Starting phenix.real_space_refine on Wed Jul 30 09:11:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vgi_31970/07_2025/7vgi_31970.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vgi_31970/07_2025/7vgi_31970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vgi_31970/07_2025/7vgi_31970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vgi_31970/07_2025/7vgi_31970.map" model { file = "/net/cci-nas-00/data/ceres_data/7vgi_31970/07_2025/7vgi_31970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vgi_31970/07_2025/7vgi_31970.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12 atoms to isotropic. 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 1 5.49 5 Mg 1 5.21 5 S 58 5.16 5 C 7828 2.51 5 N 2051 2.21 5 O 2235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12174 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2662 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 25, 'TRANS': 305} Chain: "B" Number of atoms: 9416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1162, 9416 Classifications: {'peptide': 1162} Link IDs: {'PTRANS': 31, 'TRANS': 1130} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.91, per 1000 atoms: 0.65 Number of scatterers: 12174 At special positions: 0 Unit cell: (107.06, 116.15, 163.62, 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 58 16.00 P 1 15.00 Mg 1 11.99 O 2235 8.00 N 2051 7.00 C 7828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 91 " - pdb=" SG CYS A 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG D 2 " - " MAN D 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 401 " - " ASN A 294 " " NAG A 402 " - " ASN A 107 " " NAG C 1 " - " ASN B 368 " " NAG D 1 " - " ASN A 180 " Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.6 seconds 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2820 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 11 sheets defined 39.7% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 46 through 51 removed outlier: 4.082A pdb=" N VAL A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.559A pdb=" N ILE A 56 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.780A pdb=" N PHE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 95 removed outlier: 4.081A pdb=" N LYS A 93 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS A 94 " --> pdb=" O CYS A 91 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 95 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 removed outlier: 3.858A pdb=" N LYS A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.789A pdb=" N LEU A 151 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 160 removed outlier: 3.770A pdb=" N CYS A 157 " --> pdb=" O SER A 154 " (cutoff:3.500A) Proline residue: A 159 - end of helix Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.676A pdb=" N ASN A 211 " --> pdb=" O TRP A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 250 through 253 removed outlier: 3.922A pdb=" N ILE A 253 " --> pdb=" O ASN A 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 250 through 253' Processing helix chain 'A' and resid 254 through 262 removed outlier: 3.593A pdb=" N TRP A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.512A pdb=" N ASP A 305 " --> pdb=" O HIS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 336 removed outlier: 4.355A pdb=" N GLY A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'B' and resid 72 through 76 removed outlier: 3.686A pdb=" N GLN B 76 " --> pdb=" O TYR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 118 through 131 removed outlier: 3.936A pdb=" N LEU B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 127 " --> pdb=" O TYR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 170 removed outlier: 3.555A pdb=" N THR B 155 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP B 163 " --> pdb=" O ASP B 159 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 165 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 190 through 194 Processing helix chain 'B' and resid 245 through 250 removed outlier: 3.697A pdb=" N TYR B 249 " --> pdb=" O ILE B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 291 No H-bonds generated for 'chain 'B' and resid 289 through 291' Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 335 through 364 removed outlier: 3.792A pdb=" N TYR B 339 " --> pdb=" O TYR B 335 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL B 341 " --> pdb=" O MET B 337 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 346 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 357 " --> pdb=" O ALA B 353 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY B 358 " --> pdb=" O GLY B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 390 removed outlier: 3.792A pdb=" N PHE B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 396 Processing helix chain 'B' and resid 397 through 399 No H-bonds generated for 'chain 'B' and resid 397 through 399' Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.806A pdb=" N GLU B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 415 Processing helix chain 'B' and resid 416 through 421 removed outlier: 4.173A pdb=" N ASN B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 448 removed outlier: 3.793A pdb=" N GLY B 446 " --> pdb=" O GLU B 443 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE B 448 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 519 removed outlier: 4.070A pdb=" N ILE B 513 " --> pdb=" O ASP B 509 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 