Starting phenix.real_space_refine on Fri Jun 13 09:32:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7d_41979/06_2025/8u7d_41979.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7d_41979/06_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_41979/06_2025/8u7d_41979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7d_41979/06_2025/8u7d_41979.map" model { file = "/net/cci-nas-00/data/ceres_data/8u7d_41979/06_2025/8u7d_41979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7d_41979/06_2025/8u7d_41979.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.65, per 1000 atoms: 0.65 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: 4.11 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.71 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: 5.05 Time building geometry restraints manager: 4.63 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 1192 or resid 1401)) selection = (chain 'B' and (resid 74 through 1192 or resid 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: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 36.020 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.330 ------------------------------------------------------------------------------- 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 : 5.54 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (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 TRP 0.018 0.001 TRP A 643 HIS 0.005 0.001 HIS A 928 PHE 0.037 0.001 PHE B 195 TYR 0.019 0.001 TYR A 309 ARG 0.002 0.000 ARG B 431 Details of bonding type rmsd hydrogen bonds : bond 0.12340 ( 1042) hydrogen bonds : angle 5.42029 ( 3084) covalent geometry : bond 0.00408 (15239) covalent geometry : angle 0.63298 (20710) *********************** 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 : 1.990 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: 0.3408 time to fit residues: 131.7855 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 : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 3.9990 chunk 139 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 832 GLN A 981 HIS ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.191524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.132543 restraints weight = 18359.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.131282 restraints weight = 25303.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.133015 restraints weight = 18572.809| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15239 Z= 0.251 Angle : 0.671 9.920 20710 Z= 0.331 Chirality : 0.042 0.297 2525 Planarity : 0.005 0.067 2493 Dihedral : 9.908 83.670 2767 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.01 % Allowed : 22.37 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.19), residues: 1826 helix: 1.53 (0.14), residues: 1310 sheet: -0.22 (0.48), residues: 116 loop : -0.96 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 643 HIS 0.009 0.002 HIS A 928 PHE 0.019 0.002 PHE B1032 TYR 0.021 0.002 TYR B 309 ARG 0.007 0.000 ARG B1089 Details of bonding type rmsd hydrogen bonds : bond 0.05733 ( 1042) hydrogen bonds : angle 4.16188 ( 3084) covalent geometry : bond 0.00624 (15239) covalent geometry : angle 0.67055 (20710) *********************** 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 294 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 215 time to evaluate : 1.719 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: A 199 MET cc_start: 0.8565 (mmm) cc_final: 0.8216 (tpp) REVERT: A 611 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8694 (mm) REVERT: A 817 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8673 (tp) REVERT: A 959 ASN cc_start: 0.8527 (t0) cc_final: 0.8195 (t0) REVERT: A 1173 LYS cc_start: 0.3406 (pttm) cc_final: 0.3113 (mttp) REVERT: B 172 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.7192 (m-80) REVERT: B 611 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8634 (mm) REVERT: B 1098 ILE cc_start: 0.8668 (tp) cc_final: 0.8372 (tp) REVERT: B 1173 LYS cc_start: 0.5384 (mptt) cc_final: 0.4700 (mptt) outliers start: 79 outliers final: 52 residues processed: 271 average time/residue: 0.2333 time to fit residues: 98.7227 Evaluate side-chains 257 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 201 time to evaluate : 1.808 ------------------------------------------------------------------------------- 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 261 VAL 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 424 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 584 LEU 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 898 THR Chi-restraints excluded: chain A residue 917 GLN 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 995 SER Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1058 THR 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 B residue 79 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 154 MET 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 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 424 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 592 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 814 THR Chi-restraints excluded: chain B residue 889 HIS Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1096 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 129 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 180 optimal weight: 40.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4196 r_free = 0.4196 target = 0.196138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.139901 restraints weight = 18305.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.133002 restraints weight = 24152.