Starting phenix.real_space_refine on Fri Jul 3 07:02:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7a65_11666/07_2026/7a65_11666.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a65_11666/07_2026/7a65_11666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7a65_11666/07_2026/7a65_11666.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a65_11666/07_2026/7a65_11666.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7a65_11666/07_2026/7a65_11666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a65_11666/07_2026/7a65_11666.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7a65_11666/07_2026/7a65_11666.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7a65_11666/07_2026/7a65_11666.cif" } resolution = 3.9 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= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 8075 2.51 5 N 2086 2.21 5 O 2310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 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: 12521 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9050 Classifications: {'peptide': 1164} Link IDs: {'PTRANS': 27, 'TRANS': 1136} Chain breaks: 2 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1656 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CYS%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1647 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PRO%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'CLR': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 2.69, per 1000 atoms: 0.21 Number of scatterers: 12521 At special positions: 0 Unit cell: (102.48, 207.48, 99.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 2310 8.00 N 2086 7.00 C 8075 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.05 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 201 " 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 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 554.3 milliseconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 14 sheets defined 53.9% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 35 through 40 removed outlier: 3.705A pdb=" N PHE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 82 removed outlier: 4.504A pdb=" N LEU A 65 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Proline residue: A 66 - end of helix removed outlier: 3.693A pdb=" N ASN A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 158 removed outlier: 3.642A pdb=" N TRP A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 166 Processing helix chain 'A' and resid 167 through 187 removed outlier: 4.128A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR A 176 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 211 removed outlier: 4.292A pdb=" N GLY A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.708A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 237 Processing helix chain 'A' and resid 240 through 260 removed outlier: 3.697A pdb=" N LEU A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 267 Processing helix chain 'A' and resid 269 through 323 removed outlier: 3.544A pdb=" N LEU A 274 " --> pdb=" O GLN A 270 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 284 " --> pdb=" O ASN A 280 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 348 removed outlier: 4.036A pdb=" N GLY A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 371 removed outlier: 3.680A pdb=" N ILE A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 457 through 461 removed outlier: 3.752A pdb=" N THR A 460 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 469 removed outlier: 3.810A pdb=" N ILE A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 496 through 508 Processing helix chain 'A' and resid 510 through 516 removed outlier: 3.585A pdb=" N LEU A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 529 removed outlier: 3.653A pdb=" N GLY A 528 " --> pdb=" O GLY A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 546 Processing helix chain 'A' and resid 562 through 576 Processing helix chain 'A' and resid 588 through 592 removed outlier: 3.822A pdb=" N THR A 591 " --> pdb=" O ARG A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 619 removed outlier: 3.522A pdb=" N LYS A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 699 through 706 removed outlier: 3.525A pdb=" N ASN A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 723 removed outlier: 3.914A pdb=" N PHE A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 741 removed outlier: 3.627A pdb=" N ALA A 727 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 739 " --> pdb=" O ILE A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 799 