Starting phenix.real_space_refine on Sat Aug 3 15:44:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9baz_44415/08_2024/9baz_44415.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9baz_44415/08_2024/9baz_44415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9baz_44415/08_2024/9baz_44415.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9baz_44415/08_2024/9baz_44415.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9baz_44415/08_2024/9baz_44415.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9baz_44415/08_2024/9baz_44415.cif" } resolution = 2.76 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= 0.015 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 40 5.16 5 C 5305 2.51 5 N 1477 2.21 5 O 1460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8283 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7271 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PCIS': 2, 'PTRANS': 63, 'TRANS': 899} Chain breaks: 6 Unresolved non-hydrogen bonds: 472 Unresolved non-hydrogen angles: 571 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 10, 'ASP:plan': 14, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 274 Chain: "B" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 506 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 59} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 479 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 59} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2806 SG CYS A 635 39.533 50.422 27.871 1.00170.88 S ATOM 2819 SG CYS A 637 39.129 49.591 23.881 1.00169.76 S ATOM 3230 SG CYS A 692 41.609 51.872 25.032 1.00176.61 S Time building chain proxies: 5.30, per 1000 atoms: 0.64 Number of scatterers: 8283 At special positions: 0 Unit cell: (82.017, 100.944, 140.901, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 40 16.00 O 1460 8.00 N 1477 7.00 C 5305 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: 3.04 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 637 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 635 " pdb="ZN ZN A1302 " - pdb=" ND1 HIS A 694 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 692 " Number of angles added : 3 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2022 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 13 sheets defined 31.8% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 208 through 214 removed outlier: 4.044A pdb=" N THR A 214 " --> pdb=" O GLN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.526A pdb=" N ALA A 268 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 310 Proline residue: A 289 - end of helix removed outlier: 3.843A pdb=" N TRP A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 334 through 343 removed outlier: 3.785A pdb=" N GLN A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 356 Processing helix chain 'A' and resid 356 through 367 Processing helix chain 'A' and resid 371 through 375 removed outlier: 3.635A pdb=" N GLY A 375 " --> pdb=" O ARG A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 382 removed outlier: 3.696A pdb=" N ARG A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 423 removed outlier: 4.514A pdb=" N HIS A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 687 through 691 removed outlier: 3.847A pdb=" N LEU A 690 " --> pdb=" O LYS A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 752 No H-bonds generated for 'chain 'A' and resid 750 through 752' Processing helix chain 'A' and resid 850 through 860 removed outlier: 3.580A pdb=" N GLY A 860 " --> pdb=" O LEU A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 882 Processing helix chain 'A' and resid 894 through 904 Processing helix chain 'A' and resid 938 through 959 removed outlier: 4.359A pdb=" N VAL A 948 " --> pdb=" O ASN A 944 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA A 949 " --> pdb=" O GLN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 972 No H-bonds generated for 'chain 'A' and resid 970 through 972' Processing helix chain 'A' and resid 977 through 980 Processing helix chain 'A' and resid 981 through 993 Processing helix chain 'A' and resid 1005 through 1008 Processing helix chain 'A' and resid 1068 through 1073 Processing helix chain 'A' and resid 1100 through 1110 removed outlier: 3.571A pdb=" N ILE A1110 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1124 Processing helix chain 'A' and resid 1125 through 1127 No H-bonds generated for 'chain 'A' and resid 1125 through 1127' Processing helix chain 'A' and resid 1131 through 1138 removed outlier: 3.603A pdb=" N PHE A1138 " --> pdb=" O ASP A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1197 Processing