531 Processing helix chain 'B' and resid 552 through 564 removed outlier: 3.532A pdb=" N ALA B 557 " --> pdb=" O PRO B 553 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 626 removed outlier: 3.607A pdb=" N ILE B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 626 " --> pdb=" O ASP B 622 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 621 through 626' Processing helix chain 'B' and resid 637 through 649 Processing helix chain 'B' and resid 664 through 678 removed outlier: 3.503A pdb=" N GLU B 668 " --> pdb=" O LYS B 664 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 672 " --> pdb=" O GLU B 668 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL B 678 " --> pdb=" O MET B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 692 removed outlier: 3.690A pdb=" N LYS B 689 " --> pdb=" O GLU B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 724 removed outlier: 3.663A pdb=" N LYS B 720 " --> pdb=" O GLU B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 746 Processing helix chain 'B' and resid 757 through 765 removed outlier: 3.565A pdb=" N ILE B 761 " --> pdb=" O TYR B 757 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN B 762 " --> pdb=" O GLY B 758 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER B 763 " --> pdb=" O GLU B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 770 Processing helix chain 'B' and resid 803 through 810 removed outlier: 3.554A pdb=" N GLU B 808 " --> pdb=" O SER B 804 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 810 " --> pdb=" O LEU B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 857 removed outlier: 3.888A pdb=" N LYS B 845 " --> pdb=" O ARG B 841 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 847 " --> pdb=" O GLU B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 860 No H-bonds generated for 'chain 'B' and resid 858 through 860' Processing helix chain 'B' and resid 869 through 881 removed outlier: 4.134A pdb=" N ALA B 874 " --> pdb=" O PRO B 870 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET B 875 " --> pdb=" O LYS B 871 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 880 " --> pdb=" O VAL B 876 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 881 " --> pdb=" O VAL B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 896 No H-bonds generated for 'chain 'B' and resid 894 through 896' Processing helix chain 'B' and resid 897 through 904 Processing helix chain 'B' and resid 928 through 930 No H-bonds generated for 'chain 'B' and resid 928 through 930' Processing helix chain 'B' and resid 931 through 938 Processing helix chain 'B' and resid 940 through 958 removed outlier: 3.620A pdb=" N ARG B 952 " --> pdb=" O CYS B 948 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR B 956 " --> pdb=" O ARG B 952 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN B 958 " --> pdb=" O PHE B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 963 removed outlier: 3.685A pdb=" N LEU B 963 " --> pdb=" O PHE B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 969 removed outlier: 3.802A pdb=" N TRP B 967 " --> pdb=" O LEU B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 972 No H-bonds generated for 'chain 'B' and resid 970 through 972' Processing helix chain 'B' and resid 994 through 1004 removed outlier: 3.933A pdb=" N LEU B 998 " --> pdb=" O SER B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1015 removed outlier: 3.946A pdb=" N ARG B1014 " --> pdb=" O LYS B1010 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE B1015 " --> pdb=" O LEU B1011 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1010 through 1015' Processing helix chain 'B' and resid 1016 through 1023 removed outlier: 3.565A pdb=" N VAL B1021 " --> pdb=" O LEU B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1039 Processing helix chain 'B' and resid 1042 through 1056 removed outlier: 3.837A pdb=" N PHE B1048 " --> pdb=" O SER B1044 " (cutoff:3.500A) Proline residue: B1051 - end of helix Processing helix chain 'B' and resid 1068 through 1085 removed outlier: 3.509A pdb=" N VAL B1074 " --> pdb=" O GLN B1070 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B1076 " --> pdb=" O PHE B1072 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B1077 " --> pdb=" O ALA B1073 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE B1082 " --> pdb=" O SER B1078 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR B1083 " --> pdb=" O ALA B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1106 through 1115 removed outlier: 3.660A pdb=" N PHE B1115 " --> pdb=" O PHE B1111 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1140 removed outlier: 3.918A pdb=" N LEU B1140 " --> pdb=" O ALA B1136 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1156 removed outlier: 4.175A pdb=" N ILE B1150 " --> pdb=" O TRP B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1161 through 1167 removed outlier: 3.512A pdb=" N LEU B1166 " --> pdb=" O ALA B1162 " (cutoff:3.500A) Processing helix chain 'B' and resid 1173 through 1181 removed outlier: 3.934A pdb=" N ILE B1178 " --> pdb=" O GLU B1174 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN B1179 " --> pdb=" O SER B1175 " (cutoff:3.500A) Processing helix chain 'B' and resid 1218 through 1224 removed outlier: 4.031A pdb=" N SER B1222 " --> pdb=" O ALA B1218 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 removed outlier: 3.760A pdb=" N ARG A 307 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL A 118 