Starting phenix.real_space_refine on Sat Jan 18 00:21:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r2h_18842/01_2025/8r2h_18842.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r2h_18842/01_2025/8r2h_18842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r2h_18842/01_2025/8r2h_18842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r2h_18842/01_2025/8r2h_18842.map" model { file = "/net/cci-nas-00/data/ceres_data/8r2h_18842/01_2025/8r2h_18842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r2h_18842/01_2025/8r2h_18842.cif" } resolution = 2.42 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 40 5.16 5 C 7424 2.51 5 N 1897 2.21 5 O 2117 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 11484 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5680 Classifications: {'peptide': 693} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 677} Chain breaks: 5 Chain: "B" Number of atoms: 5750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5750 Classifications: {'peptide': 701} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 685} Chain breaks: 5 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.02, per 1000 atoms: 0.70 Number of scatterers: 11484 At special positions: 0 Unit cell: (120.62, 93.98, 102.86, 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) S 40 16.00 P 4 15.00 Mg 2 11.99 O 2117 8.00 N 1897 7.00 C 7424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.5 seconds 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2642 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 8 sheets defined 56.7% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 313 through 324 removed outlier: 3.634A pdb=" N PHE A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 334 removed outlier: 4.220A pdb=" N LYS A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 346 Processing helix chain 'A' and resid 353 through 359 removed outlier: 3.526A pdb=" N LYS A 357 " --> pdb=" O TYR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.526A pdb=" N TYR A 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 390 Processing helix chain 'A' and resid 393 through 397 Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 403 through 415 Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 436 through 456 removed outlier: 3.596A pdb=" N LYS A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 454 " --> pdb=" O PHE A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 465 Processing helix chain 'A' and resid 465 through 476 Processing helix chain 'A' and resid 491 through 497 Processing helix chain 'A' and resid 534 through 553 removed outlier: 3.554A pdb=" N LYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 633 removed outlier: 3.582A pdb=" N THR A 632 " --> pdb=" O ASP A 628 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 628 through 633' Processing helix chain 'A' and resid 633 through 647 Processing helix chain 'A' and resid 676 through 683 Processing helix chain 'A' and resid 706 through 711 Processing helix chain 'A' and resid 723 through 737 Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 830 through 845 removed outlier: 3.979A pdb=" N LYS A 844 " --> pdb=" O LYS A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 868 removed outlier: 3.713A pdb=" N ARG A 867 " --> pdb=" O LYS A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 891 Processing helix chain 'A' and resid 904 through 908 Processing helix chain 'A' and resid 910 through 916 Processing helix chain 'A' and resid 938 through 942 Processing helix chain 'A' and resid 945 through 951 Processing helix chain 'A' and resid 963 through 977 Processing helix chain 'A' and resid 993 through 998 Processing helix chain 'A' and resid 1031 through 1040 Processing helix chain 'A' and resid 1080 through 1092 removed outlier: 3.799A pdb=" N VAL A1084 " --> pdb=" O MET A1080 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A1092 " --> pdb=" O ILE A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1100 Processing helix chain 'A' and resid 1115 through 1125 Processing helix chain 'A' and resid 1141 through 1154 removed outlier: 3.574A pdb=" N HIS A1145 " --> pdb=" O GLY A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1160 removed outlier: 3.535A pdb=" N LYS A1158 " --> pdb=" O ASN A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1188 through 1203 Processing helix chain 'B' and resid 313 through 324 Processing helix chain 'B' and resid 326 through 334 removed outlier: 4.259A pdb=" N LYS B 330 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 346 Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 366 through 374 removed outlier: 3.828A pdb=" N PHE B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ASP B 372 " --> pdb=" O PHE B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 390 Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 398 through 402 Processing helix chain 'B' and resid 403 through 415 Processing helix chain 'B' and resid 425 through 