Processing helix chain 'A' and resid 800 through 806 removed outlier: 3.536A pdb=" N PHE A 804 " --> pdb=" O ASP A 800 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 806 " --> pdb=" O SER A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 810 removed outlier: 3.573A pdb=" N THR A 810 " --> pdb=" O PRO A 807 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 807 through 810' Processing helix chain 'A' and resid 811 through 854 removed outlier: 3.647A pdb=" N LEU A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 819 " --> pdb=" O THR A 815 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 824 " --> pdb=" O ASN A 820 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS A 826 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER A 831 " --> pdb=" O GLY A 827 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ARG A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 863 removed outlier: 3.638A pdb=" N THR A 858 " --> pdb=" O GLY A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 881 removed outlier: 3.600A pdb=" N ILE A 868 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 903 removed outlier: 3.540A pdb=" N ILE A 901 " --> pdb=" O ALA A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 906 No H-bonds generated for 'chain 'A' and resid 904 through 906' Processing helix chain 'A' and resid 912 through 966 removed outlier: 4.582A pdb=" N VAL A 926 " --> pdb=" O GLN A 922 " (cutoff:3.500A) Proline residue: A 927 - end of helix removed outlier: 4.457A pdb=" N TYR A 950 " --> pdb=" O GLN A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 995 removed outlier: 3.633A pdb=" N ALA A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1014 removed outlier: 3.625A pdb=" N ALA A1001 " --> pdb=" O ASP A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1084 removed outlier: 4.246A pdb=" N VAL A1080 " --> pdb=" O LYS A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1113 removed outlier: 3.968A pdb=" N LEU A1109 " --> pdb=" O ASN A1105 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A1110 " --> pdb=" O VAL A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1133 Processing helix chain 'A' and resid 1141 through 1152 Processing helix chain 'A' and resid 1154 through 1160 Processing helix chain 'A' and resid 1163 through 1167 removed outlier: 3.996A pdb=" N THR A1167 " --> pdb=" O LYS A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1174 removed outlier: 3.728A pdb=" N GLY A1173 " --> pdb=" O GLY A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1191 Processing helix chain 'A' and resid 1207 through 1222 removed outlier: 3.902A pdb=" N LYS A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A1213 " --> pdb=" O GLU A1209 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A1218 " --> pdb=" O VAL A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1239 removed outlier: 4.205A pdb=" N ASN A1239 " --> pdb=" O SER A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1263 Processing helix chain 'A' and resid 1265 through 1272 removed outlier: 3.535A pdb=" N SER A1269 " --> pdb=" O GLY A1265 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 132 removed outlier: 3.593A pdb=" N SER B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.656A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 4.082A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 206 through 209 Processing sheet with id=AA1, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA2, first strand: chain 'A' and resid 470 through 473 removed outlier: 6.636A pdb=" N GLY A 471 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ASP A 555 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL A 473 " --> pdb=" O ASP A 555 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A 423 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR A 422 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ALA A 599 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA A 424 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE A 601 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 426 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLY A 600 " --> pdb=" O VAL A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1056 through 1060 removed outlier: 5.167A pdb=" N LEU A1056 " --> pdb=" O GLU A1039 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL A1040 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ALA A1091 " --> pdb=" O VAL A1040 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1114 through 1115 removed outlier: 3.638A pdb=" N GLY A1114 " --> pdb=" O ILE A1196 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A1198 " --> pdb=" O GLY A1114 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A1068 " --> pdb=" O VAL A1229 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A1245 " --> pdb=" O LYS A1252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 14 Processing sheet with id=AA7, first strand: chain 'B' and resid 50 through 53 removed outlier: 6.528A pdb=" N TRP B 40 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR B 102 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 119 through 123 removed outlier: 3.565A pdb=" N ASN B 142 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N TYR B 178 " --> pdb=" O ASN B 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 159 through 161 removed outlier: 4.257A pdb=" N TRP B 153 " --> pdb=" O GLN B 161 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.812A pdb=" N MET C 34 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N THR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.635A pdb=" N LEU C 130 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N TYR C 181 " --> pdb=" O GLY C 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.635A pdb=" N LEU C 130 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N TYR C 181 " --> pdb=" O GLY C 150 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 160 731 hydrogen bonds defined for protein. 2085 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: 2.64 Time building geometry restraints manager: 1.30 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: 3974 1.34 - 1.46: 2940 1.46 - 1.58: 5788 1.58 - 1.70: 0 1.70 - 1.82: 83 Bond restraints: 12785 Sorted by residual: bond pdb=" C TYR A1087 " pdb=" N ASP A1088 " ideal model delta sigma weight residual 1.333 1.300 0.033 1.61e-02 3.86e+03 4.24e+00 bond pdb=" C ALA B 116 " pdb=" N ALA B 117 " ideal model delta sigma weight residual 1.339 1.246 0.093 5.57e-02 3.22e+02 2.81e+00 bond pdb=" C13 CLR A1303 " pdb=" C17 CLR A1303 " ideal model delta sigma weight residual 1.550 1.517 0.033 2.00e-02 2.50e+03 2.69e+00 bond pdb=" C10 CLR A1303 " pdb=" C9 CLR A1303 " ideal model delta sigma weight residual 1.551 1.518 0.033 2.00e-02 2.50e+03 2.69e+00 bond pdb=" CA ALA A 260 " pdb=" CB ALA A 260 " ideal model delta sigma weight residual 1.527 1.488 0.040 2.48e-02 1.63e+03 2.56e+00 ... (remaining 12780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 16659 1.77 - 3.54: 579 3.54 - 5.31: 84 5.31 - 7.08: 17 7.08 - 8.85: 4 Bond angle restraints: 17343 Sorted by residual: angle pdb=" N SER A1020 " pdb=" CA SER A1020 " pdb=" C SER A1020 " ideal model delta sigma weight residual 113.97 109.29 4.68 1.28e+00 6.10e-01 1.34e+01 angle pdb=" C VAL A1273 " pdb=" CA VAL A1273 " pdb=" CB VAL A1273 " ideal model delta sigma weight residual 111.71 108.72 2.99 8.50e-01 1.38e+00 1.24e+01 angle pdb=" N VAL A 592 " pdb=" CA VAL A 592 " pdb=" C VAL A 592 " ideal model delta sigma weight residual 112.96 109.75 3.21 1.00e+00 1.00e+00 1.03e+01 angle pdb=" C TYR A1087 " pdb=" N ASP A1088 " pdb=" CA ASP A1088 " ideal model delta sigma weight residual 121.83 116.94 4.89 1.56e+00 4.11e-01 9.83e+00 angle pdb=" C SER B 68 " pdb=" N GLY B 69 " pdb=" CA GLY B 69 " ideal model delta sigma weight residual 122.73 119.95 2.78 9.30e-01 1.16e+00 8.91e+00 ... (remaining 17338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 6863 16.20 - 32.39: 531 32.39 - 48.59: 131 48.59 - 64.79: 31 64.79 - 80.98: 6 Dihedral angle restraints: 7562 sinusoidal: 2976 harmonic: 4586 Sorted by residual: dihedral pdb=" CA LYS B 55 " pdb=" C LYS B 55 " pdb=" N ILE B 56 " pdb=" CA ILE B 56 " ideal model delta harmonic sigma weight residual 180.00 -155.58 -24.42 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ASN B 216 " pdb=" C ASN B 216 " pdb=" N ARG B 217 " pdb=" CA ARG B 217 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ARG B 217 " pdb=" C ARG B 217 " pdb=" N ASN B 218 " pdb=" CA ASN B 218 " ideal model delta harmonic sigma weight residual 180.00 162.14 17.86 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 7559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1656 0.059 - 0.119: 299 0.119 - 0.178: 39 0.178 - 0.237: 6 0.237 - 0.296: 6 Chirality restraints: 2006 Sorted by residual: chirality pdb=" C13 CLR A1300 " pdb=" C12 CLR A1300 " pdb=" C14 CLR A1300 " pdb=" C17 CLR A1300 " both_signs ideal model delta sigma weight residual False -2.93 -2.64 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C13 CLR A1305 " pdb=" C12 CLR A1305 " pdb=" C14 CLR A1305 " pdb=" C17 CLR A1305 " both_signs ideal model delta sigma weight residual False -2.93 -2.66 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C13 CLR