Starting phenix.real_space_refine on Sat Oct 11 12:19:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u75_41969/10_2025/8u75_41969.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u75_41969/10_2025/8u75_41969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u75_41969/10_2025/8u75_41969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u75_41969/10_2025/8u75_41969.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u75_41969/10_2025/8u75_41969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u75_41969/10_2025/8u75_41969.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 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 P 3 5.49 5 S 74 5.16 5 C 9579 2.51 5 N 2364 2.21 5 O 2636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14656 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 907, 7131 Classifications: {'peptide': 907} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 878} Chain breaks: 3 Chain: "B" Number of atoms: 7131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 907, 7131 Classifications: {'peptide': 907} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 878} Chain breaks: 3 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 154 Unusual residues: {'AJP': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 240 Unusual residues: {'AJP': 3, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 27 Time building chain proxies: 3.67, per 1000 atoms: 0.25 Number of scatterers: 14656 At special positions: 0 Unit cell: (107.44, 120.36, 129.2, 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) S 74 16.00 P 3 15.00 O 2636 8.00 N 2364 7.00 C 9579 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 560.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 11 sheets defined 74.5% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 77 through 95 Processing helix chain 'A' and resid 102 through 120 Processing helix chain 'A' and resid 120 through 132 removed outlier: 4.932A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 141 removed outlier: 3.869A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 153 Processing helix chain 'A' and resid 156 through 188 removed outlier: 4.750A pdb=" N SER A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLN A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 209 through 221 removed outlier: 4.540A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 254 removed outlier: 3.960A pdb=" N GLY A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 273 through 292 removed outlier: 4.068A pdb=" N HIS A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 320 Processing helix chain 'A' and resid 323 through 336 removed outlier: 4.419A pdb=" N VAL A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 376 through 379 removed outlier: 3.606A pdb=" N ALA A 379 " --> pdb=" O ALA A 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 379' Processing helix chain 'A' and resid 381 through 413 removed outlier: 3.530A pdb=" N TRP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 396 " --> pdb=" O TYR A 392 " (cutoff:3.500A) Proline residue: A 408 - end of helix removed outlier: 3.675A pdb=" N ILE A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 426 removed outlier: 3.550A pdb=" N ALA A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.851A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 482 removed outlier: 4.441A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 removed outlier: 3.950A pdb=" N SER A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 530 removed outlier: 3.926A pdb=" N ALA A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 601 Processing helix chain 'A' and resid 604 through 619 Processing helix chain 'A' and resid 628 through 636 removed outlier: 3.990A pdb=" N SER A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 652 removed outlier: 3.728A pdb=" N LEU A 644 " --> pdb=" O ILE A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 858 Proline residue: A 819 - end of helix removed outlier: 3.948A pdb=" N ILE A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 823 " --> pdb=" O PRO A 819 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 824 " --> pdb=" O LYS A 820 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 832 " --> pdb=" O LYS A 828 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 835 " --> pdb=" O ASN A 831 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP A 855 " --> pdb=" O GLY A 851 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ARG A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 889 Processing helix chain 'A' and resid 889 through 919 Processing helix chain 'A' and resid 923 through 943 removed outlier: 3.535A pdb=" N THR A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 958 Processing helix chain 'A' and resid 966 through 976 removed outlier: 3.724A pdb=" N ARG A 976 " --> pdb=" O PHE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1049 Processing helix chain 'A' and resid 1070 through 1080 Processing helix chain 'A' and resid 1085 through 1107 Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1113 through 1123 removed outlier: 3.761A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1158 Processing helix chain 'B' and resid 77 through 