90) REVERT: B 29 LYS cc_start: 0.7566 (mmtt) cc_final: 0.7094 (tttt) REVERT: B 128 SER cc_start: 0.7703 (OUTLIER) cc_final: 0.7290 (p) REVERT: B 152 ASP cc_start: 0.7474 (m-30) cc_final: 0.7191 (m-30) REVERT: B 184 MET cc_start: 0.8975 (tpp) cc_final: 0.8445 (mmm) REVERT: B 230 LEU cc_start: 0.7953 (tp) cc_final: 0.7742 (tm) REVERT: B 307 ARG cc_start: 0.6807 (mtt-85) cc_final: 0.6401 (mtm-85) REVERT: B 386 PHE cc_start: 0.7770 (m-80) cc_final: 0.7495 (m-80) REVERT: B 498 LYS cc_start: 0.8334 (mmtp) cc_final: 0.7995 (mptt) REVERT: B 518 MET cc_start: 0.5499 (mmm) cc_final: 0.4789 (ttp) REVERT: B 557 ARG cc_start: 0.7250 (mtp-110) cc_final: 0.6901 (ptm160) REVERT: B 614 PHE cc_start: 0.8175 (t80) cc_final: 0.7904 (t80) REVERT: B 643 VAL cc_start: 0.7732 (OUTLIER) cc_final: 0.7530 (t) REVERT: B 656 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7782 (mm-40) REVERT: B 661 MET cc_start: 0.7025 (mmt) cc_final: 0.6617 (mtt) REVERT: B 809 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7218 (mt-10) REVERT: B 810 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.6499 (t80) REVERT: B 825 GLU cc_start: 0.8004 (tt0) cc_final: 0.7596 (tt0) REVERT: B 969 MET cc_start: 0.7687 (mtp) cc_final: 0.7273 (mmm) REVERT: C 29 LYS cc_start: 0.7598 (mtpp) cc_final: 0.7247 (ttpt) REVERT: C 48 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8068 (mmm) REVERT: C 73 ASP cc_start: 0.8509 (m-30) cc_final: 0.8279 (m-30) REVERT: C 76 MET cc_start: 0.8009 (mtt) cc_final: 0.7725 (mtm) REVERT: C 96 SER cc_start: 0.8685 (m) cc_final: 0.8367 (p) REVERT: C 149 MET cc_start: 0.7490 (mtp) cc_final: 0.7058 (ptp) REVERT: C 176 GLN cc_start: 0.8036 (mt0) cc_final: 0.7809 (tt0) REVERT: C 188 MET cc_start: 0.8808 (mtm) cc_final: 0.8515 (mtm) REVERT: C 226 LYS cc_start: 0.8401 (tptt) cc_final: 0.7443 (mppt) REVERT: C 274 SER cc_start: 0.8593 (t) cc_final: 0.8230 (p) REVERT: C 284 GLN cc_start: 0.7353 (tt0) cc_final: 0.6716 (mt0) REVERT: C 346 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6781 (mt-10) REVERT: C 356 TYR cc_start: 0.7158 (t80) cc_final: 0.6823 (t80) REVERT: C 417 GLU cc_start: 0.6865 (tm-30) cc_final: 0.6609 (tm-30) REVERT: C 432 ARG cc_start: 0.7494 (ttm-80) cc_final: 0.7079 (mtt-85) REVERT: C 435 MET cc_start: 0.8388 (mmm) cc_final: 0.7775 (mmm) REVERT: C 447 MET cc_start: 0.8043 (mmm) cc_final: 0.7782 (tpp) REVERT: C 496 MET cc_start: 0.5803 (tpt) cc_final: 0.5426 (tpt) REVERT: C 521 LYS cc_start: 0.7131 (ttpp) cc_final: 0.6720 (ptmm) REVERT: C 525 HIS cc_start: 0.5969 (t70) cc_final: 0.5646 (m90) REVERT: C 592 GLU cc_start: 0.7264 (tp30) cc_final: 0.6771 (tp30) REVERT: C 635 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7296 (mt0) REVERT: C 640 GLU cc_start: 0.6795 (pm20) cc_final: 0.6573 (pm20) REVERT: C 658 LYS cc_start: 0.5995 (mmmt) cc_final: 0.5733 (mptp) REVERT: C 680 ASP cc_start: 0.6961 (m-30) cc_final: 0.6529 (m-30) REVERT: C 917 PHE cc_start: 0.6315 (m-10) cc_final: 0.5478 (t80) REVERT: C 918 ARG cc_start: 0.7546 (mmm-85) cc_final: 0.5943 (mpt180) REVERT: C 961 GLU cc_start: 0.7628 (tt0) cc_final: 0.7091 (pm20) outliers start: 53 outliers final: 40 residues processed: 376 average time/residue: 1.3598 time to fit residues: 592.7019 Evaluate side-chains 382 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 331 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 417 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 623 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 921 THR 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 79 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 481 SER Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 647 THR 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 810 TYR Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 545 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 920 LEU Chi-restraints excluded: chain C residue 921 THR 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 194 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 226 optimal weight: 0.6980 chunk 36 optimal weight: 0.0770 chunk 68 optimal weight: 2.9990 chunk 245 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- 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 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.112083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.094628 restraints weight = 31009.615| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.68 r_work: 0.2998 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23946 Z= 0.177 Angle : 0.510 8.605 32532 Z= 0.260 Chirality : 0.041 0.203 3811 Planarity : 0.004 0.054 4170 Dihedral : 4.549 59.850 3303 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.23 % Allowed : 17.64 % Favored : 80.13 % 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: 2.06 (0.15), residues: 3092 helix: 2.44 (0.12), residues: 1736 sheet: 0.03 (0.24), residues: 421 loop : 0.02 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.002 0.000 HIS C 708 PHE 0.031 0.001 PHE A 362 TYR 0.016 0.001 TYR C 540 ARG 0.010 0.000 ARG B 557 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9388.73 seconds wall clock time: 165 minutes 56.05 seconds (9956.05 seconds total)