Starting phenix.real_space_refine on Fri Jul 3 02:44:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oh4_12893/07_2026/7oh4_12893.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oh4_12893/07_2026/7oh4_12893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7oh4_12893/07_2026/7oh4_12893.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oh4_12893/07_2026/7oh4_12893.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oh4_12893/07_2026/7oh4_12893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oh4_12893/07_2026/7oh4_12893.map" model { file = "/net/cci-nas-00/data/ceres_data/7oh4_12893/07_2026/7oh4_12893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oh4_12893/07_2026/7oh4_12893.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 7452 2.51 5 N 1859 2.21 5 O 2173 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11535 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8504 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 30, 'TRANS': 1033} Chain: "C" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2842 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 21, 'TRANS': 328} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {' MG': 1, '2Y5': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 2.74, per 1000 atoms: 0.24 Number of scatterers: 11535 At special positions: 0 Unit cell: (77.34, 108.276, 175.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 2 15.00 Mg 1 11.99 O 2173 8.00 N 1859 7.00 C 7452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 190 " distance=2.04 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=1, symmetry=0 Links applied BETA1-3 " BMA E 3 " - " BMA E 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG B 1 " - " ASN C 288 " " NAG C 501 " - " ASN C 237 " " NAG D 1 " - " ASN C 216 " " NAG E 1 " - " ASN C 199 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 469.6 milliseconds 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2676 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 11 sheets defined 45.0% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 192 through 197 removed outlier: 3.641A pdb=" N SER A 195 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 223 removed outlier: 4.309A pdb=" N PHE A 219 " --> pdb=" O PRO A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 237 Processing helix chain 'A' and resid 250 through 281 removed outlier: 3.855A pdb=" N SER A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 420 through 424 removed outlier: 4.150A pdb=" N THR A 424 " --> pdb=" O GLY A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 473 removed outlier: 3.538A pdb=" N LYS A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.806A pdb=" N LEU A 480 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 503 removed outlier: 3.641A pdb=" N PHE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 497 " --> pdb=" O LYS A 493 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 501 " --> pdb=" O THR A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 509 through 526 removed outlier: 4.355A pdb=" N GLU A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 532 Processing helix chain 'A' and resid 548 through 553 removed outlier: 3.587A pdb=" N LEU A 551 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 613 removed outlier: 3.620A pdb=" N LEU A 608 " --> pdb=" O LYS A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 630 Processing helix chain 'A' and resid 652 through 664 removed outlier: 3.556A pdb=" N GLY A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 731 removed outlier: 3.720A pdb=" N GLU A 729 " --> pdb=" O VAL A 726 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 731 " --> pdb=" O LEU A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 751 removed outlier: 3.552A pdb=" N TYR A 749 " --> pdb=" O HIS A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 782 removed outlier: 3.781A pdb=" N THR A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 796 Processing helix chain 'A' and resid 816 through 827 removed outlier: 3.743A pdb=" N HIS A 822 " --> pdb=" O PRO A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 849 Processing helix chain 'A' and resid 865 through 882 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.610A pdb=" N ASN A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 905 Processing helix chain 'A' and resid 910 through 919 removed outlier: 3.512A pdb=" N LEU A 914 " --> pdb=" O LEU A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 940 removed outlier: 3.715A pdb=" N LEU A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL A 938 " --> pdb=" O LYS A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 945 removed outlier: 3.976A pdb=" N SER A 945 " --> pdb=" O LYS A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 963 Processing helix chain 'A' and resid 992 through 997 Processing helix chain 'A' and resid 1001 through 1024 removed outlier: 4.311A pdb=" N ILE A1008 " --> pdb=" O SER A1004 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A1009 " --> pdb=" O TYR A1005 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A1010 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A1022 " --> pdb=" O LYS A1018 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET A1024 " --> pdb=" O THR A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1027 No H-bonds