Starting phenix.real_space_refine on Sat Aug 23 21:39:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7d_41979/08_2025/8u7d_41979.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7d_41979/08_2025/8u7d_41979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u7d_41979/08_2025/8u7d_41979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7d_41979/08_2025/8u7d_41979.map" model { file = "/net/cci-nas-00/data/ceres_data/8u7d_41979/08_2025/8u7d_41979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7d_41979/08_2025/8u7d_41979.cif" } resolution = 3.5 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= 0.016 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 76 5.16 5 C 9757 2.51 5 N 2412 2.21 5 O 2676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14924 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 923, 7267 Classifications: {'peptide': 923} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 893} Chain breaks: 4 Chain: "B" Number of atoms: 7267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 923, 7267 Classifications: {'peptide': 923} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 893} Chain breaks: 4 Chain: "A" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 281 Unusual residues: {'AJP': 3, 'POV': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 27 Chain: "B" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'AJP': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 3.97, per 1000 atoms: 0.27 Number of scatterers: 14924 At special positions: 0 Unit cell: (112.2, 133.96, 125.12, 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 76 16.00 P 3 15.00 O 2676 8.00 N 2412 7.00 C 9757 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: 1.37 Conformation dependent library (CDL) restraints added in 685.9 milliseconds Enol-peptide restraints added in 1.4 microseconds 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3468 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 9 sheets defined 74.7% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 77 through 95 Processing helix chain 'A' and resid 102 through 120 removed outlier: 3.525A pdb=" N LEU A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 4.700A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 141 removed outlier: 3.861A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 154 removed outlier: 3.614A pdb=" N VAL A 145 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 removed outlier: 3.675A pdb=" N SER A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 189 removed outlier: 4.054A pdb=" N ILE A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 209 through 221 removed outlier: 4.291A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 254 removed outlier: 3.691A pdb=" N PHE A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 291 removed outlier: 4.292A pdb=" N GLY A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Proline residue: A 276 - end of helix Processing helix chain 'A' and resid 296 through 317 removed outlier: 3.816A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 322 Processing helix chain 'A' and resid 323 through 337 removed outlier: 3.940A pdb=" N VAL A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 381 through 414 removed outlier: 3.617A pdb=" N TRP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A 396 " --> pdb=" O TYR A 392 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.988A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 482 removed outlier: 4.403A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 513 Processing helix chain 'A' and resid 522 through 529 removed outlier: 3.958A pdb=" N ALA A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 600 Processing helix chain 'A' and resid 604 through 621 Processing helix chain 'A' and resid 627 through 632 Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 640 through 652 removed outlier: 3.670A pdb=" N LEU A 644 " --> pdb=" O ILE A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 771 Processing helix chain 'A' and resid 807 through 810 removed outlier: 3.717A pdb=" N MET A 810 " --> pdb=" O GLY A 807 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 807 through 810' Processing helix chain 'A' and resid 811 through 851 removed outlier: 4.100A pdb=" N LYS A 815 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 816 " --> pdb=" O ARG A 812 " (cutoff:3.500A) Proline residue: A 819 - end of helix removed outlier: 3.833A pdb=" N ILE A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LEU A 835 " --> pdb=" O ASN A 831 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 836 " --> pdb=" O GLN A 832 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY A 842 " --> pdb=" O ASP A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 858 Processing helix chain 'A' and resid 860 through 889 removed outlier: 3.588A pdb=" N LEU A 864 " --> pdb=" O ASN A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 removed outlier: 3.546A pdb=" N ALA A 893 " --> pdb=" O HIS A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 942 Processing helix chain 'A' and resid 952 through 959 Processing helix chain 'A' and resid 966 through 976 removed outlier: 3.695A pdb=" N ILE A 970 " --> pdb=" O ASP A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1050 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 1124 removed outlier: 3.552A pdb=" N GLY A1124 " --> pdb=" O HIS A1120 " (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 removed outlier: 3.536A pdb=" N LEU B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 4.705A pdb=" N ASP B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL B 130 " --> pdb=" O HIS B 126 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 removed outlier: 3.870A pdb=" N LEU B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 154 removed outlier: 3.552A pdb=" N VAL B 145 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 161 removed outlier: 3.521A pdb=" N ARG B 161 " --> pdb=" O HIS B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 189 removed outlier: 3.805A pdb=" N PHE B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 205 removed outlier: 3.836A pdb=" N PHE B 201 " --> pdb=" O GLU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 220 removed outlier: 4.410A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 254 removed outlier: 3.665A pdb=" N PHE B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 291 removed outlier: 4.285A pdb=" N GLY B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 296 through 317 removed outlier: 3.801A pdb=" N GLU B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 322 Processing helix chain 'B' and resid 323 through 337 removed outlier: 3.937A pdb=" N VAL B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 375 Processing helix chain 'B' and resid 381 through 414 removed outlier: 3.623A pdb=" N TRP B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 3.663A 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 Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.970A pdb=" N LEU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 482 removed outlier: 4.398A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR B 472 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 513 Processing helix chain 'B' and resid 522 through 529 removed outlier: 3.977A pdb=" N ALA B 526 " --> pdb=" O ASP B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 600 Processing helix chain 'B' and resid 604 through 621 Processing helix chain 'B' and resid 627 through 632 Processing helix chain 'B' and resid 633 through 635 No H-bonds generated for 'chain 'B' and resid 633 through 635' Processing helix chain 'B' and resid 640 through 652 removed outlier: 3.662A pdb=" N LEU B 644 " --> pdb=" O ILE B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 771 Processing helix chain 'B' and resid 807 through 810 removed outlier: 3.833A pdb=" N MET B 810 " --> pdb=" O GLY B 807 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 807 through 810' Processing helix chain 'B' and resid 811 through 817 removed outlier: 4.114A pdb=" N LYS B 815 " --> pdb=" O LEU B 811 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B 816 " --> pdb=" O ARG B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 856 removed outlier: 3.719A pdb=" N LEU B 821 " --> pdb=" O LEU B 817 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU B 835 " --> pdb=" O ASN B 831 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY B 836 " --> pdb=" O GLN B 832 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY B 842 " --> pdb=" O ASP B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 889 removed outlier: 3.520A pdb=" N LEU B 864 " --> pdb=" O ASN B 860 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 removed outlier: 3.557A pdb=" N ALA B 893 " --> pdb=" O HIS B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 942 Processing helix chain 'B' and resid 952 through 959 Processing helix chain 'B' and resid 966 through 976 removed outlier: 3.694A pdb=" N ILE B 970 " --> pdb=" O ASP B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 1043 through 1050 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 1124 removed outlier: 3.541A pdb=" N GLY B1124 " --> pdb=" O HIS B1120 " (cutoff:3.500A) Processing helix chain 'B' and resid 1155 through 1158 Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982 removed outlier: 6.730A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1032 through 1036 Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1127 removed outlier: 4.204A pdb=" N LEU A1186 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP A1144 " --> pdb=" O VAL A1189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1136 removed outlier: 3.623A pdb=" N LEU A1174 " --> pdb=" O PHE A1136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 978 through 982 Processing sheet with id=AA6, first strand: chain 'B' and resid 978 through 982 removed outlier: 6.662A pdb=" N TYR B1066 " --> pdb=" O ILE B1001 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE B1001 " --> pdb=" O TYR B1066 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1032 through 1036 Processing sheet with id=AA8, first strand: chain 'B' and resid 1125 through 1127 removed outlier: 4.178A pdb=" N LEU B1186 " --> pdb=" O VAL B1127 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE B1187 " --> pdb=" O LEU B1147 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU B1147 " --> pdb=" O PHE B1187 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL B1189 " --> pdb=" O VAL B1145 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL B1145 " --> pdb=" O VAL B1189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1135 through 1136 removed outlier: 3.642A pdb=" N LEU B1174 " --> pdb=" O PHE B1136 " (cutoff:3.500A) 1048 hydrogen bonds defined for protein. 