431 removed outlier: 3.548A pdb=" N LYS B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 435 No H-bonds generated for 'chain 'B' and resid 433 through 435' Processing helix chain 'B' and resid 436 through 456 removed outlier: 4.222A pdb=" N ASN B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE B 454 " --> pdb=" O PHE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 465 Processing helix chain 'B' and resid 465 through 476 Processing helix chain 'B' and resid 491 through 497 Processing helix chain 'B' and resid 501 through 507 removed outlier: 4.461A pdb=" N LEU B 505 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 507 " --> pdb=" O PHE B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 552 removed outlier: 3.842A pdb=" N LYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 633 removed outlier: 3.604A pdb=" N THR B 632 " --> pdb=" O ASP B 628 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY B 633 " --> pdb=" O GLY B 629 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 628 through 633' Processing helix chain 'B' and resid 633 through 647 Processing helix chain 'B' and resid 676 through 686 Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 723 through 737 Processing helix chain 'B' and resid 821 through 823 No H-bonds generated for 'chain 'B' and resid 821 through 823' Processing helix chain 'B' and resid 830 through 845 removed outlier: 3.909A pdb=" N LYS B 844 " --> pdb=" O LYS B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 868 removed outlier: 3.863A pdb=" N ARG B 867 " --> pdb=" O LYS B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 891 Processing helix chain 'B' and resid 904 through 908 Processing helix chain 'B' and resid 909 through 916 Processing helix chain 'B' and resid 938 through 942 Processing helix chain 'B' and resid 945 through 951 removed outlier: 3.525A pdb=" N TYR B 949 " --> pdb=" O TYR B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 977 Processing helix chain 'B' and resid 993 through 1000 Processing helix chain 'B' and resid 1031 through 1040 removed outlier: 3.529A pdb=" N ILE B1040 " --> pdb=" O ILE B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1080 through 1092 removed outlier: 3.925A pdb=" N VAL B1084 " --> pdb=" O MET B1080 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU B1092 " --> pdb=" O ILE B1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1100 Processing helix chain 'B' and resid 1115 through 1125 Processing helix chain 'B' and resid 1141 through 1154 Processing helix chain 'B' and resid 1154 through 1160 Processing helix chain 'B' and resid 1177 through 1185 Processing helix chain 'B' and resid 1188 through 1203 Processing sheet with id=AA1, first strand: chain 'A' and resid 482 through 485 removed outlier: 6.539A pdb=" N ASN A 482 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ILE A 625 " --> pdb=" O ASN A 482 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE A 484 " --> pdb=" O ILE A 625 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N GLY A 627 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N HIS A 622 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE A 653 " --> pdb=" O HIS A 622 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA A 624 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ASN A 655 " --> pdb=" O ALA A 624 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE A 626 " --> pdb=" O ASN A 655 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASP A 714 " --> pdb=" O VAL A 744 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N HIS A 746 " --> pdb=" O ASP A 714 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 716 " --> pdb=" O HIS A 746 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ARG A 748 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 9.198A pdb=" N VAL A 718 " --> pdb=" O ARG A 748 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 825 through 829 removed outlier: 5.807A pdb=" N GLU A 828 " --> pdb=" O ILE A 991 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 872 through 874 removed outlier: 8.538A pdb=" N TYR A 873 " --> pdb=" O ILE A 848 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N PHE A 850 " --> pdb=" O TYR A 873 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE A 897 " --> pdb=" O LYS A 925 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ILE A 927 " --> pdb=" O ILE A 897 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A 899 " --> pdb=" O ILE A 927 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLY A 929 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A 901 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N SER A 931 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL A 926 " --> pdb=" O ILE A 984 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE A 986 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE A 928 " --> pdb=" O ILE A 986 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR A 957 " --> pdb=" O TYR A 983 