generated for 'chain 'A' and resid 1025 through 1027' Processing helix chain 'A' and resid 1044 through 1050 removed outlier: 4.076A pdb=" N ASN A1050 " --> pdb=" O MET A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1064 Processing helix chain 'A' and resid 1069 through 1074 removed outlier: 3.600A pdb=" N GLU A1074 " --> pdb=" O SER A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1078 No H-bonds generated for 'chain 'A' and resid 1076 through 1078' Processing helix chain 'A' and resid 1079 through 1086 removed outlier: 3.864A pdb=" N GLY A1083 " --> pdb=" O LEU A1079 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY A1086 " --> pdb=" O LEU A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1114 removed outlier: 3.624A pdb=" N GLY A1096 " --> pdb=" O TYR A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1154 removed outlier: 4.053A pdb=" N THR A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1183 Proline residue: A1166 - end of helix Proline residue: A1177 - end of helix Processing helix chain 'A' and resid 1184 through 1187 Processing helix chain 'A' and resid 1189 through 1193 removed outlier: 3.926A pdb=" N TYR A1193 " --> pdb=" O ARG A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1201 removed outlier: 3.653A pdb=" N HIS A1198 " --> pdb=" O GLY A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1230 removed outlier: 4.386A pdb=" N ILE A1210 " --> pdb=" O TRP A1206 " (cutoff:3.500A) Proline residue: A1213 - end of helix removed outlier: 5.073A pdb=" N ARG A1219 " --> pdb=" O PHE A1215 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASP A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1245 removed outlier: 3.864A pdb=" N GLU A1240 " --> pdb=" O HIS A1236 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 69 Proline residue: C 47 - end of helix Proline residue: C 58 - end of helix Processing helix chain 'C' and resid 79 through 84 removed outlier: 3.622A pdb=" N ALA C 84 " --> pdb=" O CYS C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 155 removed outlier: 3.750A pdb=" N GLN C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 163 removed outlier: 3.634A pdb=" N ILE C 162 " --> pdb=" O ASP C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 172 Processing helix chain 'C' and resid 181 through 185 removed outlier: 4.227A pdb=" N ASP C 184 " --> pdb=" O SER C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 removed outlier: 3.512A pdb=" N ASN C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 231 Processing helix chain 'C' and resid 266 through 273 removed outlier: 3.606A pdb=" N GLN C 270 " --> pdb=" O TRP C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 311 Processing helix chain 'C' and resid 330 through 357 removed outlier: 3.616A pdb=" N ILE C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.970A pdb=" N LYS A 369 " --> pdb=" O THR A 387 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 283 through 287 Processing sheet with id=AA3, first strand: chain 'A' and resid 307 through 310 removed outlier: 6.513A pdb=" N PHE A 414 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP A 319 " --> pdb=" O ILE A 418 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 320 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 401 " --> pdb=" O THR A 320 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.652A pdb=" N TYR A 333 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 541 through 542 removed outlier: 6.736A pdb=" N LEU A 949 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL A 969 " --> pdb=" O LEU A 949 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA A 951 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE A 971 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLY A 953 " --> pdb=" O ILE A 971 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 560 " --> pdb=" O ILE A 952 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE A 557 " --> pdb=" O TRP A 832 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU A 834 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N SER A 559 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 923 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASN A 857 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL A 896 " --> pdb=" O ASN A 857 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU A 859 " --> pdb=" O VAL A 896 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 571 through 577 removed outlier: 5.831A pdb=" N PHE A 572 " --> pdb=" O GLU A 810 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLU A 810 " --> pdb=" O PHE A 572 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 759 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA A 806 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 757 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA A 808 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG A 755 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE A 716 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A 694 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG A 710 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU A 692 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 637 through 639 Processing sheet with id=AA8, first strand: chain 'C' and resid 98 through 100 removed outlier: 6.405A pdb=" N TYR C 141 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU C 284 " --> pdb=" O TYR C 141 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 90 through 91 removed outlier: 3.716A pdb=" N THR C 201 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 90 through 91 removed outlier: 4.423A pdb=" N LYS C 297 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ASN C 301 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL C 205 " --> pdb=" O ASN C 301 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 186 through 187 removed outlier: 6.629A pdb=" N ILE C 186 " --> pdb=" O VAL C 242 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 492 hydrogen bonds defined for protein. 