Starting phenix.real_space_refine on Sat Feb 17 22:07:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3y_13797/02_2024/7q3y_13797_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3y_13797/02_2024/7q3y_13797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3y_13797/02_2024/7q3y_13797.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3y_13797/02_2024/7q3y_13797.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3y_13797/02_2024/7q3y_13797_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3y_13797/02_2024/7q3y_13797_trim.pdb" } resolution = 4.34 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= 0.003 sd= 0.048 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 S 43 5.16 5 Cl 1 4.86 5 C 6531 2.51 5 N 1695 2.21 5 O 1970 1.98 5 H 9386 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19627 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 19172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1201, 19172 Classifications: {'peptide': 1201} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 68, 'TRANS': 1129} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 6, 'water': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 9.45, per 1000 atoms: 0.48 Number of scatterers: 19627 At special positions: 0 Unit cell: (84.8, 90.1, 153.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Cl 1 17.00 S 43 16.00 O 1970 8.00 N 1695 7.00 C 6531 6.00 H 9386 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 728 " - pdb=" SG CYS A 734 " distance=2.03 Simple disulfide: pdb=" SG CYS A 928 " - pdb=" SG CYS A 946 " distance=2.03 Simple disulfide: pdb=" SG CYS A1114 " - pdb=" SG CYS A1126 " distance=2.03 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 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA J 3 " - " MAN J 4 " ALPHA1-6 " BMA B 3 " - " MAN B 4 " " BMA F 3 " - " MAN F 5 " " BMA J 3 " - " MAN J 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " BETA1-6 " NAG J 1 " - " FUC J 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1303 " - " ASN A 666 " " NAG A1304 " - " ASN A 913 " " NAG A1305 " - " ASN A 416 " " NAG A1306 " - " ASN A 82 " " NAG B 1 " - " ASN A 648 " " NAG C 1 " - " ASN A 685 " " NAG D 1 " - " ASN A 731 " " NAG E 1 " - " ASN A 9 " " NAG F 1 " - " ASN A 25 " " NAG G 1 " - " ASN A 117 " " NAG H 1 " - " ASN A 480 " " NAG I 1 " - " ASN A 45 " " NAG J 1 " - " ASN A 289 " Time building additional restraints: 17.83 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" NE2 HIS A 361 " pdb="ZN ZN A1301 " - pdb=" NE2 HIS A 365 " 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 6 sheets defined 70.7% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 13 through 45 removed outlier: 3.711A pdb=" N GLN A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 77 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 85 through 97 Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 104 through 125 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 152 through 190 Proline residue: A 170 - end of helix Proline residue: A 173 - end of helix removed outlier: 3.719A pdb=" N GLU A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.702A pdb=" N TRP A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 238 Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 251 through 254 removed outlier: 4.216A pdb=" N GLY A 254 " --> pdb=" O HIS A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 254' Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 264 through 269 removed outlier: 3.535A pdb=" N VAL A 268 " --> pdb=" O ILE A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 289 through 304 removed outlier: 3.510A pdb=" N ARG A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 317 removed outlier: 3.822A pdb=" N TRP A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 373 Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 386 through 401 removed outlier: 3.619A pdb=" N ALA A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A 392 " --> pdb=" O HIS A 388 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 417 through 433 Processing helix chain 'A' and resid 434 through 452 removed outlier: 4.505A pdb=" N PHE