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ARG A 985 " --> pdb=" O TYR A 957 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ILE A 959 " --> pdb=" O ARG A 985 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE A 958 " --> pdb=" O LEU A1111 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1044 through 1047 removed outlier: 5.081A pdb=" N ILE A1045 " --> pdb=" O ASP A1107 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASP A1107 " --> pdb=" O ILE A1045 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LYS A1070 " --> pdb=" O SER A1102 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N SER A1104 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL A1072 " --> pdb=" O SER A1104 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL A1106 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE A1074 " --> pdb=" O VAL A1106 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N MET A1108 " --> pdb=" O ILE A1074 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASN A1076 " --> pdb=" O MET A1108 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 483 through 485 removed outlier: 6.800A pdb=" N ILE B 484 " --> pdb=" O ILE B 625 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N GLY B 627 " --> pdb=" O ILE B 484 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N HIS B 622 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE B 653 " --> pdb=" O HIS B 622 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA B 624 " --> pdb=" O ILE B 653 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASN B 655 " --> pdb=" O ALA B 624 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE B 626 " --> pdb=" O ASN B 655 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP B 714 " --> pdb=" O VAL B 744 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N HIS B 746 " --> pdb=" O ASP B 714 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 716 " --> pdb=" O HIS B 746 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ARG B 748 " --> pdb=" O ILE B 716 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N VAL B 718 " --> pdb=" O ARG B 748 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 825 through 829 removed outlier: 5.056A pdb=" N ILE B 991 " --> pdb=" O SER B 826 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 872 through 874 removed outlier: 8.593A pdb=" N TYR B 873 " --> pdb=" O ILE B 848 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N PHE B 850 " --> pdb=" O TYR B 873 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE B 897 " --> pdb=" O LYS B 925 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE B 927 " --> pdb=" O ILE B 897 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU B 899 " --> pdb=" O ILE B 927 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLY B 929 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE B 901 " --> pdb=" O GLY B 929 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N SER B 931 " --> pdb=" O ILE B 901 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL B 926 " --> pdb=" O ILE B 984 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE B 986 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE B 928 " --> pdb=" O ILE B 986 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR B 957 " --> pdb=" O TYR B 983 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ARG B 985 " --> pdb=" O TYR B 957 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE B 959 " --> pdb=" O ARG B 985 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 958 " --> pdb=" O LEU B1111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1044 through 1047 removed outlier: 6.330A pdb=" N ILE B1105 " --> pdb=" O ILE B1046 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LYS B1070 " --> pdb=" O SER B1102 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N SER B1104 " --> pdb=" O LYS B1070 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL B1072 " --> pdb=" O SER B1104 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL B1106 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE B1074 " --> pdb=" O VAL B1106 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N MET B1108 " --> pdb=" O ILE B1074 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASN B1076 " --> pdb=" O MET B1108 " (cutoff:3.500A) 501 hydrogen bonds defined for protein. 