3084 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: 2.77 Time building geometry restraints manager: 1.82 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: 2432 1.32 - 1.44: 3799 1.44 - 1.57: 8862 1.57 - 1.69: 6 1.69 - 1.81: 140 Bond restraints: 15239 Sorted by residual: bond pdb=" C ILE A 488 " pdb=" N PRO A 489 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.38e-02 5.25e+03 2.86e+00 bond pdb=" C26 AJP B1402 " pdb=" O25 AJP B1402 " ideal model delta sigma weight residual 1.375 1.406 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" C26 AJP A1404 " pdb=" O25 AJP A1404 " ideal model delta sigma weight residual 1.375 1.406 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" C35 AJP A1404 " pdb=" O34 AJP A1404 " ideal model delta sigma weight residual 1.380 1.409 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C26 AJP A1405 " pdb=" O25 AJP A1405 " ideal model delta sigma weight residual 1.375 1.404 -0.029 2.00e-02 2.50e+03 2.12e+00 ... (remaining 15234 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 20262 1.89 - 3.77: 368 3.77 - 5.66: 65 5.66 - 7.55: 12 7.55 - 9.44: 3 Bond angle restraints: 20710 Sorted by residual: angle pdb=" C37 AJP A1405 " pdb=" C36 AJP A1405 " pdb=" O54 AJP A1405 " ideal model delta sigma weight residual 105.10 114.47 -9.37 3.00e+00 1.11e-01 9.76e+00 angle pdb=" CA LEU B 174 " pdb=" CB LEU B 174 " pdb=" CG LEU B 174 " ideal model delta sigma weight residual 116.30 106.86 9.44 3.50e+00 8.16e-02 7.27e+00 angle pdb=" C HIS B1156 " pdb=" N THR B1157 " pdb=" CA THR B1157 " ideal model delta sigma weight residual 121.54 126.34 -4.80 1.91e+00 2.74e-01 6.31e+00 angle pdb=" C HIS A1156 " pdb=" N THR A1157 " pdb=" CA THR A1157 " ideal model delta sigma weight residual 121.54 126.32 -4.78 1.91e+00 2.74e-01 6.26e+00 angle pdb=" C35 AJP A1405 " pdb=" C36 AJP A1405 " pdb=" O54 AJP A1405 " ideal model delta sigma weight residual 112.23 104.88 7.35 3.00e+00 1.11e-01 6.00e+00 ... (remaining 20705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.78: 8787 23.78 - 47.56: 695 47.56 - 71.34: 117 71.34 - 95.12: 24 95.12 - 118.90: 20 Dihedral angle restraints: 9643 sinusoidal: 4291 harmonic: 5352 Sorted by residual: dihedral pdb=" C29 AJP B1402 " pdb=" C30 AJP B1402 " pdb=" C32 AJP B1402 " pdb=" O33 AJP B1402 " ideal model delta sinusoidal sigma weight residual -60.96 -179.86 118.90 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" O31 AJP B1402 " pdb=" C30 AJP B1402 " pdb=" C32 AJP B1402 " pdb=" O33 AJP B1402 " ideal model delta sinusoidal sigma weight residual 177.28 59.18 118.10 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C56 AJP B1402 " pdb=" C57 AJP B1402 " pdb=" C58 AJP B1402 " pdb=" C59 AJP B1402 " ideal model delta sinusoidal sigma weight residual 57.61 -59.20 116.81 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 9640 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2214 0.063 - 0.125: 283 0.125 - 0.188: 19 0.188 - 0.250: 8 0.250 - 0.313: 1 Chirality restraints: 2525 Sorted by residual: chirality pdb=" CG LEU B 174 " pdb=" CB LEU B 174 " pdb=" CD1 LEU B 174 " pdb=" CD2 LEU B 174 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C55 AJP A1405 " pdb=" C56 AJP A1405 " pdb=" O54 AJP A1405 " pdb=" O60 AJP A1405 " both_signs ideal model delta sigma weight residual False 2.13 2.37 -0.24 2.00e-01 2.50e+01 1.46e+00 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 1.18e+00 ... (remaining 2522 not shown) Planarity restraints: 2493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 641 " 0.049 5.00e-02 4.00e+02 7.44e-02 8.86e+00 pdb=" N PRO B 642 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 642 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 642 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 641 " 0.049 5.00e-02 4.00e+02 7.34e-02 8.62e+00 pdb=" N PRO A 642 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 642 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 642 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 195 " -0.018 2.00e-02 2.50e+03 1.69e-02 5.01e+00 pdb=" CG PHE B 195 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B 195 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 195 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 195 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 195 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 195 " 0.000 2.00e-02 2.50e+03 ... (remaining 2490 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4379 2.83 - 3.34: 14505 3.34 - 3.86: 23881 3.86 - 4.38: 25448 4.38 - 4.90: 45968 Nonbonded interactions: 114181 Sorted by model distance: nonbonded pdb=" O MET A 154 " pdb=" ND2 ASN A 335 " model vdw 2.308 3.120 nonbonded pdb=" NE2 GLN A 225 " pdb=" OE1 GLN A 613 " model vdw 2.317 3.120 nonbonded pdb=" O GLY A1150 " pdb=" OG SER A1163 " model vdw 2.322 3.040 nonbonded pdb=" N ASP A 520 " pdb=" OD1 ASP A 520 " model vdw 2.323 3.120 nonbonded pdb=" OH TYR B 191 " pdb=" OD1 ASP B 384 " model vdw 2.334 3.040 ... (remaining 114176 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) selection = (chain 'B' and resid 74 through 1401) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.740 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 0.040 15239 Z= 0.185 Angle : 0.633 9.436 20710 Z= 0.315 Chirality : 0.044 0.313 2525 Planarity : 0.005 0.074 2493 Dihedral : 17.899 118.903 6175 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 23.26 % Favored : 76.74 % 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: 0.76 (0.19), residues: 1826 helix: 1.04 (0.14), residues: 1320 sheet: -0.28 (0.48), residues: 116 loop : -0.84 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 431 TYR 0.019 0.001 TYR A 309 PHE 0.037 0.001 PHE B 195 TRP 0.018 0.001 TRP A 643 HIS 0.005 0.001 HIS A 928 Details of bonding type rmsd covalent geometry : bond 0.00408 (15239) covalent geometry : angle 0.63298 (20710) hydrogen bonds : bond 0.12340 ( 1042) hydrogen bonds : angle 5.42029 ( 3084) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.7295 (ttt) cc_final: 0.6960 (ttp) REVERT: A 199 MET cc_start: 0.8473 (mmm) cc_final: 0.8081 (tpp) REVERT: A 959 ASN cc_start: 0.8412 (t0) cc_final: 0.8134 (t0) REVERT: A 1173 LYS cc_start: 0.3430 (pttm) cc_final: 0.3146 (mttp) REVERT: A 1185 ARG cc_start: 0.7141 (mtm-85) cc_final: 0.6393 (ttp80) REVERT: B 1098 ILE cc_start: 0.8895 (tp) cc_final: 0.8569 (tp) REVERT: B 1173 LYS cc_start: 0.5565 (mptt) cc_final: 0.4990 (mptt) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.1258 time to fit residues: 48.5484 Evaluate side-chains 207 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 614 HIS A 981 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.197243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.142923 restraints weight = 18433.