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LEU A 275 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N MET A 120 " --> pdb=" O TYR A 273 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 269 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 110 removed outlier: 3.777A pdb=" N GLY A 289 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 182 " --> pdb=" O THR A 296 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 163 removed outlier: 3.520A pdb=" N LYS A 166 " --> pdb=" O ASN A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 180 through 181 Processing sheet with id=AA5, first strand: chain 'B' and resid 200 through 203 removed outlier: 3.762A pdb=" N SER B 216 " --> pdb=" O HIS B 307 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B 309 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU B 214 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 237 through 241 removed outlier: 4.039A pdb=" N TYR B 225 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 277 through 279 removed outlier: 4.508A pdb=" N GLY B 277 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 435 through 436 Processing sheet with id=AA9, first strand: chain 'B' and resid 799 through 802 removed outlier: 6.129A pdb=" N LEU B 799 " --> pdb=" O ILE B 864 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N CYS B 866 " --> pdb=" O LEU B 799 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE B 801 " --> pdb=" O CYS B 866 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE B 728 " --> pdb=" O VAL B 863 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N CYS B 865 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL B 730 " --> pdb=" O CYS B 865 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE B 451 " --> pdb=" O TRP B 729 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU B 731 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N SER B 453 " --> pdb=" O LEU B 731 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR B 888 " --> pdb=" O ILE B 906 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N VAL B 908 " --> pdb=" O THR B 888 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ALA B 890 " --> pdb=" O VAL B 908 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 474 through 476 removed outlier: 3.710A pdb=" N GLN B 474 " --> pdb=" O ILE B 471 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS B 469 " --> pdb=" O TYR B 476 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU B 700 " --> pdb=" O TYR B 658 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TYR B 658 " --> pdb=" O LEU B 700 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY B 702 " --> pdb=" O LEU B 656 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 654 " --> pdb=" O THR B 704 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER B 604 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE B 593 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE B 606 " --> pdb=" O LEU B 591 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 571 " --> pdb=" O THR B 578 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER B 580 " --> pdb=" O PHE B 569 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE B 569 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 538 through 539 336 hydrogen bonds defined for protein. 921 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: 4.39 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3855 1.34 - 1.46: 2473 1.46 - 1.58: 6038 1.58 - 1.70: 0 1.70 - 1.81: 90 Bond restraints: 12456 Sorted by residual: bond pdb=" N ILE B 661 " pdb=" CA ILE B 661 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.59e+00 bond pdb=" N VAL B 66 " pdb=" CA VAL B 66 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.19e-02 7.06e+03 8.43e+00 bond pdb=" C LEU A 51 " pdb=" N PRO A 52 " ideal model delta sigma weight residual 1.331 1.352 -0.020 7.90e-03 1.60e+04 6.70e+00 bond pdb=" N MET B 834 " pdb=" CA MET B 834 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.38e-02 5.25e+03 6.67e+00 bond pdb=" N LYS B 67 " pdb=" CA LYS B 67 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.64e+00 ... (remaining 12451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 16254 1.75 - 3.50: 520 3.50 - 5.25: 66 5.25 - 6.99: 22 6.99 - 8.74: 6 Bond angle restraints: 16868 Sorted by residual: angle pdb=" N VAL B 410 " pdb=" CA VAL B 410 " pdb=" C VAL B 410 " ideal model delta sigma weight residual 112.96 107.39 5.57 1.00e+00 1.00e+00 3.11e+01 angle pdb=" N ILE A 253 " pdb=" CA ILE A 253 " pdb=" C ILE A 253 " ideal model delta sigma weight residual 112.29 108.42 3.87 9.40e-01 1.13e+00 1.70e+01 angle pdb=" N ILE A 53 " pdb=" CA ILE A 53 " pdb=" C ILE A 53 " ideal model delta sigma weight residual 113.39 108.26 5.13 1.47e+00 4.63e-01 1.22e+01 angle pdb=" C ARG B 835 " pdb=" N THR B 836 " pdb=" CA THR B 836 " ideal model delta sigma weight residual 121.54 114.90 6.64 1.91e+00 2.74e-01 1.21e+01 angle pdb=" CA ARG B 833 " pdb=" C ARG B 833 " pdb=" O ARG B 833 " ideal model delta sigma weight residual 120.81 116.64 4.17 1.24e+00 6.50e-01 1.13e+01 ... (remaining 16863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.68: 6919 22.68 - 45.36: 517 45.36 - 68.04: 52 68.04 - 90.73: 19 90.73 - 113.41: 10 Dihedral angle restraints: 7517 sinusoidal: 3140 harmonic: 4377 Sorted by residual: dihedral pdb=" CA GLN B 787 " pdb=" C GLN B 787 " pdb=" N GLU B 788 " pdb=" CA GLU B 788 " ideal model delta harmonic sigma weight residual 180.00 150.93 