1416 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: 3.75 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3614 1.34 - 1.46: 1853 1.46 - 1.57: 6168 1.57 - 1.69: 6 1.69 - 1.80: 74 Bond restraints: 11715 Sorted by residual: bond pdb=" N PHE B 527 " pdb=" CA PHE B 527 " ideal model delta sigma weight residual 1.457 1.501 -0.045 1.26e-02 6.30e+03 1.25e+01 bond pdb=" C2 TPP B1302 " pdb=" S1 TPP B1302 " ideal model delta sigma weight residual 1.675 1.701 -0.026 1.00e-02 1.00e+04 6.72e+00 bond pdb=" N ASN A 870 " pdb=" CA ASN A 870 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.31e-02 5.83e+03 6.51e+00 bond pdb=" N ASN B 399 " pdb=" CA ASN B 399 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.39e+00 bond pdb=" N LYS B 526 " pdb=" CA LYS B 526 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.19e-02 7.06e+03 6.11e+00 ... (remaining 11710 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 15643 2.05 - 4.10: 124 4.10 - 6.14: 19 6.14 - 8.19: 1 8.19 - 10.24: 3 Bond angle restraints: 15790 Sorted by residual: angle pdb=" PA TPP A1302 " pdb=" O3A TPP A1302 " pdb=" PB TPP A1302 " ideal model delta sigma weight residual 139.87 129.63 10.24 1.00e+00 1.00e+00 1.05e+02 angle pdb=" PA TPP B1302 " pdb=" O3A TPP B1302 " pdb=" PB TPP B1302 " ideal model delta sigma weight residual 139.87 130.61 9.26 1.00e+00 1.00e+00 8.57e+01 angle pdb=" CA PHE B 527 " pdb=" CB PHE B 527 " pdb=" CG PHE B 527 " ideal model delta sigma weight residual 113.80 122.14 -8.34 1.00e+00 1.00e+00 6.95e+01 angle pdb=" CA LYS B 526 " pdb=" C LYS B 526 " pdb=" N PHE B 527 " ideal model delta sigma weight residual 117.07 123.27 -6.20 1.14e+00 7.69e-01 2.95e+01 angle pdb=" C7 TPP A1302 " pdb=" O7 TPP A1302 " pdb=" PA TPP A1302 " ideal model delta sigma weight residual 124.29 119.84 4.45 1.00e+00 1.00e+00 1.98e+01 ... (remaining 15785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6680 17.99 - 35.98: 299 35.98 - 53.97: 36 53.97 - 71.95: 9 71.95 - 89.94: 3 Dihedral angle restraints: 7027 sinusoidal: 2905 harmonic: 4122 Sorted by residual: dihedral pdb=" CA LEU A 953 " pdb=" C LEU A 953 " pdb=" N ASN A 954 " pdb=" CA ASN A 954 " ideal model delta harmonic sigma weight residual 180.00 159.83 20.17 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA TYR A 374 " pdb=" C TYR A 374 " pdb=" N ASN A 375 " pdb=" CA ASN A 375 " ideal model delta harmonic sigma weight residual 180.00 164.58 15.42 0 5.00e+00 4.00e-02 9.51e+00 dihedral pdb=" CA TYR B 374 " pdb=" C TYR B 374 " pdb=" N ASN B 375 " pdb=" CA ASN B 375 " ideal model delta harmonic sigma weight residual 180.00 164.60 15.40 0 5.00e+00 4.00e-02 9.49e+00 ... (remaining 7024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1196 0.040 - 0.079: 412 0.079 - 0.118: 112 0.118 - 0.158: 13 0.158 - 0.197: 1 Chirality restraints: 1734 Sorted by residual: chirality pdb=" CA PHE B 527 " pdb=" N PHE B 527 " pdb=" C PHE B 527 " pdb=" CB PHE B 527 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CA ILE A 350 " pdb=" N ILE A 350 " pdb=" C ILE A 350 " pdb=" CB ILE A 350 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA VAL B1072 " pdb=" N VAL B1072 " pdb=" C VAL B1072 " pdb=" CB VAL B1072 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 1731 not shown) Planarity restraints: 1986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 TPP B1302 " -0.127 2.00e-02 2.50e+03 1.46e-01 4.27e+02 pdb=" C4 TPP B1302 " 0.051 2.00e-02 2.50e+03 pdb=" C5 TPP B1302 " 0.013 2.00e-02 2.50e+03 pdb=" C6 TPP B1302 " -0.223 2.00e-02 2.50e+03 pdb=" C7' TPP B1302 " -0.078 2.00e-02 2.50e+03 pdb=" CM4 TPP B1302 " 0.160 2.00e-02 2.50e+03 pdb=" N3 TPP B1302 " -0.055 2.00e-02 2.50e+03 pdb=" S1 TPP B1302 " 0.260 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 TPP A1302 " 0.095 2.00e-02 2.50e+03 1.13e-01 2.53e+02 pdb=" C4 TPP A1302 " -0.038 2.00e-02 2.50e+03 pdb=" C5 TPP A1302 " -0.005 2.00e-02 2.50e+03 pdb=" C6 TPP A1302 " 0.171 2.00e-02 2.50e+03 pdb=" C7' TPP A1302 " 0.064 2.00e-02 2.50e+03 pdb=" CM4 TPP A1302 " -0.127 2.00e-02 2.50e+03 pdb=" N3 TPP A1302 " 0.039 2.00e-02 2.50e+03 pdb=" S1 TPP A1302 " -0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 527 " -0.026 2.00e-02 2.50e+03 2.08e-02 7.58e+00 pdb=" CG PHE B 527 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B 527 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 527 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 527 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 527 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 527 " -0.005 2.00e-02 2.50e+03 ... (remaining 1983 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 86 2.51 - 3.11: 8514 3.11 - 3.71: 17578 3.71 - 4.30: 26845 4.30 - 4.90: 44175 Nonbonded interactions: 97198 Sorted by model distance: nonbonded pdb=" O GLN B 659 " pdb="MG MG B1301 " model vdw 1.914 2.170 nonbonded pdb=" O GLN A 659 " pdb="MG MG A1301 " model vdw 1.924 2.170 nonbonded pdb=" OD1 ASN B 657 " pdb="MG MG B1301 " model vdw 1.952 2.170 nonbonded pdb="MG MG A1301 " pdb=" O2A TPP A1302 " model vdw 2.045 2.170 nonbonded pdb=" OD1 ASN A 657 " pdb="MG MG A1301 " model vdw 2.108 2.170 ... (remaining 97193 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' selection = (chain 'B' and (resid 312 through 683 or resid 705 through 998 or resid 1030 thr \ ough 1204 or resid 1301 through 1302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.440 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 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 : 0.003 0.045 11715 Z= 0.211 Angle : 0.516 10.241 15790 Z= 0.322 Chirality : 0.042 0.197 1734 Planarity : 0.005 0.146 1986 Dihedral : 10.241 89.943 4385 