1365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.18 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1860 1.31 - 1.44: 3218 1.44 - 1.57: 6637 1.57 - 1.70: 3 1.70 - 1.82: 77 Bond restraints: 11795 Sorted by residual: bond pdb=" C1 NAG C 501 " pdb=" O5 NAG C 501 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C10 2Y5 A1501 " pdb=" O16 2Y5 A1501 " ideal model delta sigma weight residual 1.333 1.400 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C11 2Y5 A1501 " pdb=" O18 2Y5 A1501 " ideal model delta sigma weight residual 1.335 1.398 -0.063 2.00e-02 2.50e+03 9.81e+00 bond pdb=" O4 2Y5 A1501 " pdb=" P4 2Y5 A1501 " ideal model delta sigma weight residual 1.703 1.648 0.055 2.00e-02 2.50e+03 7.49e+00 bond pdb=" O43 2Y5 A1501 " pdb=" P4 2Y5 A1501 " ideal model delta sigma weight residual 1.551 1.509 0.042 2.00e-02 2.50e+03 4.38e+00 ... (remaining 11790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 15834 2.44 - 4.88: 119 4.88 - 7.32: 31 7.32 - 9.76: 4 9.76 - 12.21: 2 Bond angle restraints: 15990 Sorted by residual: angle pdb=" O1 2Y5 A1501 " pdb=" P1 2Y5 A1501 " pdb=" O13 2Y5 A1501 " ideal model delta sigma weight residual 97.01 109.22 -12.21 3.00e+00 1.11e-01 1.66e+01 angle pdb=" O11 2Y5 A1501 " pdb=" P1 2Y5 A1501 " pdb=" O12 2Y5 A1501 " ideal model delta sigma weight residual 121.15 109.55 11.60 3.00e+00 1.11e-01 1.49e+01 angle pdb=" C31 2Y5 A1501 " pdb=" C11 2Y5 A1501 " pdb=" O18 2Y5 A1501 " ideal model delta sigma weight residual 110.90 120.31 -9.41 3.00e+00 1.11e-01 9.85e+00 angle pdb=" O4 2Y5 A1501 " pdb=" P4 2Y5 A1501 " pdb=" O42 2Y5 A1501 " ideal model delta sigma weight residual 101.73 109.64 -7.91 3.00e+00 1.11e-01 6.95e+00 angle pdb=" N PHE A1183 " pdb=" CA PHE A1183 " pdb=" C PHE A1183 " ideal model delta sigma weight residual 109.81 115.60 -5.79 2.21e+00 2.05e-01 6.87e+00 ... (remaining 15985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.54: 6846 28.54 - 57.08: 131 57.08 - 85.62: 18 85.62 - 114.16: 4 114.16 - 142.70: 1 Dihedral angle restraints: 7000 sinusoidal: 2850 harmonic: 4150 Sorted by residual: dihedral pdb=" C33 2Y5 A1501 " pdb=" C34 2Y5 A1501 " pdb=" C35 2Y5 A1501 " pdb=" C36 2Y5 A1501 " ideal model delta sinusoidal sigma weight residual 56.12 -161.18 -142.70 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C3 2Y5 A1501 " pdb=" C1 2Y5 A1501 " pdb=" C2 2Y5 A1501 " pdb=" C6 2Y5 A1501 " ideal model delta sinusoidal sigma weight residual -53.11 57.78 -110.89 1 3.00e+01 1.11e-03 1.45e+01 dihedral pdb=" C6 2Y5 A1501 " pdb=" C1 2Y5 A1501 " pdb=" C2 2Y5 A1501 " pdb=" O2 2Y5 A1501 " ideal model delta sinusoidal sigma weight residual 171.86 64.03 107.83 1 3.00e+01 1.11e-03 1.39e+01 ... (remaining 6997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.004: 1834 1.004 - 2.008: 0 2.008 - 3.012: 0 3.012 - 4.016: 0 4.016 - 5.020: 1 Chirality restraints: 1835 Sorted by residual: chirality pdb=" C1 2Y5 A1501 " pdb=" C2 2Y5 A1501 " pdb=" C6 2Y5 A1501 " pdb=" O1 2Y5 A1501 " both_signs ideal model delta sigma weight residual False -2.53 2.49 -5.02 2.00e-01 2.50e+01 6.30e+02 chirality pdb=" C5 BMA E 4 " pdb=" C4 BMA E 4 " pdb=" C6 BMA E 4 " pdb=" O5 BMA E 4 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1832 not shown) Planarity restraints: 1999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A1056 " -0.027 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO A1057 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A1057 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1057 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 188 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO C 189 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 189 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 189 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1183 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A1184 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A1184 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1184 " 0.020 5.00e-02 4.00e+02 ... (remaining 1996 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 101 2.60 - 3.17: 9790 3.17 - 3.75: 16989 3.75 - 4.32: 24186 4.32 - 4.90: 40150 Nonbonded interactions: 91216 Sorted by model distance: nonbonded pdb="MG MG A1502 " pdb=" O HOH A1603 " model vdw 2.021 2.170 nonbonded pdb="MG MG A1502 " pdb=" O HOH A1602 " model vdw 2.044 2.170 nonbonded pdb="MG MG A1502 " pdb=" O HOH A1601 " model vdw 2.057 2.170 nonbonded pdb=" O THR A 562 " pdb="MG MG A1502 " model vdw 2.083 2.170 nonbonded pdb=" OD2 ASP A 560 " pdb="MG MG A1502 " model vdw 2.114 2.170 ... (remaining 91211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.780 