95 Processing helix chain 'B' and resid 102 through 120 Processing helix chain 'B' and resid 120 through 132 removed outlier: 4.943A pdb=" N ASP B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL B 130 " --> pdb=" O HIS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 removed outlier: 3.872A pdb=" N LEU B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 153 Processing helix chain 'B' and resid 155 through 188 removed outlier: 3.831A pdb=" N PHE B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N SER B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLN B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 209 through 221 removed outlier: 4.250A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 254 removed outlier: 3.907A pdb=" N GLY B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET B 251 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 273 through 292 removed outlier: 4.058A pdb=" N HIS B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 320 Processing helix chain 'B' and resid 323 through 336 removed outlier: 4.405A pdb=" N VAL B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 375 Processing helix chain 'B' and resid 376 through 380 removed outlier: 4.117A pdb=" N VAL B 380 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 413 removed outlier: 3.514A pdb=" N TRP B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR B 396 " --> pdb=" O TYR B 392 " (cutoff:3.500A) Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 418 through 428 removed outlier: 3.582A pdb=" N ALA B 422 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.850A pdb=" N LEU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 481 removed outlier: 4.437A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR B 472 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 514 removed outlier: 3.961A pdb=" N SER B 514 " --> pdb=" O ASN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 530 removed outlier: 3.929A pdb=" N ALA B 526 " --> pdb=" O ASP B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 601 Processing helix chain 'B' and resid 604 through 619 Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.055A pdb=" N LEU B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 652 removed outlier: 3.706A pdb=" N LEU B 644 " --> pdb=" O ILE B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 858 Proline residue: B 819 - end of helix removed outlier: 3.931A pdb=" N ILE B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 823 " --> pdb=" O PRO B 819 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL B 824 " --> pdb=" O LYS B 820 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN B 832 " --> pdb=" O LYS B 828 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU B 835 " --> pdb=" O ASN B 831 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS B 852 " --> pdb=" O GLU B 848 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE B 853 " --> pdb=" O GLU B 849 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP B 855 " --> pdb=" O GLY B 851 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG B 856 " --> pdb=" O LYS B 852 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET B 857 " --> pdb=" O ILE B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 889 removed outlier: 3.543A pdb=" N HIS B 889 " --> pdb=" O LEU B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 Processing helix chain 'B' and resid 923 through 943 removed outlier: 3.515A pdb=" N THR B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 958 Processing helix chain 'B' and resid 966 through 976 removed outlier: 3.750A pdb=" N ARG B 976 " --> pdb=" O PHE B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 1043 through 1049 Processing helix chain 'B' and resid 1070 through 1080 Processing helix chain 'B' and resid 1085 through 1107 Proline residue: B1101 - end of helix Processing helix chain 'B' and resid 1113 through 1123 Processing helix chain 'B' and resid 1155 through 1158 Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982 Processing sheet with id=AA2, first strand: chain 'A' and resid 978 through 982 removed outlier: 6.522A pdb=" N TYR A1066 " --> pdb=" O ILE A1001 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ILE A1001 " --> pdb=" O TYR A1066 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 987 through 989 removed outlier: 7.352A pdb=" N VAL A 987 " --> pdb=" O CYS A1059 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N CYS A1059 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 989 " --> pdb=" O VAL A1057 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1125 through 1127 removed outlier: 4.353A pdb=" N LEU A1186 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP A1144 " --> pdb=" O VAL A1189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1135 through 1137 Processing sheet with id=AA6, first strand: chain 'A' and resid 1151 through 1154 Processing sheet with id=AA7, first strand: chain 'B' and resid 978 through 982 removed outlier: 6.325A pdb=" N GLN B1064 " --> pdb=" O VAL B1002 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 987 through 989 removed outlier: 7.138A pdb=" N VAL B 987 " --> pdb=" O CYS B1059 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N CYS B1059 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL B 989 " --> pdb=" O VAL B1057 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1125 through 1127 removed outlier: 4.023A pdb=" N LEU B1186 " --> pdb=" O VAL B1127 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG B1185 " --> pdb=" O ILE B1148 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP B1144 " --> pdb=" O VAL B1189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1135 through 1137 Processing sheet with id=AB2, first strand: chain 'B' and resid 1151 through 1154 1046 hydrogen bonds defined for protein. 