A1303 " pdb=" C12 CLR A1303 " pdb=" C14 CLR A1303 " pdb=" C17 CLR A1303 " both_signs ideal model delta sigma weight residual False -2.93 -2.66 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 2003 not shown) Planarity restraints: 2156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 48 " 0.035 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO B 49 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 49 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 49 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 99 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO B 100 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 100 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 100 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 173 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C THR A 173 " 0.030 2.00e-02 2.50e+03 pdb=" O THR A 173 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG A 174 " -0.010 2.00e-02 2.50e+03 ... (remaining 2153 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1468 2.74 - 3.28: 12786 3.28 - 3.82: 20171 3.82 - 4.36: 23694 4.36 - 4.90: 40420 Nonbonded interactions: 98539 Sorted by model distance: nonbonded pdb=" O PHE A 623 " pdb=" OG1 THR A 627 " model vdw 2.200 3.040 nonbonded pdb=" O SER A1272 " pdb=" OG SER A1272 " model vdw 2.202 3.040 nonbonded pdb=" O PHE C 29 " pdb=" NH2 ARG C 72 " model vdw 2.218 3.120 nonbonded pdb=" O ALA A 233 " pdb=" OG SER A 237 " model vdw 2.218 3.040 nonbonded pdb=" O SER A 43 " pdb=" NZ LYS A 48 " model vdw 2.230 3.120 ... (remaining 98534 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.960 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: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.850 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 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 : 0.007 0.093 12790 Z= 0.334 Angle : 0.789 8.845 17353 Z= 0.432 Chirality : 0.049 0.296 2006 Planarity : 0.004 0.052 2156 Dihedral : 12.896 80.982 4607 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.72 % Allowed : 7.72 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.31 (0.19), residues: 1584 helix: -1.10 (0.16), residues: 759 sheet: -0.71 (0.29), residues: 283 loop : -2.42 (0.23), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 798 TYR 0.024 0.002 TYR C 95 PHE 0.020 0.002 PHE B 94 TRP 0.014 0.002 TRP C 160 HIS 0.004 0.001 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00743 / 0.33 (12785) covalent geometry : angle 0.78791 / 0.43 (17343) SS BOND : bond 0.00773 / 0.49 ( 5) SS BOND : angle 1.62653 / 0.95 ( 10) hydrogen bonds : bond 0.17741 / 11.61 ( 719) hydrogen bonds : angle 7.19739 / 5.32 ( 2085) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 282 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 TRP cc_start: 0.7992 (t60) cc_final: 0.7673 (t60) REVERT: A 499 GLU cc_start: 0.6276 (mt-10) cc_final: 0.6021 (mm-30) REVERT: A 514 MET cc_start: 0.5423 (mtm) cc_final: 0.4642 (tmm) REVERT: A 799 GLN cc_start: 0.7907 (mm110) cc_final: 0.7680 (mm-40) REVERT: A 816 THR cc_start: 0.7941 (m) cc_final: 0.7392 (t) REVERT: A 1183 ARG cc_start: 0.5891 (mtm180) cc_final: 0.5525 (mtp85) REVERT: A 1270 MET cc_start: -0.0552 (OUTLIER) cc_final: -0.0880 (mtt) REVERT: B 171 GLN cc_start: 0.8046 (tt0) cc_final: 0.6997 (tt0) REVERT: C 25 SER cc_start: 0.8624 (p) cc_final: 0.8135 (t) REVERT: C 121 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8177 (ptmm) REVERT: C 173 PRO cc_start: 0.8225 (Cg_endo) cc_final: 0.7801 (Cg_exo) outliers start: 23 outliers final: 7 residues processed: 297 average time/residue: 0.1267 time to fit residues: 51.9634 Evaluate side-chains 158 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 1270 MET Chi-restraints excluded: chain A residue 1271 VAL Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 121 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 0.0670 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 HIS ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN A 398 HIS A 438 GLN A 462 ASN A 475 GLN A 612 HIS A 704 ASN A 750 GLN A 799 GLN A 912 GLN A 914 GLN A 946 GLN A 966 HIS A1054 GLN A1105 ASN ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1182 GLN ** A1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1248 ASN B 18 GLN B 129 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.155044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.122869 restraints weight = 27728.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.120769 restraints weight = 49452.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.122432 restraints weight = 38941.