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.55 % Allowed : 5.97 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.09 (0.22), residues: 1370 helix: 0.42 (0.20), residues: 640 sheet: 0.97 (0.43), residues: 156 loop : -0.83 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 547 HIS 0.003 0.001 HIS B 915 PHE 0.047 0.002 PHE B 527 TYR 0.014 0.001 TYR B 983 ARG 0.003 0.000 ARG B 741 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 216 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 GLU cc_start: 0.6135 (mm-30) cc_final: 0.5799 (mm-30) REVERT: A 504 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7138 (m-80) REVERT: A 980 HIS cc_start: 0.7865 (m90) cc_final: 0.7658 (m90) outliers start: 7 outliers final: 0 residues processed: 222 average time/residue: 1.1675 time to fit residues: 282.8531 Evaluate side-chains 202 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 732 ASN A 990 ASN A1154 ASN B 406 ASN B 435 GLN B 710 ASN B 732 ASN B 737 ASN ** B 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.172232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.157228 restraints weight = 14216.948| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 1.32 r_work: 0.4060 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3935 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11715 Z= 0.290 Angle : 0.568 8.496 15790 Z= 0.309 Chirality : 0.045 0.157 1734 Planarity : 0.004 0.040 1986 Dihedral : 6.516 76.209 1536 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.73 % Allowed : 10.60 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.03 (0.22), residues: 1370 helix: 0.46 (0.19), residues: 661 sheet: 0.70 (0.46), residues: 137 loop : -0.67 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 547 HIS 0.005 0.001 HIS B 915 PHE 0.022 0.002 PHE B1146 TYR 0.018 0.002 TYR B 983 ARG 0.004 0.000 ARG B 673 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 1.275 Fit side-chains revert: symmetry clash REVERT: A 504 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7165 (m-80) REVERT: B 411 LYS cc_start: 0.7325 (ttpt) cc_final: 0.7086 (ttpt) outliers start: 22 outliers final: 8 residues processed: 218 average time/residue: 1.1429 time to fit residues: 273.4617 Evaluate side-chains 208 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 199 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 1080 MET Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 936 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 114 optimal weight: 0.4980 chunk 129 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 732 ASN A 907 GLN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN A1153 ASN B 406 ASN ** B 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.172186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.157337 restraints weight = 14378.989| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 1.32 r_work: 0.4059 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3936 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11715 Z= 0.273 Angle : 0.552 8.351 15790 Z= 0.298 Chirality : 0.044 0.153 1734 Planarity : 0.004 0.041 1986 Dihedral : 6.476 76.997 1536 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.36 % Allowed : 11.94 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.04 (0.22), residues: 1370 helix: 0.55 (0.20), residues: 647 sheet: 0.34 (0.47), residues: 128 loop : -0.65 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 547 HIS 0.005 0.001 HIS B 915 PHE 0.020 0.002 PHE B1146 TYR 0.016 0.002 TYR B 983 ARG 0.004 0.000 ARG B 673 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 1.381 Fit side-chains revert: symmetry clash REVERT: A 885 PHE cc_start: 0.7493 (t80) cc_final: 0.7275 (t80) REVERT: B 440 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6605 (mt) REVERT: B 1048 MET cc_start: 0.5288 (mmt) cc_final: 0.4979 (mmm) outliers start: 30 outliers final: 10 residues processed: 212 average time/residue: 1.1207 time to fit residues: 260.7054 Evaluate side-chains 207 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 196 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 1080 MET Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 936 GLU Chi-restraints excluded: chain B residue 1123 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 126 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 81 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 ASN A 907 GLN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN B 482 ASN ** B 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1153 ASN B1154 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.174161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.159446 restraints weight = 14275.792| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.32 r_work: 0.4068 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3945 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11715 Z= 0.230 Angle : 0.532 8.050 15790 Z= 0.285 Chirality : 0.043 0.162 1734 Planarity : 0.003 0.042 1986 