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 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 : 0.003 0.079 11807 Z= 0.144 Angle : 0.588 12.205 16021 Z= 0.281 Chirality : 0.124 5.020 1835 Planarity : 0.003 0.040 1995 Dihedral : 11.593 142.697 4318 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.36 % Allowed : 5.03 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.19), residues: 1410 helix: -1.74 (0.19), residues: 594 sheet: -1.81 (0.31), residues: 219 loop : -2.37 (0.21), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 391 TYR 0.012 0.001 TYR C 141 PHE 0.014 0.001 PHE A1205 TRP 0.009 0.001 TRP A1134 HIS 0.003 0.001 HIS A 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (11795) covalent geometry : angle 0.58653 / 0.28 (15990) SS BOND : bond 0.00357 / 0.25 ( 2) SS BOND : angle 0.98895 / 0.61 ( 4) hydrogen bonds : bond 0.13085 / 8.66 ( 476) hydrogen bonds : angle 5.60300 / 4.06 ( 1365) Misc. bond : bond 0.00032 / 0.02 ( 1) link_BETA1-3 : bond 0.00514 / 0.34 ( 1) link_BETA1-3 : angle 1.58349 / 0.96 ( 3) link_BETA1-4 : bond 0.00386 / 0.23 ( 4) link_BETA1-4 : angle 1.18445 / 0.85 ( 12) link_NAG-ASN : bond 0.00226 / 0.16 ( 4) link_NAG-ASN : angle 0.89812 / 0.53 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 HIS cc_start: 0.8237 (t-90) cc_final: 0.7835 (p90) REVERT: A 299 TRP cc_start: 0.6890 (m-10) cc_final: 0.6115 (m100) REVERT: A 647 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8156 (mmpt) REVERT: A 961 MET cc_start: 0.7757 (ttm) cc_final: 0.7556 (ttt) REVERT: A 1042 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6825 (mm-30) REVERT: A 1212 LEU cc_start: 0.6385 (OUTLIER) cc_final: 0.6175 (mp) outliers start: 17 outliers final: 3 residues processed: 152 average time/residue: 0.4224 time to fit residues: 71.1915 Evaluate side-chains 93 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 1042 GLU Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain C residue 365 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN A 338 ASN A 699 ASN A 883 HIS A 888 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.178344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.111546 restraints weight = 14473.302| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.68 r_work: 0.3611 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11807 Z= 0.122 Angle : 0.568 8.245 16021 Z= 0.283 Chirality : 0.043 0.246 1835 Planarity : 0.004 0.059 1995 Dihedral : 9.074 128.575 1619 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.55 % Allowed : 10.61 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.21), residues: 1410 helix: -0.75 (0.22), residues: 585 sheet: -1.47 (0.32), residues: 217 loop : -1.97 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.016 0.001 TYR C 147 PHE 0.021 0.001 PHE A1109 TRP 0.012 0.001 TRP A1056 HIS 0.008 0.001 HIS A 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (11795) covalent geometry : angle 0.56578 / 0.28 (15990) SS BOND : bond 0.00490 / 0.35 ( 2) SS BOND : angle 1.24803 / 0.74 ( 4) hydrogen bonds : bond 0.03641 / 2.37 ( 476) hydrogen bonds : angle 4.11859 / 2.96 ( 1365) Misc. bond : bond 0.00003 / 0.00 ( 1) link_BETA1-3 : bond 0.00864 / 0.58 ( 1) link_BETA1-3 : angle 1.48324 / 0.89 ( 3) link_BETA1-4 : bond 0.00364 / 0.24 ( 4) link_BETA1-4 : angle 1.13591 / 0.68 ( 12) link_NAG-ASN : bond 0.00086 / 0.05 ( 4) link_NAG-ASN : angle 1.27357 / 0.75 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 202 HIS cc_start: 0.7934 (t-90) cc_final: 0.7632 (p-80) REVERT: A 280 ASN cc_start: 0.5379 (OUTLIER) cc_final: 0.5007 (t0) REVERT: A 299 TRP cc_start: 0.6777 (m-10) cc_final: 0.5926 (m100) REVERT: A 359 ASP cc_start: 0.6907 (t0) cc_final: 0.6375 (t0) REVERT: A 464 ILE cc_start: 0.5808 (OUTLIER) cc_final: 0.5460 (mp) REVERT: A 978 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7813 (mm110) REVERT: A 1042 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6814 (tm-30) REVERT: A 1212 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6748 (mp) outliers start: 32 outliers final: 15 residues processed: 109 average time/residue: 0.4437 time to fit residues: 53.4434 Evaluate side-chains 100 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1042 GLU Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain C residue 33 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 34 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 47 optimal weight: 30.0000 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 30.0000 chunk 86 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 63 optimal weight: 0.0470 chunk 73 optimal weight: 1.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 HIS A 888 HIS C 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.172927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.105697 restraints weight = 14756.247| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.67 r_work: 0.3527 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11807 Z= 0.190 Angle : 0.637 10.403 16021 Z= 0.320 Chirality : 0.047 0.327 1835 Planarity : 0.004 0.061 1995 Dihedral : 8.945 125.106 1614 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.83 % Allowed : 11.09 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.21), residues: 1410 helix: -0.83 (0.21), residues: 589 sheet: -1.20 (0.32), residues: 220 loop : -1.88 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 755 TYR 0.028 0.002 TYR C 147 PHE 0.022 0.002 PHE A1205 TRP 0.009 0.001 TRP A1056 HIS 0.005 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 (11795) covalent geometry : angle 0.63351 / 0.32 (15990) SS BOND : bond 0.00795 / 0.57 ( 2) SS BOND : angle 1.67748 / 0.99 ( 4) hydrogen bonds : bond 0.04229 / 2.75 ( 476) hydrogen bonds : angle 4.25517 / 3.05 ( 1365) Misc. bond : bond 0.00051 / 0.03 ( 1) link_BETA1-3 : bond 0.00724 / 0.48 ( 1) link_BETA1-3 : angle 1.62327 / 0.90 ( 3) link_BETA1-4 : bond 0.00309 / 0.20 ( 4) link_BETA1-4 : angle 1.32810 / 0.74 ( 12) link_NAG-ASN : bond 0.00618 / 0.43 ( 4) link_NAG-ASN : angle 1.93417 / 1.