A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP A 443 " --> pdb=" O GLY A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 458 through 472 Processing helix chain 'A' and resid 484 through 489 Processing helix chain 'A' and resid 498 through 519 removed outlier: 3.830A pdb=" N PHE A 502 " --> pdb=" O TYR A 498 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 509 " --> pdb=" O PHE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 Processing helix chain 'A' and resid 533 through 546 Processing helix chain 'A' and resid 551 through 560 Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'A' and resid 574 through 589 Processing helix chain 'A' and resid 616 through 648 removed outlier: 3.923A pdb=" N ALA A 620 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 633 " --> pdb=" O ARG A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 676 Processing helix chain 'A' and resid 677 through 678 No H-bonds generated for 'chain 'A' and resid 677 through 678' Processing helix chain 'A' and resid 679 through 683 removed outlier: 3.718A pdb=" N GLN A 682 " --> pdb=" O ASP A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'A' and resid 704 through 725 Processing helix chain 'A' and resid 739 through 748 Processing helix chain 'A' and resid 750 through 769 removed outlier: 3.897A pdb=" N ARG A 767 " --> pdb=" O ASP A 763 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 769 " --> pdb=" O ALA A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 787 Processing helix chain 'A' and resid 791 through 799 removed outlier: 3.848A pdb=" N MET A 799 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 836 removed outlier: 3.505A pdb=" N LEU A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Proline residue: A 818 - end of helix removed outlier: 3.600A pdb=" N HIS A 834 " --> pdb=" O ALA A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 861 No H-bonds generated for 'chain 'A' and resid 859 through 861' Processing helix chain 'A' and resid 862 through 867 Processing helix chain 'A' and resid 876 through 884 Processing helix chain 'A' and resid 887 through 902 Processing helix chain 'A' and resid 910 through 915 Processing helix chain 'A' and resid 950 through 970 removed outlier: 3.627A pdb=" N TYR A 970 " --> pdb=" O TYR A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 978 Processing helix chain 'A' and resid 982 through 996 removed outlier: 3.608A pdb=" N HIS A 986 " --> pdb=" O ASN A 982 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 990 " --> pdb=" O HIS A 986 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP A 991 " --> pdb=" O GLU A 987 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 993 " --> pdb=" O ILE A 989 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A 994 " --> pdb=" O GLY A 990 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N SER A 996 " --> pdb=" O VAL A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1006 Processing helix chain 'A' and resid 1015 through 1031 removed outlier: 3.691A pdb=" N ASP A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP A1029 " --> pdb=" O LYS A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1049 removed outlier: 3.870A pdb=" N PHE A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1055 No H-bonds generated for 'chain 'A' and resid 1053 through 1055' Processing helix chain 'A' and resid 1056 through 1070 Processing helix chain 'A' and resid 1082 through 1087 Processing helix chain 'A' and resid 1096 through 1117 removed outlier: 3.887A pdb=" N PHE A1100 " --> pdb=" O TYR A1096 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N PHE A1107 " --> pdb=" O PHE A1103 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN A1108 " --> pdb=" O ILE A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1126 Processing helix chain 'A' and resid 1131 through 1143 removed outlier: 3.571A pdb=" N GLN A1136 " --> pdb=" O LYS A1132 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A1141 " --> pdb=" O ARG A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1159 removed outlier: 3.961A pdb=" N ALA A1153 " --> pdb=" O PRO A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1186 Proline residue: A1174 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 249 removed outlier: 5.988A pdb=" N ILE A 248 " --> pdb=" O CYS A 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 333 through 335 Processing sheet with id=AA4, first strand: chain 'A' and resid 727 through 728 Processing sheet with id=AA5, first strand: chain 'A' and resid 846 through 847 removed outlier: 6.356A pdb=" N ILE A 846 " --> pdb=" O CYS A1072 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 931 through 934 570 hydrogen bonds defined for protein. 