helix chain 'A' and resid 1208 through 1218 Processing helix chain 'A' and resid 1221 through 1237 Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 236 through 246 removed outlier: 3.897A pdb=" N MET B 240 " --> pdb=" O CYS B 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 228 through 236 removed outlier: 3.880A pdb=" N ILE C 232 " --> pdb=" O THR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 247 removed outlier: 3.656A pdb=" N MET C 240 " --> pdb=" O CYS C 236 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 248 through 249 removed outlier: 5.985A pdb=" N VAL A 132 " --> pdb=" O ARG C 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 148 removed outlier: 3.922A pdb=" N GLN B 226 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 206 removed outlier: 3.653A pdb=" N GLU A 205 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU A 190 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS A 228 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ASP A 192 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL A 226 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N PHE A 223 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY A 238 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 205 through 206 removed outlier: 3.653A pdb=" N GLU A 205 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP A 192 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASN A 194 " --> pdb=" O PRO A 279 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 400 through 402 Processing sheet with id=AA6, first strand: chain 'A' and resid 411 through 412 removed outlier: 5.650A pdb=" N THR A 411 " --> pdb=" O ARG A 431 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 559 removed outlier: 4.594A pdb=" N PHE A 582 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP A 606 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL A 588 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N SER A 604 " --> pdb=" O VAL A 588 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 607 " --> pdb=" O HIS A 634 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N HIS A 634 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N TRP A 609 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU A 629 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N TYR A 675 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU A 631 " --> pdb=" O TYR A 675 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 671 " --> pdb=" O ASP A 657 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 556 through 559 removed outlier: 4.594A pdb=" N PHE A 582 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP A 606 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL A 588 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N SER A 604 " --> pdb=" O VAL A 588 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 607 " --> pdb=" O HIS A 634 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N HIS A 634 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N TRP A 609 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU A 629 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N TYR A 675 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU A 631 " --> pdb=" O TYR A 675 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 776 through 779 removed outlier: 3.616A pdb=" N GLY A 778 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 11.821A pdb=" N ASP A 723 " --> pdb=" O ARG A 748 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N ARG A 748 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N TYR A 725 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU A 746 " --> pdb=" O TYR A 725 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL A 727 " --> pdb=" O ARG A 744 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG A 744 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 729 " --> pdb=" O ARG A 742 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASP A 767 " --> pdb=" O LYS A 745 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU A 747 " --> pdb=" O THR A 765 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR A 765 " --> pdb=" O LEU A 747 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU A 762 " --> pdb=" O ILE A 806 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N HIS A 808 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLU A 766 " --> pdb=" O GLN A 810 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE A 781 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE A 806 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 776 through 779 removed outlier: 3.616A pdb=" N GLY A 778 