Starting phenix.real_space_refine on Sun Aug 4 21:27:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2h_18842/08_2024/8r2h_18842.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2h_18842/08_2024/8r2h_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2h_18842/08_2024/8r2h_18842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2h_18842/08_2024/8r2h_18842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2h_18842/08_2024/8r2h_18842.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2h_18842/08_2024/8r2h_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 Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 7.87, per 1000 atoms: 0.69 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.08 Conformation dependent library (CDL) restraints added in 2.1 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: 1.53 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: 4.04 Time building geometry restraints manager: 4.49 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: 89.20 - 98.16: 2 98.16 - 107.11: 214 107.11 - 116.06: 7331 116.06 - 125.01: 8156 125.01 - 133.96: 87 Bond angle restraints: 15790 Sorted by residual: angle pdb=" PA TPP A1302 " pdb=" O3A TPP A1302 " pdb=" PB TPP A1302 " ideal model delta sigma weight residual 139.87 129.63 10.24 1.00e+00 1.00e+00 1.05e+02 angle pdb=" PA TPP B1302 " pdb=" O3A TPP B1302 " pdb=" PB TPP B1302 " ideal model delta sigma weight residual 139.87 130.61 9.26 1.00e+00 1.00e+00 8.57e+01 angle pdb=" CA PHE B 527 " pdb=" CB PHE B 527 " pdb=" CG PHE B 527 " ideal model delta sigma weight residual 113.80 122.14 -8.34 1.00e+00 1.00e+00 6.95e+01 angle pdb=" CA LYS B 526 " pdb=" C LYS B 526 " pdb=" N PHE B 527 " ideal model delta sigma weight residual 117.07 123.27 -6.20 1.14e+00 7.69e-01 2.95e+01 angle pdb=" C7 TPP A1302 " pdb=" O7 TPP A1302 " pdb=" PA TPP A1302 " ideal model delta sigma weight residual 124.29 119.84 4.45 1.00e+00 1.00e+00 1.98e+01 ... (remaining 15785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6680 17.99 - 35.98: 299 35.98 - 53.97: 36 53.97 - 71.95: 9 71.95 - 89.94: 3 Dihedral angle restraints: 7027 sinusoidal: 2905 harmonic: 4122 Sorted by residual: dihedral pdb=" CA LEU A 953 " pdb=" C LEU A 953 " pdb=" N ASN A 954 " pdb=" CA ASN A 954 " ideal model delta harmonic sigma weight residual 180.00 159.83 20.17 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA TYR A 374 " pdb=" C TYR A 374 " pdb=" N ASN A 375 " pdb=" CA ASN A 375 " ideal model delta harmonic sigma weight residual 180.00 164.58 15.42 0 5.00e+00 4.00e-02 9.51e+00 dihedral pdb=" CA TYR B 374 " pdb=" C TYR B 374 " pdb=" N ASN B 375 " pdb=" CA ASN B 375 " ideal model delta harmonic sigma weight residual 180.00 164.60 15.40 0 5.00e+00 4.00e-02 9.49e+00 ... (remaining 7024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1196 0.040 - 0.079: 412 0.079 - 0.118: 112 0.118 - 0.158: 13 0.158 - 0.197: 1 Chirality restraints: 1734 Sorted by residual: chirality pdb=" CA PHE B 527 " pdb=" N PHE B 527 " pdb=" C PHE B 527 " pdb=" CB PHE B 527 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CA ILE A 350 " pdb=" N ILE A 350 " pdb=" C ILE A 350 " pdb=" CB ILE A 350 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA VAL B1072 " pdb=" N VAL B1072 " pdb=" C VAL B1072 " pdb=" CB VAL B1072 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 1731 not shown) Planarity restraints: 1986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 TPP B1302 " -0.127 2.00e-02 2.50e+03 1.46e-01 4.27e+02 pdb=" C4 TPP B1302 " 0.051 2.00e-02 2.50e+03 pdb=" C5 TPP B1302 " 0.013 2.00e-02 2.50e+03 pdb=" C6 TPP B1302 " -0.223 2.00e-02 2.50e+03 pdb=" C7' TPP B1302 " -0.078 2.00e-02 2.50e+03 pdb=" CM4 TPP B1302 " 0.160 2.00e-02 2.50e+03 pdb=" N3 TPP B1302 " -0.055 2.00e-02 2.50e+03 pdb=" S1 TPP B1302 " 0.260 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 TPP A1302 " 0.095 2.00e-02 2.50e+03 1.13e-01 2.53e+02 pdb=" C4 TPP A1302 " -0.038 2.00e-02 2.50e+03 pdb=" C5 TPP A1302 " -0.005 2.00e-02 2.50e+03 pdb=" C6 TPP A1302 " 0.171 2.00e-02 2.50e+03 pdb=" C7' TPP A1302 " 0.064 2.00e-02 2.50e+03 pdb=" CM4 TPP A1302 " -0.127 2.00e-02 2.50e+03 pdb=" N3 TPP A1302 " 0.039 2.00e-02 2.50e+03 pdb=" S1 TPP A1302 " -0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 527 " -0.026 2.00e-02 2.50e+03 2.08e-02 7.58e+00 pdb=" CG PHE B 527 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B 527 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 527 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 527 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 527 