1626 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: 7.13 Time building geometry restraints manager: 18.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9384 1.03 - 1.23: 286 1.23 - 1.43: 4409 1.43 - 1.63: 5772 1.63 - 1.83: 72 Bond restraints: 19923 Sorted by residual: bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" C5 BMA H 3 " pdb=" O5 BMA H 3 " ideal model delta sigma weight residual 1.417 1.456 -0.039 2.00e-02 2.50e+03 3.88e+00 bond pdb=" C1 MAN B 4 " pdb=" C2 MAN B 4 " ideal model delta sigma weight residual 1.526 1.564 -0.038 2.00e-02 2.50e+03 3.52e+00 bond pdb=" CB TRP A1062 " pdb=" CG TRP A1062 " ideal model delta sigma weight residual 1.498 1.442 0.056 3.10e-02 1.04e+03 3.21e+00 bond pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sigma weight residual 1.417 1.452 -0.035 2.00e-02 2.50e+03 3.03e+00 ... (remaining 19918 not shown) Histogram of bond angle deviations from ideal: 98.18 - 105.37: 274 105.37 - 112.55: 22141 112.55 - 119.74: 5628 119.74 - 126.92: 7430 126.92 - 134.11: 221 Bond angle restraints: 35694 Sorted by residual: angle pdb=" C CYS A 928 " pdb=" N HIS A 929 " pdb=" CA HIS A 929 " ideal model delta sigma weight residual 121.24 116.55 4.69 1.44e+00 4.82e-01 1.06e+01 angle pdb=" N ASN A1196 " pdb=" CA ASN A1196 " pdb=" C ASN A1196 " ideal model delta sigma weight residual 107.41 113.66 -6.25 2.02e+00 2.45e-01 9.57e+00 angle pdb=" C LYS A 341 " pdb=" N ASP A 342 " pdb=" CA ASP A 342 " ideal model delta sigma weight residual 121.62 116.09 5.53 1.83e+00 2.99e-01 9.14e+00 angle pdb=" CA CYS A 928 " pdb=" C CYS A 928 " pdb=" N HIS A 929 " ideal model delta sigma weight residual 118.59 123.49 -4.90 1.63e+00 3.76e-01 9.05e+00 angle pdb=" CA TRP A1062 " pdb=" CB TRP A1062 " pdb=" CG TRP A1062 " ideal model delta sigma weight residual 113.60 108.00 5.60 1.90e+00 2.77e-01 8.70e+00 ... (remaining 35689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.49: 9277 21.49 - 42.97: 445 42.97 - 64.46: 153 64.46 - 85.95: 72 85.95 - 107.43: 32 Dihedral angle restraints: 9979 sinusoidal: 5598 harmonic: 4381 Sorted by residual: dihedral pdb=" CB CYS A 928 " pdb=" SG CYS A 928 " pdb=" SG CYS A 946 " pdb=" CB CYS A 946 " ideal model delta sinusoidal sigma weight residual 93.00 168.62 -75.62 1 1.00e+01 1.00e-02 7.22e+01 dihedral pdb=" O4 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.72 107.43 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C3 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sinusoidal sigma weight residual 47.62 -58.12 105.74 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 9976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1409 0.070 - 0.141: 169 0.141 - 0.211: 15 0.211 - 0.282: 5 0.282 - 0.352: 5 Chirality restraints: 1603 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 666 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 1600 not shown) Planarity restraints: 2950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 508 " -0.037 2.00e-02 2.50e+03 4.25e-02 2.71e+01 pdb=" CD GLN A 508 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN A 508 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN A 508 " 0.061 2.00e-02 2.50e+03 pdb="HE21 GLN A 508 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN A 508 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 446 " -0.090 9.50e-02 1.11e+02 3.77e-02 1.27e+01 pdb=" NE ARG A 446 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 446 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG A 446 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 446 " 0.043 2.00e-02 2.50e+03 pdb="HH11 ARG A 446 