Starting phenix.real_space_refine on Sat Aug 23 10:35:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r2h_18842/08_2025/8r2h_18842.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r2h_18842/08_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_18842/08_2025/8r2h_18842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r2h_18842/08_2025/8r2h_18842.map" model { file = "/net/cci-nas-00/data/ceres_data/8r2h_18842/08_2025/8r2h_18842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r2h_18842/08_2025/8r2h_18842.cif" } resolution = 2.42 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.93, per 1000 atoms: 0.26 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: 0.66 Conformation dependent library (CDL) restraints added in 396.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.46 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: 2.05 Time building geometry restraints manager: 0.88 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 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: 6.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.280 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.960 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG B 741 TYR 0.014 0.001 TYR B 983 PHE 0.047 0.002 PHE B 527 TRP 0.004 0.002 TRP A 547 HIS 0.003 0.001 HIS B 915 Details of bonding type rmsd covalent geometry : bond 0.00329 (11715) covalent geometry : angle 0.51561 (15790) hydrogen bonds : bond 0.18680 ( 501) hydrogen bonds : angle 7.56515 ( 1416) *********************** 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 : 0.425 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: 0.4645 time to fit residues: 113.1906 Evaluate side-chains 201 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.0270 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.1980 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 GLN A 732 ASN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN A1154 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 = 0.4342 r_free = 0.4342 target = 0.174413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.159451 restraints weight = 14315.100| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 1.34 r_work: 0.4086 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3960 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.1275 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= 0.132 Angle : 0.504 7.982 15790 Z= 0.274 Chirality : 0.043 0.138 1734 Planarity : 0.003 0.037 1986 Dihedral : 6.268 71.678 1536 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.49 % Allowed : 10.29 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.22), residues: 1370 helix: 0.77 (0.20), residues: 664 sheet: 1.10 (0.45), residues: 146 loop : -0.66 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 673 TYR 0.017 0.001 TYR B 474 PHE 0.017 0.002 PHE B 885 TRP 0.004 0.001 TRP A 547 HIS 0.003 0.001 HIS B 915 Details of bonding type rmsd covalent geometry : bond 0.00283 (11715) covalent geometry : angle 0.50377 (15790) hydrogen bonds : bond 0.04814 ( 501) hydrogen bonds : angle 5.73311 ( 1416) *********************** 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 227 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 504 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.7074 (m-80) REVERT: A 885 PHE cc_start: 0.7463 (t80) cc_final: 0.7243 (t80) outliers start: 19 outliers final: 7 residues processed: 218 average time/residue: 0.4362 time to fit residues: 104.2051 Evaluate side-chains 210 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 202 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 882 SER 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 47 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 3 optimal weight: 0.0770 chunk 66 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 112 optimal weight: 0.2980 chunk 130 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN A 836 ASN A 907 GLN A 918 ASN A 990 ASN A1153 ASN B 406 ASN B 482 ASN ** B 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1153 ASN B1154 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.171367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.156314 restraints weight = 14255.713| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 1.34 r_work: 0.4046 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3920 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11715 Z= 0.239 Angle : 0.609 9.089 15790 Z= 0.326 Chirality : 0.047 0.170 1734 Planarity : 0.004 0.040 1986 Dihedral : 6.578 77.868 1536 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.44 % Allowed : 12.73 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.22), residues: 1370 helix: 0.44 (0.20), residues: 648 sheet: 0.86 (0.48), residues: 120 loop : -0.74 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 673 TYR 0.021 0.002 TYR B 983 PHE 0.024 0.002 PHE B1146 TRP 0.007 0.003 TRP B 547 HIS 0.007 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00547 (11715) covalent geometry : angle 0.60924 (15790) hydrogen bonds : bond 0.05744 ( 501) hydrogen bonds : angle 5.92647 ( 1416) *********************** 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 235 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 GLU cc_start: 0.6668 (mm-30) cc_final: 0.6236 (mm-30) REVERT: B 440 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6595 (mt) REVERT: B 1048 MET cc_start: 0.5400 (mmt) cc_final: 0.5047 (mmm) outliers start: 31 outliers final: 10 residues processed: 220 average time/residue: 0.5009 time to fit residues: 120.9415 