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.133962 restraints weight = 22946.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.131585 restraints weight = 17063.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.132589 restraints weight = 13938.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.132336 restraints weight = 12691.463| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15239 Z= 0.123 Angle : 0.560 9.334 20710 Z= 0.274 Chirality : 0.038 0.251 2525 Planarity : 0.004 0.067 2493 Dihedral : 9.347 79.997 2767 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.04 % Allowed : 23.83 % Favored : 73.13 % 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: 1.67 (0.20), residues: 1826 helix: 1.86 (0.14), residues: 1312 sheet: -0.31 (0.47), residues: 120 loop : -0.98 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1089 TYR 0.018 0.001 TYR B 309 PHE 0.019 0.001 PHE B1032 TRP 0.023 0.001 TRP B 643 HIS 0.009 0.001 HIS A 928 Details of bonding type rmsd covalent geometry : bond 0.00263 (15239) covalent geometry : angle 0.56045 (20710) hydrogen bonds : bond 0.04575 ( 1042) hydrogen bonds : angle 3.97011 ( 3084) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 225 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 611 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8746 (mm) REVERT: A 817 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8630 (mp) REVERT: A 959 ASN cc_start: 0.8615 (t0) cc_final: 0.8263 (t0) REVERT: A 1173 LYS cc_start: 0.3586 (pttm) cc_final: 0.3352 (mttp) REVERT: B 172 PHE cc_start: 0.7421 (OUTLIER) cc_final: 0.7080 (m-80) REVERT: B 611 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8681 (mm) REVERT: B 1098 ILE cc_start: 0.8632 (tp) cc_final: 0.8355 (tp) REVERT: B 1173 LYS cc_start: 0.5796 (mptt) cc_final: 0.5134 (mptt) outliers start: 48 outliers final: 23 residues processed: 255 average time/residue: 0.1066 time to fit residues: 42.4128 Evaluate side-chains 237 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 210 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 643 TRP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 889 HIS Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1037 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 181 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.196289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.140776 restraints weight = 18559.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.132493 restraints weight = 24114.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.129766 restraints weight = 16028.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.129711 restraints weight = 13049.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.130026 restraints weight = 10905.324| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15239 Z= 0.127 Angle : 0.539 8.786 20710 Z= 0.267 Chirality : 0.038 0.261 2525 Planarity : 0.004 0.066 2493 Dihedral : 7.508 67.785 2767 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.93 % Allowed : 22.88 % Favored : 73.19 % 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: 1.93 (0.20), residues: 1826 helix: 2.09 (0.14), residues: 1310 sheet: -0.26 (0.47), residues: 120 loop : -0.99 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 420 TYR 0.019 0.001 TYR A 309 PHE 0.025 0.001 PHE B 972 TRP 0.026 0.001 TRP A 962 HIS 0.009 0.001 HIS B 928 Details of bonding type rmsd covalent geometry : bond 0.00289 (15239) covalent geometry : angle 0.53910 (20710) hydrogen bonds : bond 0.04390 ( 1042) hydrogen bonds : angle 3.73948 ( 3084) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 225 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8505 (mmm) cc_final: 0.8199 (tpp) REVERT: A 531 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7669 (tm-30) REVERT: A 611 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8716 (mm) REVERT: A 817 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8691 (tp) REVERT: A 959 ASN cc_start: 0.8672 (t0) cc_final: 0.8294 (t0) REVERT: A 1044 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7608 (mt-10) REVERT: A 1173 LYS cc_start: 0.3591 (pttm) cc_final: 0.3378 (mttp) REVERT: B 172 PHE cc_start: 0.7427 (OUTLIER) cc_final: 0.7100 (m-80) REVERT: B 199 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7498 (mpp) REVERT: B 611 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8694 (mm) REVERT: B 1033 GLU cc_start: 0.8581 (pm20) cc_final: 0.8333 (pm20) REVERT: B 1072 ASP cc_start: 0.7618 (m-30) cc_final: 0.7384 (m-30) REVERT: B 1173 LYS cc_start: 0.5733 (mptt) cc_final: 0.4985 (mptt) outliers start: 62 outliers final: 41 residues processed: 263 average time/residue: 0.0997 time to fit residues: 41.5694 Evaluate side-chains 254 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 207 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 643 TRP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 889 HIS Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1045 MET Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1174 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 88 optimal weight: 6.9990 chunk 166 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 152 optimal weight: 0.0070 chunk 20 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 133 optimal weight: 0.0170 chunk 170 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1040 ASN B 981 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.198256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.143411 restraints weight = 18656.