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 76 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 202 HIS cc_start: 0.8040 (t-90) cc_final: 0.7647 (p-80) REVERT: A 299 TRP cc_start: 0.6819 (m-10) cc_final: 0.6001 (m100) REVERT: A 359 ASP cc_start: 0.7071 (t0) cc_final: 0.6541 (t0) REVERT: A 437 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7911 (ptp-110) REVERT: A 464 ILE cc_start: 0.5971 (OUTLIER) cc_final: 0.5463 (mp) REVERT: A 809 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.6991 (tp) REVERT: A 912 ASP cc_start: 0.8196 (t0) cc_final: 0.7772 (t0) REVERT: A 978 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7821 (mm110) REVERT: A 1042 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6928 (tm-30) REVERT: A 1212 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6692 (mp) REVERT: C 102 LYS cc_start: 0.7987 (tptt) cc_final: 0.7700 (tptp) REVERT: C 297 LYS cc_start: 0.8176 (mttt) cc_final: 0.7665 (mtpp) outliers start: 48 outliers final: 22 residues processed: 112 average time/residue: 0.4348 time to fit residues: 54.6438 Evaluate side-chains 103 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1042 GLU Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1234 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 205 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 76 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 131 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 61 optimal weight: 50.0000 chunk 1 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN A 883 HIS A 888 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.175009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.108054 restraints weight = 14632.322| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.61 r_work: 0.3561 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11807 Z= 0.118 Angle : 0.563 8.813 16021 Z= 0.279 Chirality : 0.044 0.271 1835 Planarity : 0.004 0.061 1995 Dihedral : 8.794 125.684 1614 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.55 % Allowed : 13.25 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.22), residues: 1410 helix: -0.48 (0.22), residues: 585 sheet: -1.07 (0.32), residues: 222 loop : -1.62 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1228 TYR 0.024 0.001 TYR C 147 PHE 0.015 0.001 PHE A 669 TRP 0.008 0.001 TRP A1134 HIS 0.005 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (11795) covalent geometry : angle 0.55944 / 0.28 (15990) SS BOND : bond 0.00544 / 0.39 ( 2) SS BOND : angle 1.41259 / 0.85 ( 4) hydrogen bonds : bond 0.03548 / 2.30 ( 476) hydrogen bonds : angle 4.04643 / 2.89 ( 1365) Misc. bond : bond 0.00045 / 0.03 ( 1) link_BETA1-3 : bond 0.00844 / 0.56 ( 1) link_BETA1-3 : angle 1.48348 / 0.87 ( 3) link_BETA1-4 : bond 0.00286 / 0.17 ( 4) link_BETA1-4 : angle 1.13403 / 0.65 ( 12) link_NAG-ASN : bond 0.00422 / 0.30 ( 4) link_NAG-ASN : angle 1.70315 / 1.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 299 TRP cc_start: 0.6814 (m-10) cc_final: 0.6006 (m100) REVERT: A 359 ASP cc_start: 0.7105 (t0) cc_final: 0.6563 (t0) REVERT: A 437 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7845 (ptp-110) REVERT: A 464 ILE cc_start: 0.5911 (OUTLIER) cc_final: 0.5424 (mp) REVERT: A 809 ILE cc_start: 0.6959 (OUTLIER) cc_final: 0.6759 (tp) REVERT: A 911 GLU cc_start: 0.7915 (pm20) cc_final: 0.7695 (pm20) REVERT: A 912 ASP cc_start: 0.8137 (t0) cc_final: 0.7701 (t0) REVERT: A 1042 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6843 (tm-30) REVERT: A 1212 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6639 (mp) REVERT: C 102 LYS cc_start: 0.7895 (tptt) cc_final: 0.7639 (tptp) outliers start: 32 outliers final: 18 residues processed: 101 average time/residue: 0.4474 time to fit residues: 50.6596 Evaluate side-chains 97 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1042 GLU Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain C residue 363 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 2 optimal weight: 0.0270 chunk 90 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.174327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.107486 restraints weight = 14470.052| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.67 r_work: 0.3551 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11807 Z= 0.123 Angle : 0.567 8.829 16021 Z= 0.281 Chirality : 0.044 0.279 1835 Planarity : 0.004 0.057 1995 Dihedral : 8.714 126.068 1614 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.55 % Allowed : 13.97 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.22), residues: 1410 helix: -0.28 (0.22), residues: 580 sheet: -0.86 (0.33), residues: 216 loop : -1.52 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1228 TYR 0.023 0.001 TYR C 147 PHE 0.016 0.001 PHE A1205 TRP 0.008 0.001 TRP A1134 HIS 0.005 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (11795) covalent geometry : angle 0.56385 / 0.28 (15990) SS BOND : bond 0.00555 / 0.40 ( 2) SS BOND : angle 1.32734 / 0.79 ( 4) hydrogen bonds : bond 0.03509 / 2.28 ( 476) hydrogen bonds : angle 4.02913 / 2.88 ( 1365) Misc. bond : bond 0.00039 / 0.03 ( 1) link_BETA1-3 : bond 0.00782 / 0.52 ( 1) link_BETA1-3 : angle 1.41469 / 0.83 ( 3) link_BETA1-4 : bond 0.00297 / 0.19 ( 4) link_BETA1-4 : angle 1.15357 / 0.65 ( 12) link_NAG-ASN : bond 0.00454 / 0.32 ( 4) link_NAG-ASN : angle 1.63361 / 0.