29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA THR B 398 " pdb=" C THR B 398 " pdb=" N MET B 399 " pdb=" CA MET B 399 " ideal model delta harmonic sigma weight residual 180.00 153.40 26.60 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA ARG B 652 " pdb=" C ARG B 652 " pdb=" N THR B 653 " pdb=" CA THR B 653 " ideal model delta harmonic sigma weight residual -180.00 -155.28 -24.72 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 7514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1813 0.107 - 0.213: 64 0.213 - 0.320: 1 0.320 - 0.427: 0 0.427 - 0.534: 1 Chirality restraints: 1879 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN B 368 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.12e+00 chirality pdb=" CB ILE B 136 " pdb=" CA ILE B 136 " pdb=" CG1 ILE B 136 " pdb=" CG2 ILE B 136 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C2 NAG C 1 " pdb=" C1 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" N2 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.29 -0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1876 not shown) Planarity restraints: 2140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 659 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.16e+00 pdb=" C LYS B 659 " 0.052 2.00e-02 2.50e+03 pdb=" O LYS B 659 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU B 660 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 246 " -0.046 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO A 247 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1191 " -0.027 2.00e-02 2.50e+03 1.57e-02 6.19e+00 pdb=" CG TRP B1191 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP B1191 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP B1191 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B1191 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B1191 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B1191 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1191 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1191 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B1191 " -0.003 2.00e-02 2.50e+03 ... (remaining 2137 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 137 2.61 - 3.18: 10410 3.18 - 3.75: 16903 3.75 - 4.33: 25489 4.33 - 4.90: 41653 Nonbonded interactions: 94592 Sorted by model distance: nonbonded pdb=" OD2 PHD B 454 " pdb="MG MG B1401 " model vdw 2.032 2.170 nonbonded pdb=" OE2 GLU B 829 " pdb=" N THR B 836 " model vdw 2.083 3.120 nonbonded pdb=" O LEU B 279 " pdb=" OG SER B 285 " model vdw 2.138 3.040 nonbonded pdb=" O PRO A 287 " pdb=" OH TYR A 291 " model vdw 2.174 3.040 nonbonded pdb=" OG SER B 416 " pdb=" OD1 ASN B 442 " model vdw 2.216 3.040 ... (remaining 94587 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 32.260 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.005 0.047 12464 Z= 0.243 Angle : 0.772 12.621 16891 Z= 0.422 Chirality : 0.049 0.534 1879 Planarity : 0.004 0.069 2136 Dihedral : 16.047 113.407 4694 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.46 % Favored : 89.34 % Rotamer: Outliers : 0.38 % Allowed : 0.76 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.18), residues: 1482 helix: -3.53 (0.16), residues: 556 sheet: -0.92 (0.40), residues: 168 loop : -2.91 (0.20), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B1191 HIS 0.005 0.001 HIS B1039 PHE 0.026 0.002 PHE B 275 TYR 0.025 0.002 TYR B 142 ARG 0.006 0.001 ARG B 946 Details of bonding type rmsd link_NAG-ASN : bond 0.01402 ( 4) link_NAG-ASN : angle 5.92664 ( 12) link_ALPHA1-4 : bond 0.00753 ( 1) link_ALPHA1-4 : angle 3.56799 ( 3) link_BETA1-4 : bond 0.00895 ( 2) link_BETA1-4 : angle 2.75904 ( 6) hydrogen bonds : bond 0.30191 ( 336) hydrogen bonds : angle 9.99362 ( 921) SS BOND : bond 0.00340 ( 1) SS BOND : angle 0.69816 ( 2) covalent geometry : bond 0.00534 (12456) covalent geometry : angle 0.75255 (16868) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 1.478 Fit side-chains TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. REVERT: B 198 ASP cc_start: 0.7779 (m-30) cc_final: 0.7442 (m-30) REVERT: B 511 TYR cc_start: 0.7694 (t80) cc_final: 0.7070 (t80) outliers start: 5 outliers final: 1 residues processed: 133 average time/residue: 0.2630 time to fit residues: 51.2999 Evaluate side-chains 114 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 692 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 913 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.158849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126160 restraints weight = 14675.477| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.72 r_work: 0.2826 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 12464 Z= 0.159 Angle : 0.680 11.339 16891 Z= 0.352 Chirality : 0.047 0.367 1879 Planarity : 0.005 0.048 2136 Dihedral : 10.092 97.129 1789 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 0.69 % Allowed : 7.47 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.20), residues: 1482 helix: -2.35 (0.19), residues: 556 sheet: -0.38 (0.41), residues: 164 loop : -2.81 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B1191 HIS 0.003 0.001 HIS B 510 PHE 0.022 0.001 PHE B 666 TYR 0.016 0.001 TYR B 142 ARG 0.010 0.000 ARG B 835 Details of bonding type rmsd link_NAG-ASN : bond 0.01148 ( 4) link_NAG-ASN : angle 5.25341 ( 12) link_ALPHA1-4 : bond 0.01584 ( 1) link_ALPHA1-4 : angle 3.24986 ( 3) link_BETA1-4 : bond 0.00367 ( 2) link_BETA1-4 : angle 2.21003 ( 6) hydrogen bonds : bond 0.05323 ( 336) hydrogen