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.133747 restraints weight = 22418.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.131569 restraints weight = 14870.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.132720 restraints weight = 11832.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.133120 restraints weight = 9369.610| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15239 Z= 0.103 Angle : 0.505 8.978 20710 Z= 0.251 Chirality : 0.037 0.218 2525 Planarity : 0.004 0.064 2493 Dihedral : 7.000 67.534 2767 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.68 % Allowed : 24.33 % Favored : 71.99 % 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: 2.18 (0.20), residues: 1826 helix: 2.26 (0.14), residues: 1310 sheet: 0.11 (0.53), residues: 100 loop : -0.92 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 420 TYR 0.015 0.001 TYR B 309 PHE 0.022 0.001 PHE B1032 TRP 0.028 0.001 TRP B 962 HIS 0.008 0.001 HIS A 928 Details of bonding type rmsd covalent geometry : bond 0.00214 (15239) covalent geometry : angle 0.50493 (20710) hydrogen bonds : bond 0.03901 ( 1042) hydrogen bonds : angle 3.57495 ( 3084) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 217 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8516 (mmm) cc_final: 0.8101 (tpp) REVERT: A 531 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7722 (tm-30) REVERT: B 154 MET cc_start: 0.8168 (ppp) cc_final: 0.7947 (ppp) REVERT: B 172 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.7071 (m-80) REVERT: B 611 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8711 (mm) REVERT: B 857 MET cc_start: 0.6543 (mmp) cc_final: 0.5712 (tmm) REVERT: B 1033 GLU cc_start: 0.8538 (pm20) cc_final: 0.8321 (pm20) REVERT: B 1072 ASP cc_start: 0.7624 (m-30) cc_final: 0.7349 (m-30) REVERT: B 1173 LYS cc_start: 0.5723 (mptt) cc_final: 0.4978 (mptt) outliers start: 58 outliers final: 32 residues processed: 253 average time/residue: 0.1062 time to fit residues: 42.5153 Evaluate side-chains 241 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 643 TRP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 889 HIS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1045 MET Chi-restraints excluded: chain B residue 1174 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 34 optimal weight: 9.9990 chunk 162 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 137 optimal weight: 0.0470 chunk 174 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 86 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 181 optimal weight: 20.0000 chunk 28 optimal weight: 0.6980 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1040 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.198036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.138308 restraints weight = 18581.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.136282 restraints weight = 23917.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.138183 restraints weight = 17578.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.138720 restraints weight = 11963.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.139105 restraints weight = 11194.954| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15239 Z= 0.105 Angle : 0.517 9.845 20710 Z= 0.253 Chirality : 0.037 0.219 2525 Planarity : 0.004 0.061 2493 Dihedral : 6.859 67.589 2767 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.99 % Allowed : 24.40 % 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: 2.27 (0.20), residues: 1826 helix: 2.32 (0.14), residues: 1310 sheet: -0.08 (0.50), residues: 112 loop : -0.80 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 491 TYR 0.021 0.001 TYR B1125 PHE 0.026 0.001 PHE B1032 TRP 0.026 0.001 TRP A 643 HIS 0.009 0.001 HIS A 928 Details of bonding type rmsd covalent geometry : bond 0.00226 (15239) covalent geometry : angle 0.51734 (20710) hydrogen bonds : bond 0.03840 ( 1042) hydrogen bonds : angle 3.50166 ( 3084) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 218 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8093 (tt) REVERT: A 477 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8604 (tt) REVERT: A 483 MET cc_start: 0.8311 (mmp) cc_final: 0.7942 (mmt) REVERT: A 531 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7702 (tm-30) REVERT: A 611 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8699 (mm) REVERT: A 1044 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7469 (mt-10) REVERT: A 1173 LYS cc_start: 0.5052 (mtmt) cc_final: 0.4747 (mptt) REVERT: B 154 MET cc_start: 0.8111 (ppp) cc_final: 0.7875 (ppp) REVERT: B 172 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.7030 (m-80) REVERT: B 611 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8683 (mm) REVERT: B 857 MET cc_start: 0.6320 (mmp) cc_final: 0.5822 (tmm) REVERT: B 872 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7890 (tm-30) REVERT: B 1173 LYS cc_start: 0.5597 (mptt) cc_final: 0.5047 (mptt) outliers start: 63 outliers final: 41 residues processed: 256 average time/residue: 0.0939 time to fit residues: 38.1598 Evaluate side-chains 259 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 212 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 643 TRP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 889 HIS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1174 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 74 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1040 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.194787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.135908 restraints weight = 18433.