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 0.369 Fit side-chains REVERT: A 299 TRP cc_start: 0.6757 (m-10) cc_final: 0.5943 (m100) REVERT: A 359 ASP cc_start: 0.7153 (t0) cc_final: 0.6579 (t0) REVERT: A 366 MET cc_start: 0.4170 (tpp) cc_final: 0.0860 (mtm) REVERT: A 437 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7851 (ptp-110) REVERT: A 464 ILE cc_start: 0.5920 (OUTLIER) cc_final: 0.5429 (mp) REVERT: A 705 MET cc_start: 0.7080 (ppp) cc_final: 0.6530 (ppp) REVERT: A 863 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7591 (mt-10) REVERT: A 912 ASP cc_start: 0.8153 (t0) cc_final: 0.7697 (t0) REVERT: A 1042 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7199 (tm-30) REVERT: A 1212 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6638 (mp) REVERT: C 102 LYS cc_start: 0.7821 (tptt) cc_final: 0.7556 (tptp) outliers start: 32 outliers final: 21 residues processed: 101 average time/residue: 0.4322 time to fit residues: 49.1274 Evaluate side-chains 96 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1042 GLU Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 363 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 140 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.173178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.106052 restraints weight = 14672.859| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.68 r_work: 0.3529 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11807 Z= 0.148 Angle : 0.591 10.110 16021 Z= 0.294 Chirality : 0.045 0.291 1835 Planarity : 0.004 0.049 1995 Dihedral : 8.758 129.005 1614 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.95 % Allowed : 13.65 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.22), residues: 1410 helix: -0.36 (0.22), residues: 583 sheet: -0.81 (0.33), residues: 216 loop : -1.54 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1228 TYR 0.023 0.001 TYR C 147 PHE 0.019 0.002 PHE A1205 TRP 0.008 0.001 TRP A1134 HIS 0.005 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (11795) covalent geometry : angle 0.58779 / 0.29 (15990) SS BOND : bond 0.00872 / 0.62 ( 2) SS BOND : angle 1.81575 / 1.11 ( 4) hydrogen bonds : bond 0.03812 / 2.49 ( 476) hydrogen bonds : angle 4.12369 / 2.95 ( 1365) Misc. bond : bond 0.00053 / 0.04 ( 1) link_BETA1-3 : bond 0.00788 / 0.53 ( 1) link_BETA1-3 : angle 1.41683 / 0.81 ( 3) link_BETA1-4 : bond 0.00265 / 0.19 ( 4) link_BETA1-4 : angle 1.20099 / 0.67 ( 12) link_NAG-ASN : bond 0.00455 / 0.32 ( 4) link_NAG-ASN : angle 1.80970 / 1.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 73 time to evaluate : 0.509 Fit side-chains REVERT: A 299 TRP cc_start: 0.6838 (m-10) cc_final: 0.6057 (m100) REVERT: A 359 ASP cc_start: 0.7194 (t0) cc_final: 0.6640 (t0) REVERT: A 437 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7832 (ptp-110) REVERT: A 464 ILE cc_start: 0.5957 (OUTLIER) cc_final: 0.5474 (mp) REVERT: A 705 MET cc_start: 0.7174 (ppp) cc_final: 0.6659 (ppp) REVERT: A 863 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7588 (mt-10) REVERT: A 911 GLU cc_start: 0.8049 (pm20) cc_final: 0.7841 (pm20) REVERT: A 912 ASP cc_start: 0.8142 (t0) cc_final: 0.7875 (t0) REVERT: A 1212 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6646 (mp) REVERT: C 102 LYS cc_start: 0.7817 (tptt) cc_final: 0.7569 (tptp) outliers start: 37 outliers final: 22 residues processed: 100 average time/residue: 0.4618 time to fit residues: 51.8613 Evaluate side-chains 96 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 363 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 132 optimal weight: 0.7980 chunk 16 optimal weight: 0.0000 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 50.0000 chunk 72 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 117 optimal weight: 0.0170 overall best weight: 0.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN A 888 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.175765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.108604 restraints weight = 14679.977| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.74 r_work: 0.3564 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11807 Z= 0.105 Angle : 0.542 9.884 16021 Z= 0.268 Chirality : 0.043 0.251 1835 Planarity : 0.004 0.046 1995 Dihedral : 8.154 131.065 1611 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.39 % Allowed : 14.60 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.22), residues: 1410 helix: -0.02 (0.23), residues: 583 sheet: -0.84 (0.32), residues: 222 loop : -1.32 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 755 TYR 0.015 0.001 TYR C 147 PHE 0.013 0.001 PHE A1205 TRP 0.009 0.001 TRP A1134 HIS 0.004 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 (11795) covalent geometry : angle 0.53954 / 0.27 (15990) SS BOND : bond 0.00517 / 0.37 ( 2) SS BOND : angle 1.19596 / 0.70 ( 4) hydrogen bonds : bond 0.03191 / 2.07 ( 476) hydrogen bonds : angle 3.94619 / 2.82 ( 1365) Misc. bond : bond 0.00040 / 0.03 ( 1) link_BETA1-3 : bond 0.00831 / 0.55 ( 1) link_BETA1-3 : angle 1.35251 / 0.82 ( 3) link_BETA1-4 : bond 0.00292 / 0.18 ( 4) link_BETA1-4 : angle 1.11192 / 0.64 ( 12) link_NAG-ASN : bond 0.00414 / 0.29 ( 4) link_NAG-ASN : angle 1.54498 / 0.