3075 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: 2.84 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2446 1.32 - 1.44: 3652 1.44 - 1.57: 8721 1.57 - 1.69: 6 1.69 - 1.81: 136 Bond restraints: 14961 Sorted by residual: bond pdb=" C35 AJP B1404 " pdb=" O34 AJP B1404 " ideal model delta sigma weight residual 1.380 1.412 -0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" C LYS B1051 " pdb=" N PRO B1052 " ideal model delta sigma weight residual 1.331 1.351 -0.019 1.21e-02 6.83e+03 2.58e+00 bond pdb=" C26 AJP B1404 " pdb=" O25 AJP B1404 " ideal model delta sigma weight residual 1.375 1.406 -0.031 2.00e-02 2.50e+03 2.45e+00 bond pdb=" C26 AJP B1402 " pdb=" O25 AJP B1402 " ideal model delta sigma weight residual 1.375 1.405 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" C26 AJP A1403 " pdb=" O25 AJP A1403 " ideal model delta sigma weight residual 1.375 1.405 -0.030 2.00e-02 2.50e+03 2.24e+00 ... (remaining 14956 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 19935 2.03 - 4.05: 323 4.05 - 6.08: 57 6.08 - 8.10: 19 8.10 - 10.13: 4 Bond angle restraints: 20338 Sorted by residual: angle pdb=" CA GLU A 233 " pdb=" CB GLU A 233 " pdb=" CG GLU A 233 " ideal model delta sigma weight residual 114.10 121.98 -7.88 2.00e+00 2.50e-01 1.55e+01 angle pdb=" CB GLU A 233 " pdb=" CG GLU A 233 " pdb=" CD GLU A 233 " ideal model delta sigma weight residual 112.60 119.08 -6.48 1.70e+00 3.46e-01 1.45e+01 angle pdb=" N VAL B 130 " pdb=" CA VAL B 130 " pdb=" C VAL B 130 " ideal model delta sigma weight residual 112.96 109.31 3.65 1.00e+00 1.00e+00 1.33e+01 angle pdb=" N VAL A 130 " pdb=" CA VAL A 130 " pdb=" C VAL A 130 " ideal model delta sigma weight residual 112.96 109.34 3.62 1.00e+00 1.00e+00 1.31e+01 angle pdb=" CA MET B1107 " pdb=" CB MET B1107 " pdb=" CG MET B1107 " ideal model delta sigma weight residual 114.10 121.09 -6.99 2.00e+00 2.50e-01 1.22e+01 ... (remaining 20333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.25: 8760 27.25 - 54.51: 606 54.51 - 81.76: 73 81.76 - 109.01: 26 109.01 - 136.26: 24 Dihedral angle restraints: 9489 sinusoidal: 4227 harmonic: 5262 Sorted by residual: dihedral pdb=" C29 POV A1401 " pdb="C210 POV A1401 " pdb="C211 POV A1401 " pdb="C212 POV A1401 " ideal model delta sinusoidal sigma weight residual 112.25 -111.49 -136.26 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" O31 AJP B1403 " pdb=" C30 AJP B1403 " pdb=" C32 AJP B1403 " pdb=" O33 AJP B1403 " ideal model delta sinusoidal sigma weight residual 177.28 -51.04 -131.68 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C29 AJP B1403 " pdb=" C30 AJP B1403 " pdb=" C32 AJP B1403 " pdb=" O33 AJP B1403 " ideal model delta sinusoidal sigma weight residual -60.96 69.57 -130.53 1 3.00e+01 1.11e-03 1.76e+01 ... (remaining 9486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1792 0.043 - 0.086: 533 0.086 - 0.129: 139 0.129 - 0.172: 15 0.172 - 0.215: 10 Chirality restraints: 2489 Sorted by residual: chirality pdb=" C10 AJP B1402 " pdb=" C08 AJP B1402 " pdb=" C11 AJP B1402 " pdb=" O82 AJP B1402 " both_signs ideal model delta sigma weight residual False 2.61 2.39 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C10 AJP B1404 " pdb=" C08 AJP B1404 " pdb=" C11 AJP B1404 " pdb=" O82 AJP B1404 " both_signs ideal model delta sigma weight residual False 2.61 2.39 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C10 AJP B1403 " pdb=" C08 AJP B1403 " pdb=" C11 AJP B1403 " pdb=" O82 AJP B1403 " both_signs ideal model delta sigma weight residual False 2.61 2.39 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2486 not shown) Planarity restraints: 2449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 641 " 0.052 5.00e-02 4.00e+02 7.84e-02 9.83e+00 pdb=" N PRO B 642 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 642 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 642 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 949 " 0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO A 950 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 950 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 950 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 268 " -0.010 2.00e-02 2.50e+03 1.55e-02 4.20e+00 pdb=" CG PHE A 268 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 268 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 268 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 268 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 268 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 268 " 0.001 2.00e-02 2.50e+03 ... (remaining 2446 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3685 2.80 - 3.33: 