Dihedral : 6.128 76.478 1534 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.12 % Allowed : 13.51 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.00 (0.22), residues: 1370 helix: 0.63 (0.20), residues: 651 sheet: 0.26 (0.45), residues: 136 loop : -0.69 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 547 HIS 0.004 0.001 HIS B 915 PHE 0.017 0.002 PHE B 885 TYR 0.017 0.001 TYR B 474 ARG 0.003 0.000 ARG B 673 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1118 MET cc_start: 0.6166 (tpp) cc_final: 0.5865 (tpp) REVERT: A 1123 ILE cc_start: 0.5470 (OUTLIER) cc_final: 0.5178 (mt) REVERT: B 411 LYS cc_start: 0.7316 (ttpt) cc_final: 0.7086 (ttpt) REVERT: B 440 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6550 (mt) REVERT: B 1048 MET cc_start: 0.5279 (mmt) cc_final: 0.5027 (mmm) outliers start: 27 outliers final: 15 residues processed: 213 average time/residue: 1.1252 time to fit residues: 263.2531 Evaluate side-chains 213 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 1077 MET Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 936 GLU Chi-restraints excluded: chain B residue 1077 MET Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1123 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 129 optimal weight: 0.7980 chunk 46 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 GLN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN A1153 ASN B 482 ASN ** B 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1154 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.174544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.159737 restraints weight = 14206.856| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.33 r_work: 0.4067 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3944 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11715 Z= 0.233 Angle : 0.530 8.077 15790 Z= 0.286 Chirality : 0.044 0.223 1734 Planarity : 0.003 0.041 1986 Dihedral : 6.080 76.287 1534 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.36 % Allowed : 14.14 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.01 (0.22), residues: 1370 helix: 0.62 (0.20), residues: 651 sheet: 0.22 (0.44), residues: 143 loop : -0.66 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 547 HIS 0.004 0.001 HIS B 915 PHE 0.017 0.002 PHE B1146 TYR 0.014 0.001 TYR B 983 ARG 0.004 0.000 ARG B 908 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1118 MET cc_start: 0.6158 (tpp) cc_final: 0.5872 (tpp) REVERT: A 1123 ILE cc_start: 0.5449 (OUTLIER) cc_final: 0.5157 (mt) REVERT: B 440 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6565 (mt) outliers start: 30 outliers final: 15 residues processed: 208 average time/residue: 1.0500 time to fit residues: 240.4218 Evaluate side-chains 210 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 193 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 1077 MET Chi-restraints excluded: chain A residue 1080 MET Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 936 GLU Chi-restraints excluded: chain B residue 1077 MET Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1123 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 95 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 120 optimal weight: 0.0770 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 54 optimal weight: 0.0770 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 GLN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN B 482 ASN ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 ASN B1153 ASN B1182 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.175476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.160729 restraints weight = 14379.392| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 1.33 r_work: 0.4079 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3956 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11715 Z= 0.193 Angle : 0.523 10.163 15790 Z= 0.277 Chirality : 0.043 0.304 1734 Planarity : 0.003 0.042 1986 Dihedral : 5.914 74.343 1534 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.36 % Allowed : 14.22 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.15 (0.22), residues: 1370 helix: 0.79 (0.20), residues: 653 sheet: 0.34 (0.46), residues: 136 loop : -0.68 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 547 HIS 0.003 0.001 HIS B 915 PHE 0.017 0.001 PHE A 885 TYR 0.019 0.001 TYR B 474 ARG 0.004 0.000 ARG B 908 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: A 504 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7168 (m-80) REVERT: A 885 PHE cc_start: 0.7450 (t80) cc_final: 0.7219 (t80) REVERT: A 1118 MET cc_start: 0.6090 (OUTLIER) cc_final: 0.5795 (tpp) REVERT: A 1123 ILE cc_start: 0.5458 (OUTLIER) cc_final: 0.5183 (mt) REVERT: B 440 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6483 (tt) REVERT: B 1077 MET cc_start: 0.5861 (OUTLIER) cc_final: 0.5010 (ttm) REVERT: B 1147 ASN cc_start: 0.5807 (m-40) cc_final: 0.5443 (p0) outliers start: 30 outliers final: 14 residues processed: 209 