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 299 TRP cc_start: 0.6844 (m-10) cc_final: 0.6100 (m100) REVERT: A 359 ASP cc_start: 0.7211 (t0) cc_final: 0.6658 (t0) REVERT: A 366 MET cc_start: 0.4063 (tpp) cc_final: 0.0884 (mtm) REVERT: A 437 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7788 (ptp-110) REVERT: A 464 ILE cc_start: 0.6005 (OUTLIER) cc_final: 0.5512 (mp) REVERT: A 705 MET cc_start: 0.7406 (ppp) cc_final: 0.6955 (ppp) REVERT: A 912 ASP cc_start: 0.8091 (t0) cc_final: 0.7749 (t0) REVERT: A 1212 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6616 (mp) REVERT: C 102 LYS cc_start: 0.7757 (tptt) cc_final: 0.7495 (tptp) outliers start: 30 outliers final: 17 residues processed: 96 average time/residue: 0.4519 time to fit residues: 48.7176 Evaluate side-chains 88 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 229 HIS Chi-restraints excluded: chain C residue 255 TYR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 363 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 24 optimal weight: 10.0000 chunk 99 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 8 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.175149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.107958 restraints weight = 14722.983| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.73 r_work: 0.3553 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11807 Z= 0.114 Angle : 0.557 9.883 16021 Z= 0.278 Chirality : 0.043 0.272 1835 Planarity : 0.004 0.043 1995 Dihedral : 8.126 133.799 1609 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.71 % Allowed : 14.76 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.22), residues: 1410 helix: 0.02 (0.23), residues: 583 sheet: -0.76 (0.33), residues: 222 loop : -1.30 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 755 TYR 0.017 0.001 TYR C 147 PHE 0.015 0.001 PHE A1205 TRP 0.008 0.001 TRP A1134 HIS 0.003 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (11795) covalent geometry : angle 0.55427 / 0.28 (15990) SS BOND : bond 0.00606 / 0.43 ( 2) SS BOND : angle 1.38516 / 0.78 ( 4) hydrogen bonds : bond 0.03278 / 2.14 ( 476) hydrogen bonds : angle 3.93730 / 2.80 ( 1365) Misc. bond : bond 0.00047 / 0.03 ( 1) link_BETA1-3 : bond 0.00930 / 0.62 ( 1) link_BETA1-3 : angle 1.41224 / 0.82 ( 3) link_BETA1-4 : bond 0.00355 / 0.22 ( 4) link_BETA1-4 : angle 1.17905 / 0.68 ( 12) link_NAG-ASN : bond 0.00399 / 0.28 ( 4) link_NAG-ASN : angle 1.57643 / 0.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 73 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 HIS cc_start: 0.7884 (OUTLIER) cc_final: 0.7432 (p90) REVERT: A 299 TRP cc_start: 0.6854 (m-10) cc_final: 0.6104 (m100) REVERT: A 359 ASP cc_start: 0.7255 (t0) cc_final: 0.6690 (t0) REVERT: A 366 MET cc_start: 0.4101 (tpp) cc_final: 0.0883 (mtm) REVERT: A 437 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7758 (ptp-110) REVERT: A 464 ILE cc_start: 0.6000 (OUTLIER) cc_final: 0.5688 (mp) REVERT: A 705 MET cc_start: 0.7420 (ppp) cc_final: 0.6968 (ppp) REVERT: A 912 ASP cc_start: 0.8069 (t0) cc_final: 0.7829 (t0) REVERT: A 1212 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6637 (mp) REVERT: C 102 LYS cc_start: 0.7743 (tptt) cc_final: 0.7362 (tptp) outliers start: 34 outliers final: 19 residues processed: 99 average time/residue: 0.4552 time to fit residues: 50.4192 Evaluate side-chains 91 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 229 HIS Chi-restraints excluded: chain C residue 255 TYR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 363 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 59 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 50.0000 chunk 65 optimal weight: 0.1980 chunk 11 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 HIS C 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.174578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.107537 restraints weight = 14527.297| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.63 r_work: 0.3546 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11807 Z= 0.126 Angle : 0.577 10.237 16021 Z= 0.286 Chirality : 0.044 0.281 1835 Planarity : 0.004 0.041 1995 Dihedral : 8.185 139.122 1609 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.31 % Allowed : 15.32 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.22), residues: 1410 helix: -0.02 (0.23), residues: 583 sheet: -0.71 (0.33), residues: 222 loop : -1.30 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 755 TYR 0.018 0.001 TYR C 147 PHE 0.017 0.001 PHE A1205 TRP 0.008 0.001 TRP A1134 HIS 0.003 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (11795) covalent geometry : angle 0.57432 / 0.29 (15990) SS BOND : bond 0.00620 / 0.44 ( 2) SS BOND : angle 1.24273 / 0.71 ( 4) hydrogen bonds : bond 0.03433 / 2.24 ( 476) hydrogen bonds : angle 3.98649 / 2.84 ( 1365) Misc. bond : bond 0.00053 / 0.04 ( 1) link_BETA1-3 : bond 0.00791 / 0.53 ( 1) link_BETA1-3 : angle 1.40521 / 0.81 ( 3) link_BETA1-4 : bond 0.00285 / 0.18 ( 4) link_BETA1-4 : angle 1.19655 / 0.68 ( 12) link_NAG-ASN : bond 0.00409 / 0.29 ( 4) link_NAG-ASN : angle 1.65856 / 1.