13899 3.33 - 3.85: 23828 3.85 - 4.38: 25804 4.38 - 4.90: 47304 Nonbonded interactions: 114520 Sorted by model distance: nonbonded pdb=" OE1 GLU A 233 " pdb=" ND2 ASN A 237 " model vdw 2.280 3.120 nonbonded pdb=" O GLN B 140 " pdb=" OH TYR B 312 " model vdw 2.303 3.040 nonbonded pdb=" O GLN A 140 " pdb=" OH TYR A 312 " model vdw 2.308 3.040 nonbonded pdb=" O LEU B 174 " pdb=" OG SER B 178 " model vdw 2.311 3.040 nonbonded pdb=" O42 AJP A1403 " pdb=" O64 AJP B1404 " model vdw 2.312 3.040 ... (remaining 114515 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 74 through 1401 or resid 1403)) selection = (chain 'B' and (resid 74 through 1401 or resid 1403)) } 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: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.910 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 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 0.045 14961 Z= 0.188 Angle : 0.674 10.128 20338 Z= 0.336 Chirality : 0.045 0.215 2489 Planarity : 0.005 0.078 2449 Dihedral : 19.444 136.263 6081 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 26.71 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.20), residues: 1798 helix: 1.48 (0.14), residues: 1242 sheet: -0.51 (0.43), residues: 114 loop : -1.06 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 856 TYR 0.016 0.001 TYR A 309 PHE 0.035 0.002 PHE A 268 TRP 0.015 0.001 TRP B 635 HIS 0.002 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00414 (14961) covalent geometry : angle 0.67380 (20338) hydrogen bonds : bond 0.11196 ( 1040) hydrogen bonds : angle 5.04859 ( 3075) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1087 time to fit residues: 28.8346 Evaluate side-chains 169 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS B 981 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.230784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.187410 restraints weight = 15206.462| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.13 r_work: 0.3624 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14961 Z= 0.128 Angle : 0.531 8.015 20338 Z= 0.266 Chirality : 0.038 0.150 2489 Planarity : 0.004 0.076 2449 Dihedral : 12.081 132.934 2739 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.97 % Allowed : 24.45 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.20), residues: 1798 helix: 2.09 (0.15), residues: 1256 sheet: -0.55 (0.43), residues: 114 loop : -1.11 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 976 TYR 0.016 0.001 TYR A 309 PHE 0.020 0.001 PHE A 268 TRP 0.014 0.001 TRP B 635 HIS 0.004 0.001 HIS A 889 Details of bonding type rmsd covalent geometry : bond 0.00287 (14961) covalent geometry : angle 0.53052 (20338) hydrogen bonds : bond 0.04645 ( 1040) hydrogen bonds : angle 4.06723 ( 3075) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 869 HIS cc_start: 0.4591 (OUTLIER) cc_final: 0.4163 (t70) REVERT: A 937 LYS cc_start: 0.7734 (mtpp) cc_final: 0.7481 (mmtm) REVERT: A 1092 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7786 (tpt-90) outliers start: 46 outliers final: 27 residues processed: 199 average time/residue: 0.0936 time to fit residues: 29.1988 Evaluate side-chains 192 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 869 HIS Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 412 ARG Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 981 HIS Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1126 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 158 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN A 981 HIS B 889 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.229384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.184220 restraints weight = 15677.895| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.45 r_work: 0.3543 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14961 Z= 0.136 Angle : 0.517 9.277 20338 Z= 0.262 Chirality : 0.038 0.158 2489 Planarity : 0.004 0.075 2449 Dihedral : 10.048 132.247 2739 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.13 % Allowed : 23.29 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.20), residues: 1798 helix: 2.21 (0.14), residues: 1256 sheet: -0.52 (0.44), residues: 110 loop : -1.04 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 976 TYR 0.017 0.001 TYR B1125 PHE 0.017 0.001 PHE B 201 TRP 0.012 0.001 TRP B 635 HIS 0.005 0.001 HIS B 981 Details of bonding type rmsd covalent geometry : bond 0.00317 (14961) covalent geometry : angle 0.51738 (20338) hydrogen bonds : bond 0.04610 ( 1040) hydrogen bonds : angle 3.99402 ( 3075) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 171 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 869 HIS cc_start: 0.4831 (OUTLIER) cc_final: 0.4329 (t70) REVERT: B 889 HIS cc_start: 0.7271 (OUTLIER) cc_final: 0.6492 (m90) REVERT: B 937 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7403 (mmtm) outliers start: 64 outliers final: 42 residues processed: 213 average time/residue: 0.0981 time to fit residues: 32.9867 Evaluate side-chains 210 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 165 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 869 HIS Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 412 ARG Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 