Starting phenix.real_space_refine on Tue Dec 31 12:16:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bfh_44496/12_2024/9bfh_44496_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bfh_44496/12_2024/9bfh_44496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bfh_44496/12_2024/9bfh_44496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bfh_44496/12_2024/9bfh_44496.map" model { file = "/net/cci-nas-00/data/ceres_data/9bfh_44496/12_2024/9bfh_44496_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bfh_44496/12_2024/9bfh_44496_trim.cif" } resolution = 2.62 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= 0.001 sd= 0.112 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 23519 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 132 5.16 5 Cl 2 4.86 5 C 15172 2.51 5 N 3888 2.21 5 O 4383 1.98 5 H 24002 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 47579 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 15857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 15857 Classifications: {'peptide': 1034} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 988} Chain: "B" Number of atoms: 15849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 15849 Classifications: {'peptide': 1033} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 987} Chain: "C" Number of atoms: 15849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 15849 Classifications: {'peptide': 1033} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 987} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 24 Unusual residues: {'A1AN8': 1} Classifications: {'undetermined': 1, 'water': 5} Link IDs: {None: 5} Time building chain proxies: 17.30, per 1000 atoms: 0.36 Number of scatterers: 47579 At special positions: 0 Unit cell: (115.56, 123.05, 146.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 132 16.00 O 4383 8.00 N 3888 7.00 C 15172 6.00 H 24002 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.10 Conformation dependent library (CDL) restraints added in 3.0 seconds 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5666 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 24 sheets defined 60.6% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 3.519A pdb=" N ASP A 7 " --> pdb=" O ASN A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 30 Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 67 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 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 329 through 360 Processing helix chain 'A' and resid 361 through 386 removed outlier: 3.749A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 424 removed outlier: 4.333A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 454 removed outlier: 5.467A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.139A 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: 3.639A pdb=" N GLN A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 510 through 537 removed outlier: 3.530A pdb=" N SER A 537 " --> pdb=" O GLY A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 559 removed outlier: 4.037A pdb=" N TYR A 541 " --> pdb=" O SER A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 601 Processing helix chain 'A' and resid 633 through 637 Processing helix chain 'A' and resid 639 through 642 Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'A' and resid 691 through 708 Processing helix chain 'A' and resid 732 through 739 Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 777 through 780 removed outlier: 3.517A pdb=" N ARG A 780 " --> pdb=" O ALA A 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 777 through 780' Processing helix chain 'A' and resid 782 through 788 Processing helix chain 'A' and resid 836 through 850 removed outlier: 3.724A pdb=" N LYS A 850 " --> pdb=" O GLN A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 870 removed outlier: 3.530A pdb=" N GLN A 865 " --> pdb=" O GLY A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 893 removed outlier: 4.076A pdb=" N SER A 875 " --> pdb=" O ASN A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 903 removed outlier: 3.989A pdb=" N SER A 900 " --> pdb=" O SER A 896 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 901 " --> pdb=" O ILE A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 920 removed outlier: 3.917A pdb=" N GLY A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 956 Processing helix chain 'A' and resid 959 through 992 removed outlier: 4.751A pdb=" N ARG A 973 " --> pdb=" O ARG A 969 " (cutoff:3.500A) Proline residue: A 974 - end of helix Proline residue: A 988 - end of helix Processing helix chain 'A' and resid 996 through 1033 removed outlier: 4.201A pdb=" N GLY A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A1007 " --> pdb=" O VAL A1003 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A1019 " --> pdb=" O THR A1015 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE A1020 " --> pdb=" O VAL A1016 " (cutoff:3.500A) Proline residue: A1023 - end of helix Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 8 through 30 Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 67 Processing helix chain 'B' and resid 99 through 115 removed outlier: 4.160A pdb=" N LEU B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA B 114 " --> pdb=" O LYS B 110 " (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 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 Processing helix chain 'B' and resid 361 through 386 removed outlier: 3.779A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 424 removed outlier: 4.379A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 454 removed outlier: 5.455A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 463 through 497 removed outlier: 4.014A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.620A 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 511 through 536 removed outlier: 3.604A pdb=" N ARG B 536 " --> pdb=" O GLY B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 558 removed outlier: 3.556A pdb=" N TYR B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG B 558 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 601 Processing helix chain 'B' and resid 633 through 637 Processing helix chain 'B' and resid 643 through 656 Processing helix chain 'B' and resid 691 through 708 Processing helix chain 'B' and resid 732 through 739 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 777 