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.123326 restraints weight = 23575.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.123798 restraints weight = 21330.443| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12790 Z= 0.157 Angle : 0.614 8.374 17353 Z= 0.319 Chirality : 0.042 0.179 2006 Planarity : 0.004 0.038 2156 Dihedral : 6.234 59.850 1795 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.37 % Allowed : 14.38 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.56 (0.20), residues: 1584 helix: 0.54 (0.18), residues: 787 sheet: 0.02 (0.31), residues: 276 loop : -1.95 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 538 TYR 0.015 0.002 TYR A1133 PHE 0.018 0.002 PHE A 200 TRP 0.019 0.002 TRP A 698 HIS 0.004 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (12785) covalent geometry : angle 0.61369 / 0.32 (17343) SS BOND : bond 0.00557 / 0.32 ( 5) SS BOND : angle 1.09452 / 0.61 ( 10) hydrogen bonds : bond 0.05960 / 3.90 ( 719) hydrogen bonds : angle 5.11092 / 3.80 ( 2085) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.7526 (mmm) cc_final: 0.7230 (tpp) REVERT: A 232 TRP cc_start: 0.7819 (t60) cc_final: 0.7516 (t60) REVERT: A 393 GLU cc_start: 0.5551 (tm-30) cc_final: 0.3949 (pm20) REVERT: A 514 MET cc_start: 0.4788 (mtm) cc_final: 0.4264 (tmm) REVERT: A 948 MET cc_start: 0.7535 (tpt) cc_final: 0.7283 (tpp) REVERT: A 949 MET cc_start: 0.8124 (tmm) cc_final: 0.7643 (tpt) REVERT: A 973 ASP cc_start: 0.8016 (t0) cc_final: 0.7612 (m-30) REVERT: A 1270 MET cc_start: 0.0281 (tpt) cc_final: -0.0412 (mtt) REVERT: C 173 PRO cc_start: 0.7732 (Cg_endo) cc_final: 0.7411 (Cg_exo) outliers start: 45 outliers final: 20 residues processed: 216 average time/residue: 0.1018 time to fit residues: 32.1977 Evaluate side-chains 158 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain A residue 1271 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 138 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 83 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 HIS ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1182 GLN B 18 GLN B 142 ASN C 170 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.149441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.117425 restraints weight = 27983.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.115438 restraints weight = 42603.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.116660 restraints weight = 35189.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.117795 restraints weight = 21209.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.118123 restraints weight = 18542.585| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12790 Z= 0.188 Angle : 0.643 11.166 17353 Z= 0.337 Chirality : 0.044 0.170 2006 Planarity : 0.004 0.046 2156 Dihedral : 5.491 52.908 1772 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.19 % Allowed : 16.85 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.12 (0.20), residues: 1584 helix: 0.92 (0.18), residues: 776 sheet: 0.23 (0.31), residues: 277 loop : -1.72 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 492 TYR 0.018 0.002 TYR B 54 PHE 0.022 0.002 PHE A 200 TRP 0.013 0.002 TRP B 153 HIS 0.014 0.002 HIS C 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (12785) covalent geometry : angle 0.64197 / 0.34 (17343) SS BOND : bond 0.00893 / 0.56 ( 5) SS BOND : angle 1.76307 / 1.21 ( 10) hydrogen bonds : bond 0.05859 / 3.81 ( 719) hydrogen bonds : angle 4.93148 / 3.65 ( 2085) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 152 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 514 MET cc_start: 0.4993 (mtm) cc_final: 0.4579 (tmm) REVERT: A 786 LYS cc_start: 0.7901 (tmtt) cc_final: 0.7615 (tmtt) REVERT: A 799 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7929 (tp40) REVERT: A 814 LEU cc_start: 0.8360 (mt) cc_final: 0.7859 (mt) REVERT: A 948 MET cc_start: 0.7647 (tpt) cc_final: 0.7351 (tpp) REVERT: A 949 MET cc_start: 0.8125 (tmm) cc_final: 0.7617 (tpt) REVERT: A 1010 MET cc_start: 0.5827 (ptt) cc_final: 0.5128 (ttp) REVERT: A 1119 GLU cc_start: 0.3241 (OUTLIER) cc_final: 0.3016 (pt0) REVERT: A 1270 MET cc_start: -0.0072 (tpt) cc_final: -0.0668 (mtt) REVERT: B 110 GLU cc_start: 0.7430 (tp30) cc_final: 0.7126 (tp30) REVERT: B 172 ASP cc_start: 0.5962 (t70) cc_final: 0.5672 (t70) outliers start: 56 outliers final: 31 residues processed: 196 average time/residue: 0.1038 time to fit residues: 30.2481 Evaluate side-chains 157 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1119 GLU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain A residue 1182 GLN Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 213 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 27 optimal weight: 0.6980 chunk 47 optimal weight: 0.0030 chunk 148 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN B 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.149483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.118259 restraints weight = 27904.