Evaluate side-chains 204 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 193 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 GLN 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 440 LEU 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 1123 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 97 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 56 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 990 ASN B 406 ASN ** B 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 ASN B1154 ASN B1182 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.175576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.160763 restraints weight = 14446.779| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 1.33 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: 0.6936 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11715 Z= 0.130 Angle : 0.507 9.097 15790 Z= 0.271 Chirality : 0.043 0.168 1734 Planarity : 0.003 0.040 1986 Dihedral : 5.982 72.556 1534 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.12 % Allowed : 13.90 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.22), residues: 1370 helix: 0.78 (0.20), residues: 652 sheet: 0.63 (0.44), residues: 139 loop : -0.70 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 673 TYR 0.012 0.001 TYR A1130 PHE 0.017 0.001 PHE B 885 TRP 0.003 0.001 TRP A 547 HIS 0.003 0.001 HIS B 915 Details of bonding type rmsd covalent geometry : bond 0.00288 (11715) covalent geometry : angle 0.50662 (15790) hydrogen bonds : bond 0.04419 ( 501) hydrogen bonds : angle 5.52286 ( 1416) *********************** 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 224 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 504 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.7104 (m-80) REVERT: A 1123 ILE cc_start: 0.5626 (OUTLIER) cc_final: 0.5383 (mt) REVERT: B 440 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6475 (mt) REVERT: B 480 TYR cc_start: 0.8236 (t80) cc_final: 0.8024 (t80) REVERT: B 1048 MET cc_start: 0.5267 (mmt) cc_final: 0.5007 (mmm) outliers start: 27 outliers final: 11 residues processed: 210 average time/residue: 0.5072 time to fit residues: 116.8673 Evaluate side-chains 208 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 A residue 1139 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 707 ILE Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 840 LYS Chi-restraints excluded: chain B residue 936 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 36 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 119 optimal weight: 0.0470 chunk 21 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN A 907 GLN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN A1153 ASN ** B1076 ASN ** 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 = 0.4329 r_free = 0.4329 target = 0.173567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.158773 restraints weight = 14349.108| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 1.32 r_work: 0.4077 rms_B_bonded: 1.97 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: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11715 Z= 0.153 Angle : 0.530 8.530 15790 Z= 0.281 Chirality : 0.044 0.233 1734 Planarity : 0.003 0.041 1986 Dihedral : 5.959 73.537 1534 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.44 % Allowed : 14.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.22), residues: 1370 helix: 0.77 (0.20), residues: 651 sheet: 0.35 (0.46), residues: 135 loop : -0.67 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 673 TYR 0.018 0.001 TYR B 474 PHE 0.019 0.002 PHE B 417 TRP 0.004 0.001 TRP B 547 HIS 0.004 0.001 HIS B 915 Details of bonding type rmsd covalent geometry : bond 0.00347 (11715) covalent geometry : angle 0.53027 (15790) hydrogen bonds : bond 0.04624 ( 501) hydrogen bonds : angle 5.52622 ( 1416) *********************** 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: 31 poor density : 194 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1042 LYS cc_start: 0.8036 (mttp) cc_final: 0.7836 (mtpp) REVERT: A 1123 ILE cc_start: 0.5497 (OUTLIER) cc_final: 0.5215 (mt) REVERT: A 1144 THR cc_start: 0.6453 (m) cc_final: 0.6247 (m) REVERT: B 440 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6543 (mt) REVERT: B 480 TYR cc_start: 0.8256 (t80) cc_final: 0.8021 (t80) outliers start: 31 outliers final: 15 residues processed: 206 average time/residue: 0.5011 time to fit residues: 113.5849 Evaluate side-chains 208 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 1139 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 840 LYS Chi-restraints excluded: chain B residue 936 GLU Chi-restraints excluded: chain B residue 997 MET Chi-restraints excluded: chain B residue 1091 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 7 optimal weight: 0.0470 chunk 5 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 117 optimal weight: 0.0010 chunk 74 optimal weight: 0.0010 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 81 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.2490 ------------------------------------------------------------------------------- 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 990 ASN ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 HIS ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.177931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.163182 restraints weight = 14427.262| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 1.35 r_work: 0.4108 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3981 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 