through 780 Processing helix chain 'B' and resid 782 through 788 Processing helix chain 'B' and resid 836 through 849 Processing helix chain 'B' and resid 860 through 869 removed outlier: 3.795A pdb=" N GLN B 865 " --> pdb=" O GLY B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 893 Processing helix chain 'B' and resid 896 through 903 removed outlier: 3.906A pdb=" N SER B 900 " --> pdb=" O SER B 896 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 920 removed outlier: 3.758A pdb=" N VAL B 909 " --> pdb=" O VAL B 905 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 957 Processing helix chain 'B' and resid 959 through 992 removed outlier: 4.926A pdb=" N ARG B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Proline residue: B 974 - end of helix Proline residue: B 988 - end of helix Processing helix chain 'B' and resid 998 through 1033 removed outlier: 4.075A pdb=" N ILE B1019 " --> pdb=" O THR B1015 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE B1020 " --> pdb=" O VAL B1016 " (cutoff:3.500A) Proline residue: B1023 - end of helix Processing helix chain 'C' and resid 2 through 7 removed outlier: 3.586A 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 68 removed outlier: 4.036A pdb=" N ASN C 68 " --> pdb=" O VAL C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 removed outlier: 4.135A pdb=" N LEU C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 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 168 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 312 Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 329 through 360 Processing helix chain 'C' and resid 361 through 386 Proline residue: C 368 - end of helix removed outlier: 4.009A pdb=" N ALA C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 391 through 424 removed outlier: 4.261A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASP C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 452 removed outlier: 4.147A pdb=" N GLY C 440 " --> pdb=" O GLY C 436 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ALA C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 443 " --> pdb=" O GLN C 439 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY C 444 " --> pdb=" O GLY C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 Processing helix chain 'C' and resid 460 through 496 removed outlier: 3.773A pdb=" N GLN C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 4.485A 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 511 through 537 removed outlier: 3.631A pdb=" N TRP C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 559 removed outlier: 3.731A pdb=" N VAL C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU C 544 " --> pdb=" O ARG C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 601 Processing helix chain 'C' and resid 633 through 637 Processing helix chain 'C' and resid 639 through 642 Processing helix chain 'C' and resid 643 through 656 Processing helix chain 'C' and resid 691 through 708 Processing helix chain 'C' and resid 732 through 740 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 777 through 780 Processing helix chain 'C' and resid 782 through 788 removed outlier: 3.557A pdb=" N ILE C 786 " --> pdb=" O PRO C 783 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY C 787 " --> pdb=" O ASP C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 849 Processing helix chain 'C' and resid 861 through 893 Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 895 through 903 removed outlier: 3.501A pdb=" N PHE C 899 " --> pdb=" O TRP C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 920 removed outlier: 3.704A pdb=" N GLY C 908 " --> pdb=" O VAL C 904 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 957 removed outlier: 3.737A pdb=" N ILE C 945 " --> pdb=" O ASN C 941 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 991 removed outlier: 5.119A pdb=" N ARG C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Proline residue: C 974 - end of helix Proline residue: C 988 - end of helix Processing helix chain 'C' and resid 996 through 1017 removed outlier: 3.589A pdb=" N GLN C1000 " --> pdb=" O GLY C 996 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL C1007 " --> pdb=" O VAL C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1033 Proline residue: C1023 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 131 removed outlier: 4.021A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ARG A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N GLU A 826 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLU A 826 " --> pdb=" O PRO A 718 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU A 828 " --> pdb=" O VAL A 716 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL A 716 " --> pdb=" O LEU A 828 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 131 removed outlier: 4.021A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ARG A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N GLU A 826 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.544A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN A 144 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 7.261A 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: 3.544A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 4.602A 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: 7.362A pdb=" N TYR A 182 " --> pdb=" O LYS A 770 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N TYR A 772 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N MET A 184 " --> pdb=" O TYR A 772 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N MET A 774 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE A 186 " --> pdb=" O MET A 774 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ARG A 767 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE A 763 " --> pdb=" O ARG A 767 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LYS A 769 " --> pdb=" O ASP A 761 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ASP A 761 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL A 771 " --> pdb=" O VAL A 759 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 217 through 219 removed outlier: 4.281A pdb=" N GLY A 217 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER A 233 " --> pdb=" O PRO C 725 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 250 through 253 removed outlier: 3.571A pdb=" N LYS A 252 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 