Starting phenix.real_space_refine on Tue Jul 29 16:28:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r2h_18842/07_2025/8r2h_18842.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r2h_18842/07_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_18842/07_2025/8r2h_18842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r2h_18842/07_2025/8r2h_18842.map" model { file = "/net/cci-nas-00/data/ceres_data/8r2h_18842/07_2025/8r2h_18842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r2h_18842/07_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 8.42, per 1000 atoms: 0.73 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: 3.06 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: 1.87 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: 3.80 Time building geometry restraints manager: 3.44 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: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.910 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.080 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:12.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.190 ------------------------------------------------------------------------------- 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= 0.169 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 Details of bonding type rmsd hydrogen bonds : bond 0.18680 ( 501) hydrogen bonds : angle 7.56515 ( 1416) covalent geometry : bond 0.00329 (11715) covalent geometry : angle 0.51561 (15790) *********************** 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 : 1.334 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: 1.0866 time to fit residues: 264.2579 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 : 1.113 ------------------------------------------------------------------------------- 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 = 34)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.157227 restraints weight = 14216.937| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 1.32 r_work: 0.4061 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: 0.6978 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= 0.201 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 Details of bonding type rmsd hydrogen bonds : bond 0.05587 ( 501) hydrogen bonds : angle 5.98616 ( 1416) covalent geometry : bond 0.00452 (11715) covalent geometry : angle 0.56848 (15790) *********************** 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 : 1.392 Fit side-chains revert: symmetry clash REVERT: A 504 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7165 (m-80) REVERT: B 411 LYS cc_start: 0.7325 (ttpt) cc_final: 0.7088 (ttpt) outliers start: 22 outliers final: 8 residues processed: 218 average time/residue: 1.3753 time to fit residues: 330.5286 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 : 1.356 ------------------------------------------------------------------------------- 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: 0.6980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 0.0370 chunk 99 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 69 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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** B1083 ASN B1182 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.175062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.160253 restraints weight = 14403.417| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 1.33 r_work: 0.4075 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3952 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11715 Z= 0.143 Angle : 0.508 8.095 15790 Z= 0.275 Chirality : 0.043 0.138 1734 Planarity : 0.003 0.040 1986 Dihedral : 6.306 74.725 1536 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.04 % Allowed : 12.25 % 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: 0.18 (0.22), residues: 1370 helix: 0.76 (0.20), residues: 650 sheet: 0.63 (0.44), residues: 145 loop : -0.67 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 547 HIS 0.004 0.001 HIS B 915 PHE 0.017 0.002 PHE B 885 TYR 0.013 0.001 TYR B 949 ARG 0.003 0.000 ARG B 673 Details of bonding type rmsd hydrogen bonds : bond 0.04700 ( 501) hydrogen bonds : angle 5.59932 ( 1416) covalent geometry : bond 0.00318 (11715) covalent geometry : angle 0.50787 (15790) *********************** 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 227 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 1.286 Fit side-chains revert: symmetry clash REVERT: A 504 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.7097 (m-80) REVERT: A 840 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7380 (ttmm) REVERT: A 885 PHE cc_start: 0.7462 (t80) cc_final: 0.7249 (t80) REVERT: B 1048 MET cc_start: 0.5280 (mmt) cc_final: 0.4970 (mmm) outliers start: 26 outliers final: 9 residues processed: 213 average time/residue: 0.9996 time to fit residues: 234.6232 Evaluate side-chains 208 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 197 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 882 SER 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 0.0770 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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** B1083 ASN B1153 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.172976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.158183 restraints weight = 14280.567| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 1.33 r_work: 0.4068 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3945 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11715 Z= 0.161 Angle : 0.532 7.796 15790 Z= 0.284 Chirality : 0.044 0.228 1734 Planarity : 0.003 0.041 1986 Dihedral : 6.253 75.347 1536 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.59 % Allowed : 13.20 % Favored : 84.21 % 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: 0.12 (0.22), residues: 1370 helix: 0.72 (0.20), residues: 651 sheet: 0.69 (0.46), residues: 131 loop : -0.72 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 547 HIS 0.004 0.001 HIS B 915 PHE 0.017 0.002 PHE B1146 TYR 0.018 0.001 TYR B 474 ARG 0.003 0.000 ARG B 673 Details of bonding type rmsd hydrogen bonds : bond 0.04781 ( 501) hydrogen bonds : angle 5.59363 ( 1416) covalent geometry : bond 0.00363 (11715) covalent geometry : angle 0.53178 (15790) *********************** 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 231 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7240 (t0) cc_final: 0.7036 (t0) REVERT: A 504 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7146 (m-80) REVERT: A 840 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7380 (ttmm) REVERT: A 1123 ILE cc_start: 0.5481 (OUTLIER) cc_final: 0.5183 (mt) REVERT: A 1144 THR cc_start: 0.6457 (m) cc_final: 0.6242 (m) REVERT: B 480 TYR cc_start: 0.8241 (t80) cc_final: 0.8009 (t80) REVERT: B 1048 MET cc_start: 0.5303 (mmt) cc_final: 0.5056 (mmm) REVERT: B 1077 MET cc_start: 0.5739 (OUTLIER) cc_final: 0.4834 (ttm) outliers start: 33 outliers final: 16 residues processed: 212 average time/residue: 1.0562 time to fit residues: 246.0853 Evaluate side-chains 215 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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 840 LYS 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 434 LYS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 465 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: 2.9990 chunk 63 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 122 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 46 optimal weight: 0.0870 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN A1153 ASN ** B 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.174170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.159512 restraints weight = 14270.754| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 1.31 r_work: 0.4083 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3961 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.1807 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= 0.133 Angle : 0.507 8.823 15790 Z= 0.271 Chirality : 0.043 0.306 1734 Planarity : 0.003 0.041 1986 Dihedral : 6.089 73.122 1536 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.28 % Allowed : 14.22 % 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: 0.21 (0.22), residues: 1370 helix: 0.84 (0.20), residues: 651 sheet: 0.32 (0.45), residues: 143 loop : -0.64 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 547 HIS 0.003 0.001 HIS B 915 PHE 0.019 0.001 PHE A 885 TYR 0.011 0.001 TYR B 983 ARG 0.002 0.000 ARG B 673 Details of bonding type rmsd hydrogen bonds : bond 0.04390 ( 501) hydrogen bonds : angle 5.44731 ( 1416) covalent geometry : bond 0.00296 (11715) covalent geometry : angle 0.50695 (15790) *********************** 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 225 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 1.415 Fit side-chains revert: symmetry clash REVERT: A 504 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.7115 (m-80) REVERT: A 1118 MET cc_start: 0.6153 (tpp) cc_final: 0.5847 (tpp) REVERT: A 1123 ILE cc_start: 0.5498 (OUTLIER) cc_final: 0.5216 (mt) REVERT: B 480 TYR cc_start: 0.8216 (t80) cc_final: 0.7963 (t80) outliers start: 29 outliers final: 14 residues processed: 209 average time/residue: 1.0352 time to fit residues: 239.0871 Evaluate side-chains 208 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 PHE 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 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: 2.9990 chunk 102 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 54 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 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 942 GLN ** 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 = 0.4329 r_free = 0.4329 target = 0.173616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.158893 restraints weight = 14418.680| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 1.33 r_work: 0.4074 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3951 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11715 Z= 0.154 Angle : 0.546 11.060 15790 Z= 0.287 Chirality : 0.044 0.346 1734 Planarity : 0.003 0.047 1986 Dihedral : 6.107 73.322 1536 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.12 % Allowed : 14.61 % Favored : 83.27 % 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: 0.11 (0.22), residues: 1370 helix: 0.76 (0.20), residues: 657 sheet: 0.31 (0.46), residues: 143 loop : -0.71 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 547 HIS 0.004 0.001 HIS B 915 PHE 0.016 0.002 PHE B 885 TYR 0.018 0.001 TYR B 474 ARG 0.004 0.000 ARG B 908 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 501) hydrogen bonds : angle 5.51296 ( 1416) covalent geometry : bond 0.00347 (11715) covalent geometry : angle 0.54577 (15790) *********************** 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 224 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 1.351 Fit side-chains revert: symmetry clash REVERT: A 504 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7149 (m-80) REVERT: A 885 PHE cc_start: 0.7449 (t80) cc_final: 0.7235 (t80) REVERT: A 1118 MET cc_start: 0.6158 (tpp) cc_final: 0.5845 (tpp) REVERT: A 1123 ILE cc_start: 0.5503 (OUTLIER) cc_final: 0.5222 (mt) REVERT: B 414 LEU cc_start: 0.7494 (mm) cc_final: 0.7227 (mt) REVERT: B 440 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6564 (mt) REVERT: B 480 TYR cc_start: 0.8223 (t80) cc_final: 0.7974 (t80) outliers start: 