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 446 " 0.009 2.00e-02 2.50e+03 pdb="HH21 ARG A 446 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 446 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 371 " 0.024 2.00e-02 2.50e+03 2.85e-02 1.22e+01 pdb=" CD GLN A 371 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN A 371 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN A 371 " -0.044 2.00e-02 2.50e+03 pdb="HE21 GLN A 371 " 0.000 2.00e-02 2.50e+03 pdb="HE22 GLN A 371 " 0.043 2.00e-02 2.50e+03 ... (remaining 2947 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 290 2.05 - 2.69: 29670 2.69 - 3.32: 59137 3.32 - 3.96: 72516 3.96 - 4.60: 115764 Nonbonded interactions: 277377 Sorted by model distance: nonbonded pdb=" OD2 ASP A1041 " pdb=" H ILE A1097 " model vdw 1.411 1.850 nonbonded pdb=" H THR A 948 " pdb=" OD2 ASP A 953 " model vdw 1.500 1.850 nonbonded pdb=" HG1 THR A 454 " pdb=" OD2 ASP A 462 " model vdw 1.514 1.850 nonbonded pdb=" OD2 ASP A 443 " pdb=" H ILE A 499 " model vdw 1.515 1.850 nonbonded pdb=" HG1 THR A 468 " pdb=" O ILE A 473 " model vdw 1.566 1.850 ... (remaining 277372 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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 group one per residue 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: 0.710 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: 0.280 Extract box with map and model: 4.460 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 70.580 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 : 0.007 0.056 10537 Z= 0.440 Angle : 0.904 6.974 14348 Z= 0.479 Chirality : 0.050 0.352 1603 Planarity : 0.008 0.095 1808 Dihedral : 17.139 107.431 4371 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.19 % Allowed : 2.31 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.22), residues: 1199 helix: -0.73 (0.16), residues: 715 sheet: -0.82 (1.11), residues: 20 loop : -0.89 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP A 552 HIS 0.013 0.003 HIS A 388 PHE 0.032 0.003 PHE A1107 TYR 0.026 0.004 TYR A 501 ARG 0.023 0.003 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.8547 (m-10) cc_final: 0.8200 (m-80) REVERT: A 182 SER cc_start: 0.9071 (t) cc_final: 0.8863 (m) REVERT: A 183 ASN cc_start: 0.8527 (m-40) cc_final: 0.7527 (t0) REVERT: A 293 MET cc_start: 0.8985 (mtp) cc_final: 0.8550 (mmm) REVERT: A 606 ASN cc_start: 0.9013 (m-40) cc_final: 0.8370 (m-40) REVERT: A 779 LEU cc_start: 0.9500 (mt) cc_final: 0.9084 (mt) REVERT: A 916 MET cc_start: 0.9012 (ttp) cc_final: 0.8656 (tmm) REVERT: A 943 ILE cc_start: 0.9536 (mt) cc_final: 0.9291 (tp) REVERT: A 968 MET cc_start: 0.9401 (mtm) cc_final: 0.9184 (mtp) REVERT: A 1190 LEU cc_start: 0.8351 (mt) cc_final: 0.8141 (pt) outliers start: 2 outliers final: 2 residues processed: 192 average time/residue: 0.5333 time to fit residues: 140.2519 Evaluate side-chains 123 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 31 optimal weight: 0.0020 chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 108 optimal weight: 0.4980 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 575 GLN A 832 HIS ** A 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 GLN ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10537 Z= 0.216 Angle : 0.681 6.459 14348 Z= 0.355 Chirality : 0.041 0.286 1603 Planarity : 0.005 0.061 1808 Dihedral : 11.424 68.169 2021 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 0.28 (0.23), residues: 1199 helix: 0.43 (0.17), residues: 740 sheet: 0.52 (1.88), residues: 10 loop : -0.01 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 257 HIS 0.012 0.002 HIS A 491 PHE 0.018 0.002 PHE A 83 TYR 0.026 0.002 TYR A 368 ARG 0.006 0.001 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASN cc_start: 0.8455 (m-40) cc_final: 0.7286 (t0) REVERT: A 293 MET cc_start: 0.8935 (mtp) cc_final: 0.8662 (mtp) REVERT: A 428 MET cc_start: 0.8005 (tpp) cc_final: 0.7785 (tpp) REVERT: A 826 TYR cc_start: 0.8991 (t80) cc_final: 0.8494 (t80) REVERT: A 916 MET cc_start: 0.8982 (ttp) cc_final: 0.8561 (tmm) REVERT: A 1017 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7957 (mp0) REVERT: A 1020 ILE cc_start: 0.8954 (mm) cc_final: 0.8628 (tp) REVERT: A 1190 LEU cc_start: 0.8363 (mt) cc_final: 0.8061 (pt) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.5436 time to fit residues: 111.7415 Evaluate side-chains 116 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 824 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10537 Z= 0.252 Angle : 0.630 5.884 14348 Z= 0.328 Chirality : 0.040 0.248 1603 Planarity : 0.004 0.056 1808 Dihedral : 9.190 59.764 2021 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 0.56 (0.24), residues: 1199 helix: 0.56 (0.18), residues: 741 sheet: -0.04 (1.79), residues: 10 loop : 0.31 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 40 HIS 0.007 0.001 HIS A 824 PHE 0.022 0.002 PHE A 505 TYR 0.014 0.002 TYR A 368 ARG 0.003 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.8747 (m-10) cc_final: 0.8190 (m-80) REVERT: A 183 ASN cc_start: 0.8325 (m-40) cc_final: 0.7297 (t0) REVERT: A 293 MET cc_start: 0.8946 (mtp) cc_final: 0.8693 (mtp) REVERT: A 489 LYS cc_start: 0.8025 (tppt) cc_final: 0.7794 (mptt) REVERT: A 916 MET cc_start: 0.8940 (ttp) cc_final: 0.8556 (tmm) REVERT: A 1017 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7918 (mp0) REVERT: A 1020 ILE cc_start: 0.8975 (mm) cc_final: 0.8650 (tp) REVERT: A 1190 LEU cc_start: 0.8392 (mt) cc_final: 0.8053 (pt) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.5326 time to fit residues: 97.8435 Evaluate side-chains 109 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 56 optimal weight: 0.0370 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 overall best weight: 1.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10537 Z= 0.194 Angle : 0.564 5.760 14348 Z= 0.292 Chirality : 0.037 0.225 1603 Planarity : 0.004 0.050 1808 Dihedral : 6.884 48.362 2021 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.24), residues: 1199 helix: 0.95 (0.18), residues: 739 sheet: 0.04 (1.88), residues: 10 loop : 0.58 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 758 HIS 0.008 0.001 HIS A 824 PHE 0.018 0.002 PHE A 178 TYR 0.012 0.001 TYR A 368 ARG 0.004 0.000 ARG A1044 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASN cc_start: 0.8433 (m-40) cc_final: 0.7330 (t0) REVERT: A 420 SER cc_start: 0.9052 (t) cc_final: 0.8801 (p) REVERT: A 662 MET cc_start: 0.8531 (ttt) cc_final: 0.7869 (tmm) REVERT: A 961 MET cc_start: 0.8588 (mmm) cc_final: 0.8307 (mmm) REVERT: A 1017 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7979 (mp0) REVERT: A 1020 ILE cc_start: 0.8965 (mm) cc_final: 0.8642 (tp) REVERT: A 1190 LEU cc_start: 0.8390 (mt) cc_final: 0.7985 (pt) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.5122 time to fit residues: 94.8789 Evaluate side-chains 113 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 0.0270 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 824 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 HIS ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10537 Z= 0.215 Angle : 0.554 5.854 14348 Z= 0.289 Chirality : 0.037 0.213 1603 Planarity : 0.004 0.048 1808 Dihedral : 6.311 41.752 2021 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.25), residues: 1199 helix: 1.15 (0.18), residues: 739 sheet: -0.20 (1.76), residues: 10 loop : 0.68 (0.33), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 758 HIS 0.006 0.001 HIS A 824 PHE 0.013 0.001 PHE A 505 TYR 0.014 0.001 TYR A 372 ARG 0.003 0.000 ARG A1065 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.8818 (m-10) cc_final: 0.8360 (m-80) REVERT: A 183 ASN cc_start: 0.8357 (m-40) cc_final: 0.7320 (t0) REVERT: A 320 GLU cc_start: 0.8637 (pm20) cc_final: 0.8188 (pm20) REVERT: A 420 SER cc_start: 0.8963 (t) cc_final: 0.8669 (p) REVERT: A 428 MET cc_start: 0.7924 (tpp) cc_final: 0.7681 (tpp) REVERT: A 662 MET cc_start: 0.8489 (ttt) cc_final: 0.7813 (tmm) REVERT: A 961 MET cc_start: 0.8565 (mmm) cc_final: 0.8312 (mmm) REVERT: A 1017 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7939 (mp0) REVERT: A 1020 ILE cc_start: 0.8965 (mm) cc_final: 0.8656 (tp) REVERT: A 1190 LEU cc_start: 0.8420 (mt) cc_final: 0.7974 (pt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.4817 time to fit residues: 