889 HIS Chi-restraints excluded: chain B residue 937 LYS Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1186 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 85 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS A 981 HIS B 889 HIS B 914 HIS B 981 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.225843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.171708 restraints weight = 15261.042| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.51 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14961 Z= 0.197 Angle : 0.562 8.330 20338 Z= 0.287 Chirality : 0.040 0.147 2489 Planarity : 0.004 0.074 2449 Dihedral : 9.250 137.727 2739 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.29 % Allowed : 22.71 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.20), residues: 1798 helix: 2.09 (0.14), residues: 1254 sheet: -0.46 (0.45), residues: 110 loop : -1.08 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 499 TYR 0.016 0.002 TYR A 309 PHE 0.020 0.002 PHE B 201 TRP 0.009 0.001 TRP A 635 HIS 0.011 0.001 HIS B 889 Details of bonding type rmsd covalent geometry : bond 0.00490 (14961) covalent geometry : angle 0.56222 (20338) hydrogen bonds : bond 0.05205 ( 1040) hydrogen bonds : angle 4.09100 ( 3075) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 165 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 869 HIS cc_start: 0.4019 (OUTLIER) cc_final: 0.3621 (t70) REVERT: B 923 ASP cc_start: 0.5696 (OUTLIER) cc_final: 0.5340 (m-30) REVERT: B 937 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7462 (mmtm) outliers start: 82 outliers final: 57 residues processed: 225 average time/residue: 0.0969 time to fit residues: 34.3060 Evaluate side-chains 224 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 164 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 869 HIS Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 412 ARG Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain B residue 923 ASP Chi-restraints excluded: chain B residue 937 LYS Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1186 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 78 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 126 optimal weight: 0.0980 chunk 120 optimal weight: 0.5980 chunk 124 optimal weight: 0.0370 chunk 177 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS A 832 GLN A 981 HIS B 889 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.229980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.190946 restraints weight = 15327.008| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 1.95 r_work: 0.3518 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14961 Z= 0.105 Angle : 0.475 8.299 20338 Z= 0.245 Chirality : 0.037 0.140 2489 Planarity : 0.004 0.074 2449 Dihedral : 8.068 129.536 2739 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.90 % Allowed : 25.03 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.20), residues: 1798 helix: 2.39 (0.14), residues: 1256 sheet: -0.45 (0.44), residues: 110 loop : -0.98 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 499 TYR 0.013 0.001 TYR A 309 PHE 0.018 0.001 PHE B 268 TRP 0.015 0.001 TRP B 635 HIS 0.017 0.001 HIS B 914 Details of bonding type rmsd covalent geometry : bond 0.00210 (14961) covalent geometry : angle 0.47533 (20338) hydrogen bonds : bond 0.04096 ( 1040) hydrogen bonds : angle 3.87575 ( 3075) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.6921 (mp) REVERT: A 869 HIS cc_start: 0.5124 (OUTLIER) cc_final: 0.4567 (t70) REVERT: B 233 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7078 (tm-30) REVERT: B 923 ASP cc_start: 0.5933 (OUTLIER) cc_final: 0.5491 (m-30) REVERT: B 937 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7364 (mmtm) outliers start: 45 outliers final: 26 residues processed: 196 average time/residue: 0.0997 time to fit residues: 30.8856 Evaluate side-chains 191 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 869 HIS Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 923 ASP Chi-restraints excluded: chain B residue 937 LYS Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1186 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 142 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 137 optimal weight: 30.0000 chunk 41 optimal weight: 0.0030 chunk 178 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS A 831 ASN A 914 HIS A 981 HIS B 292 HIS B 981 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.228607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.182892 restraints weight = 15412.070| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 2.26 r_work: 0.3545 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14961 Z= 0.123 Angle : 0.498 8.244 20338 Z= 0.254 Chirality : 0.038 0.322 2489 Planarity : 0.004 0.073 2449 Dihedral : 7.582 128.120 2739 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.00 % Allowed : 24.06 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.20), residues: 1798 helix: 2.43 (0.14), residues: 1256 sheet: -0.42 (0.44), residues: 110 loop : -0.91 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 609 TYR 0.016 0.001 TYR A 309 PHE 0.016 0.001 PHE B 201 TRP 0.012 0.001 TRP A 635 HIS 0.003 0.001 HIS B 914 Details of bonding type