805 through 812 removed outlier: 8.221A pdb=" N ILE B 235 " --> pdb=" O PRO A 725 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE A 727 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 790 through 792 Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 130 removed outlier: 4.046A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 12.232A pdb=" N ARG B 815 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N GLU B 826 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLU B 826 " --> pdb=" O PRO B 718 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU B 828 " --> pdb=" O VAL B 716 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL B 716 " --> pdb=" O LEU B 828 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 128 through 130 removed outlier: 4.046A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 12.232A pdb=" N ARG B 815 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N GLU B 826 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 6.647A pdb=" N VAL B 172 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ALA B 294 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ILE B 143 " --> pdb=" O PRO B 285 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER B 287 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLY B 141 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 289 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL B 139 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 291 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU B 293 " --> pdb=" O SER B 135 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N SER B 135 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 9.954A pdb=" N LEU B 137 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ASP B 328 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 6.832A 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: 6.647A pdb=" N VAL B 172 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ALA B 294 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 266 through 272 removed outlier: 7.441A pdb=" N TYR B 182 " --> pdb=" O LYS B 770 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N TYR B 772 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N MET B 184 " --> pdb=" O TYR B 772 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N MET B 774 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE B 186 " --> pdb=" O MET B 774 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN B 760 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL B 773 " --> pdb=" O TYR B 758 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N TYR B 758 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 250 through 253 Processing sheet with id=AB7, first strand: chain 'B' and resid 805 through 812 removed outlier: 8.596A pdb=" N ILE C 235 " --> pdb=" O PRO B 725 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE B 727 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLY C 217 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 790 through 792 Processing sheet with id=AB9, first strand: chain 'C' and resid 128 through 132 removed outlier: 4.505A pdb=" N ALA C 42 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 11.903A pdb=" N ARG C 815 " --> pdb=" O GLU C 826 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N GLU C 826 " --> pdb=" O ARG C 815 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU C 817 " --> pdb=" O SER C 824 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN C 830 " --> pdb=" O SER C 715 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N SER C 715 " --> pdb=" O GLN C 830 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 128 through 132 removed outlier: 4.505A pdb=" N ALA C 42 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 11.903A pdb=" N ARG C 815 " --> pdb=" O GLU C 826 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N GLU C 826 " --> pdb=" O ARG C 815 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU C 817 " --> pdb=" O SER C 824 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY C 829 " --> pdb=" O PHE C 680 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 177 removed outlier: 5.733A pdb=" N LYS C 292 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL C 175 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY C 290 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU C 177 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY C 288 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASN C 144 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET C 138 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU C 293 " --> pdb=" O PHE C 136 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N PHE C 136 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 9.699A pdb=" N LEU C 137 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ASP C 328 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 6.539A 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: 5.733A pdb=" N LYS C 292 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL C 175 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY C 290 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU C 177 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY C 288 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 266 through 270 removed outlier: 5.854A pdb=" N MET C 184 " --> pdb=" O TYR C 772 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N MET C 774 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ILE C 186 " --> pdb=" O MET C 774 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN C 760 " --> pdb=" O VAL C 771 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL C 773 " --> pdb=" O TYR C 758 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N TYR C 758 " --> pdb=" O VAL C 773 " (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 790 through 792 1665 hydrogen bonds defined for protein. 4815 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: 19.07 Time building geometry restraints manager: 13.