bonds : angle 5.93036 ( 921) SS BOND : bond 0.00407 ( 1) SS BOND : angle 1.15902 ( 2) covalent geometry : bond 0.00369 (12456) covalent geometry : angle 0.66295 (16868) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 1.395 Fit side-chains TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. REVERT: B 128 LEU cc_start: 0.8723 (tp) cc_final: 0.8493 (tt) REVERT: B 198 ASP cc_start: 0.8245 (m-30) cc_final: 0.7903 (m-30) REVERT: B 658 TYR cc_start: 0.8020 (p90) cc_final: 0.7643 (p90) REVERT: B 685 GLU cc_start: 0.7192 (pm20) cc_final: 0.6888 (tt0) REVERT: B 688 ASP cc_start: 0.7393 (t0) cc_final: 0.6702 (t70) outliers start: 9 outliers final: 7 residues processed: 126 average time/residue: 0.2428 time to fit residues: 45.4896 Evaluate side-chains 114 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 1027 LEU Chi-restraints excluded: chain B residue 1052 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 92 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 31 optimal weight: 0.0060 chunk 124 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 461 GLN B 479 HIS B 913 GLN B1138 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.157434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.128157 restraints weight = 15002.413| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.63 r_work: 0.2800 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12464 Z= 0.194 Angle : 0.681 10.040 16891 Z= 0.346 Chirality : 0.047 0.311 1879 Planarity : 0.004 0.048 2136 Dihedral : 9.008 88.422 1789 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 1.14 % Allowed : 10.98 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.20), residues: 1482 helix: -1.84 (0.21), residues: 559 sheet: -0.45 (0.40), residues: 174 loop : -2.78 (0.20), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B1191 HIS 0.005 0.001 HIS B 479 PHE 0.022 0.002 PHE B 666 TYR 0.015 0.002 TYR B 123 ARG 0.004 0.000 ARG B 946 Details of bonding type rmsd link_NAG-ASN : bond 0.00938 ( 4) link_NAG-ASN : angle 4.63606 ( 12) link_ALPHA1-4 : bond 0.01411 ( 1) link_ALPHA1-4 : angle 3.54807 ( 3) link_BETA1-4 : bond 0.00391 ( 2) link_BETA1-4 : angle 2.43660 ( 6) hydrogen bonds : bond 0.04668 ( 336) hydrogen bonds : angle 5.26155 ( 921) SS BOND : bond 0.00365 ( 1) SS BOND : angle 0.97122 ( 2) covalent geometry : bond 0.00471 (12456) covalent geometry : angle 0.66709 (16868) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 1.492 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. REVERT: A 207 TRP cc_start: 0.8357 (t60) cc_final: 0.8136 (t60) REVERT: B 198 ASP cc_start: 0.8314 (m-30) cc_final: 0.7900 (m-30) REVERT: B 648 ASN cc_start: 0.8162 (t0) cc_final: 0.7816 (t0) REVERT: B 658 TYR cc_start: 0.8166 (p90) cc_final: 0.7910 (p90) REVERT: B 688 ASP cc_start: 0.7310 (t0) cc_final: 0.6609 (t70) outliers start: 15 outliers final: 9 residues processed: 126 average time/residue: 0.2503 time to fit residues: 47.2634 Evaluate side-chains 117 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 1027 LEU Chi-restraints excluded: chain B residue 1052 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 32 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 131 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 28 optimal weight: 0.0870 chunk 114 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN B 359 HIS B 442 ASN B 479 HIS B 575 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.162226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.132095 restraints weight = 14602.357| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.58 r_work: 0.2884 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12464 Z= 0.105 Angle : 0.588 9.739 16891 Z= 0.299 Chirality : 0.044 0.324 1879 Planarity : 0.004 0.052 2136 Dihedral : 7.947 90.822 1786 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 1.07 % Allowed : 13.03 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.21), residues: 1482 helix: -1.35 (0.22), residues: 549 sheet: -0.13 (0.41), residues: 164 loop : -2.57 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1191 HIS 0.003 0.001 HIS B 359 PHE 0.022 0.001 PHE B 280 TYR 0.013 0.001 TYR B 658 ARG 0.002 0.000 ARG B 833 Details of bonding type rmsd link_NAG-ASN : bond 0.00909 ( 4) link_NAG-ASN : angle 4.02009 ( 12) link_ALPHA1-4 : bond 0.01619 ( 1) link_ALPHA1-4 : angle 3.36710 ( 3) link_BETA1-4 : bond 0.00413 ( 2) link_BETA1-4 : angle 1.64702 ( 6) hydrogen bonds : bond 0.03246 ( 336) hydrogen bonds : angle 4.83973 ( 921) SS BOND : bond 0.00299 ( 1) SS BOND : angle 0.91936 ( 2) covalent geometry : bond 0.00228 (12456) covalent geometry : angle 0.57548 (16868) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 1.439 Fit side-chains TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. REVERT: A 56 ILE cc_start: 0.8769 (mm) cc_final: 0.8463 (mt) REVERT: B 67 LYS cc_start: 0.8032 (tptm) cc_final: 0.7720 (tptt) REVERT: B 110 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7553 (mtt) REVERT: B 198 ASP cc_start: 0.8249 (m-30) cc_final: 0.7854 (m-30) REVERT: B 479 HIS cc_start: 0.5249 (OUTLIER) cc_final: 0.5035 (m-70) REVERT: B 490 ILE cc_start: 0.6009 (OUTLIER) cc_final: 0.5201 (mt) REVERT: B 528 PHE cc_start: 0.8181 (m-80) cc_final: 0.7906 (m-80) REVERT: B 648 ASN cc_start: 0.8028 (t0) cc_final: 0.7679 (t0) REVERT: B 685 GLU cc_start: 0.7591 (pm20) cc_final: 0.6917 (tt0) REVERT: B 688 ASP cc_start: 0.7337 (t0) cc_final: 0.6560 (t0) REVERT: B 760 ASP cc_start: 0.6945 (t0) cc_final: 