rmsd covalent geometry : bond 0.00283 (14961) covalent geometry : angle 0.49769 (20338) hydrogen bonds : bond 0.04305 ( 1040) hydrogen bonds : angle 3.86743 ( 3075) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 167 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.6925 (mp) REVERT: A 869 HIS cc_start: 0.4774 (OUTLIER) cc_final: 0.4240 (t70) REVERT: B 233 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7409 (tm-30) REVERT: B 923 ASP cc_start: 0.6012 (OUTLIER) cc_final: 0.5525 (m-30) REVERT: B 937 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7494 (mmtm) outliers start: 62 outliers final: 39 residues processed: 211 average time/residue: 0.1016 time to fit residues: 33.5768 Evaluate side-chains 204 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 869 HIS Chi-restraints excluded: chain A residue 914 HIS Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 412 ARG Chi-restraints excluded: chain B residue 923 ASP Chi-restraints excluded: chain B residue 937 LYS Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1186 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 84 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 30 optimal weight: 0.2980 chunk 173 optimal weight: 5.9990 chunk 17 optimal weight: 0.2980 chunk 12 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS A 981 HIS B 292 HIS B 981 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.230641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.179971 restraints weight = 15234.607| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.35 r_work: 0.3440 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14961 Z= 0.107 Angle : 0.487 8.935 20338 Z= 0.248 Chirality : 0.037 0.234 2489 Planarity : 0.004 0.072 2449 Dihedral : 7.121 124.492 2739 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.13 % Allowed : 24.13 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.20), residues: 1798 helix: 2.50 (0.14), residues: 1256 sheet: -0.42 (0.44), residues: 110 loop : -0.87 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 976 TYR 0.014 0.001 TYR A 309 PHE 0.020 0.001 PHE B 268 TRP 0.014 0.001 TRP B 635 HIS 0.011 0.001 HIS A 914 Details of bonding type rmsd covalent geometry : bond 0.00231 (14961) covalent geometry : angle 0.48728 (20338) hydrogen bonds : bond 0.04021 ( 1040) hydrogen bonds : angle 3.80957 ( 3075) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 158 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 405 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6880 (mp) REVERT: A 869 HIS cc_start: 0.5241 (OUTLIER) cc_final: 0.4647 (t70) REVERT: A 1115 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7246 (pt0) REVERT: B 233 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: B 923 ASP cc_start: 0.5919 (OUTLIER) cc_final: 0.5345 (m-30) REVERT: B 937 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7345 (mmtm) outliers start: 64 outliers final: 44 residues processed: 201 average time/residue: 0.1015 time to fit residues: 32.1442 Evaluate side-chains 206 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 156 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 869 HIS Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 412 ARG Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 923 ASP Chi-restraints excluded: chain B residue 937 LYS Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1186 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 105 optimal weight: 0.9990 chunk 72 optimal weight: 0.1980 chunk 159 optimal weight: 0.0050 chunk 70 optimal weight: 0.3980 chunk 129 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 144 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.232552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.185331 restraints weight = 15352.032| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.26 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14961 Z= 0.099 Angle : 0.475 11.005 20338 Z= 0.240 Chirality : 0.037 0.198 2489 Planarity : 0.004 0.072 2449 Dihedral : 6.612 114.501 2739 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.03 % Allowed : 24.84 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.20), residues: 1798 helix: 2.62 (0.14), residues: 1256 sheet: -0.39 (0.44), residues: 110 loop : -0.82 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 940 TYR 0.014 0.001 TYR A 594 PHE 0.012 0.001 PHE B 201 TRP 0.016 0.001 TRP B 635 HIS 0.002 0.000 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00206 (14961) covalent geometry : angle 0.47539 (20338) hydrogen bonds : bond 0.03674 ( 1040) hydrogen bonds : angle 3.72467 ( 3075) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 165 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 405 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7014 (mp) REVERT: A 869 HIS cc_start: 0.3724 (OUTLIER) cc_final: 0.3276 (t70) REVERT: B 405 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.6966 (mp) outliers start: 47 outliers final: 36 residues processed: 194 average time/residue: 0.1053 time to fit residues: 31.5729 Evaluate side-chains 196 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 869 HIS Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1179 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 