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 23996 1.02 - 1.22: 37 1.22 - 1.41: 9479 1.41 - 1.61: 14252 1.61 - 1.81: 261 Bond restraints: 48025 Sorted by residual: bond pdb=" C02 A1AN8 A1101 " pdb=" C03 A1AN8 A1101 " ideal model delta sigma weight residual 1.542 1.259 0.283 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C06 A1AN8 A1101 " pdb=" N05 A1AN8 A1101 " ideal model delta sigma weight residual 1.444 1.208 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C GLY C 440 " pdb=" O GLY C 440 " ideal model delta sigma weight residual 1.234 1.107 0.127 1.29e-02 6.01e+03 9.64e+01 bond pdb=" C19 A1AN8 A1101 " pdb=" N05 A1AN8 A1101 " ideal model delta sigma weight residual 1.452 1.280 0.172 2.00e-02 2.50e+03 7.40e+01 bond pdb=" CA GLN C 439 " pdb=" C GLN C 439 " ideal model delta sigma weight residual 1.523 1.424 0.098 1.35e-02 5.49e+03 5.32e+01 ... (remaining 48020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 86955 3.35 - 6.69: 143 6.69 - 10.04: 3 10.04 - 13.38: 0 13.38 - 16.73: 2 Bond angle restraints: 87103 Sorted by residual: angle pdb=" C GLY C 440 " pdb=" N ALA C 441 " pdb=" CA ALA C 441 " ideal model delta sigma weight residual 120.58 135.97 -15.39 1.71e+00 3.42e-01 8.10e+01 angle pdb=" N ILE C 438 " pdb=" CA ILE C 438 " pdb=" C ILE C 438 " ideal model delta sigma weight residual 113.22 121.49 -8.27 1.23e+00 6.61e-01 4.52e+01 angle pdb=" C GLY C 440 " pdb=" N ALA C 441 " pdb=" H ALA C 441 " ideal model delta sigma weight residual 124.86 108.13 16.73 3.00e+00 1.11e-01 3.11e+01 angle pdb=" CA GLY C 440 " pdb=" C GLY C 440 " pdb=" N ALA C 441 " ideal model delta sigma weight residual 117.34 122.35 -5.01 1.01e+00 9.80e-01 2.46e+01 angle pdb=" CA MET C 435 " pdb=" C MET C 435 " pdb=" N GLY C 436 " ideal model delta sigma weight residual 117.07 122.67 -5.60 1.14e+00 7.69e-01 2.41e+01 ... (remaining 87098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 20329 17.72 - 35.44: 1612 35.44 - 53.16: 446 53.16 - 70.88: 156 70.88 - 88.59: 20 Dihedral angle restraints: 22563 sinusoidal: 12360 harmonic: 10203 Sorted by residual: dihedral pdb=" CA ASP C 730 " pdb=" CB ASP C 730 " pdb=" CG ASP C 730 " pdb=" OD1 ASP C 730 " ideal model delta sinusoidal sigma weight residual -30.00 -86.34 56.34 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CB GLU B 269 " pdb=" CG GLU B 269 " pdb=" CD GLU B 269 " pdb=" OE1 GLU B 269 " ideal model delta sinusoidal sigma weight residual 0.00 88.59 -88.59 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CG ARG C 767 " pdb=" CD ARG C 767 " pdb=" NE ARG C 767 " pdb=" CZ ARG C 767 " ideal model delta sinusoidal sigma weight residual 180.00 137.11 42.89 2 1.50e+01 4.44e-03 9.88e+00 ... (remaining 22560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3642 0.092 - 0.184: 192 0.184 - 0.276: 3 0.276 - 0.367: 1 0.367 - 0.459: 2 Chirality restraints: 3840 Sorted by residual: chirality pdb=" C02 A1AN8 A1101 " pdb=" C03 A1AN8 A1101 " pdb=" C19 A1AN8 A1101 " pdb=" N01 A1AN8 A1101 " both_signs ideal model delta sigma weight residual False 2.78 2.32 0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" CA MET C 435 " pdb=" N MET C 435 " pdb=" C MET C 435 " pdb=" CB MET C 435 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CA ILE C 438 " pdb=" N ILE C 438 " pdb=" C ILE C 438 " pdb=" CB ILE C 438 " both_signs ideal model delta sigma weight residual False 2.43 2.14 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 3837 not shown) Planarity restraints: 7132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN C 437 " 0.235 2.00e-02 2.50e+03 3.26e-01 1.59e+03 pdb=" CD GLN C 437 " -0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN C 437 " -0.236 2.00e-02 2.50e+03 pdb=" NE2 GLN C 437 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN C 437 " 0.522 2.00e-02 2.50e+03 pdb="HE22 GLN C 437 " -0.503 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 415 " -0.134 2.00e-02 2.50e+03 1.33e-01 2.67e+02 pdb=" CG ASN C 415 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN C 415 " 0.132 2.00e-02 2.50e+03 pdb=" ND2 ASN C 415 " -0.005 2.00e-02 2.50e+03 pdb="HD21 ASN C 415 " -0.189 2.00e-02 2.50e+03 pdb="HD22 ASN C 415 " 0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 439 " 0.030 2.00e-02 2.50e+03 3.29e-02 1.62e+01 pdb=" CD GLN C 439 " 0.000 2.00e-02 2.50e+03 pdb=" OE1 GLN C 439 " -0.030 2.00e-02 2.50e+03 pdb=" NE2 GLN C 439 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN C 439 " -0.048 2.00e-02 2.50e+03 pdb="HE22 GLN C 439 " 0.049 2.00e-02 2.50e+03 ... (remaining 7129 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 2879 2.21 - 2.80: 101481 2.80 - 3.40: 137491 3.40 - 4.00: 185343 4.00 - 4.60: 284863 Nonbonded interactions: 712057 Sorted by model distance: nonbonded pdb=" OE2 GLU A 845 " pdb="HH22 ARG A 867 " model vdw 1.608 2.450 nonbonded pdb=" HH TYR C 758 " pdb=" OD1 ASP C 761 " model vdw 1.641 2.450 nonbonded pdb=" OE1 GLU A 641 " pdb=" H GLU A 641 " model vdw 1.642 2.450 nonbonded pdb=" O HIS A 596 " pdb=" HG1 THR A 600 " model vdw 1.647 2.450 nonbonded pdb=" O PRO B 427 " pdb=" HG1 THR B 431 " model vdw 1.655 2.450 ... (remaining 712052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 532 or (resid 533 and (name N or name CA or name \ C or name O or name HA2 or name HA3)) or resid 534 through 551 or (resid 552 an \ d (name N or name CA or name C or name O or name CB or name CG or name SD or nam \ e CE or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE1 or n \ ame HE2 or name HE3)) or resid 553 through 1033)) selection = (chain 'B' and (resid 1 through 108 or (resid 109 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ )) or resid 110 through 551 or (resid 552 and (name N or name CA or name C or na \ me O or name CB or name CG or name SD or name CE or name HA or name HB2 or name \ HB3 or name HG2 or name HG3 or name HE1 or name HE2 or name HE3)) or resid 553 t \ hrough 1033)) selection = (chain 'C' and (resid 1 through 108 or (resid 109 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ )) or resid 110 through 532 or (resid 533 and (name N or name CA or name C or na \ me O or name HA2 or name HA3)) or resid 534 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: 4.