85.3277 Evaluate side-chains 104 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.4980 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 ASN A 585 ASN ** A 824 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 10537 Z= 0.309 Angle : 0.600 5.957 14348 Z= 0.319 Chirality : 0.038 0.201 1603 Planarity : 0.004 0.049 1808 Dihedral : 6.092 39.808 2021 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.10 % Allowed : 1.34 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 0.98 (0.25), residues: 1199 helix: 0.90 (0.18), residues: 737 sheet: 0.07 (1.77), residues: 10 loop : 0.46 (0.33), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 758 HIS 0.005 0.001 HIS A 963 PHE 0.021 0.002 PHE A 892 TYR 0.015 0.002 TYR A 372 ARG 0.005 0.001 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.8891 (m-10) cc_final: 0.8435 (m-80) REVERT: A 183 ASN cc_start: 0.8406 (m-40) cc_final: 0.7383 (t0) REVERT: A 320 GLU cc_start: 0.8777 (pm20) cc_final: 0.8353 (pm20) REVERT: A 420 SER cc_start: 0.9067 (t) cc_final: 0.8778 (p) REVERT: A 662 MET cc_start: 0.8465 (ttt) cc_final: 0.8097 (tmm) REVERT: A 826 TYR cc_start: 0.9030 (t80) cc_final: 0.8569 (t80) REVERT: A 961 MET cc_start: 0.8612 (mmm) cc_final: 0.8375 (mmm) REVERT: A 1017 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7927 (mp0) REVERT: A 1020 ILE cc_start: 0.8978 (mm) cc_final: 0.8661 (tp) REVERT: A 1190 LEU cc_start: 0.8367 (mt) cc_final: 0.7818 (pt) outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.5041 time to fit residues: 83.2268 Evaluate side-chains 101 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 ASN ** A 824 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10537 Z= 0.305 Angle : 0.592 6.017 14348 Z= 0.316 Chirality : 0.038 0.193 1603 Planarity : 0.004 0.050 1808 Dihedral : 6.006 41.879 2021 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.10 % Allowed : 0.77 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 0.87 (0.25), residues: 1199 helix: 0.86 (0.18), residues: 737 sheet: -0.13 (1.83), residues: 10 loop : 0.34 (0.33), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 758 HIS 0.008 0.001 HIS A1089 PHE 0.024 0.002 PHE A 511 TYR 0.016 0.002 TYR A 498 ARG 0.004 0.000 ARG A1065 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.8946 (m-10) cc_final: 0.8470 (m-80) REVERT: A 183 ASN cc_start: 0.8374 (m-40) cc_final: 0.7401 (t0) REVERT: A 320 GLU cc_start: 0.8850 (pm20) cc_final: 0.8457 (pm20) REVERT: A 662 MET cc_start: 0.8513 (ttt) cc_final: 0.8117 (tmm) REVERT: A 826 TYR cc_start: 0.9050 (t80) cc_final: 0.8574 (t80) REVERT: A 961 MET cc_start: 0.8618 (mmm) cc_final: 0.8349 (mmm) REVERT: A 1017 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7961 (mp0) REVERT: A 1020 ILE cc_start: 0.8983 (mm) cc_final: 0.8664 (tp) REVERT: A 1172 PHE cc_start: 0.8871 (m-80) cc_final: 0.8670 (m-10) REVERT: A 1190 LEU cc_start: 0.8395 (mt) cc_final: 0.7791 (pt) outliers start: 1 outliers final: 1 residues processed: 116 average time/residue: 0.5115 time to fit residues: 84.3013 Evaluate side-chains 99 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 chunk 78 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 824 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10537 Z= 0.183 Angle : 0.536 5.822 14348 Z= 0.277 Chirality : 0.036 0.200 1603 Planarity : 0.004 0.048 1808 Dihedral : 5.665 38.925 2021 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.10 % Allowed : 0.38 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.25), residues: 1199 helix: 1.21 (0.19), residues: 736 sheet: -0.12 (1.90), residues: 10 loop : 0.59 (0.33), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 761 HIS 0.004 0.001 HIS A 824 PHE 0.028 0.001 PHE A 967 TYR 0.014 0.001 TYR A 773 ARG 0.002 0.000 ARG A 541 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.8936 (m-10) cc_final: 0.8459 (m-80) REVERT: A 183 ASN cc_start: 0.8357 (m-40) cc_final: 0.7380 (t0) REVERT: A 320 GLU cc_start: 0.8811 (pm20) cc_final: 0.8526 (pm20) REVERT: A 662 MET cc_start: 0.8484 (ttt) cc_final: 0.8110 (tmm) REVERT: A 961 MET cc_start: 0.8424 (mmm) cc_final: 0.8160 (mmm) REVERT: A 1017 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7939 (mp0) REVERT: A 1020 ILE cc_start: 0.8954 (mm) cc_final: 0.8637 (tp) REVERT: A 1190 LEU cc_start: 0.8415 (mt) cc_final: 0.7768 (pt) outliers start: 1 outliers final: 1 residues processed: 117 average time/residue: 0.4852 time to fit residues: 81.6453 Evaluate side-chains 99 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 97 optimal weight: 0.0980 chunk 70 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 824 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10537 Z= 0.194 Angle : 0.530 5.838 14348 Z= 0.274 Chirality : 0.036 0.198 1603 Planarity : 0.004 0.047 1808 Dihedral : 5.373 37.868 2021 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.25), residues: 1199 helix: 1.38 (0.19), residues: 738 sheet: -0.59 (1.62), residues: 10 loop : 0.53 (0.33), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 758 HIS 0.004 0.001 HIS A 491 PHE 0.023 0.001 PHE A 967 TYR 0.014 0.001 TYR A 372 ARG 0.004 0.000 ARG A 942 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASN cc_start: 0.8294 (m-40) cc_final: 0.7362 (t0) REVERT: A 320 GLU cc_start: 0.8862 (pm20) cc_final: 0.8592 (pm20) REVERT: A 662 MET cc_start: 0.8514 (ttt) cc_final: 0.8108 (tmm) REVERT: A 961 MET cc_start: 0.8427 (mmm) cc_final: 0.8131 (mmm) REVERT: A 1017 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7934 (mp0) REVERT: A 1020 ILE cc_start: 0.8952 (mm) cc_final: 0.8637 (tp) REVERT: A 1190 LEU cc_start: 0.8418 (mt) cc_final: 0.7757 (pt) outliers start: 1 outliers final: 1 residues processed: 112 average time/residue: 0.5257 time to fit residues: 82.5744 Evaluate side-chains 98 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 119 optimal weight: 0.5980 chunk 110 optimal weight: 0.0010 chunk 95 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 824 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10537 Z= 0.176 Angle : 0.518 5.832 14348 Z= 0.267 Chirality : 0.035 0.195 1603 Planarity : 0.004 0.048 1808 Dihedral : 5.154 37.006 2021 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.17 % Favored : 96.75 % Rotamer: Outliers : 0.10 % Allowed : 0.00 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.25), residues: 1199 helix: 1.47 (0.19), residues: 739 sheet: -0.28 (1.72), residues: 10 loop : 0.59 (0.33), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 761 HIS 0.004 0.001 HIS A 824 PHE 0.023 0.001 PHE A 967 TYR 0.014 0.001 TYR A 372 ARG 0.003 0.000 ARG A 380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASN cc_start: 0.8301 (m-40) cc_final: 0.7365 (t0) REVERT: A 320 GLU cc_start: 0.8828 (pm20) cc_final: 0.8578 (pm20) REVERT: A 662 MET cc_start: 0.8505 (ttt) cc_final: 0.8014 (tmm) REVERT: A 961 MET cc_start: 0.8429 (mmm) cc_final: 0.8128 (mmm) REVERT: A 1017 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7929 (mp0) REVERT: A 1020 ILE cc_start: 0.8948 (mm) cc_final: 0.8628 (tp) REVERT: A 1190 LEU cc_start: 0.8410 (mt) cc_final: 0.7738 (pt) outliers start: 1 outliers final: 1 residues processed: 112 average time/residue: 0.4961 time to fit residues: 79.8199 Evaluate side-chains 97 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.084118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.064559 restraints weight = 103786.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.068313 restraints weight = 49281.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.070889 restraints weight = 30556.097| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10537 Z= 0.169 Angle : 0.506 5.906 14348 Z= 0.261 Chirality : 0.035 0.193 1603 Planarity : 0.004 0.048 1808 Dihedral : 4.937 36.179 2021 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.00 % Favored : 96.91 % Rotamer: Outliers : 0.10 % Allowed : 0.10 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.25), residues: 1199 helix: 1.63 (0.19), residues: 741 sheet: -0.26 (1.74), residues: 10 loop : 0.57 (0.33), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 761 HIS 0.004 0.001 HIS A 361 PHE 0.021 0.001 PHE A 967 TYR 0.022 0.001 TYR A 498 ARG 0.003 0.000 ARG A 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3985.99 seconds wall clock time: 71 minutes 40.44 seconds (4300.44 seconds total)