average time/residue: 1.0482 time to fit residues: 241.1897 Evaluate side-chains 209 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 1077 MET Chi-restraints excluded: chain A residue 1118 MET Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 936 GLU Chi-restraints excluded: chain B residue 1045 ILE Chi-restraints excluded: chain B residue 1077 MET Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1123 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 96 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 GLN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN A1153 ASN ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 ASN ** B 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.173827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.159036 restraints weight = 14409.087| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 1.33 r_work: 0.4063 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3939 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11715 Z= 0.266 Angle : 0.560 11.439 15790 Z= 0.298 Chirality : 0.045 0.351 1734 Planarity : 0.004 0.042 1986 Dihedral : 6.051 75.764 1534 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.12 % Allowed : 15.08 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.00 (0.22), residues: 1370 helix: 0.64 (0.20), residues: 651 sheet: 0.24 (0.46), residues: 132 loop : -0.69 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 547 HIS 0.005 0.001 HIS A 915 PHE 0.018 0.002 PHE B1146 TYR 0.016 0.002 TYR B 983 ARG 0.004 0.000 ARG B 908 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 885 PHE cc_start: 0.7507 (t80) cc_final: 0.7240 (t80) REVERT: A 1118 MET cc_start: 0.6146 (OUTLIER) cc_final: 0.5867 (tpp) REVERT: A 1123 ILE cc_start: 0.5502 (OUTLIER) cc_final: 0.5192 (mt) REVERT: B 414 LEU cc_start: 0.7499 (mm) cc_final: 0.7229 (mt) REVERT: B 440 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6613 (mt) outliers start: 27 outliers final: 19 residues processed: 207 average time/residue: 1.0841 time to fit residues: 248.0780 Evaluate side-chains 212 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 1077 MET Chi-restraints excluded: chain A residue 1080 MET Chi-restraints excluded: chain A residue 1118 MET Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 934 VAL Chi-restraints excluded: chain B residue 936 GLU Chi-restraints excluded: chain B residue 1045 ILE Chi-restraints excluded: chain B residue 1077 MET Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1123 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 118 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 GLN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 ASN B1153 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.174678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.159879 restraints weight = 14349.728| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 1.34 r_work: 0.4067 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3943 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11715 Z= 0.239 Angle : 0.564 11.296 15790 Z= 0.297 Chirality : 0.045 0.358 1734 Planarity : 0.003 0.041 1986 Dihedral : 6.030 75.281 1534 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.04 % Allowed : 15.71 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.05 (0.22), residues: 1370 helix: 0.68 (0.20), residues: 651 sheet: 0.40 (0.50), residues: 117 loop : -0.68 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 547 HIS 0.004 0.001 HIS A 915 PHE 0.016 0.002 PHE B 885 TYR 0.014 0.001 TYR B 983 ARG 0.003 0.000 ARG B 673 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 885 PHE cc_start: 0.7479 (t80) cc_final: 0.7225 (t80) REVERT: A 1118 MET cc_start: 0.6139 (OUTLIER) cc_final: 0.5846 (tpp) REVERT: A 1123 ILE cc_start: 0.5504 (OUTLIER) cc_final: 0.5218 (mt) REVERT: B 440 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6577 (mt) REVERT: B 480 TYR cc_start: 0.8211 (t80) cc_final: 0.7969 (t80) REVERT: B 1147 ASN cc_start: 0.5809 (m-40) cc_final: 0.5460 (p0) outliers start: 26 outliers final: 19 residues processed: 204 average time/residue: 1.0714 time to fit residues: 240.1970 Evaluate side-chains 211 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 1077 MET Chi-restraints excluded: chain A residue 1080 MET Chi-restraints excluded: chain A residue 1118 MET Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 934 VAL Chi-restraints excluded: chain B residue 936 GLU Chi-restraints excluded: chain B residue 1045 ILE Chi-restraints excluded: chain B residue 1077 MET Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1123 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 36 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 80 optimal weight: 0.0050 chunk 71 optimal weight: 1.9990 chunk 83 optimal weight: 0.0980 chunk 116 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 GLN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN A1153 ASN ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 ASN