139 optimal weight: 4.9990 chunk 68 optimal weight: 0.0070 chunk 137 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 123 optimal weight: 0.1980 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.8404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN A 981 HIS B 270 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.227613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.176463 restraints weight = 15342.810| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.45 r_work: 0.3480 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14961 Z= 0.162 Angle : 0.547 10.254 20338 Z= 0.276 Chirality : 0.039 0.167 2489 Planarity : 0.004 0.072 2449 Dihedral : 7.343 129.996 2739 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.29 % Allowed : 25.16 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.20), residues: 1798 helix: 2.39 (0.14), residues: 1256 sheet: -0.30 (0.45), residues: 110 loop : -0.85 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 516 TYR 0.016 0.001 TYR A 309 PHE 0.023 0.002 PHE B 268 TRP 0.012 0.001 TRP A 595 HIS 0.003 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00392 (14961) covalent geometry : angle 0.54728 (20338) hydrogen bonds : bond 0.04732 ( 1040) hydrogen bonds : angle 3.90252 ( 3075) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 159 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 405 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.6975 (mp) REVERT: A 869 HIS cc_start: 0.4928 (OUTLIER) cc_final: 0.4365 (t70) REVERT: B 405 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6860 (mp) outliers start: 51 outliers final: 42 residues processed: 194 average time/residue: 0.1022 time to fit residues: 30.7424 Evaluate side-chains 203 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 869 HIS Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 981 HIS Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1179 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 28 optimal weight: 0.7980 chunk 177 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 160 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 162 optimal weight: 0.0670 chunk 147 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS B 831 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.230866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.182760 restraints weight = 15325.377| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 2.34 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14961 Z= 0.110 Angle : 0.501 10.933 20338 Z= 0.254 Chirality : 0.037 0.160 2489 Planarity : 0.004 0.073 2449 Dihedral : 6.926 123.983 2739 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.52 % Allowed : 25.81 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.20), residues: 1798 helix: 2.51 (0.14), residues: 1256 sheet: -0.30 (0.44), residues: 110 loop : -0.80 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 976 TYR 0.013 0.001 TYR A 309 PHE 0.014 0.001 PHE B 201 TRP 0.014 0.001 TRP A 635 HIS 0.002 0.000 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00241 (14961) covalent geometry : angle 0.50112 (20338) hydrogen bonds : bond 0.04043 ( 1040) hydrogen bonds : angle 3.79581 ( 3075) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7013 (mp) REVERT: A 869 HIS cc_start: 0.3694 (OUTLIER) cc_final: 0.3264 (t70) REVERT: B 405 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.6945 (mp) outliers start: 39 outliers final: 34 residues processed: 184 average time/residue: 0.1009 time to fit residues: 28.9838 Evaluate side-chains 196 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 869 HIS Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1179 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 17 optimal weight: 0.2980 chunk 80 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 167 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 108 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 8 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 126 optimal weight: 0.3980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN A 981 HIS B 908 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.232201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.191062 restraints weight = 15497.105| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 2.22 r_work: 0.3599 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14961 Z= 0.105 Angle : 0.489 10.988 20338 Z= 0.248 Chirality : 0.037 0.144 2489 Planarity : 0.004 0.073 2449 Dihedral : 6.615 115.810 2739 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.52 % Allowed : 25.87 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.20), residues: 1798 helix: 2.60 (0.14), residues: 1256 sheet: -0.25 (0.44), residues: 110 loop : -0.77 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 875 TYR 0.014 0.001 TYR A 309 PHE 0.014 0.001 PHE B 201 TRP 0.017 0.001 TRP A 635 HIS 0.003 0.000 HIS B 869 Details of bonding type rmsd covalent geometry : bond 0.00228 (14961) covalent geometry : angle 0.48927 (20338) hydrogen bonds : bond 0.03807 ( 1040) hydrogen bonds : angle 3.73601 ( 3075) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2989.98 seconds wall clock time: 52 minutes 11.02 seconds (3131.02 seconds total)