0.6679 (t0) REVERT: B 842 LEU cc_start: 0.7750 (mm) cc_final: 0.7474 (mt) REVERT: B 1088 ILE cc_start: 0.9069 (tp) cc_final: 0.8799 (tp) outliers start: 14 outliers final: 5 residues processed: 137 average time/residue: 0.2345 time to fit residues: 48.1129 Evaluate side-chains 123 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 479 HIS Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 749 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 54 optimal weight: 10.0000 chunk 12 optimal weight: 0.1980 chunk 148 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 7 optimal weight: 0.1980 chunk 142 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 479 HIS B 575 ASN ** B1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.160020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.130398 restraints weight = 14658.304| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.58 r_work: 0.2840 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12464 Z= 0.138 Angle : 0.607 10.369 16891 Z= 0.306 Chirality : 0.045 0.315 1879 Planarity : 0.004 0.050 2136 Dihedral : 7.532 87.166 1786 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 1.30 % Allowed : 14.33 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.21), residues: 1482 helix: -1.21 (0.22), residues: 549 sheet: -0.06 (0.41), residues: 164 loop : -2.55 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 207 HIS 0.004 0.001 HIS B1039 PHE 0.024 0.001 PHE B 666 TYR 0.012 0.001 TYR B 123 ARG 0.003 0.000 ARG B 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00984 ( 4) link_NAG-ASN : angle 4.48669 ( 12) link_ALPHA1-4 : bond 0.01549 ( 1) link_ALPHA1-4 : angle 3.50798 ( 3) link_BETA1-4 : bond 0.00364 ( 2) link_BETA1-4 : angle 2.32445 ( 6) hydrogen bonds : bond 0.03563 ( 336) hydrogen bonds : angle 4.72418 ( 921) SS BOND : bond 0.00304 ( 1) SS BOND : angle 0.84682 ( 2) covalent geometry : bond 0.00328 (12456) covalent geometry : angle 0.59224 (16868) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 1.350 Fit side-chains TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. REVERT: A 56 ILE cc_start: 0.8766 (mm) cc_final: 0.8414 (mt) REVERT: B 110 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7610 (mtt) REVERT: B 198 ASP cc_start: 0.8270 (m-30) cc_final: 0.7859 (m-30) REVERT: B 490 ILE cc_start: 0.6072 (OUTLIER) cc_final: 0.5272 (mt) REVERT: B 528 PHE cc_start: 0.8202 (m-80) cc_final: 0.7943 (m-80) REVERT: B 648 ASN cc_start: 0.8058 (t0) cc_final: 0.7726 (t0) REVERT: B 688 ASP cc_start: 0.7202 (t0) cc_final: 0.6442 (t0) REVERT: B 760 ASP cc_start: 0.7020 (t0) cc_final: 0.6748 (t0) REVERT: B 842 LEU cc_start: 0.7693 (mm) cc_final: 0.7398 (mt) REVERT: B 1088 ILE cc_start: 0.9131 (tp) cc_final: 0.8829 (tp) REVERT: B 1113 ILE cc_start: 0.8058 (tt) cc_final: 0.7693 (tt) outliers start: 17 outliers final: 10 residues processed: 130 average time/residue: 0.2624 time to fit residues: 51.1881 Evaluate side-chains 126 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 479 HIS Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 1052 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 58 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 479 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.158103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.133304 restraints weight = 14968.923| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.37 r_work: 0.2921 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12464 Z= 0.196 Angle : 0.645 10.274 16891 Z= 0.326 Chirality : 0.047 0.302 1879 Planarity : 0.004 0.047 2136 Dihedral : 7.367 80.886 1786 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 1.52 % Allowed : 14.79 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.21), residues: 1482 helix: -1.24 (0.22), residues: 551 sheet: -0.04 (0.41), residues: 165 loop : -2.63 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B1191 HIS 0.005 0.001 HIS B1039 PHE 0.025 0.001 PHE B 666 TYR 0.015 0.001 TYR B 123 ARG 0.003 0.000 ARG B 867 Details of bonding type rmsd link_NAG-ASN : bond 0.00975 ( 4) link_NAG-ASN : angle 4.22469 ( 12) link_ALPHA1-4 : bond 0.01528 ( 1) link_ALPHA1-4 : angle 3.66909 ( 3) link_BETA1-4 : bond 0.00351 ( 2) link_BETA1-4 : angle 2.32230 ( 6) hydrogen bonds : bond 0.04007 ( 336) hydrogen bonds : angle 4.75694 ( 921) SS BOND : bond 0.00322 ( 1) SS BOND : angle 0.75944 ( 2) covalent geometry : bond 0.00479 (12456) covalent geometry : angle 0.63182 (16868) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 1.367 Fit side-chains REVERT: B 110 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7722 (mtt) REVERT: B 198 ASP cc_start: 0.8364 (m-30) cc_final: 0.7984 (m-30) REVERT: B 490 ILE cc_start: 0.6246 (OUTLIER) cc_final: 0.5363 (mt) REVERT: B 648 ASN cc_start: 0.8098 (t0) cc_final: 0.7786 (t0) REVERT: B 760 ASP cc_start: 0.7019 (t0) cc_final: 0.6739 (t0) REVERT: B 842 LEU cc_start: 0.7760 (mm) cc_final: 0.7467 (mt) REVERT: B 1088 ILE cc_start: 0.9175 (tp) cc_final: 0.8874 (tp) outliers start: 20 outliers final: 15 residues processed: 124 average time/residue: 0.2396 time to fit residues: 44.1425 Evaluate side-chains 123 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 1027 LEU Chi-restraints excluded: chain B residue 1052 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 5 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 104 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 100 optimal weight: 