A1203 ASN ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 ASN ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.176251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.161793 restraints weight = 14417.705| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 1.33 r_work: 0.4090 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3965 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11715 Z= 0.165 Angle : 0.523 12.874 15790 Z= 0.275 Chirality : 0.043 0.365 1734 Planarity : 0.003 0.042 1986 Dihedral : 5.798 73.947 1534 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.34 % Allowed : 16.42 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.29 (0.22), residues: 1370 helix: 0.94 (0.20), residues: 650 sheet: 0.34 (0.48), residues: 136 loop : -0.62 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 547 HIS 0.003 0.001 HIS B 915 PHE 0.016 0.001 PHE B 885 TYR 0.018 0.001 TYR B 474 ARG 0.002 0.000 ARG B 908 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 193 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 885 PHE cc_start: 0.7441 (t80) cc_final: 0.7210 (t80) REVERT: A 1118 MET cc_start: 0.6078 (tpp) cc_final: 0.5773 (tpp) REVERT: A 1123 ILE cc_start: 0.5538 (OUTLIER) cc_final: 0.5269 (mt) REVERT: B 440 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6510 (mt) REVERT: B 1147 ASN cc_start: 0.5723 (m-40) cc_final: 0.5401 (p0) outliers start: 17 outliers final: 12 residues processed: 201 average time/residue: 1.0486 time to fit residues: 232.7194 Evaluate side-chains 203 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 189 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 934 VAL Chi-restraints excluded: chain B residue 936 GLU Chi-restraints excluded: chain B residue 1045 ILE Chi-restraints excluded: chain B residue 1091 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 GLN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1153 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.173158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.158344 restraints weight = 14299.899| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 1.33 r_work: 0.4054 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3928 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11715 Z= 0.321 Angle : 0.634 13.005 15790 Z= 0.330 Chirality : 0.047 0.398 1734 Planarity : 0.004 0.041 1986 Dihedral : 6.149 76.697 1534 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.81 % Allowed : 16.42 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.08 (0.22), residues: 1370 helix: 0.56 (0.20), residues: 651 sheet: 0.39 (0.50), residues: 116 loop : -0.74 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 547 HIS 0.007 0.001 HIS A 915 PHE 0.020 0.002 PHE B 417 TYR 0.020 0.002 TYR B 983 ARG 0.004 0.000 ARG B 673 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 885 PHE cc_start: 0.7523 (t80) cc_final: 0.7289 (t80) REVERT: A 1118 MET cc_start: 0.6212 (OUTLIER) cc_final: 0.5929 (tpp) REVERT: A 1123 ILE cc_start: 0.5479 (OUTLIER) cc_final: 0.5153 (mt) REVERT: B 440 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6652 (mt) REVERT: B 480 TYR cc_start: 0.8244 (t80) cc_final: 0.8007 (t80) outliers start: 23 outliers final: 14 residues processed: 199 average time/residue: 1.0472 time to fit residues: 230.3564 Evaluate side-chains 204 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 1118 MET Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 934 VAL Chi-restraints excluded: chain B residue 936 GLU Chi-restraints excluded: chain B residue 1045 ILE Chi-restraints excluded: chain B residue 1091 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 0.9990 chunk 122 optimal weight: 0.2980 chunk 129 optimal weight: 0.4980 chunk 113 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 100 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 GLN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 GLN B 482 ASN ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1076 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.175262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.160625 restraints weight = 14343.049| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 1.32 r_work: 0.4081 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3958 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11715 Z= 0.196 Angle : 0.564 12.223 15790 Z= 0.294 Chirality : 0.044 0.308 1734 Planarity : 0.003 0.042 1986 Dihedral : 5.919 73.443 1534 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.49 % Allowed : 16.73 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.13 (0.22), residues: 1370 helix: 0.80 (0.20), residues: 651 sheet: 0.46 (0.51), residues: 116 loop : -0.72 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 547 HIS 0.004 0.001 HIS B 915 PHE 0.018 0.002 PHE B 417 TYR 0.018 0.001 TYR B 474 ARG 0.002 0.000 ARG B 673 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9812.25 seconds wall clock time: 176 minutes 34.55 seconds (10594.55 seconds total)