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.330 Construct map_model_manager: 0.640 Extract box with map and model: 1.460 Check model and map are aligned: 0.290 Set scattering table: 0.360 Process input model: 83.890 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.130 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:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.005 0.283 24023 Z= 0.311 Angle : 0.542 15.392 32624 Z= 0.301 Chirality : 0.042 0.459 3840 Planarity : 0.004 0.070 4172 Dihedral : 13.421 88.594 8693 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.04 % Allowed : 0.16 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.99 (0.16), residues: 3094 helix: 2.18 (0.13), residues: 1694 sheet: 0.01 (0.25), residues: 386 loop : 0.50 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 789 HIS 0.002 0.000 HIS B 526 PHE 0.022 0.001 PHE A 362 TYR 0.022 0.001 TYR A 49 ARG 0.011 0.000 ARG B 969 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 457 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7948 (mmtm) cc_final: 0.7371 (pttt) REVERT: A 138 MET cc_start: 0.8224 (ttm) cc_final: 0.7738 (ttp) REVERT: A 681 ASP cc_start: 0.7348 (t0) cc_final: 0.7106 (t70) REVERT: B 505 HIS cc_start: 0.7443 (m-70) cc_final: 0.7027 (m-70) REVERT: B 953 MET cc_start: 0.7943 (mtp) cc_final: 0.7741 (mtm) REVERT: C 29 LYS cc_start: 0.7570 (mmpt) cc_final: 0.7352 (pttt) REVERT: C 437 GLN cc_start: 0.8426 (mt0) cc_final: 0.8152 (mt0) REVERT: C 681 ASP cc_start: 0.8640 (t0) cc_final: 0.8423 (t0) REVERT: C 956 GLU cc_start: 0.7703 (mp0) cc_final: 0.7366 (mp0) REVERT: C 962 GLU cc_start: 0.7371 (tt0) cc_final: 0.7161 (tt0) outliers start: 1 outliers final: 1 residues processed: 458 average time/residue: 2.3620 time to fit residues: 1252.6610 Evaluate side-chains 370 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 369 time to evaluate : 2.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 566 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 2.9990 chunk 234 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 125 optimal weight: 0.0770 chunk 242 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24023 Z= 0.230 Angle : 0.521 5.909 32624 Z= 0.280 Chirality : 0.041 0.175 3840 Planarity : 0.005 0.059 4172 Dihedral : 4.743 73.187 3309 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.31 % Allowed : 7.82 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 3094 helix: 2.21 (0.12), residues: 1702 sheet: 0.10 (0.26), residues: 375 loop : 0.42 (0.21), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 789 HIS 0.003 0.001 HIS B 338 PHE 0.016 0.001 PHE B 664 TYR 0.016 0.001 TYR B 49 ARG 0.006 0.000 ARG B 969 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 375 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8195 (mmtm) cc_final: 0.7637 (pttt) REVERT: A 138 MET cc_start: 0.8289 (ttm) cc_final: 0.7839 (ttp) REVERT: A 681 ASP cc_start: 0.7479 (t0) cc_final: 0.7160 (t0) REVERT: A 866 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6554 (tm-30) REVERT: A 966 ASP cc_start: 0.6796 (OUTLIER) cc_final: 0.6258 (t0) REVERT: A 977 MET cc_start: 0.8353 (ptm) cc_final: 0.8121 (ptm) REVERT: B 450 SER cc_start: 0.8668 (m) cc_final: 0.8400 (p) REVERT: B 505 HIS cc_start: 0.7459 (m-70) cc_final: 0.7145 (m-70) REVERT: B 825 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8353 (mtt) REVERT: B 953 MET cc_start: 0.7892 (mtp) cc_final: 0.7636 (mtm) REVERT: C 29 LYS cc_start: 0.7640 (mmpt) cc_final: 0.7385 (pttt) REVERT: C 423 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7372 (mt-10) REVERT: C 956 GLU cc_start: 0.7654 (mp0) cc_final: 0.7368 (mp0) REVERT: C 962 GLU cc_start: 0.7380 (tt0) cc_final: 0.7132 (tt0) outliers start: 33 outliers final: 15 residues processed: 392 average time/residue: 2.3538 time to fit residues: 1071.9126 Evaluate side-chains 383 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 364 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 938 SER Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 640 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 423 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 281 optimal weight: 0.4980 chunk 303 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24023 Z= 0.348 Angle : 0.562 5.632 32624 Z= 0.302 Chirality : 0.043 0.174 3840 Planarity : 0.005 0.051 4172 Dihedral : 4.856 56.957 3309 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.87 % Allowed : 9.09 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.64 (0.15), residues: 3094 helix: 1.90 (0.12), residues: 1704 sheet: 0.09 (0.26), residues: 382 loop : 0.21 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 789 HIS 0.004 0.001 HIS B 338 PHE 0.018 0.002 PHE A 617 TYR 0.026 0.002 TYR B 49 ARG 0.005 0.001 ARG C 637 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 369 time to evaluate : 3.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8172 (mmtm) cc_final: 0.7525 (pttt) REVERT: A 130 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7175 (pm20) REVERT: A 138 MET cc_start: 0.8377 (ttm) cc_final: 0.8047 (ttp) REVERT: A 866 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6588 (tm-30) REVERT: A 966 ASP cc_start: 0.6873 (OUTLIER) cc_final: 0.6459 (t0) REVERT: A 977 MET cc_start: 0.8491 (ptm) cc_final: 0.8083 (ptm) REVERT: B 505 HIS cc_start: 0.7564 (m-70) cc_final: 0.7226 (m-70) REVERT: B 573 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7967 (mtp) REVERT: B 825 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8117 (mtt) REVERT: B 953 MET cc_start: 0.7984 (mtp) cc_final: 0.7589 (mtm) REVERT: C 29 LYS cc_start: 0.7761 (mmpt) cc_final: 0.7435 (pttt) REVERT: C 66 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7862 (pt0) REVERT: C 432 ARG cc_start: 0.7466 (mtt-85) cc_final: 0.7241 (mtt-85) REVERT: C 687 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.6606 (mm-40) REVERT: C 962 GLU cc_start: 0.7461 (tt0) cc_final: 0.7184 (tt0) outliers start: 47 outliers final: 22 residues processed: 389 average time/residue: 2.3571 time to fit residues: 1066.2827 Evaluate side-chains 380 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 351 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 938 SER Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 573 MET Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 640 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 987 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 687 GLN Chi-restraints excluded: chain C residue 714 THR Chi-restraints excluded: chain C residue 896 SER 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: 4.9990 chunk 31 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 188 optimal weight: 4.9990 chunk 282 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 267 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24023 Z= 0.236 Angle : 0.514 5.458 32624 Z= 0.276 Chirality : 0.041 0.171 3840 Planarity : 0.004 0.062 4172 Dihedral : 4.758 57.294 3309 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.63 % Allowed : 10.21 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.74 (0.15), residues: 3094 helix: 2.00 (0.12), residues: 1705 sheet: 0.12 (0.26), residues: 360 loop : 0.21 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 789 HIS 0.003 0.001 HIS B 338 PHE 0.013 0.001 PHE A 682 TYR 0.016 0.001 TYR A 554 ARG 0.003 0.000 ARG B 558 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 368 time to evaluate : 3.