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.130218 restraints weight = 15321.245| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15239 Z= 0.118 Angle : 0.534 8.362 20710 Z= 0.266 Chirality : 0.038 0.272 2525 Planarity : 0.004 0.065 2493 Dihedral : 7.620 68.968 2767 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.93 % Allowed : 24.02 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.20), residues: 1826 helix: 1.99 (0.14), residues: 1310 sheet: -0.16 (0.49), residues: 116 loop : -0.98 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 643 HIS 0.009 0.001 HIS B 928 PHE 0.025 0.001 PHE B 972 TYR 0.017 0.001 TYR B1125 ARG 0.005 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.04402 ( 1042) hydrogen bonds : angle 3.79240 ( 3084) covalent geometry : bond 0.00250 (15239) covalent geometry : angle 0.53442 (20710) *********************** 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 284 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 222 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 611 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8709 (mm) REVERT: A 868 LYS cc_start: 0.8989 (mmtm) cc_final: 0.8748 (mmmm) REVERT: A 959 ASN cc_start: 0.8704 (t0) cc_final: 0.8278 (t0) REVERT: A 1044 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: A 1173 LYS cc_start: 0.3481 (pttm) cc_final: 0.3199 (mttp) REVERT: B 154 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7303 (ppp) REVERT: B 611 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8670 (mm) REVERT: B 1072 ASP cc_start: 0.7608 (m-30) cc_final: 0.7366 (m-30) REVERT: B 1173 LYS cc_start: 0.5773 (mptt) cc_final: 0.5025 (mptt) outliers start: 62 outliers final: 29 residues processed: 258 average time/residue: 0.2962 time to fit residues: 119.2479 Evaluate side-chains 236 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 1.959 ------------------------------------------------------------------------------- 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 373 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 424 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 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 1005 LEU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 424 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 963 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 74 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 chunk 157 optimal weight: 0.8980 chunk 174 optimal weight: 0.4980 chunk 150 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.194646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.140061 restraints weight = 18848.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.130253 restraints weight = 24285.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.126332 restraints weight = 17411.401| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15239 Z= 0.154 Angle : 0.559 9.537 20710 Z= 0.278 Chirality : 0.039 0.242 2525 Planarity : 0.004 0.064 2493 Dihedral : 7.463 68.680 2767 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.07 % Allowed : 23.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.20), residues: 1826 helix: 2.03 (0.14), residues: 1308 sheet: -0.30 (0.46), residues: 128 loop : -0.93 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 643 HIS 0.008 0.001 HIS B 928 PHE 0.024 0.001 PHE B1032 TYR 0.020 0.001 TYR A 309 ARG 0.005 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.04672 ( 1042) hydrogen bonds : angle 3.72959 ( 3084) covalent geometry : bond 0.00370 (15239) covalent geometry : angle 0.55926 (20710) *********************** 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 296 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 216 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ASN cc_start: 0.7537 (OUTLIER) cc_final: 0.7072 (m110) REVERT: A 611 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8733 (mm) REVERT: A 1173 LYS cc_start: 0.3521 (pttm) cc_final: 0.3134 (mttp) REVERT: B 172 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.7201 (m-80) REVERT: B 611 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8685 (mm) REVERT: B 1072 ASP cc_start: 0.7593 (m-30) cc_final: 0.7285 (m-30) REVERT: B 1173 LYS cc_start: 0.5700 (mptt) cc_final: 0.4867 (mptt) outliers start: 80 outliers final: 52 residues processed: 263 average time/residue: 0.2957 time to fit residues: 121.8145 Evaluate side-chains 261 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 205 time to evaluate : 2.873 ------------------------------------------------------------------------------- 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 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 444 ASN Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 483 MET 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 814 THR Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 914 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 989 VAL Chi-restraints excluded: chain A residue 1005 LEU 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 1189 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 154 MET 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 405 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 889 HIS Chi-restraints excluded: chain B residue 948 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 43 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1040 ASN ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1040 ASN ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.190979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130297 restraints weight = 18605.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.127126 restraints weight = 24390.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.129372 restraints weight = 17410.482| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15239 Z= 0.220 Angle : 0.621 9.931 20710 Z= 0.309 Chirality : 0.041 0.281 2525 Planarity : 0.004 0.063 2493 Dihedral : 7.710 68.652 2767 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 6.08 % Allowed : 22.