27 outliers final: 15 residues processed: 211 average time/residue: 0.9822 time to fit residues: 228.8444 Evaluate side-chains 208 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 75 optimal weight: 0.8980 chunk 129 optimal weight: 0.2980 chunk 107 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 118 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 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 = 0.174364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.159599 restraints weight = 14410.330| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 1.33 r_work: 0.4069 rms_B_bonded: 1.97 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: 0.6965 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11715 Z= 0.168 Angle : 0.551 10.153 15790 Z= 0.293 Chirality : 0.045 0.347 1734 Planarity : 0.004 0.044 1986 Dihedral : 6.154 73.537 1536 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.04 % Allowed : 15.24 % Favored : 82.72 % 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: 0.70 (0.20), residues: 657 sheet: 0.24 (0.47), residues: 132 loop : -0.71 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP B 547 HIS 0.004 0.001 HIS A 915 PHE 0.017 0.002 PHE B1146 TYR 0.015 0.001 TYR B 983 ARG 0.004 0.000 ARG B 908 Details of bonding type rmsd hydrogen bonds : bond 0.04718 ( 501) hydrogen bonds : angle 5.55803 ( 1416) covalent geometry : bond 0.00382 (11715) covalent geometry : angle 0.55103 (15790) *********************** 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 220 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: A 504 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7177 (m-80) REVERT: A 885 PHE cc_start: 0.7472 (t80) cc_final: 0.7241 (t80) REVERT: A 1118 MET cc_start: 0.6167 (tpp) cc_final: 0.5860 (tpp) REVERT: A 1123 ILE cc_start: 0.5505 (OUTLIER) cc_final: 0.5208 (mt) REVERT: B 407 ILE cc_start: 0.5632 (OUTLIER) cc_final: 0.5334 (mm) REVERT: B 440 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6584 (mt) REVERT: B 480 TYR cc_start: 0.8230 (t80) cc_final: 0.7975 (t80) REVERT: B 1147 ASN cc_start: 0.5810 (m-40) cc_final: 0.5442 (p0) outliers start: 26 outliers final: 16 residues processed: 206 average time/residue: 1.0041 time to fit residues: 228.2888 Evaluate side-chains 210 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 1.227 ------------------------------------------------------------------------------- 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 1123 ILE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 407 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 0.0870 chunk 112 optimal weight: 0.7980 chunk 73 optimal weight: 0.0980 chunk 118 optimal weight: 0.9980 chunk 5 optimal weight: 0.0370 chunk 133 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 114 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 overall best weight: 0.2636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN A 907 GLN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1076 ASN B1083 ASN B1153 ASN B1154 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.177344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.162971 restraints weight = 14421.326| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 1.34 r_work: 0.4102 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3978 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11715 Z= 0.110 Angle : 0.519 12.253 15790 Z= 0.269 Chirality : 0.043 0.357 1734 Planarity : 0.003 0.042 1986 Dihedral : 5.823 73.306 1536 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.65 % Allowed : 15.71 % Favored : 82.64 % 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: 0.40 (0.22), residues: 1370 helix: 1.06 (0.20), residues: 652 sheet: 0.31 (0.47), residues: 138 loop : -0.60 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 547 HIS 0.002 0.001 HIS B 915 PHE 0.017 0.001 PHE A 885 TYR 0.010 0.001 TYR B 402 ARG 0.004 0.000 ARG B 908 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 501) hydrogen bonds : angle 5.27187 ( 1416) covalent geometry : bond 0.00243 (11715) covalent geometry : angle 0.51894 (15790) *********************** 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 216 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 1.758 Fit side-chains revert: symmetry clash REVERT: A 504 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.7029 (m-80) REVERT: A 1118 MET cc_start: 0.6039 (tpp) cc_final: 0.5746 (tpp) REVERT: A 1123 ILE cc_start: 0.5630 (OUTLIER) cc_final: 0.5387 (mt) REVERT: B 414 LEU cc_start: 0.7476 (mm) cc_final: 0.7193 (mt) REVERT: B 1147 ASN cc_start: 0.5741 (m-40) cc_final: 0.5395 (p0) outliers start: 21 outliers final: 11 residues processed: 206 average time/residue: 1.4468 time to fit residues: 329.4963 Evaluate side-chains 210 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 1.711 ------------------------------------------------------------------------------- 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 1077 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 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 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: 0.8980 chunk 122 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 80 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 83 optimal weight: 0.0670 chunk 116 optimal weight: 2.9990 chunk 9 optimal weight: 0.0870 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- 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 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.174676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.159747 restraints weight = 14388.487| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 1.36 r_work: 0.4084 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3959 