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 : 0.002 0.033 11715 Z= 0.105 Angle : 0.493 10.226 15790 Z= 0.258 Chirality : 0.043 0.297 1734 Planarity : 0.003 0.041 1986 Dihedral : 5.606 73.814 1534 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.51 % Allowed : 14.61 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.22), residues: 1370 helix: 1.10 (0.20), residues: 647 sheet: 0.66 (0.45), residues: 150 loop : -0.63 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 908 TYR 0.011 0.001 TYR B 402 PHE 0.018 0.001 PHE A 885 TRP 0.009 0.001 TRP A 547 HIS 0.002 0.001 HIS B 915 Details of bonding type rmsd covalent geometry : bond 0.00230 (11715) covalent geometry : angle 0.49272 (15790) hydrogen bonds : bond 0.03831 ( 501) hydrogen bonds : angle 5.21999 ( 1416) *********************** 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 236 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1123 ILE cc_start: 0.5641 (OUTLIER) cc_final: 0.5411 (mt) REVERT: B 440 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6357 (tt) REVERT: B 1147 ASN cc_start: 0.5779 (m-40) cc_final: 0.5419 (p0) outliers start: 32 outliers final: 12 residues processed: 220 average time/residue: 0.4749 time to fit residues: 114.8737 Evaluate side-chains 214 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 1123 ILE Chi-restraints excluded: chain A residue 1139 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 707 ILE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 48 optimal weight: 0.0870 chunk 39 optimal weight: 0.8980 chunk 128 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 GLN A 990 ASN A1153 ASN ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 ASN 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 = 0.4346 r_free = 0.4346 target = 0.175805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.160884 restraints weight = 14303.264| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 1.35 r_work: 0.4078 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3952 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11715 Z= 0.160 Angle : 0.548 11.575 15790 Z= 0.285 Chirality : 0.044 0.365 1734 Planarity : 0.003 0.041 1986 Dihedral : 5.779 71.549 1534 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.04 % Allowed : 15.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.22), residues: 1370 helix: 0.93 (0.20), residues: 652 sheet: 0.44 (0.48), residues: 130 loop : -0.65 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 908 TYR 0.018 0.001 TYR B 474 PHE 0.018 0.002 PHE A 885 TRP 0.006 0.002 TRP A 547 HIS 0.004 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00366 (11715) covalent geometry : angle 0.54815 (15790) hydrogen bonds : bond 0.04530 ( 501) hydrogen bonds : angle 5.42824 ( 1416) *********************** 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 217 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1123 ILE cc_start: 0.5461 (OUTLIER) cc_final: 0.5178 (mt) REVERT: A 1144 THR cc_start: 0.6463 (m) cc_final: 0.6256 (m) REVERT: B 414 LEU cc_start: 0.7489 (mm) cc_final: 0.7196 (mt) REVERT: B 440 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6499 (mt) outliers start: 26 outliers final: 14 residues processed: 202 average time/residue: 0.4974 time to fit residues: 110.6880 Evaluate side-chains 206 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 1123 ILE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 400 THR 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 707 ILE Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 936 GLU Chi-restraints excluded: chain B residue 997 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 127 optimal weight: 0.6980 chunk 113 optimal weight: 0.0970 chunk 91 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 GLN A 990 ASN ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.175902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.161118 restraints weight = 14309.379| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 1.35 r_work: 0.4080 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3957 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11715 Z= 0.150 Angle : 0.546 11.322 15790 Z= 0.285 Chirality : 0.044 0.361 1734 Planarity : 0.003 0.039 1986 Dihedral : 5.774 72.001 1534 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.12 % Allowed : 16.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.22), residues: 1370 helix: 0.88 (0.20), residues: 658 sheet: 0.39 (0.48), residues: 130 loop : -0.64 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 908 TYR 0.017 0.001 TYR B 474 PHE 0.016 0.002 PHE B 885 TRP 0.009 0.002 TRP A 547 HIS 0.004 0.001 HIS B 915 Details of bonding type rmsd covalent geometry : bond 0.00340 (11715) covalent geometry : angle 0.54558 (15790) hydrogen bonds : bond 0.04421 ( 501) hydrogen bonds : angle 5.43276 ( 1416) *********************** 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 215 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1123 ILE cc_start: 0.5494 (OUTLIER) cc_final: 0.5219 (mt) REVERT: A 1144 THR cc_start: 0.6442 (m) cc_final: 0.6232 (m) REVERT: B 440 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6529 (mt) REVERT: B 1147 ASN cc_start: 0.5845 (m-40) cc_final: 0.5480 (p0) outliers start: 27 outliers final: 13 residues processed: 199 average time/residue: 0.4508 time to fit residues: 98.7652 Evaluate side-chains 203 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 1123 ILE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 440 LEU 