0.4980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.161926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.132208 restraints weight = 14638.150| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.53 r_work: 0.2994 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12464 Z= 0.106 Angle : 0.576 9.835 16891 Z= 0.290 Chirality : 0.044 0.317 1879 Planarity : 0.004 0.049 2136 Dihedral : 6.793 75.652 1786 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 1.22 % Allowed : 15.70 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.21), residues: 1482 helix: -0.87 (0.23), residues: 540 sheet: 0.09 (0.40), residues: 165 loop : -2.44 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 207 HIS 0.003 0.001 HIS B 449 PHE 0.024 0.001 PHE B 666 TYR 0.010 0.001 TYR B 123 ARG 0.003 0.000 ARG B 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00953 ( 4) link_NAG-ASN : angle 3.91975 ( 12) link_ALPHA1-4 : bond 0.01857 ( 1) link_ALPHA1-4 : angle 3.73906 ( 3) link_BETA1-4 : bond 0.00343 ( 2) link_BETA1-4 : angle 1.67145 ( 6) hydrogen bonds : bond 0.03078 ( 336) hydrogen bonds : angle 4.52424 ( 921) SS BOND : bond 0.00253 ( 1) SS BOND : angle 0.80918 ( 2) covalent geometry : bond 0.00238 (12456) covalent geometry : angle 0.56415 (16868) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.402 Fit side-chains REVERT: B 110 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7708 (mtt) REVERT: B 185 ARG cc_start: 0.7890 (ptp-110) cc_final: 0.7631 (ptp-170) REVERT: B 198 ASP cc_start: 0.8288 (m-30) cc_final: 0.7970 (m-30) REVERT: B 464 MET cc_start: 0.7926 (mmt) cc_final: 0.7409 (mmt) REVERT: B 490 ILE cc_start: 0.6178 (OUTLIER) cc_final: 0.5337 (mt) REVERT: B 648 ASN cc_start: 0.8050 (t0) cc_final: 0.7778 (t0) REVERT: B 760 ASP cc_start: 0.6958 (t0) cc_final: 0.6662 (t0) REVERT: B 842 LEU cc_start: 0.7706 (mm) cc_final: 0.7422 (mt) REVERT: B 1113 ILE cc_start: 0.8053 (tt) cc_final: 0.7683 (tt) outliers start: 16 outliers final: 8 residues processed: 133 average time/residue: 0.2699 time to fit residues: 53.3641 Evaluate side-chains 125 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 540 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 93 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 43 optimal weight: 0.0770 chunk 33 optimal weight: 0.0870 chunk 9 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 143 optimal weight: 0.1980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.164104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.133556 restraints weight = 14844.054| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.66 r_work: 0.3019 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 12464 Z= 0.098 Angle : 0.573 9.747 16891 Z= 0.285 Chirality : 0.043 0.317 1879 Planarity : 0.003 0.047 2136 Dihedral : 6.227 62.757 1786 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.07 % Allowed : 16.62 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.22), residues: 1482 helix: -0.59 (0.23), residues: 540 sheet: 0.35 (0.41), residues: 162 loop : -2.30 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 207 HIS 0.003 0.001 HIS B 167 PHE 0.020 0.001 PHE B 666 TYR 0.009 0.001 TYR B 691 ARG 0.003 0.000 ARG B 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00849 ( 4) link_NAG-ASN : angle 3.70069 ( 12) link_ALPHA1-4 : bond 0.01971 ( 1) link_ALPHA1-4 : angle 3.88459 ( 3) link_BETA1-4 : bond 0.00348 ( 2) link_BETA1-4 : angle 1.55792 ( 6) hydrogen bonds : bond 0.02805 ( 336) hydrogen bonds : angle 4.41982 ( 921) SS BOND : bond 0.00025 ( 1) SS BOND : angle 0.88281 ( 2) covalent geometry : bond 0.00213 (12456) covalent geometry : angle 0.56174 (16868) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 1.330 Fit side-chains TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. REVERT: B 110 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7814 (mtt) REVERT: B 198 ASP cc_start: 0.8251 (m-30) cc_final: 0.7928 (m-30) REVERT: B 490 ILE cc_start: 0.6174 (OUTLIER) cc_final: 0.5393 (mt) REVERT: B 603 MET cc_start: 0.8634 (ttp) cc_final: 0.8371 (ttm) REVERT: B 648 ASN cc_start: 0.7961 (t0) cc_final: 0.7677 (t0) REVERT: B 760 ASP cc_start: 0.7039 (t0) cc_final: 0.6703 (t0) REVERT: B 842 LEU cc_start: 0.7633 (mm) cc_final: 0.7361 (mt) REVERT: B 1113 ILE cc_start: 0.7944 (tt) cc_final: 0.7563 (tt) outliers start: 14 outliers final: 9 residues processed: 134 average time/residue: 0.2570 time to fit residues: 51.2596 Evaluate side-chains 123 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 749 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 86 optimal weight: 0.1980 chunk 72 optimal weight: 0.5980 chunk 33 optimal weight: 0.0010 chunk 6 optimal weight: 0.0570 chunk 37 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 overall best weight: 0.9706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.163703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.133173 restraints weight = 14800.929| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.71 r_work: 0.3021 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12464 Z= 0.105 Angle : 0.566 9.823 16891 Z= 0.283 Chirality : 0.043 0.305 1879 Planarity : 0.003 0.047 2136 Dihedral : 5.783 55.352 1786 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 1.14 % Allowed : 16.92 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.22), residues: 1482 helix: -0.48 (0.23), residues: 546 sheet: 0.41 (0.41), residues: 162 loop : -2.28 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 207 HIS 0.002 0.001 HIS B 359 PHE 0.025 0.001 PHE B 