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 11.821A pdb=" N ASP A 723 " --> pdb=" O ARG A 748 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N ARG A 748 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N TYR A 725 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU A 746 " --> pdb=" O TYR A 725 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL A 727 " --> pdb=" O ARG A 744 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG A 744 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 729 " --> pdb=" O ARG A 742 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASP A 767 " --> pdb=" O LYS A 745 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU A 747 " --> pdb=" O THR A 765 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR A 765 " --> pdb=" O LEU A 747 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU A 762 " --> pdb=" O ILE A 806 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N HIS A 808 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLU A 766 " --> pdb=" O GLN A 810 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 862 through 866 removed outlier: 5.512A pdb=" N LEU A 840 " --> pdb=" O GLU A 863 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ARG A 865 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLY A 842 " --> pdb=" O ARG A 865 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ARG A 841 " --> pdb=" O PHE A 919 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ALA A 921 " --> pdb=" O ARG A 841 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N MET A 843 " --> pdb=" O ALA A 921 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 920 " --> pdb=" O VAL A 964 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N GLU A 966 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA A 922 " --> pdb=" O GLU A 966 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N VAL A 968 " --> pdb=" O ALA A 922 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 868 through 869 removed outlier: 3.534A pdb=" N ASP A 869 " --> pdb=" O PHE A 891 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 199 through 206 309 hydrogen bonds defined for protein. 843 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.81 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2729 1.34 - 1.46: 2075 1.46 - 1.58: 3656 1.58 - 1.70: 0 1.70 - 1.82: 59 Bond restraints: 8519 Sorted by residual: bond pdb=" CA SER A1221 " pdb=" CB SER A1221 " ideal model delta sigma weight residual 1.531 1.477 0.054 1.69e-02 3.50e+03 1.01e+01 bond pdb=" N VAL A1216 " pdb=" CA VAL A1216 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.21e-02 6.83e+03 8.16e+00 bond pdb=" N VAL A1220 " pdb=" CA VAL A1220 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.19e-02 7.06e+03 6.28e+00 bond pdb=" N SER A1219 " pdb=" CA SER A1219 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.14e-02 7.69e+03 6.09e+00 bond pdb=" N ASN A1218 " pdb=" CA ASN A1218 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.32e-02 5.74e+03 5.66e+00 ... (remaining 8514 not shown) Histogram of bond angle deviations from ideal: 97.53 - 104.92: 206 104.92 - 112.31: 4266 112.31 - 119.70: 2824 119.70 - 127.09: 4176 127.09 - 134.47: 152 Bond angle restraints: 11624 Sorted by residual: angle pdb=" N ARG A1222 " pdb=" CA ARG A1222 " pdb=" C ARG A1222 " ideal model delta sigma weight residual 113.01 106.42 6.59 1.20e+00 6.94e-01 3.02e+01 angle pdb=" C SER A1221 " pdb=" CA SER A1221 " pdb=" CB SER A1221 " ideal model delta sigma weight residual 109.80 115.93 -6.13 1.23e+00 6.61e-01 2.49e+01 angle pdb=" N SER A1221 " pdb=" CA SER A1221 " pdb=" C SER A1221 " ideal model delta sigma weight residual 110.64 103.48 7.16 1.48e+00 4.57e-01 2.34e+01 angle pdb=" CA THR B 225 " pdb=" CB THR B 225 " pdb=" OG1 THR B 225 " ideal model delta sigma weight residual 109.60 103.41 6.19 1.50e+00 4.44e-01 1.70e+01 angle pdb=" CB LYS A 215 " pdb=" CG LYS A 215 " pdb=" CD LYS A 215 " ideal model delta sigma weight residual 111.30 119.68 -8.38 2.30e+00 1.89e-01 1.33e+01 ... (remaining 11619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 4280 16.94 - 33.87: 493 33.87 - 50.81: 158 50.81 - 67.75: 28 67.75 - 84.69: 9 Dihedral angle restraints: 4968 sinusoidal: 1822 harmonic: 3146 Sorted by residual: dihedral pdb=" CA VAL A 862 " pdb=" C VAL A 862 " pdb=" N GLU A 863 " pdb=" CA GLU A 863 " ideal model delta harmonic sigma weight residual 180.00 162.79 17.21 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" N MET B 214 " pdb=" CA MET B 214 " pdb=" CB MET B 214 " pdb=" CG MET B 214 " ideal model delta sinusoidal sigma weight residual -180.00 -120.01 -59.99 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET A 206 " pdb=" CG MET A 206 " pdb=" SD MET A 206 " pdb=" CE MET A 206 " ideal model delta sinusoidal sigma weight residual -60.00 -118.79 58.79 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 4965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1128 0.068 - 0.135: 127 0.135 - 0.202: 5 0.202 - 0.270: 2 0.270 - 0.337: 1 Chirality restraints: 1263 Sorted by residual: chirality pdb=" CA VAL A1220 " pdb=" N VAL A1220 " pdb=" C VAL A1220 " pdb=" CB VAL A1220 " both_signs ideal model delta sigma weight residual False 2.44 2.78 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA ARG A1222 " pdb=" N ARG A1222 " pdb=" C ARG A1222 " pdb=" CB ARG A1222 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB VAL A1220 " pdb=" CA VAL A1220 " pdb=" CG1 VAL A1220 " pdb=" CG2 VAL A1220 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1260 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A1215 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.92e+00 pdb=" C LEU A1215 " -0.038 2.00e-02 2.50e+03 pdb=" O LEU A1215 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL A1216 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 616 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO A 617 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 617 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 617 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1222 " 0.182 9.50e-02 1.11e+02 8.14e-02 4.08e+00 pdb=" NE ARG A1222 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A1222 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A1222 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A1222 " 0.006 2.00e-02 2.50e+03 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 177 2.67 - 3.23: 7829 3.23 - 3.79: 13595 3.79 - 4.34: 17776 4.34 - 4.90: 29447 Nonbonded interactions: 68824 Sorted by model distance: nonbonded pdb=" OH TYR A 249 " pdb=" OE1 GLU A 363 " model vdw 2.117 3.040 nonbonded pdb=" OG SER A 722 " pdb=" O PRO A1061 " model vdw 2.153 3.040 nonbonded pdb=" OD2 ASP A 869 " pdb=" O3' SAH A1301 " model vdw 2.162 3.040 nonbonded pdb=" O ARG A 207 " pdb=" OH TYR A 283 " model vdw 2.228 3.040 nonbonded pdb=" O ASP A 872 " pdb=" ND1 HIS A 876 " model vdw 2.229 3.120 ... (remaining 68819 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 'B' and (resid 191 through 195 or (resid 196 through 197 and (name N or n \ ame CA or name C or name O or name CB )) or resid 198 through 200 or (resid 201 \ and (name N or name CA or name C or name O or name CB )) or resid 202 or (resid \ 203 through 204 and (name N or name CA or name C or name O or name CB )) or resi \ d 205 or (resid 206 and (name N or name CA or name C or name O or name CB )) or \ resid 207 through 211 or (resid 212 through 214 and (name N or name CA or name C \ or name O or name CB )) or resid 215 through 251)) selection = (chain 'C' and (resid 191 through 207 or (resid 208 through 209 and (name N or n \ ame CA or name C or name O or name CB )) or resid 210 through 233 or (resid 234 \ and (name N or name CA or name C or name O or name CB )) or resid 235 through 24 \ 8 or (resid 249 and (name N or name CA or name C or name O or name CB )) or resi \ d 250 through 251)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.320 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.470 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 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 : 0.004 0.054 8519 Z= 0.240 Angle : 0.633 9.473 11624 Z= 0.321 Chirality : 0.044 0.337 1263 Planarity : 0.005 0.081 1514 Dihedral : 16.560 84.686 2946 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.50 % Allowed : 33.33 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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 (0.26), residues: 1071 helix: 0.71 (0.31), residues: 302 sheet: -0.46 (0.39), residues: 182 loop : 0.14 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 361 HIS 0.003 0.001 HIS A1223 PHE 0.012 0.001 PHE A 805 TYR 0.009 0.001 TYR A 725 ARG 0.007 0.000 ARG A 744 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 133 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 215 LYS cc_start: 0.8648 (mmmt) cc_final: 0.8082 (tmtp) REVERT: A 954 PHE cc_start: 0.7672 (m-80) cc_final: 0.7206 (m-80) REVERT: B 244 TYR cc_start: 0.7698 (m-10) cc_final: 0.7377 (m-10) REVERT: C 198 HIS cc_start: 0.8170 (m170) cc_final: 0.7827 (m-70) REVERT: C 242 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8139 (mm-40) REVERT: C 249 ARG cc_start: 0.7581 (ttp-170) cc_final: 0.7362 (mmt-90) outliers start: 4 outliers final: 5 residues processed: 134 average time/residue: 