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11715 Z= 0.139 Angle : 0.548 12.132 15790 Z= 0.283 Chirality : 0.044 0.367 1734 Planarity : 0.003 0.041 1986 Dihedral : 5.896 71.300 1536 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.49 % Allowed : 16.42 % Favored : 82.09 % 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: 0.34 (0.22), residues: 1370 helix: 1.01 (0.20), residues: 650 sheet: 0.24 (0.46), residues: 143 loop : -0.60 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 547 HIS 0.008 0.001 HIS B1159 PHE 0.019 0.002 PHE B 417 TYR 0.019 0.001 TYR B 474 ARG 0.005 0.000 ARG B 908 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 501) hydrogen bonds : angle 5.39307 ( 1416) covalent geometry : bond 0.00313 (11715) covalent geometry : angle 0.54804 (15790) *********************** 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 211 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 1.286 Fit side-chains revert: symmetry clash REVERT: A 504 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.7096 (m-80) REVERT: A 885 PHE cc_start: 0.7401 (t80) cc_final: 0.7198 (t80) REVERT: A 1118 MET cc_start: 0.6098 (tpp) cc_final: 0.5770 (tpp) REVERT: A 1123 ILE cc_start: 0.5503 (OUTLIER) cc_final: 0.5238 (mt) REVERT: B 440 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6535 (mt) outliers start: 19 outliers final: 9 residues processed: 200 average time/residue: 2.0153 time to fit residues: 445.1775 Evaluate side-chains 203 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 3.845 ------------------------------------------------------------------------------- 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 1077 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 522 SER Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 1045 ILE Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1123 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 55 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 97 optimal weight: 0.0000 chunk 122 optimal weight: 0.9980 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.173604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.158668 restraints weight = 14310.440| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 1.35 r_work: 0.4071 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3945 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.2044 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= 0.166 Angle : 0.586 13.010 15790 Z= 0.302 Chirality : 0.045 0.393 1734 Planarity : 0.004 0.040 1986 Dihedral : 6.014 70.226 1536 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.10 % Allowed : 17.05 % Favored : 81.85 % 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: 0.21 (0.22), residues: 1370 helix: 0.87 (0.20), residues: 651 sheet: 0.24 (0.46), residues: 143 loop : -0.66 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 547 HIS 0.006 0.001 HIS B1159 PHE 0.020 0.002 PHE B 417 TYR 0.018 0.001 TYR B 474 ARG 0.005 0.000 ARG B 908 Details of bonding type rmsd hydrogen bonds : bond 0.04600 ( 501) hydrogen bonds : angle 5.53048 ( 1416) covalent geometry : bond 0.00377 (11715) covalent geometry : angle 0.58585 (15790) ********************** 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 203 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 189 time to evaluate : 1.257 Fit side-chains REVERT: A 504 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7156 (m-80) REVERT: A 885 PHE cc_start: 0.7463 (t80) cc_final: 0.7211 (t80) REVERT: A 889 MET cc_start: 0.8414 (mtp) cc_final: 0.8207 (ttm) REVERT: A 1118 MET cc_start: 0.6172 (OUTLIER) cc_final: 0.5865 (tpp) REVERT: A 1123 ILE cc_start: 0.5474 (OUTLIER) cc_final: 0.5203 (mt) REVERT: B 440 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6596 (mt) outliers start: 14 outliers final: 9 residues processed: 196 average time/residue: 1.0641 time to fit residues: 229.7873 Evaluate side-chains 201 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 1.262 ------------------------------------------------------------------------------- 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 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 522 SER Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 1045 ILE Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1123 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 100 optimal weight: 0.4980 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 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 482 ASN ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.172765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.158118 restraints weight = 14356.474| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 1.31 r_work: 0.4067 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3942 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.2044 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= 0.184 Angle : 0.593 13.076 15790 Z= 0.309 Chirality : 0.045 0.393 1734 Planarity : 0.004 0.040 1986 Dihedral : 6.080 71.233 1536 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.26 % Allowed : 17.28 % Favored : 81.46 % 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: 0.06 (0.22), residues: 1370 helix: 0.71 (0.20), residues: 652 sheet: 0.30 (0.48), residues: 130 loop : -0.71 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 547 HIS 0.005 0.001 HIS A 915 PHE 0.020 0.002 PHE B 417 TYR 0.018 0.002 TYR B 474 ARG 0.006 0.000 ARG B 908 Details of bonding type rmsd hydrogen bonds : bond 0.04817 ( 501) hydrogen bonds : angle 5.63668 ( 1416) covalent geometry : bond 0.00420 (11715) covalent geometry : angle 0.59324 (15790) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10564.69 seconds wall clock time: 188 minutes 26.15 seconds (11306.15 seconds total)