666 TYR 0.009 0.001 TYR B 691 ARG 0.002 0.000 ARG B 867 Details of bonding type rmsd link_NAG-ASN : bond 0.00790 ( 4) link_NAG-ASN : angle 3.53194 ( 12) link_ALPHA1-4 : bond 0.02097 ( 1) link_ALPHA1-4 : angle 4.16173 ( 3) link_BETA1-4 : bond 0.00357 ( 2) link_BETA1-4 : angle 1.68559 ( 6) hydrogen bonds : bond 0.02927 ( 336) hydrogen bonds : angle 4.36032 ( 921) SS BOND : bond 0.00218 ( 1) SS BOND : angle 0.77253 ( 2) covalent geometry : bond 0.00238 (12456) covalent geometry : angle 0.55502 (16868) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 2.502 Fit side-chains TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. REVERT: B 110 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7828 (mtt) REVERT: B 198 ASP cc_start: 0.8280 (m-30) cc_final: 0.7942 (m-30) REVERT: B 490 ILE cc_start: 0.6195 (OUTLIER) cc_final: 0.5398 (mt) REVERT: B 603 MET cc_start: 0.8665 (ttp) cc_final: 0.8411 (ttm) REVERT: B 648 ASN cc_start: 0.7954 (t0) cc_final: 0.7675 (t0) REVERT: B 694 ILE cc_start: 0.7709 (mt) cc_final: 0.7460 (mt) REVERT: B 760 ASP cc_start: 0.7059 (t0) cc_final: 0.6728 (t0) REVERT: B 842 LEU cc_start: 0.7673 (mm) cc_final: 0.7374 (mt) REVERT: B 1113 ILE cc_start: 0.7972 (tt) cc_final: 0.7590 (tt) outliers start: 15 outliers final: 11 residues processed: 124 average time/residue: 0.3260 time to fit residues: 62.4561 Evaluate side-chains 123 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 575 ASN Chi-restraints excluded: chain B residue 749 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 79 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 71 optimal weight: 0.4980 chunk 56 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1085 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.158194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127710 restraints weight = 14830.758| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.74 r_work: 0.2788 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12464 Z= 0.213 Angle : 0.667 10.235 16891 Z= 0.336 Chirality : 0.048 0.304 1879 Planarity : 0.004 0.044 2136 Dihedral : 5.973 55.954 1786 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 1.45 % Allowed : 16.92 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.21), residues: 1482 helix: -0.90 (0.22), residues: 561 sheet: 0.02 (0.39), residues: 175 loop : -2.48 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B1191 HIS 0.007 0.001 HIS B 965 PHE 0.026 0.002 PHE B 666 TYR 0.016 0.002 TYR A 122 ARG 0.005 0.000 ARG B 946 Details of bonding type rmsd link_NAG-ASN : bond 0.00727 ( 4) link_NAG-ASN : angle 3.48999 ( 12) link_ALPHA1-4 : bond 0.01826 ( 1) link_ALPHA1-4 : angle 4.48886 ( 3) link_BETA1-4 : bond 0.00399 ( 2) link_BETA1-4 : angle 2.61427 ( 6) hydrogen bonds : bond 0.04211 ( 336) hydrogen bonds : angle 4.61342 ( 921) SS BOND : bond 0.00310 ( 1) SS BOND : angle 0.63553 ( 2) covalent geometry : bond 0.00523 (12456) covalent geometry : angle 0.65594 (16868) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.432 Fit side-chains TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. REVERT: B 198 ASP cc_start: 0.8260 (m-30) cc_final: 0.7790 (m-30) REVERT: B 464 MET cc_start: 0.7841 (mmt) cc_final: 0.7214 (mmt) REVERT: B 603 MET cc_start: 0.8730 (ttp) cc_final: 0.8457 (ttm) REVERT: B 648 ASN cc_start: 0.8022 (t0) cc_final: 0.7714 (t0) REVERT: B 694 ILE cc_start: 0.7833 (mt) cc_final: 0.7561 (mt) REVERT: B 760 ASP cc_start: 0.7072 (t0) cc_final: 0.6740 (t0) REVERT: B 842 LEU cc_start: 0.7636 (mm) cc_final: 0.7359 (mt) REVERT: B 913 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6660 (mt0) outliers start: 19 outliers final: 14 residues processed: 126 average time/residue: 0.2551 time to fit residues: 48.3741 Evaluate side-chains 121 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 575 ASN Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 913 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 63 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 78 optimal weight: 0.0170 chunk 15 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 90 optimal weight: 0.1980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.162997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.131993 restraints weight = 14638.313| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.62 r_work: 0.3038 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12464 Z= 0.100 Angle : 0.571 9.702 16891 Z= 0.288 Chirality : 0.043 0.307 1879 Planarity : 0.003 0.049 2136 Dihedral : 5.527 55.205 1786 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.91 % Allowed : 17.61 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.22), residues: 1482 helix: -0.44 (0.23), residues: 546 sheet: 0.36 (0.41), residues: 165 loop : -2.31 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 207 HIS 0.004 0.001 HIS B 965 PHE 0.022 0.001 PHE B 666 TYR 0.010 0.001 TYR B 658 ARG 0.002 0.000 ARG B 572 Details of bonding type rmsd link_NAG-ASN : bond 0.00811 ( 4) link_NAG-ASN : angle 3.31247 ( 12) link_ALPHA1-4 : bond 0.01695 ( 1) link_ALPHA1-4 : angle 4.57173 ( 3) link_BETA1-4 : bond 0.00335 ( 2) link_BETA1-4 : angle 1.76284 ( 6) hydrogen bonds : bond 0.02883 ( 336) hydrogen bonds : angle 4.41067 ( 921) SS BOND : bond 0.00193 ( 1) SS BOND : angle 0.79497 ( 2) covalent geometry : bond 0.00219 (12456) covalent geometry : angle 0.56061 (16868) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6365.59 seconds wall clock time: 116 minutes 9.52 seconds (6969.52 seconds total)