0.7405 time to fit residues: 109.7824 Evaluate side-chains 123 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 118 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1092 ASP Chi-restraints excluded: chain C residue 230 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.0050 chunk 84 optimal weight: 0.0970 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN C 211 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8519 Z= 0.207 Angle : 0.560 9.406 11624 Z= 0.273 Chirality : 0.042 0.151 1263 Planarity : 0.004 0.052 1514 Dihedral : 4.482 42.556 1194 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.91 % Allowed : 26.67 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.24 (0.26), residues: 1071 helix: 0.89 (0.31), residues: 304 sheet: -0.52 (0.39), residues: 178 loop : 0.12 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 361 HIS 0.003 0.001 HIS A1007 PHE 0.012 0.001 PHE A 323 TYR 0.010 0.001 TYR A 730 ARG 0.005 0.000 ARG A 744 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 130 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7413 (mp10) REVERT: A 844 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7042 (m-30) REVERT: A 947 LEU cc_start: 0.8270 (mt) cc_final: 0.8057 (mp) REVERT: A 954 PHE cc_start: 0.7788 (m-80) cc_final: 0.7174 (m-80) REVERT: A 1085 ASP cc_start: 0.8483 (t70) cc_final: 0.8201 (t70) REVERT: B 244 TYR cc_start: 0.7734 (m-10) cc_final: 0.7317 (m-10) REVERT: C 198 HIS cc_start: 0.8121 (m170) cc_final: 0.7906 (m-70) REVERT: C 242 GLN cc_start: 0.8601 (mm-40) cc_final: 0.7997 (mm-40) REVERT: C 249 ARG cc_start: 0.7836 (ttp-170) cc_final: 0.7534 (mmt180) outliers start: 47 outliers final: 17 residues processed: 157 average time/residue: 0.6322 time to fit residues: 110.8005 Evaluate side-chains 136 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 1209 THR Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 248 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 0.3980 chunk 81 optimal weight: 0.1980 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.0770 chunk 98 optimal weight: 0.9980 chunk 106 optimal weight: 0.0770 chunk 87 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8519 Z= 0.165 Angle : 0.545 9.350 11624 Z= 0.261 Chirality : 0.041 0.156 1263 Planarity : 0.004 0.051 1514 Dihedral : 3.966 23.725 1187 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.65 % Allowed : 27.67 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1071 helix: 0.97 (0.31), residues: 305 sheet: -0.53 (0.39), residues: 173 loop : 0.20 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 361 HIS 0.002 0.000 HIS A1113 PHE 0.012 0.001 PHE A 605 TYR 0.009 0.001 TYR A 725 ARG 0.003 0.000 ARG A 783 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 132 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 284 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7446 (mp10) REVERT: A 761 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7802 (mm-30) REVERT: A 779 LYS cc_start: 0.7616 (tttp) cc_final: 0.7412 (tttt) REVERT: A 892 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7931 (tt) REVERT: A 947 LEU cc_start: 0.8322 (mt) cc_final: 0.8069 (mp) REVERT: A 954 PHE cc_start: 0.7712 (m-80) cc_final: 0.6955 (m-80) REVERT: B 240 MET cc_start: 0.8575 (tpt) cc_final: 0.8100 (tpt) REVERT: B 244 TYR cc_start: 0.7872 (m-10) cc_final: 0.7341 (m-10) REVERT: C 242 GLN cc_start: 0.8623 (mm-40) cc_final: 0.7995 (mm-40) REVERT: C 249 ARG cc_start: 0.7800 (ttp-170) cc_final: 0.7569 (mmt180) outliers start: 37 outliers final: 18 residues processed: 153 average time/residue: 0.6914 time to fit residues: 117.5912 Evaluate side-chains 139 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1092 ASP Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 248 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 ASN ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8519 Z= 0.353 Angle : 0.631 9.549 11624 Z= 0.309 Chirality : 0.044 0.150 1263 Planarity : 0.005 0.054 1514 Dihedral : 4.362 30.897 1187 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.66 % Allowed : 26.67 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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 (0.26), residues: 1071 helix: 0.71 (0.30), residues: 312 sheet: -0.63 (0.39), residues: 166 loop : 0.00 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 361 HIS 0.008 0.001 HIS C 198 PHE 0.016 0.002 PHE A 146 TYR 0.010 0.002 TYR A 286 ARG 0.003 0.000 ARG A1186 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 120 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7347 (mp10) REVERT: A 320 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7602 (mmtp) REVERT: A 761 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.7836 (mm-30) REVERT: A 947 LEU cc_start: 0.8246 (mt) cc_final: 0.7998 (mp) REVERT: A 954 PHE cc_start: 0.8001 (m-80) cc_final: 0.7414 (m-80) REVERT: A 1085 ASP cc_start: 0.8469 (t70) cc_final: 0.7993 (t70) REVERT: B 240 MET cc_start: 0.8611 (tpt) cc_final: 0.8105 (tpt) REVERT: B 244 TYR cc_start: 0.7939 (m-10) cc_final: 0.7379 (m-10) REVERT: C 198 HIS cc_start: 0.7499 (m-70) cc_final: 0.7236 (m90) REVERT: C 249 ARG cc_start: 0.7903 (ttp-170) cc_final: 0.7607 (mmt-90) outliers start: 45 outliers final: 23 residues processed: 145 average time/residue: 0.7433 time to fit residues: 119.0782 Evaluate side-chains 138 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1130 MET Chi-restraints excluded: chain A residue 1209 THR Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 248 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.0670 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 0.0670 chunk 72 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 26 optimal weight: 0.0270 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 ASN B 198 HIS C 211 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8519 Z= 0.167 Angle : 0.558 9.402 11624 Z= 0.268 Chirality : 0.041 0.145 1263 Planarity : 0.004 0.052 1514 Dihedral : 4.035 22.223 1185 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.53 % Allowed : 27.92 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.24 (0.26), residues: 1071 helix: 0.88 (0.31), residues: 311 sheet: -0.63 (0.39), residues: 171 loop : 0.14 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 361 HIS 0.002 0.000 HIS C 198 PHE 0.015 0.001 PHE A 146 TYR 0.010 0.001 TYR A1188 ARG 0.005 0.000 ARG A 744 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 126 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7397 (mp10) REVERT: A 761 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7760 (mm-30) REVERT: A 844 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.6998 (m-30) REVERT: A 947 LEU cc_start: 0.8273 (mt) cc_final: 0.8003 (mp) REVERT: A 954 PHE cc_start: 0.7790 (m-80) cc_final: 0.6913 (m-80) REVERT: A 980 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6424 (mp10) REVERT: A 1085 ASP cc_start: 0.8429 (t70) cc_final: 0.7904 (t70) REVERT: B 240 MET cc_start: 0.8552 (tpt) cc_final: 0.7974 (tpt) REVERT: B 244 TYR cc_start: 0.7771 (m-10) cc_final: 0.7297 (m-10) REVERT: C 198 HIS cc_start: 0.7522 (m-70) cc_final: 0.7198 (m90) REVERT: C 199 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8157 (mt) REVERT: C 249 ARG cc_start: 0.7893 (ttp-170) cc_final: 0.7609 (mmt180) outliers start: 36 outliers final: 18 residues processed: 150 average time/residue: 0.7530 time to fit residues: 124.3644 Evaluate side-chains 144 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 980 GLN Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1209 THR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 248 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 86 optimal weight: 0.1980 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 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 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8519 Z= 0.214 Angle : 0.572 9.470 11624 Z= 0.276 Chirality : 0.042 0.146 1263 Planarity : 0.004 0.052 1514 Dihedral : 4.066 22.812 1185 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.65 % Allowed : 28.55 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.23 (0.26), residues: 1071 helix: 0.88 (0.30), residues: 312 sheet: -0.58 (0.40), residues: 161 loop : 0.10 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 361 HIS 0.002 0.000 HIS A 344 PHE 0.017 0.001 PHE A 323 TYR 0.010 0.001 TYR A 725 ARG 0.005 0.000 ARG A 744 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 284 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7378 (mp10) REVERT: A 742 ARG cc_start: 0.7018 (tpp80) cc_final: 0.6262 (mmt-90) REVERT: A 761 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.7787 (mm-30) REVERT: A 768 LEU cc_start: 0.8770 (mp) cc_final: 0.8112 (tm) REVERT: A 947 LEU cc_start: 0.8283 (mt) cc_final: 0.7996 (mp) REVERT: A 954 PHE cc_start: 0.7901 (m-80) cc_final: 0.6984 (m-80) REVERT: A 1085 ASP cc_start: 0.8423 (t70) cc_final: 0.7882 (t70) REVERT: B 240 MET cc_start: 0.8573 (tpt) cc_final: 0.7966 (tpt) REVERT: B 244 TYR cc_start: 0.7858 (m-10) cc_final: 0.7382 (m-10) REVERT: C 198 HIS cc_start: 0.7629 (m-70) cc_final: 0.7310 (m90) REVERT: C 199 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8254 (mt) REVERT: C 249 ARG cc_start: 0.7939 (ttp-170) cc_final: 0.7656 (mmt180) outliers