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 527 " -0.005 2.00e-02 2.50e+03 ... (remaining 1983 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 86 2.51 - 3.11: 8514 3.11 - 3.71: 17578 3.71 - 4.30: 26845 4.30 - 4.90: 44175 Nonbonded interactions: 97198 Sorted by model distance: nonbonded pdb=" O GLN B 659 " pdb="MG MG B1301 " model vdw 1.914 2.170 nonbonded pdb=" O GLN A 659 " pdb="MG MG A1301 " model vdw 1.924 2.170 nonbonded pdb=" OD1 ASN B 657 " pdb="MG MG B1301 " model vdw 1.952 2.170 nonbonded pdb="MG MG A1301 " pdb=" O2A TPP A1302 " model vdw 2.045 2.170 nonbonded pdb=" OD1 ASN A 657 " pdb="MG MG A1301 " model vdw 2.108 2.170 ... (remaining 97193 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 312 through 683 or resid 705 through 998 or resid 1030 thr \ ough 1204 or resid 1301 through 1302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.450 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 34.580 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11715 Z= 0.211 Angle : 0.516 10.241 15790 Z= 0.322 Chirality : 0.042 0.197 1734 Planarity : 0.005 0.146 1986 Dihedral : 10.241 89.943 4385 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.55 % Allowed : 5.97 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.22), residues: 1370 helix: 0.42 (0.20), residues: 640 sheet: 0.97 (0.43), residues: 156 loop : -0.83 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 547 HIS 0.003 0.001 HIS B 915 PHE 0.047 0.002 PHE B 527 TYR 0.014 0.001 TYR B 983 ARG 0.003 0.000 ARG B 741 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 216 time to evaluate : 1.178 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: 1.0370 time to fit residues: 252.6367 Evaluate side-chains 202 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11715 Z= 0.290 Angle : 0.568 8.496 15790 Z= 0.309 Chirality : 0.045 0.157 1734 Planarity : 0.004 0.040 1986 Dihedral : 6.516 76.209 1536 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.73 % Allowed : 10.60 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1370 helix: 0.46 (0.19), residues: 661 sheet: 0.70 (0.46), residues: 137 loop : -0.67 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 547 HIS 0.005 0.001 HIS B 915 PHE 0.022 0.002 PHE B1146 TYR 0.018 0.002 TYR B 983 ARG 0.004 0.000 ARG B 673 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 207 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 504 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.7244 (m-80) REVERT: B 411 LYS cc_start: 0.7352 (ttpt) cc_final: 0.7105 (ttpt) outliers start: 22 outliers final: 8 residues processed: 218 average time/residue: 1.0171 time to fit residues: 243.9903 Evaluate side-chains 208 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 199 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 70 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 732 ASN A 907 GLN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN A1153 ASN B 406 ASN ** B 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.1492 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= 0.234 Angle : 0.526 8.345 15790 Z= 0.285 Chirality : 0.044 0.135 1734 Planarity : 0.003 0.041 1986 Dihedral : 6.377 75.705 1536 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.12 % Allowed : 12.10 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.22), residues: 1370 helix: 0.68 (0.20), residues: 647 sheet: 0.62 (0.45), residues: 137 loop : -0.65 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 547 HIS 0.004 0.001 HIS B 915 PHE 0.018 0.002 PHE B 885 TYR 0.015 0.001 TYR A1130 ARG 0.003 0.000 ARG B 673 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 202 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: A 504 PHE cc_start: 0.7720 (OUTLIER) cc_final: 0.7209 (m-80) REVERT: A 840 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7421 (ttmm) REVERT: A 885 PHE cc_start: 0.7686 (t80) cc_final: 0.7387 (t80) REVERT: B 440 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6609 (mt) REVERT: B 1048 MET cc_start: 0.5272 (mmt) cc_final: 0.5020 (mmm) outliers start: 27 outliers final: 9 residues processed: 215 average time/residue: 0.9761 time to fit residues: 231.7451 Evaluate side-chains 210 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 198 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 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 124 optimal weight: 0.4980 chunk 95 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1153 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11715 Z= 0.285 Angle : 0.563 8.309 15790 Z= 0.302 Chirality : 0.045 0.162 1734 Planarity : 