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8094 (mmtm) cc_final: 0.7414 (pttt) REVERT: A 130 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7263 (pm20) REVERT: A 138 MET cc_start: 0.8320 (ttm) cc_final: 0.8041 (ttp) REVERT: A 540 ARG cc_start: 0.7213 (mtm110) cc_final: 0.6922 (ttm-80) REVERT: A 866 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6547 (tm-30) REVERT: A 966 ASP cc_start: 0.6946 (OUTLIER) cc_final: 0.6526 (t0) REVERT: A 977 MET cc_start: 0.8424 (ptm) cc_final: 0.8085 (ptm) REVERT: B 450 SER cc_start: 0.8671 (m) cc_final: 0.8400 (p) REVERT: B 505 HIS cc_start: 0.7593 (m-70) cc_final: 0.7238 (m-70) REVERT: B 573 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7960 (mtp) REVERT: B 761 ASP cc_start: 0.8034 (m-30) cc_final: 0.7800 (m-30) REVERT: B 825 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8149 (mtt) REVERT: B 953 MET cc_start: 0.7991 (mtp) cc_final: 0.7627 (mtm) REVERT: C 29 LYS cc_start: 0.7711 (mmpt) cc_final: 0.7396 (pttt) REVERT: C 89 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7412 (tp40) REVERT: C 956 GLU cc_start: 0.7605 (mp0) cc_final: 0.7385 (mp0) REVERT: C 962 GLU cc_start: 0.7432 (tt0) cc_final: 0.7156 (tt0) outliers start: 41 outliers final: 24 residues processed: 387 average time/residue: 2.3377 time to fit residues: 1051.7637 Evaluate side-chains 387 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 357 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 938 SER Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 573 MET Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 640 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 987 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 714 THR Chi-restraints excluded: chain C residue 896 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 0.3980 chunk 169 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 206 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24023 Z= 0.217 Angle : 0.501 5.238 32624 Z= 0.268 Chirality : 0.040 0.169 3840 Planarity : 0.004 0.049 4172 Dihedral : 4.681 57.556 3309 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.71 % Allowed : 10.41 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.83 (0.15), residues: 3094 helix: 2.10 (0.12), residues: 1707 sheet: 0.20 (0.27), residues: 349 loop : 0.18 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 754 HIS 0.003 0.001 HIS B 338 PHE 0.013 0.001 PHE A 682 TYR 0.013 0.001 TYR B 49 ARG 0.005 0.000 ARG B 558 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 370 time to evaluate : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8128 (mmtm) cc_final: 0.7431 (pttt) REVERT: A 130 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7295 (pm20) REVERT: A 138 MET cc_start: 0.8315 (ttm) cc_final: 0.8052 (ttp) REVERT: A 540 ARG cc_start: 0.7215 (mtm110) cc_final: 0.7013 (ttm-80) REVERT: A 866 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6519 (tm-30) REVERT: A 966 ASP cc_start: 0.6952 (OUTLIER) cc_final: 0.6523 (t0) REVERT: B 450 SER cc_start: 0.8687 (m) cc_final: 0.8381 (p) REVERT: B 505 HIS cc_start: 0.7570 (m-70) cc_final: 0.7203 (m-70) REVERT: B 761 ASP cc_start: 0.8079 (m-30) cc_final: 0.7857 (m-30) REVERT: B 825 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8090 (mtt) REVERT: B 830 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7843 (mt0) REVERT: B 953 MET cc_start: 0.7930 (mtp) cc_final: 0.7590 (mtm) REVERT: C 29 LYS cc_start: 0.7723 (mmpt) cc_final: 0.7375 (pttt) REVERT: C 66 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7791 (pt0) REVERT: C 334 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7426 (ttpp) REVERT: C 423 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7493 (mt-10) REVERT: C 962 GLU cc_start: 0.7427 (tt0) cc_final: 0.7146 (tt0) outliers start: 43 outliers final: 20 residues processed: 389 average time/residue: 2.3564 time to fit residues: 1068.7408 Evaluate side-chains 393 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 365 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 938 SER Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 640 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 830 GLN Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 714 THR Chi-restraints excluded: chain C residue 896 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 4.9990 chunk 268 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 298 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24023 Z= 0.281 Angle : 0.526 5.384 32624 Z= 0.281 Chirality : 0.041 0.167 3840 Planarity : 0.005 0.049 4172 Dihedral : 4.759 57.533 3309 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.79 % Allowed : 10.68 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.73 (0.15), residues: 3094 helix: 2.01 (0.12), residues: 1706 sheet: 0.19 (0.27), residues: 352 loop : 0.14 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 789 HIS 0.003 0.001 HIS B 338 PHE 0.014 0.001 PHE A 458 TYR 0.019 0.001 TYR A 554 ARG 0.007 0.000 ARG C 540 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 367 time to evaluate : 2.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7444 (pttt) REVERT: A 130 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7317 (pm20) REVERT: A 138 MET cc_start: 0.8329 (ttm) cc_final: 0.8064 (ttp) REVERT: A 540 ARG cc_start: 0.7237 (mtm110) cc_final: 0.7036 (ttm-80) REVERT: A 866 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6601 (tm-30) REVERT: A 966 ASP cc_start: 0.6965 (OUTLIER) cc_final: 0.6535 (t0) REVERT: B 450 SER cc_start: 0.8678 (m) cc_final: 0.8392 (p) REVERT: B 505 HIS cc_start: 0.7583 (m-70) cc_final: 0.7220 (m-70) REVERT: B 761 ASP cc_start: 0.8130 (m-30) cc_final: 0.7912 (m-30) REVERT: B 825 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8010 (mtt) REVERT: B 830 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7854 (mt0) REVERT: B 953 MET cc_start: 0.7969 (mtp) cc_final: 0.7617 (mtm) REVERT: C 29 LYS cc_start: 0.7788 (mmpt) cc_final: 0.7404 (pttt) REVERT: C 66 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7835 (pt0) REVERT: C 89 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7407 (tp40) REVERT: C 197 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8210 (mp-120) REVERT: C 280 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8066 (mt-10) REVERT: C 334 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7430 (ttpp) REVERT: C 956 GLU cc_start: 0.7658 (mp0) cc_final: 0.7297 (mp0) REVERT: C 962 GLU cc_start: 0.7502 (tt0) cc_final: 0.7218 (tt0) outliers start: 45 outliers final: 27 residues processed: 391 average time/residue: 2.4444 time to fit residues: 1112.9168 Evaluate side-chains 400 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 363 time to evaluate : 2.