start: 37 outliers final: 21 residues processed: 151 average time/residue: 0.7387 time to fit residues: 123.1009 Evaluate side-chains 146 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1092 ASP Chi-restraints excluded: chain A residue 1209 THR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 248 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 59 optimal weight: 0.0670 chunk 76 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 0.0980 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 64 optimal weight: 0.3980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8519 Z= 0.185 Angle : 0.575 9.440 11624 Z= 0.274 Chirality : 0.041 0.143 1263 Planarity : 0.004 0.053 1514 Dihedral : 4.050 20.482 1185 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.40 % Allowed : 29.18 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.26), residues: 1071 helix: 0.92 (0.30), residues: 311 sheet: -0.59 (0.40), residues: 161 loop : 0.15 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 361 HIS 0.002 0.000 HIS A1007 PHE 0.011 0.001 PHE A 146 TYR 0.009 0.001 TYR A 725 ARG 0.007 0.000 ARG A 744 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 130 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8051 (tttt) REVERT: A 243 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7762 (tm-30) REVERT: A 284 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7376 (mp10) REVERT: A 742 ARG cc_start: 0.7039 (tpp80) cc_final: 0.6267 (mmt-90) REVERT: A 761 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.7815 (mm-30) REVERT: A 768 LEU cc_start: 0.8770 (mp) cc_final: 0.8056 (tm) REVERT: A 947 LEU cc_start: 0.8281 (mt) cc_final: 0.8012 (mp) REVERT: A 954 PHE cc_start: 0.7850 (m-80) cc_final: 0.6861 (m-80) REVERT: A 1085 ASP cc_start: 0.8401 (t70) cc_final: 0.7862 (t70) REVERT: B 240 MET cc_start: 0.8572 (tpt) cc_final: 0.7893 (tpt) REVERT: B 244 TYR cc_start: 0.7822 (m-10) cc_final: 0.7331 (m-10) REVERT: C 198 HIS cc_start: 0.7715 (m-70) cc_final: 0.7441 (m90) REVERT: C 199 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8343 (mt) REVERT: C 249 ARG cc_start: 0.7961 (ttp-170) cc_final: 0.7666 (mmt180) outliers start: 35 outliers final: 23 residues processed: 151 average time/residue: 0.7368 time to fit residues: 122.9617 Evaluate side-chains 149 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1092 ASP Chi-restraints excluded: chain A residue 1209 THR Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 248 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.0170 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8519 Z= 0.286 Angle : 0.615 9.521 11624 Z= 0.298 Chirality : 0.043 0.152 1263 Planarity : 0.004 0.053 1514 Dihedral : 4.290 28.864 1185 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.28 % Allowed : 29.18 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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 (0.26), residues: 1071 helix: 0.84 (0.30), residues: 312 sheet: -0.73 (0.39), residues: 166 loop : 0.02 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 361 HIS 0.004 0.001 HIS A 344 PHE 0.013 0.002 PHE A 290 TYR 0.009 0.001 TYR A 286 ARG 0.008 0.000 ARG A 744 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 125 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7577 (tm-30) REVERT: A 284 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7348 (mp10) REVERT: A 742 ARG cc_start: 0.7028 (tpp80) cc_final: 0.6213 (mmt-90) REVERT: A 761 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.7847 (mm-30) REVERT: A 768 LEU cc_start: 0.8803 (mp) cc_final: 0.8072 (tm) REVERT: A 947 LEU cc_start: 0.8272 (mt) cc_final: 0.7980 (mp) REVERT: A 1085 ASP cc_start: 0.8433 (t70) cc_final: 0.7906 (t70) REVERT: B 240 MET cc_start: 0.8633 (tpt) cc_final: 0.7986 (tpt) REVERT: B 244 TYR cc_start: 0.7727 (m-10) cc_final: 0.7210 (m-10) REVERT: C 198 HIS cc_start: 0.7832 (m-70) cc_final: 0.7500 (m90) REVERT: C 199 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8387 (mt) REVERT: C 249 ARG cc_start: 0.7995 (ttp-170) cc_final: 0.7715 (mpt180) outliers start: 34 outliers final: 22 residues processed: 144 average time/residue: 0.8019 time to fit residues: 127.6813 Evaluate side-chains 145 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1092 ASP Chi-restraints excluded: chain A residue 1209 THR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 248 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.0770 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 0.0970 chunk 87 optimal weight: 0.0970 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.0570 chunk 63 optimal weight: 0.9990 overall best weight: 