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.20), residues: 1826 helix: 1.88 (0.14), residues: 1308 sheet: -0.31 (0.46), residues: 128 loop : -0.88 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 643 HIS 0.008 0.001 HIS B 928 PHE 0.027 0.002 PHE B1032 TYR 0.020 0.002 TYR A 309 ARG 0.003 0.000 ARG B 976 Details of bonding type rmsd hydrogen bonds : bond 0.05338 ( 1042) hydrogen bonds : angle 3.84164 ( 3084) covalent geometry : bond 0.00547 (15239) covalent geometry : angle 0.62065 (20710) *********************** 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 307 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 211 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8498 (mmm) cc_final: 0.8233 (tpp) REVERT: A 444 ASN cc_start: 0.7661 (OUTLIER) cc_final: 0.7294 (m110) REVERT: A 483 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7960 (mmt) REVERT: A 611 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8712 (mm) REVERT: A 1044 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: A 1173 LYS cc_start: 0.3484 (pttm) cc_final: 0.3047 (mttp) REVERT: B 172 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.7182 (m-80) REVERT: B 611 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8685 (mm) REVERT: B 1173 LYS cc_start: 0.5590 (mptt) cc_final: 0.4818 (mptt) outliers start: 96 outliers final: 66 residues processed: 278 average time/residue: 0.2260 time to fit residues: 99.0312 Evaluate side-chains 279 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 207 time to evaluate : 1.777 ------------------------------------------------------------------------------- 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 321 VAL Chi-restraints excluded: chain A residue 373 THR 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 403 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 483 MET 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 823 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 934 VAL 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 989 VAL 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 1112 TRP Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 154 MET 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 321 VAL Chi-restraints excluded: chain B residue 373 THR 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 403 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 584 LEU 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 817 LEU Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 889 HIS Chi-restraints excluded: chain B residue 934 VAL Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 957 LEU 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 1127 VAL Chi-restraints excluded: chain B residue 1174 LEU Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 46 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 136 optimal weight: 8.9990 chunk 158 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.193467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.132412 restraints weight = 18495.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.131057 restraints weight = 20847.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.132807 restraints weight = 16802.955| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15239 Z= 0.147 Angle : 0.562 11.250 20710 Z= 0.278 Chirality : 0.039 0.409 2525 Planarity : 0.004 0.061 2493 Dihedral : 7.381 68.808 2767 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 5.20 % Allowed : 23.89 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.20), residues: 1826 helix: 2.03 (0.14), residues: 1310 sheet: -0.38 (0.45), residues: 128 loop : -0.90 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 643 HIS 0.009 0.001 HIS A 928 PHE 0.027 0.001 PHE B1032 TYR 0.018 0.001 TYR A 309 ARG 0.005 0.000 ARG B 976 Details of bonding type rmsd hydrogen bonds : bond 0.04697 ( 1042) hydrogen bonds : angle 3.70469 ( 3084) covalent geometry : bond 0.00347 (15239) covalent geometry : angle 0.56206 (20710) *********************** 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 292 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 210 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8460 (mmm) cc_final: 0.8075 (tpp) REVERT: A 444 ASN cc_start: 0.7660 (OUTLIER) cc_final: 0.7249 (m110) REVERT: A 611 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8704 (mm) REVERT: A 1044 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7736 (mt-10) REVERT: A 1173 LYS cc_start: 0.3456 (pttm) cc_final: 0.3120 (mttp) REVERT: B 611 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8666 (mm) REVERT: B 1173 LYS cc_start: 0.5722 (mptt) cc_final: 0.4983 (mptt) outliers start: 82 outliers final: 60 residues processed: 264 average time/residue: 0.2703 time to fit residues: 115.1801 Evaluate side-chains 273 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 209 time to evaluate : 1.677 ------------------------------------------------------------------------------- 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 261 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 373 THR 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 424 ILE Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 483 MET 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 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 914 HIS 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 79 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 SER 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 380 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 424 ILE 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 817 LEU Chi-restraints excluded: chain B residue 889 HIS Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 957 LEU Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 970 ILE 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 Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 110 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.194841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.136600 restraints weight = 18804.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.134202 restraints weight = 29107.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.136355 restraints weight = 21144.998| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1990 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= 0.138 Angle : 0.566 10.540 20710 Z= 0.277 Chirality : 0.039 0.352 2525 Planarity : 0.004 0.060 2493 Dihedral : 7.263 68.798 2767 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 5.20 % Allowed : 23.89 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.20), residues: 1826 helix: 2.10 (0.14), residues: 1310 sheet: -0.43 (0.45), residues: 128 loop : -0.86 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 643 HIS 0.010 0.001 HIS A 928 PHE 0.031 0.001 PHE B1032 TYR 0.020 0.001 TYR A1125 ARG 0.003 0.000 ARG B 976 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 1042) hydrogen bonds : angle 3.64610 ( 3084) covalent geometry : bond 0.00324 (15239) covalent geometry : angle 0.56569 (20710) *********************** 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 