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 938 SER Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 640 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 830 GLN Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 987 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 433 LYS Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 714 THR Chi-restraints excluded: chain C residue 896 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 170 optimal weight: 6.9990 chunk 218 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 251 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 297 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 181 optimal weight: 0.5980 chunk 137 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24023 Z= 0.169 Angle : 0.483 4.966 32624 Z= 0.257 Chirality : 0.040 0.165 3840 Planarity : 0.004 0.047 4172 Dihedral : 4.590 59.562 3309 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.19 % Allowed : 11.76 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 3094 helix: 2.23 (0.12), residues: 1708 sheet: 0.22 (0.27), residues: 349 loop : 0.23 (0.20), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 754 HIS 0.003 0.001 HIS B 338 PHE 0.014 0.001 PHE A 682 TYR 0.011 0.001 TYR B 541 ARG 0.008 0.000 ARG B 558 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 370 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8117 (mmtm) cc_final: 0.7490 (pttt) REVERT: A 138 MET cc_start: 0.8298 (ttm) cc_final: 0.8027 (ttp) REVERT: A 540 ARG cc_start: 0.7236 (mtm110) cc_final: 0.7034 (ttm-80) REVERT: A 966 ASP cc_start: 0.6949 (OUTLIER) cc_final: 0.6515 (t0) REVERT: B 450 SER cc_start: 0.8622 (m) cc_final: 0.8356 (p) REVERT: B 505 HIS cc_start: 0.7548 (m-70) cc_final: 0.7181 (m-70) REVERT: B 546 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8469 (mm) REVERT: B 761 ASP cc_start: 0.7989 (m-30) cc_final: 0.7788 (m-30) REVERT: B 825 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8123 (mtt) REVERT: B 830 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7834 (mt0) REVERT: B 953 MET cc_start: 0.7941 (mtp) cc_final: 0.7603 (mtm) REVERT: C 29 LYS cc_start: 0.7758 (mmpt) cc_final: 0.7379 (pttt) REVERT: C 197 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8305 (mp-120) REVERT: C 334 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7420 (ttpp) REVERT: C 435 MET cc_start: 0.8474 (mmm) cc_final: 0.8244 (mmm) REVERT: C 962 GLU cc_start: 0.7437 (tt0) cc_final: 0.7155 (tt0) REVERT: C 1032 ARG cc_start: 0.7531 (mmt90) cc_final: 0.7174 (mpt-90) outliers start: 30 outliers final: 13 residues processed: 386 average time/residue: 2.3215 time to fit residues: 1040.2048 Evaluate side-chains 381 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 362 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 938 SER Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 830 GLN Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 734 GLU Chi-restraints excluded: chain C residue 896 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 0.1980 chunk 118 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24023 Z= 0.324 Angle : 0.539 5.435 32624 Z= 0.288 Chirality : 0.042 0.169 3840 Planarity : 0.005 0.051 4172 Dihedral : 4.733 57.731 3307 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.75 % Allowed : 11.32 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.76 (0.15), residues: 3094 helix: 2.03 (0.12), residues: 1707 sheet: 0.20 (0.27), residues: 352 loop : 0.14 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 789 HIS 0.003 0.001 HIS B 526 PHE 0.015 0.002 PHE A 458 TYR 0.016 0.002 TYR C 182 ARG 0.007 0.001 ARG B 558 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 364 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8135 (mmtm) cc_final: 0.7503 (pttt) REVERT: A 130 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7324 (pm20) REVERT: A 138 MET cc_start: 0.8326 (ttm) cc_final: 0.8093 (ttp) REVERT: A 423 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6575 (mp0) REVERT: A 866 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6520 (tm-30) REVERT: A 966 ASP cc_start: 0.6974 (OUTLIER) cc_final: 0.6536 (t0) REVERT: B 505 HIS cc_start: 0.7620 (m-70) cc_final: 0.7242 (m-70) REVERT: B 546 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8491 (mm) REVERT: B 761 ASP cc_start: 0.8092 (m-30) cc_final: 0.7886 (m-30) REVERT: B 825 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8004 (mtt) REVERT: B 830 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7863 (mt0) REVERT: B 867 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6709 (mtp-110) REVERT: B 953 MET cc_start: 0.8005 (mtp) cc_final: 0.7683 (mtm) REVERT: C 29 LYS cc_start: 0.7823 (mmpt) cc_final: 0.7415 (pttt) REVERT: C 66 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7856 (pt0) REVERT: C 197 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8256 (mp-120) REVERT: C 334 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7426 (ttpp) REVERT: C 956 GLU cc_start: 0.7652 (mp0) cc_final: 0.7253 (mp0) REVERT: C 962 GLU cc_start: 0.7499 (tt0) cc_final: 0.7211 (tt0) outliers start: 44 outliers final: 24 residues processed: 391 average time/residue: 2.4221 time to fit residues: 1101.7593 Evaluate side-chains 397 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 362 time to evaluate : 3.