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 707 ILE Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 997 MET 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 75 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 98 optimal weight: 0.2980 chunk 60 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 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 907 GLN 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** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 ASN B1153 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.175220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.160738 restraints weight = 14270.459| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 1.33 r_work: 0.4077 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3952 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2030 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= 0.157 Angle : 0.560 12.629 15790 Z= 0.290 Chirality : 0.044 0.389 1734 Planarity : 0.003 0.039 1986 Dihedral : 5.810 72.227 1534 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.73 % Allowed : 15.95 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.22), residues: 1370 helix: 0.84 (0.20), residues: 658 sheet: 0.36 (0.48), residues: 131 loop : -0.67 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 908 TYR 0.017 0.001 TYR B 474 PHE 0.016 0.002 PHE B 905 TRP 0.010 0.002 TRP A 547 HIS 0.004 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00357 (11715) covalent geometry : angle 0.55956 (15790) hydrogen bonds : bond 0.04510 ( 501) hydrogen bonds : angle 5.46035 ( 1416) *********************** 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 213 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1123 ILE cc_start: 0.5519 (OUTLIER) cc_final: 0.5224 (mt) REVERT: A 1144 THR cc_start: 0.6455 (m) cc_final: 0.6250 (m) REVERT: B 440 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6523 (mt) REVERT: B 1147 ASN cc_start: 0.5775 (m-40) cc_final: 0.5423 (p0) outliers start: 22 outliers final: 14 residues processed: 201 average time/residue: 0.4472 time to fit residues: 99.0462 Evaluate side-chains 205 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 840 LYS Chi-restraints excluded: chain B residue 997 MET 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 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 0.0970 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 A 990 ASN ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.174060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.159181 restraints weight = 14445.921| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 1.35 r_work: 0.4062 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3935 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11715 Z= 0.191 Angle : 0.597 13.052 15790 Z= 0.310 Chirality : 0.046 0.401 1734 Planarity : 0.004 0.040 1986 Dihedral : 5.948 72.207 1534 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.73 % Allowed : 16.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.22), residues: 1370 helix: 0.65 (0.20), residues: 660 sheet: 0.40 (0.48), residues: 124 loop : -0.71 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 908 TYR 0.018 0.002 TYR B 983 PHE 0.019 0.002 PHE B1146 TRP 0.009 0.003 TRP A 547 HIS 0.006 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00436 (11715) covalent geometry : angle 0.59655 (15790) hydrogen bonds : bond 0.04932 ( 501) hydrogen bonds : angle 5.61367 ( 1416) ********************** 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 216 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1123 ILE cc_start: 0.5496 (OUTLIER) cc_final: 0.5229 (mt) REVERT: A 1144 THR cc_start: 0.6483 (m) cc_final: 0.6273 (m) REVERT: B 440 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6550 (mt) outliers start: 22 outliers final: 15 residues processed: 206 average time/residue: 0.4430 time to fit residues: 100.3810 Evaluate side-chains 209 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 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 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 997 MET 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 118 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 3 optimal weight: 0.0010 chunk 86 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 A 990 ASN ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1076 ASN B1083 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.174733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.159927 restraints weight = 14418.238| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 1.35 r_work: 0.4076 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3951 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11715 Z= 0.153 Angle : 0.562 12.055 15790 Z= 0.294 Chirality : 0.044 0.325 1734 Planarity : 0.003 0.039 1986 Dihedral : 5.839 71.391 1534 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.73 % Allowed : 16.58 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.22), residues: 1370 helix: 0.78 (0.20), residues: 658 sheet: 0.40 (0.48), residues: 124 loop : -0.70 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 908 TYR 0.014 0.001 TYR B 983 PHE 0.022 0.002 PHE B 417 TRP 0.012 0.003 TRP A 547 HIS 0.004 0.001 HIS B 915 Details of bonding type rmsd covalent geometry : bond 0.00345 (11715) covalent geometry : angle 0.56155 (15790) hydrogen bonds : bond 0.04499 ( 501) hydrogen bonds : angle 5.50679 ( 1416) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4541.15 seconds wall clock time: 78 minutes 10.79 seconds (4690.79 seconds total)