295 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 213 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8513 (mmm) cc_final: 0.8093 (tpp) REVERT: A 444 ASN cc_start: 0.7609 (OUTLIER) cc_final: 0.7196 (m110) REVERT: A 611 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8713 (mm) REVERT: A 1044 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: A 1173 LYS cc_start: 0.3466 (pttm) cc_final: 0.3145 (mttp) REVERT: B 611 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8643 (mm) REVERT: B 857 MET cc_start: 0.6276 (mmp) cc_final: 0.5957 (tmm) REVERT: B 1173 LYS cc_start: 0.5673 (mptt) cc_final: 0.4963 (mptt) outliers start: 82 outliers final: 61 residues processed: 266 average time/residue: 0.2187 time to fit residues: 92.4391 Evaluate side-chains 273 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 208 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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 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 444 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 465 LEU 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 811 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 914 HIS 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 79 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 373 THR 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 424 ILE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 588 LYS 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 817 LEU Chi-restraints excluded: chain B residue 889 HIS Chi-restraints excluded: chain B residue 948 ILE 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 1127 VAL Chi-restraints excluded: chain B residue 1174 LEU Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 71 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 23 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4196 r_free = 0.4196 target = 0.196347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.141406 restraints weight = 18718.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131555 restraints weight = 23847.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.127482 restraints weight = 17352.805| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2118 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= 0.123 Angle : 0.567 9.976 20710 Z= 0.276 Chirality : 0.038 0.342 2525 Planarity : 0.004 0.060 2493 Dihedral : 7.016 68.722 2767 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.63 % Allowed : 24.84 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.20), residues: 1826 helix: 2.20 (0.14), residues: 1312 sheet: -0.44 (0.45), residues: 128 loop : -0.82 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 643 HIS 0.011 0.001 HIS A 928 PHE 0.032 0.001 PHE B1032 TYR 0.016 0.001 TYR A 309 ARG 0.002 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.04223 ( 1042) hydrogen bonds : angle 3.57334 ( 3084) covalent geometry : bond 0.00277 (15239) covalent geometry : angle 0.56687 (20710) *********************** 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 287 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 214 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8565 (mmm) cc_final: 0.8162 (tpp) REVERT: A 444 ASN cc_start: 0.7565 (OUTLIER) cc_final: 0.7092 (m110) REVERT: A 477 LEU cc_start: 0.8877 (tp) cc_final: 0.8630 (tt) REVERT: A 611 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8733 (mm) REVERT: A 1044 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: A 1067 PHE cc_start: 0.8441 (t80) cc_final: 0.8039 (t80) REVERT: A 1173 LYS cc_start: 0.3473 (pttm) cc_final: 0.2989 (mttp) REVERT: B 611 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8681 (mm) REVERT: B 857 MET cc_start: 0.6633 (mmp) cc_final: 0.6044 (tmm) REVERT: B 1173 LYS cc_start: 0.5707 (mptt) cc_final: 0.4906 (mptt) outliers start: 73 outliers final: 55 residues processed: 262 average time/residue: 0.2209 time to fit residues: 91.6675 Evaluate side-chains 269 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 210 time to evaluate : 2.095 ------------------------------------------------------------------------------- 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 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 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 811 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 898 THR 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 1127 VAL Chi-restraints excluded: chain A residue 1174 LEU 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 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 SER 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 380 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 477 LEU 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 913 ILE 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 1096 ILE Chi-restraints excluded: chain B residue 1127 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 102 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.4189 r_free = 0.4189 target = 0.195580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.138972 restraints weight = 18794.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.132482 restraints weight = 25387.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.127542 restraints weight = 18224.152| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15239 Z= 0.140 Angle : 0.584 9.845 20710 Z= 0.283 Chirality : 0.039 0.358 2525 Planarity : 0.004 0.059 2493 Dihedral : 7.071 69.213 2767 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.25 % Allowed : 25.16 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.20), residues: 1826 helix: 2.18 (0.14), residues: 1310 sheet: -0.37 (0.45), residues: 128 loop : -0.83 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 643 HIS 0.011 0.001 HIS A 928 PHE 0.032 0.001 PHE B1032 TYR 0.019 0.001 TYR A1125 ARG 0.003 0.000 ARG B1185 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 1042) hydrogen bonds : angle 3.58664 ( 3084) covalent geometry : bond 0.00330 (15239) covalent geometry : angle 0.58364 (20710) *********************** 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 283 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 216 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8621 (mmm) cc_final: 0.8152 (tpp) REVERT: A 444 ASN cc_start: 0.7570 (OUTLIER) cc_final: 0.7170 (m110) REVERT: A 477 LEU cc_start: 0.8883 (tp) cc_final: 0.8624 (tt) REVERT: A 611 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8724 (mm) REVERT: A 810 MET cc_start: 0.6274 (mmt) cc_final: 0.5759 (mmt) REVERT: A 1044 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: A 1067 PHE cc_start: 0.8400 (t80) cc_final: 0.7999 (t80) REVERT: A 1173 LYS cc_start: 0.3431 (pttm) cc_final: 0.2974 (mttp) REVERT: B 195 PHE cc_start: 0.6761 (t80) cc_final: 0.6430 (t80) REVERT: B 611 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8696 (mm) REVERT: B 1173 LYS cc_start: 0.5710 (mptt) cc_final: 0.4967 (mptt) outliers start: 67 outliers final: 56 residues processed: 260 average time/residue: 0.2327 time to fit residues: 95.0227 Evaluate side-chains 271 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 211 time to evaluate : 1.606 ------------------------------------------------------------------------------- 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 373 THR 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 424 ILE Chi-restraints excluded: chain A residue 444 ASN 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 811 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 898 THR 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 1174 LEU 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 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 SER 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 380 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 468 VAL 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 913 ILE 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 1096 ILE Chi-restraints excluded: chain B residue 1127 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 84 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.194491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.137842 restraints weight = 18846.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.131719 restraints weight = 25937.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127736 restraints weight = 17041.145| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15239 Z= 0.161 Angle : 0.618 11.145 20710 Z= 0.298 Chirality : 0.040 0.340 2525 Planarity : 0.004 0.060 2493 Dihedral : 7.198 69.678 2767 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.31 % Allowed : 25.35 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.20), residues: 1826 helix: 2.11 (0.14), residues: 1310 sheet: -0.35 (0.45), residues: 128 loop : -0.83 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 643 HIS 0.011 0.001 HIS A 928 PHE 0.033 0.002 PHE B1032 TYR 0.019 0.001 TYR B 309 ARG 0.002 0.000 ARG B 990 Details of bonding type rmsd hydrogen bonds : bond 0.04604 ( 1042) hydrogen bonds : angle 3.63338 ( 3084) covalent geometry : bond 0.00391 (15239) covalent geometry : angle 0.61832 (20710) ********************** 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 282 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 214 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ASN cc_start: 0.7577 (OUTLIER) cc_final: 0.7160 (m110) REVERT: A 477 LEU cc_start: 0.8897 (tp) cc_final: 0.8608 (tt) REVERT: A 611 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8708 (mm) REVERT: A 810 MET cc_start: 0.6347 (mmt) cc_final: 0.5858 (mmt) REVERT: A 1044 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: A 1067 PHE cc_start: 0.8368 (t80) cc_final: 0.7977 (t80) REVERT: A 1173 LYS cc_start: 0.3484 (pttm) cc_final: 0.3006 (mttp) REVERT: B 611 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8693 (mm) REVERT: B 857 MET cc_start: 0.6356 (mmp) cc_final: 0.5937 (tmm) REVERT: B 1173 LYS cc_start: 0.5683 (mptt) cc_final: 0.4946 (mptt) outliers start: 68 outliers final: 60 residues processed: 260 average time/residue: 0.2083 time to fit residues: 86.4950 Evaluate side-chains 274 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 210 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 380 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 463 VAL 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 811 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 898 THR 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 1189 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 SER 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 380 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 477 LEU 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 913 ILE Chi-restraints excluded: chain B residue 948 ILE 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 1096 ILE Chi-restraints excluded: chain B residue 1127 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 52 optimal weight: 0.4980 chunk 77 optimal weight: 0.0570 chunk 99 optimal weight: 0.5980 chunk 166 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 overall best weight: 1.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 959 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.195288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.138653 restraints weight = 18889.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.132999 restraints weight = 25550.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.127290 restraints weight = 18659.936| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2256 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= 0.142 Angle : 0.604 10.249 20710 Z= 0.290 Chirality : 0.039 0.320 2525 Planarity : 0.004 0.060 2493 Dihedral : 7.124 69.821 2767 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.31 % Allowed : 25.41 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.20), residues: 1826 helix: 2.17 (0.14), residues: 1310 sheet: -0.34 (0.45), residues: 128 loop : -0.86 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 643 HIS 0.011 0.001 HIS A 928 PHE 0.034 0.001 PHE B1032 TYR 0.019 0.001 TYR A1125 ARG 0.004 0.000 ARG B 812 Details of bonding type rmsd hydrogen bonds : bond 0.04437 ( 1042) hydrogen bonds : angle 3.61266 ( 3084) covalent geometry : bond 0.00336 (15239) covalent geometry : angle 0.60364 (20710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6088.13 seconds wall clock time: 108 minutes 46.84 seconds (6526.84 seconds total)