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 938 SER Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 687 GLN Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 830 GLN Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 987 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 714 THR Chi-restraints excluded: chain C residue 896 SER Chi-restraints excluded: chain C residue 947 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 0.2980 chunk 285 optimal weight: 2.9990 chunk 260 optimal weight: 0.7980 chunk 277 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 262 optimal weight: 0.8980 chunk 276 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24023 Z= 0.174 Angle : 0.490 5.067 32624 Z= 0.261 Chirality : 0.040 0.165 3840 Planarity : 0.005 0.103 4172 Dihedral : 4.591 59.947 3307 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.31 % Allowed : 11.68 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 3094 helix: 2.22 (0.12), residues: 1707 sheet: 0.21 (0.27), residues: 349 loop : 0.21 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 754 HIS 0.003 0.001 HIS B 526 PHE 0.013 0.001 PHE A 682 TYR 0.019 0.001 TYR A 554 ARG 0.011 0.000 ARG A 540 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 367 time to evaluate : 2.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8117 (mmtm) cc_final: 0.7498 (pttt) REVERT: A 138 MET cc_start: 0.8298 (ttm) cc_final: 0.8064 (ttp) REVERT: A 540 ARG cc_start: 0.7354 (mtm110) cc_final: 0.6977 (ttm-80) REVERT: A 966 ASP cc_start: 0.6957 (OUTLIER) cc_final: 0.6520 (t0) REVERT: B 450 SER cc_start: 0.8623 (m) cc_final: 0.8353 (p) REVERT: B 505 HIS cc_start: 0.7602 (m-70) cc_final: 0.7225 (m-70) REVERT: B 546 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8463 (mm) REVERT: B 825 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8098 (mtt) REVERT: B 830 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: B 867 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6795 (ttp-110) REVERT: B 953 MET cc_start: 0.7929 (mtp) cc_final: 0.7566 (mtm) REVERT: C 29 LYS cc_start: 0.7741 (mmpt) cc_final: 0.7365 (pttt) REVERT: C 197 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8320 (mp-120) REVERT: C 334 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7419 (ttpp) REVERT: C 956 GLU cc_start: 0.7589 (mp0) cc_final: 0.7094 (mp0) REVERT: C 962 GLU cc_start: 0.7475 (tt0) cc_final: 0.7193 (tt0) outliers start: 33 outliers final: 19 residues processed: 383 average time/residue: 2.3880 time to fit residues: 1069.6131 Evaluate side-chains 384 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 358 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 938 SER Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 687 GLN Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 830 GLN Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 987 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 896 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 0.1980 chunk 293 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 307 optimal weight: 3.9990 chunk 283 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 189 optimal weight: 0.0370 chunk 150 optimal weight: 4.9990 overall best weight: 1.2464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24023 Z= 0.196 Angle : 0.494 5.007 32624 Z= 0.263 Chirality : 0.040 0.164 3840 Planarity : 0.004 0.083 4172 Dihedral : 4.572 59.416 3307 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.11 % Allowed : 12.23 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 3094 helix: 2.24 (0.12), residues: 1707 sheet: 0.22 (0.27), residues: 352 loop : 0.20 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 754 HIS 0.004 0.001 HIS B 526 PHE 0.013 0.001 PHE A 682 TYR 0.014 0.001 TYR B 182 ARG 0.014 0.000 ARG A 540 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 362 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8124 (mmtm) cc_final: 0.7502 (pttt) REVERT: A 130 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7294 (pm20) REVERT: A 138 MET cc_start: 0.8308 (ttm) cc_final: 0.8107 (ttp) REVERT: A 540 ARG cc_start: 0.7373 (mtm110) cc_final: 0.6997 (ttm-80) REVERT: A 966 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6526 (t0) REVERT: B 450 SER cc_start: 0.8655 (m) cc_final: 0.8361 (p) REVERT: B 505 HIS cc_start: 0.7590 (m-70) cc_final: 0.7205 (m-70) REVERT: B 522 LYS cc_start: 0.8226 (ttpp) cc_final: 0.7647 (ttmm) REVERT: B 546 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8457 (mm) REVERT: B 825 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8038 (mtt) REVERT: B 830 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7851 (mt0) REVERT: B 867 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6795 (ttp-110) REVERT: B 953 MET cc_start: 0.7937 (mtp) cc_final: 0.7579 (mtm) REVERT: C 29 LYS cc_start: 0.7789 (mmpt) cc_final: 0.7389 (pttt) REVERT: C 197 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8320 (mp-120) REVERT: C 334 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7416 (ttpp) REVERT: C 956 GLU cc_start: 0.7592 (mp0) cc_final: 0.7125 (mp0) REVERT: C 962 GLU cc_start: 0.7478 (tt0) cc_final: 0.7202 (tt0) REVERT: C 1032 ARG cc_start: 0.7526 (mmt90) cc_final: 0.7159 (mpt-90) outliers start: 28 outliers final: 17 residues processed: 375 average time/residue: 2.3863 time to fit residues: 1039.1471 Evaluate side-chains 385 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 360 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 938 SER Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 687 GLN Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 830 GLN Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 987 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 896 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 68 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.116049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.098141 restraints weight = 75620.941| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.25 r_work: 0.2942 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24023 Z= 0.184 Angle : 0.490 4.929 32624 Z= 0.260 Chirality : 0.040 0.164 3840 Planarity : 0.004 0.079 4172 Dihedral : 4.540 59.833 3307 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.23 % Allowed : 12.27 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.00 (0.15), residues: 3094 helix: 2.25 (0.12), residues: 1713 sheet: 0.24 (0.27), residues: 352 loop : 0.23 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 754 HIS 0.004 0.001 HIS B 526 PHE 0.013 0.001 PHE A 682 TYR 0.022 0.001 TYR A 554 ARG 0.013 0.000 ARG A 540 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 15224.44 seconds wall clock time: 260 minutes 14.12 seconds (15614.12 seconds total)