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.134001 restraints weight = 26025.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.135579 restraints weight = 19633.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.135736 restraints weight = 13189.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.136818 restraints weight = 12279.690| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15239 Z= 0.156 Angle : 0.564 9.164 20710 Z= 0.276 Chirality : 0.038 0.253 2525 Planarity : 0.004 0.061 2493 Dihedral : 7.115 67.589 2767 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.69 % Allowed : 23.57 % 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: 2.10 (0.20), residues: 1826 helix: 2.23 (0.14), residues: 1310 sheet: -0.37 (0.46), residues: 120 loop : -0.95 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 976 TYR 0.021 0.001 TYR A 309 PHE 0.030 0.002 PHE B1032 TRP 0.021 0.001 TRP A 643 HIS 0.009 0.001 HIS B 928 Details of bonding type rmsd covalent geometry : bond 0.00377 (15239) covalent geometry : angle 0.56362 (20710) hydrogen bonds : bond 0.04444 ( 1042) hydrogen bonds : angle 3.57286 ( 3084) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 221 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8489 (mmm) cc_final: 0.8226 (tpp) REVERT: A 477 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8618 (tt) REVERT: A 483 MET cc_start: 0.8307 (mmp) cc_final: 0.7923 (mmt) REVERT: A 531 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7667 (tm-30) REVERT: A 611 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8709 (mm) REVERT: A 1044 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7484 (mt-10) REVERT: A 1067 PHE cc_start: 0.8313 (t80) cc_final: 0.7956 (t80) REVERT: A 1173 LYS cc_start: 0.5037 (mtmt) cc_final: 0.4739 (mptt) REVERT: B 172 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.7041 (m-80) REVERT: B 483 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7892 (mmt) REVERT: B 611 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8678 (mm) REVERT: B 857 MET cc_start: 0.6320 (mmp) cc_final: 0.5958 (tmm) REVERT: B 1173 LYS cc_start: 0.5440 (mptt) cc_final: 0.4914 (mptt) outliers start: 74 outliers final: 56 residues processed: 263 average time/residue: 0.0902 time to fit residues: 37.3345 Evaluate side-chains 275 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 213 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 889 HIS Chi-restraints excluded: chain B residue 957 LEU Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1045 MET Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1174 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 65 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 chunk 127 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 103 optimal weight: 0.0870 chunk 50 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.197909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.142662 restraints weight = 18405.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.134256 restraints weight = 24099.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.133024 restraints weight = 14557.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.131964 restraints weight = 11550.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.132614 restraints weight = 9866.279| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15239 Z= 0.103 Angle : 0.523 8.651 20710 Z= 0.254 Chirality : 0.037 0.245 2525 Planarity : 0.004 0.060 2493 Dihedral : 6.774 67.669 2767 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.99 % Allowed : 24.97 % Favored : 71.04 % 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: 2.35 (0.20), residues: 1826 helix: 2.38 (0.14), residues: 1312 sheet: 0.23 (0.52), residues: 100 loop : -0.88 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 491 TYR 0.018 0.001 TYR B1125 PHE 0.026 0.001 PHE B1032 TRP 0.024 0.001 TRP B1112 HIS 0.010 0.001 HIS B 928 Details of bonding type rmsd covalent geometry : bond 0.00216 (15239) covalent geometry : angle 0.52320 (20710) hydrogen bonds : bond 0.03810 ( 1042) hydrogen bonds : angle 3.44718 ( 3084) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 222 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8454 (mmm) cc_final: 0.8118 (tpp) REVERT: A 477 LEU cc_start: 0.8821 (tp) cc_final: 0.8558 (tt) REVERT: A 483 MET cc_start: 0.8341 (mmp) cc_final: 0.8051 (mmt) REVERT: A 531 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7834 (tm-30) REVERT: A 611 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8734 (mm) REVERT: A 1044 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7499 (mt-10) REVERT: A 1067 PHE cc_start: 0.8375 (t80) cc_final: 0.7898 (t80) REVERT: A 1173 LYS cc_start: 0.5088 (mtmt) cc_final: 0.4695 (mptt) REVERT: B 172 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.7097 (m-80) REVERT: B 483 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8058 (mmt) REVERT: B 611 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8710 (mm) REVERT: B 857 MET cc_start: 0.6697 (mmp) cc_final: 0.6027 (tmm) REVERT: B 872 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8117 (tm-30) REVERT: B 1173 LYS cc_start: 0.5565 (mptt) cc_final: 0.4917 (mptt) outliers start: 63 outliers final: 45 residues processed: 263 average time/residue: 0.0958 time to fit residues: 40.3977 Evaluate side-chains 261 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 211 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 643 TRP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 889 HIS Chi-restraints excluded: chain B residue 957 LEU Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1045 MET Chi-restraints excluded: chain B residue 1174 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 66 optimal weight: 0.9990 chunk 171 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 137 optimal weight: 0.0370 chunk 156 optimal weight: 1.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1040 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.196988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.139940 restraints weight = 18506.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.132670 restraints weight = 24350.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.130282 restraints weight = 15427.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130662 restraints weight = 11884.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.131239 restraints weight = 10247.015| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15239 Z= 0.118 Angle : 0.558 9.080 20710 Z= 0.268 Chirality : 0.038 0.238 2525 Planarity : 0.004 0.060 2493 Dihedral : 6.809 67.819 2767 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.12 % Allowed : 25.03 % Favored : 70.85 % 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: 1826 helix: 2.38 (0.14), residues: 1312 sheet: 0.51 (0.52), residues: 96 loop : -0.86 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 609 TYR 0.018 0.001 TYR A 309 PHE 0.032 0.001 PHE B1032 TRP 0.027 0.001 TRP A 643 HIS 0.011 0.001 HIS B 928 Details of bonding type rmsd covalent geometry : bond 0.00267 (15239) covalent geometry : angle 0.55842 (20710) hydrogen bonds : bond 0.03949 ( 1042) hydrogen bonds : angle 3.43490 ( 3084) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 215 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8487 (mmm) cc_final: 0.8119 (tpp) REVERT: A 477 LEU cc_start: 0.8819 (tp) cc_final: 0.8549 (tt) REVERT: A 531 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7858 (tm-30) REVERT: A 611 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8724 (mm) REVERT: A 1044 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7551 (mt-10) REVERT: A 1067 PHE cc_start: 0.8363 (t80) cc_final: 0.7904 (t80) REVERT: A 1173 LYS cc_start: 0.5082 (mtmt) cc_final: 0.4799 (mttp) REVERT: B 172 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.7111 (m-80) REVERT: B 483 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7973 (mmt) REVERT: B 611 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8687 (mm) REVERT: B 1173 LYS cc_start: 0.5537 (mptt) cc_final: 0.4925 (mptt) outliers start: 65 outliers final: 52 residues processed: 255 average time/residue: 0.0896 time to fit residues: 36.5413 Evaluate side-chains 267 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 210 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 156 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 643 TRP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 889 HIS Chi-restraints excluded: chain B residue 957 LEU Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1174 LEU Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 91 optimal weight: 0.5980 chunk 118 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 148 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.196999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.140102 restraints weight = 18483.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.133847 restraints weight = 23555.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.131520 restraints weight = 14865.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.131901 restraints weight = 12634.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.132330 restraints weight = 10966.360| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15239 Z= 0.120 Angle : 0.563 10.000 20710 Z= 0.270 Chirality : 0.038 0.241 2525 Planarity : 0.004 0.060 2493 Dihedral : 6.815 67.797 2767 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.12 % Allowed : 24.84 % Favored : 71.04 % 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: 2.40 (0.20), residues: 1826 helix: 2.38 (0.14), residues: 1312 sheet: 0.64 (0.53), residues: 96 loop : -0.80 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 609 TYR 0.020 0.001 TYR A1125 PHE 0.032 0.001 PHE B1032 TRP 0.023 0.001 TRP A 643 HIS 0.011 0.001 HIS B 928 Details of bonding type rmsd covalent geometry : bond 0.00273 (15239) covalent geometry : angle 0.56333 (20710) hydrogen bonds : bond 0.03959 ( 1042) hydrogen bonds : angle 3.43565 ( 3084) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 215 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8519 (mmm) cc_final: 0.8100 (tpp) REVERT: A 444 ASN cc_start: 0.7553 (OUTLIER) cc_final: 0.7058 (m110) REVERT: A 477 LEU cc_start: 0.8834 (tp) cc_final: 0.8576 (tt) REVERT: A 531 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7893 (tm-30) REVERT: A 611 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8714 (mm) REVERT: A 1044 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7532 (mt-10) REVERT: A 1067 PHE cc_start: 0.8359 (t80) cc_final: 0.7903 (t80) REVERT: A 1173 LYS cc_start: 0.5035 (mtmt) cc_final: 0.4731 (mttp) REVERT: B 172 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.7086 (m-80) REVERT: B 477 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8517 (tt) REVERT: B 483 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7994 (mmt) REVERT: B 611 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8700 (mm) REVERT: B 857 MET cc_start: 0.6425 (mmp) cc_final: 0.5975 (tmm) REVERT: B 1173 LYS cc_start: 0.5593 (mptt) cc_final: 0.4719 (mptt) outliers start: 65 outliers final: 55 residues processed: 257 average time/residue: 0.1081 time to fit residues: 44.4735 Evaluate side-chains 271 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 209 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 156 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 643 TRP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 889 HIS Chi-restraints excluded: chain B residue 957 LEU Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1045 MET Chi-restraints excluded: chain B residue 1174 LEU Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 103 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 132 optimal weight: 0.0970 chunk 102 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.197044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.140226 restraints weight = 18946.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.145131 restraints weight = 29013.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.142901 restraints weight = 16852.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.142423 restraints weight = 13024.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.143164 restraints weight = 11673.474| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15239 Z= 0.130 Angle : 0.578 10.233 20710 Z= 0.276 Chirality : 0.039 0.306 2525 Planarity : 0.004 0.060 2493 Dihedral : 6.897 67.961 2767 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.12 % Allowed : 24.65 % Favored : 71.23 % 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: 1826 helix: 2.35 (0.14), residues: 1310 sheet: 0.17 (0.48), residues: 116 loop : -0.82 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 990 TYR 0.019 0.001 TYR B 309 PHE 0.033 0.001 PHE B1032 TRP 0.022 0.001 TRP A 643 HIS 0.011 0.001 HIS B 928 Details of bonding type rmsd covalent geometry : bond 0.00303 (15239) covalent geometry : angle 0.57770 (20710) hydrogen bonds : bond 0.04118 ( 1042) hydrogen bonds : angle 3.47788 ( 3084) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 213 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8464 (mmm) cc_final: 0.8097 (tpp) REVERT: A 444 ASN cc_start: 0.7577 (OUTLIER) cc_final: 0.7110 (m110) REVERT: A 477 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8635 (tt) REVERT: A 531 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7847 (tm-30) REVERT: A 611 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8703 (mm) REVERT: A 1044 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: A 1067 PHE cc_start: 0.8248 (t80) cc_final: 0.7883 (t80) REVERT: A 1173 LYS cc_start: 0.4972 (mtmt) cc_final: 0.4651 (mttp) REVERT: B 172 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6981 (m-80) REVERT: B 483 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7917 (mmt) REVERT: B 611 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8730 (mm) REVERT: B 857 MET cc_start: 0.6195 (mmp) cc_final: 0.5913 (tmm) REVERT: B 1173 LYS cc_start: 0.5519 (mptt) cc_final: 0.4712 (mptt) outliers start: 65 outliers final: 52 residues processed: 254 average time/residue: 0.1105 time to fit residues: 44.8174 Evaluate side-chains 271 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 212 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 156 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 643 TRP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 889 HIS Chi-restraints excluded: chain B residue 957 LEU Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 972 PHE Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1174 LEU Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 15 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.197546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137665 restraints weight = 18461.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.138344 restraints weight = 26630.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.138920 restraints weight = 16563.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.137767 restraints weight = 13084.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.138463 restraints weight = 11706.210| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15239 Z= 0.114 Angle : 0.574 10.420 20710 Z= 0.273 Chirality : 0.038 0.307 2525 Planarity : 0.004 0.060 2493 Dihedral : 6.778 68.100 2767 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.68 % Allowed : 25.22 % Favored : 71.10 % 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: 2.43 (0.20), residues: 1826 helix: 2.40 (0.14), residues: 1310 sheet: 0.84 (0.53), residues: 96 loop : -0.82 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 990 TYR 0.019 0.001 TYR A1125 PHE 0.033 0.001 PHE B1032 TRP 0.022 0.001 TRP A 643 HIS 0.012 0.001 HIS B 928 Details of bonding type rmsd covalent geometry : bond 0.00256 (15239) covalent geometry : angle 0.57413 (20710) hydrogen bonds : bond 0.03884 ( 1042) hydrogen bonds : angle 3.44115 ( 3084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2647.27 seconds wall clock time: 46 minutes 34.86 seconds (2794.86 seconds total)