0.004 0.042 1986 Dihedral : 6.413 77.495 1536 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.28 % Allowed : 13.83 % Favored : 83.90 % 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: 0.53 (0.20), residues: 649 sheet: 0.28 (0.47), residues: 128 loop : -0.66 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 547 HIS 0.005 0.001 HIS A 915 PHE 0.020 0.002 PHE B1146 TYR 0.017 0.002 TYR B 474 ARG 0.003 0.000 ARG B 673 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 199 time to evaluate : 1.147 Fit side-chains REVERT: A 1118 MET cc_start: 0.6284 (tpp) cc_final: 0.6012 (tpp) REVERT: A 1123 ILE cc_start: 0.5590 (OUTLIER) cc_final: 0.5286 (mt) REVERT: B 440 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6654 (mt) REVERT: B 1048 MET cc_start: 0.5302 (mmt) cc_final: 0.5079 (mmm) outliers start: 29 outliers final: 16 residues processed: 212 average time/residue: 1.0593 time to fit residues: 246.4495 Evaluate side-chains 210 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 192 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 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 440 LEU Chi-restraints excluded: chain B residue 446 ILE 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 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 111 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 114 optimal weight: 0.1980 chunk 92 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 120 optimal weight: 0.0020 chunk 33 optimal weight: 0.5980 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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 482 ASN ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 ASN B1182 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.1817 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= 0.187 Angle : 0.506 7.985 15790 Z= 0.273 Chirality : 0.043 0.140 1734 Planarity : 0.003 0.042 1986 Dihedral : 5.942 74.404 1534 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.44 % Allowed : 14.14 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.22), residues: 1370 helix: 0.76 (0.20), residues: 651 sheet: 0.22 (0.44), residues: 149 loop : -0.62 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 547 HIS 0.003 0.001 HIS B 915 PHE 0.017 0.001 PHE B 885 TYR 0.012 0.001 TYR A1130 ARG 0.002 0.000 ARG B 673 *********************** 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 fitting. rotamer outliers: 31 poor density : 194 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 504 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7206 (m-80) REVERT: A 885 PHE cc_start: 0.7648 (t80) cc_final: 0.7263 (t80) REVERT: A 1118 MET cc_start: 0.6212 (tpp) cc_final: 0.5932 (tpp) REVERT: A 1123 ILE cc_start: 0.5602 (OUTLIER) cc_final: 0.5321 (mt) REVERT: B 1147 ASN cc_start: 0.6081 (m-40) cc_final: 0.5739 (p0) outliers start: 31 outliers final: 13 residues processed: 210 average time/residue: 0.9969 time to fit residues: 231.0752 Evaluate side-chains 207 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 192 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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 1123 ILE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 936 GLU 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 45 optimal weight: 0.9980 chunk 120 optimal weight: 0.0370 chunk 26 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 134 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 ASN B1153 ASN B1154 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.1884 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= 0.196 Angle : 0.521 7.950 15790 Z= 0.276 Chirality : 0.043 0.221 1734 Planarity : 0.003 0.042 1986 Dihedral : 5.871 73.387 1534 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.20 % Allowed : 14.45 % Favored : 83.35 % 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: 0.19 (0.22), residues: 1370 helix: 0.79 (0.20), residues: 658 sheet: 0.29 (0.46), residues: 138 loop : -0.61 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 547 HIS 0.003 0.001 HIS B 915 PHE 0.016 0.001 PHE B 885 TYR 0.019 0.001 TYR B 474 ARG 0.004 0.000 ARG B 908 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 504 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7209 (m-80) REVERT: A 885 PHE cc_start: 0.7637 (t80) cc_final: 0.7335 (t80) REVERT: A 1077 MET cc_start: 0.5765 (OUTLIER) cc_final: 0.5455 (ttm) REVERT: A 1118 MET cc_start: 0.6197 (OUTLIER) cc_final: 0.5914 (tpp) REVERT: A 1123 ILE cc_start: 0.5662 (OUTLIER) cc_final: 0.5369 (mt) REVERT: B 480 TYR cc_start: 0.8353 (t80) cc_final: 0.8094 (t80) outliers start: 28 outliers final: 15 residues processed: 212 average time/residue: 0.9811 time to fit residues: 229.9331 Evaluate side-chains 212 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 193 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 1118 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 462 VAL 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 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 129 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 98 optimal weight: 0.0370 chunk 113 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 133 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 A1153 ASN ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.1935 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= 0.222 Angle : 0.535 10.672 15790 Z= 0.285 Chirality : 0.044 0.326 1734 Planarity : 0.003 0.043 1986 Dihedral : 5.890 73.112 1534 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.20 % Allowed : 15.00 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.22), residues: 1370 helix: 0.77 (0.20), residues: 651 sheet: 0.26 (0.47), residues: 138 loop : -0.62 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 547 HIS 0.004 0.001 HIS A 915 PHE 0.016 0.002 PHE B 885 TYR 0.017 0.001 TYR B 474 ARG 0.004 0.000 ARG B 908 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 197 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 885 PHE cc_start: 0.7672 (t80) cc_final: 0.7325 (t80) REVERT: A 1077 MET cc_start: 0.5732 (OUTLIER) cc_final: 0.5374 (ttm) REVERT: A 1118 MET cc_start: 0.6210 (OUTLIER) cc_final: 0.5929 (tpp) REVERT: A 1123 ILE cc_start: 0.5637 (OUTLIER) cc_final: 0.5344 (mt) REVERT: B 440 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6627 (mt) REVERT: B 480 TYR cc_start: 0.8368 (t80) cc_final: 0.8094 (t80) REVERT: B 1147 ASN cc_start: 0.6090 (m-40) cc_final: 0.5733 (p0) outliers start: 28 outliers final: 15 residues processed: 209 average time/residue: 1.0054 time to fit residues: 231.7675 Evaluate side-chains 212 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 193 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 1077 MET Chi-restraints excluded: chain A residue 1080 MET Chi-restraints excluded: chain A residue 1118 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 462 VAL Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 936 GLU Chi-restraints excluded: chain B residue 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 53 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 105 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 ASN B1153 ASN B1154 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11715 Z= 0.261 Angle : 0.577 12.083 15790 Z= 0.303 Chirality : 0.045 0.374 1734 Planarity : 0.004 0.043 1986 Dihedral : 5.990 74.208 1534 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.20 % Allowed : 15.24 % Favored : 82.56 % 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: 0.68 (0.20), residues: 651 sheet: 0.29 (0.47), residues: 131 loop : -0.66 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 547 HIS 0.005 0.001 HIS A 915 PHE 0.017 0.002 PHE B1146 TYR 0.017 0.002 TYR A1130 ARG 0.004 0.000 ARG B 908 *********************** 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 224 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 196 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: A 885 PHE cc_start: 0.7677 (t80) cc_final: 0.7387 (t80) REVERT: A 1077 MET cc_start: 0.5761 (OUTLIER) cc_final: 0.5267 (ttm) REVERT: A 1118 MET cc_start: 0.6265 (OUTLIER) cc_final: 0.5996 (tpp) REVERT: A 1123 ILE cc_start: 0.5662 (OUTLIER) cc_final: 0.5363 (mt) REVERT: B 414 LEU cc_start: 0.7506 (mm) cc_final: 0.7221 (mt) REVERT: B 440 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6652 (mt) REVERT: B 480 TYR cc_start: 0.8383 (t80) cc_final: 0.8097 (t80) outliers start: 28 outliers final: 17 residues processed: 208 average time/residue: 1.0084 time to fit residues: 231.1359 Evaluate side-chains 214 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 193 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 1077 MET Chi-restraints excluded: chain A residue 1080 MET Chi-restraints excluded: chain A residue 1118 MET Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 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 128 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.0030 chunk 38 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 118 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 132 optimal weight: 0.0040 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 