0.2252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN C 211 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8519 Z= 0.168 Angle : 0.598 10.080 11624 Z= 0.284 Chirality : 0.041 0.148 1263 Planarity : 0.004 0.053 1514 Dihedral : 4.101 21.563 1185 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.27 % Allowed : 30.57 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.26), residues: 1071 helix: 0.91 (0.30), residues: 311 sheet: -0.65 (0.39), residues: 171 loop : 0.20 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 361 HIS 0.002 0.000 HIS A1113 PHE 0.018 0.001 PHE A 605 TYR 0.009 0.001 TYR A 725 ARG 0.008 0.000 ARG A 744 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7552 (tm-30) REVERT: A 284 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7381 (mp10) REVERT: A 742 ARG cc_start: 0.7081 (tpp80) cc_final: 0.6354 (mmt-90) REVERT: A 761 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.7818 (mm-30) REVERT: A 768 LEU cc_start: 0.8734 (mp) cc_final: 0.8002 (tm) REVERT: A 947 LEU cc_start: 0.8316 (mt) cc_final: 0.8057 (mp) REVERT: A 1085 ASP cc_start: 0.8387 (t70) cc_final: 0.7846 (t70) REVERT: B 201 GLN cc_start: 0.8499 (tm-30) cc_final: 0.7468 (tm-30) REVERT: B 203 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7590 (m-30) REVERT: B 220 LYS cc_start: 0.6907 (pttt) cc_final: 0.6462 (pmtt) REVERT: B 240 MET cc_start: 0.8672 (tpt) cc_final: 0.7992 (tpt) REVERT: B 244 TYR cc_start: 0.7540 (m-10) cc_final: 0.7056 (m-10) REVERT: C 198 HIS cc_start: 0.7791 (m-70) cc_final: 0.7521 (m90) REVERT: C 249 ARG cc_start: 0.7979 (ttp-170) cc_final: 0.7673 (mmt180) outliers start: 26 outliers final: 19 residues processed: 148 average time/residue: 0.7634 time to fit residues: 124.5638 Evaluate side-chains 146 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1209 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 0.2980 chunk 68 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8519 Z= 0.247 Angle : 0.629 10.215 11624 Z= 0.299 Chirality : 0.043 0.153 1263 Planarity : 0.004 0.053 1514 Dihedral : 4.210 26.721 1185 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.14 % Allowed : 31.57 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.24 (0.26), residues: 1071 helix: 0.88 (0.30), residues: 312 sheet: -0.59 (0.40), residues: 161 loop : 0.12 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 361 HIS 0.002 0.001 HIS A 876 PHE 0.016 0.002 PHE A 605 TYR 0.010 0.001 TYR A 725 ARG 0.009 0.000 ARG A 744 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7531 (tm-30) REVERT: A 284 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7352 (mp10) REVERT: A 742 ARG cc_start: 0.7080 (tpp80) cc_final: 0.6325 (mmt-90) REVERT: A 761 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.7789 (mm-30) REVERT: A 768 LEU cc_start: 0.8762 (mp) cc_final: 0.8038 (tm) REVERT: A 844 ASP cc_start: 0.7148 (m-30) cc_final: 0.6756 (m-30) REVERT: A 947 LEU cc_start: 0.8287 (mt) cc_final: 0.8004 (mp) REVERT: A 1085 ASP cc_start: 0.8418 (t70) cc_final: 0.7906 (t70) REVERT: B 240 MET cc_start: 0.8618 (tpt) cc_final: 0.7812 (tpt) REVERT: B 244 TYR cc_start: 0.7610 (m-10) cc_final: 0.7108 (m-10) REVERT: C 249 ARG cc_start: 0.8011 (ttp-170) cc_final: 0.7685 (mmt180) outliers start: 25 outliers final: 19 residues processed: 143 average time/residue: 0.7585 time to fit residues: 119.6239 Evaluate side-chains 140 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1209 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 26 optimal weight: 0.0270 chunk 79 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 0.2980 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 HIS C 211 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.138311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.118046 restraints weight = 16061.793| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.44 r_work: 0.3619 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8519 Z= 0.201 Angle : 0.613 10.238 11624 Z= 0.291 Chirality : 0.042 0.150 1263 Planarity : 0.004 0.052 1514 Dihedral : 4.189 24.652 1185 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.89 % Allowed : 32.08 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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 (0.26), residues: 1071 helix: 0.89 (0.30), residues: 311 sheet: -0.63 (0.40), residues: 161 loop : 0.17 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 361 HIS 0.003 0.000 HIS C 198 PHE 0.017 0.001 PHE A 323 TYR 0.010 0.001 TYR A1188 ARG 0.009 0.000 ARG A 744 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3010.35 seconds wall clock time: 53 minutes 17.34 seconds (3197.34 seconds total)