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 HIS cc_start: 0.8002 (OUTLIER) cc_final: 0.7528 (p90) REVERT: A 299 TRP cc_start: 0.6887 (m-10) cc_final: 0.6162 (m100) REVERT: A 359 ASP cc_start: 0.7280 (t0) cc_final: 0.6714 (t0) REVERT: A 366 MET cc_start: 0.4173 (tpp) cc_final: 0.0972 (mtm) REVERT: A 437 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7778 (ptp-110) REVERT: A 464 ILE cc_start: 0.6024 (OUTLIER) cc_final: 0.5715 (mp) REVERT: A 705 MET cc_start: 0.7368 (ppp) cc_final: 0.6926 (ppp) REVERT: A 912 ASP cc_start: 0.8167 (t0) cc_final: 0.7902 (t0) REVERT: A 1212 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6629 (mp) outliers start: 29 outliers final: 20 residues processed: 92 average time/residue: 0.4219 time to fit residues: 43.3855 Evaluate side-chains 90 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 229 HIS Chi-restraints excluded: chain C residue 255 TYR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 363 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 32 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 123 optimal weight: 0.0010 chunk 82 optimal weight: 0.6980 chunk 23 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.173956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.106723 restraints weight = 14766.967| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.66 r_work: 0.3533 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11807 Z= 0.133 Angle : 0.587 10.051 16021 Z= 0.292 Chirality : 0.044 0.287 1835 Planarity : 0.004 0.040 1995 Dihedral : 8.264 141.152 1609 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.31 % Allowed : 15.56 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.22), residues: 1410 helix: -0.00 (0.23), residues: 576 sheet: -0.67 (0.33), residues: 222 loop : -1.27 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 755 TYR 0.019 0.001 TYR C 147 PHE 0.017 0.001 PHE A1205 TRP 0.008 0.001 TRP A1134 HIS 0.004 0.001 HIS A1198 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (11795) covalent geometry : angle 0.58424 / 0.29 (15990) SS BOND : bond 0.00662 / 0.47 ( 2) SS BOND : angle 1.31395 / 0.75 ( 4) hydrogen bonds : bond 0.03582 / 2.33 ( 476) hydrogen bonds : angle 4.01718 / 2.85 ( 1365) Misc. bond : bond 0.00051 / 0.03 ( 1) link_BETA1-3 : bond 0.00890 / 0.59 ( 1) link_BETA1-3 : angle 1.42388 / 0.81 ( 3) link_BETA1-4 : bond 0.00269 / 0.17 ( 4) link_BETA1-4 : angle 1.21312 / 0.68 ( 12) link_NAG-ASN : bond 0.00424 / 0.30 ( 4) link_NAG-ASN : angle 1.71058 / 1.06 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 299 TRP cc_start: 0.6896 (m-10) cc_final: 0.6195 (m100) REVERT: A 359 ASP cc_start: 0.7252 (t0) cc_final: 0.6693 (t0) REVERT: A 366 MET cc_start: 0.4252 (tpp) cc_final: 0.1096 (mtm) REVERT: A 437 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7794 (ptp-110) REVERT: A 464 ILE cc_start: 0.5894 (OUTLIER) cc_final: 0.5397 (mp) REVERT: A 912 ASP cc_start: 0.8174 (t0) cc_final: 0.7963 (t0) REVERT: A 1212 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6618 (mp) outliers start: 29 outliers final: 21 residues processed: 91 average time/residue: 0.4460 time to fit residues: 45.4999 Evaluate side-chains 93 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1234 THR Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 229 HIS Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 363 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 135 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 62 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 ASN A 888 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.172923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.105625 restraints weight = 14824.787| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.67 r_work: 0.3516 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11807 Z= 0.147 Angle : 0.612 9.873 16021 Z= 0.302 Chirality : 0.045 0.294 1835 Planarity : 0.004 0.040 1995 Dihedral : 8.110 127.540 1609 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.39 % Allowed : 15.48 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.22), residues: 1410 helix: -0.07 (0.22), residues: 574 sheet: -0.72 (0.33), residues: 230 loop : -1.30 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 755 TYR 0.022 0.001 TYR C 147 PHE 0.017 0.002 PHE A1205 TRP 0.008 0.001 TRP A1206 HIS 0.004 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (11795) covalent geometry : angle 0.60848 / 0.30 (15990) SS BOND : bond 0.00750 / 0.54 ( 2) SS BOND : angle 1.30344 / 0.75 ( 4) hydrogen bonds : bond 0.03770 / 2.46 ( 476) hydrogen bonds : angle 4.07389 / 2.90 ( 1365) Misc. bond : bond 0.00053 / 0.04 ( 1) link_BETA1-3 : bond 0.00894 / 0.60 ( 1) link_BETA1-3 : angle 1.42144 / 0.81 ( 3) link_BETA1-4 : bond 0.00288 / 0.18 ( 4) link_BETA1-4 : angle 1.27187 / 0.70 ( 12) link_NAG-ASN : bond 0.00440 / 0.31 ( 4) link_NAG-ASN : angle 1.81699 / 1.13 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4976.89 seconds wall clock time: 85 minutes 29.84 seconds (5129.84 seconds total)