GLN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.2028 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= 0.177 Angle : 0.526 12.335 15790 Z= 0.278 Chirality : 0.044 0.373 1734 Planarity : 0.003 0.042 1986 Dihedral : 5.781 70.999 1534 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.34 % Allowed : 16.03 % 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: 0.27 (0.22), residues: 1370 helix: 0.90 (0.20), residues: 650 sheet: 0.27 (0.47), residues: 143 loop : -0.59 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 547 HIS 0.003 0.001 HIS B 915 PHE 0.016 0.001 PHE B 885 TYR 0.012 0.001 TYR A1130 ARG 0.003 0.000 ARG B 908 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 198 time to evaluate : 1.494 Fit side-chains revert: symmetry clash REVERT: A 885 PHE cc_start: 0.7570 (t80) cc_final: 0.7321 (t80) REVERT: A 1077 MET cc_start: 0.5691 (OUTLIER) cc_final: 0.5362 (ttm) REVERT: A 1118 MET cc_start: 0.6187 (tpp) cc_final: 0.5884 (tpp) REVERT: A 1123 ILE cc_start: 0.5787 (OUTLIER) cc_final: 0.5517 (mt) REVERT: B 440 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6574 (mt) REVERT: B 480 TYR cc_start: 0.8366 (t80) cc_final: 0.8145 (t80) REVERT: B 1147 ASN cc_start: 0.6043 (m-40) cc_final: 0.5698 (p0) outliers start: 17 outliers final: 12 residues processed: 205 average time/residue: 1.0219 time to fit residues: 230.8194 Evaluate side-chains 211 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 196 time to evaluate : 1.291 ------------------------------------------------------------------------------- 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 434 LYS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 0.0980 chunk 62 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 127 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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** ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.1989 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= 0.261 Angle : 0.589 13.301 15790 Z= 0.307 Chirality : 0.045 0.401 1734 Planarity : 0.004 0.041 1986 Dihedral : 5.934 73.301 1534 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.57 % Allowed : 16.42 % Favored : 82.01 % 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: 0.10 (0.22), residues: 1370 helix: 0.72 (0.20), residues: 651 sheet: 0.29 (0.47), residues: 137 loop : -0.66 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 547 HIS 0.005 0.001 HIS A 915 PHE 0.019 0.002 PHE B 417 TYR 0.017 0.001 TYR B 983 ARG 0.004 0.000 ARG B 908 ********************** 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 217 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 197 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1077 MET cc_start: 0.5736 (OUTLIER) cc_final: 0.5281 (ttm) REVERT: A 1118 MET cc_start: 0.6270 (tpp) cc_final: 0.5988 (tpp) REVERT: A 1123 ILE cc_start: 0.5619 (OUTLIER) cc_final: 0.5320 (mt) REVERT: B 440 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6652 (mt) REVERT: B 480 TYR cc_start: 0.8386 (t80) cc_final: 0.8097 (t80) outliers start: 20 outliers final: 12 residues processed: 206 average time/residue: 1.0481 time to fit residues: 237.4064 Evaluate side-chains 208 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 193 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 434 LYS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 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 33 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 6 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 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** B1154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.172367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.157527 restraints weight = 14254.516| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 1.33 r_work: 0.4059 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3934 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11715 Z= 0.289 Angle : 0.593 11.717 15790 Z= 0.314 Chirality : 0.046 0.331 1734 Planarity : 0.004 0.044 1986 Dihedral : 6.059 74.826 1534 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.73 % Allowed : 16.50 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.22), residues: 1370 helix: 0.59 (0.20), residues: 652 sheet: 0.38 (0.49), residues: 124 loop : -0.72 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 547 HIS 0.006 0.001 HIS A 915 PHE 0.020 0.002 PHE B 417 TYR 0.018 0.002 TYR B 983 ARG 0.004 0.000 ARG B 908 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4850.65 seconds wall clock time: 86 minutes 6.92 seconds (5166.92 seconds total)