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.118084 restraints weight = 44483.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.119729 restraints weight = 31739.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.119632 restraints weight = 20663.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.120921 restraints weight = 17791.885| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12790 Z= 0.144 Angle : 0.576 10.463 17353 Z= 0.299 Chirality : 0.041 0.137 2006 Planarity : 0.004 0.047 2156 Dihedral : 5.264 57.480 1771 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.75 % Allowed : 18.50 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.25 (0.21), residues: 1584 helix: 1.23 (0.18), residues: 784 sheet: 0.42 (0.32), residues: 273 loop : -1.59 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1085 TYR 0.014 0.001 TYR C 95 PHE 0.022 0.001 PHE A 200 TRP 0.020 0.001 TRP A 803 HIS 0.003 0.001 HIS A1007 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (12785) covalent geometry : angle 0.57509 / 0.30 (17343) SS BOND : bond 0.00664 / 0.44 ( 5) SS BOND : angle 1.40504 / 0.81 ( 10) hydrogen bonds : bond 0.05175 / 3.37 ( 719) hydrogen bonds : angle 4.65922 / 3.45 ( 2085) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 141 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 220 " (corrupted residue). Skipping it. REVERT: A 514 MET cc_start: 0.4895 (mtm) cc_final: 0.4627 (tmm) REVERT: A 799 GLN cc_start: 0.8253 (mm-40) cc_final: 0.8000 (tp40) REVERT: A 891 GLU cc_start: 0.7207 (tt0) cc_final: 0.6527 (pp20) REVERT: A 948 MET cc_start: 0.7595 (tpt) cc_final: 0.7250 (tpp) REVERT: A 949 MET cc_start: 0.8096 (tmm) cc_final: 0.7550 (tpt) REVERT: A 1119 GLU cc_start: 0.3241 (OUTLIER) cc_final: 0.2424 (pp20) REVERT: A 1270 MET cc_start: 0.0033 (tpt) cc_final: -0.0713 (mtt) outliers start: 50 outliers final: 32 residues processed: 183 average time/residue: 0.1034 time to fit residues: 28.5912 Evaluate side-chains 153 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1119 GLU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain A residue 1182 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 179 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 135 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN A1153 ASN A1182 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.148662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.119003 restraints weight = 28073.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.118717 restraints weight = 54081.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.119956 restraints weight = 40839.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.119964 restraints weight = 26304.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.120528 restraints weight = 22575.718| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12790 Z= 0.137 Angle : 0.571 10.069 17353 Z= 0.296 Chirality : 0.041 0.199 2006 Planarity : 0.003 0.048 2156 Dihedral : 5.185 55.069 1771 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.67 % Allowed : 19.33 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.45 (0.21), residues: 1584 helix: 1.39 (0.18), residues: 784 sheet: 0.60 (0.33), residues: 263 loop : -1.51 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 699 TYR 0.014 0.001 TYR B 54 PHE 0.023 0.001 PHE A 200 TRP 0.013 0.001 TRP A 803 HIS 0.003 0.001 HIS A1007 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (12785) covalent geometry : angle 0.56828 / 0.29 (17343) SS BOND : bond 0.00937 / 0.61 ( 5) SS BOND : angle 2.39326 / 1.42 ( 10) hydrogen bonds : bond 0.04982 / 3.25 ( 719) hydrogen bonds : angle 4.55270 / 3.36 ( 2085) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 139 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 155 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8590 (tt) REVERT: A 273 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7076 (mm-30) REVERT: A 514 MET cc_start: 0.4841 (mtm) cc_final: 0.4565 (tmm) REVERT: A 814 LEU cc_start: 0.8455 (mt) cc_final: 0.8136 (mt) REVERT: A 891 GLU cc_start: 0.6992 (tt0) cc_final: 0.6385 (pp20) REVERT: A 948 MET cc_start: 0.7605 (tpt) cc_final: 0.7277 (tpp) REVERT: A 949 MET cc_start: 0.8127 (tmm) cc_final: 0.7711 (tpt) REVERT: A 1270 MET cc_start: 0.0497 (tpt) cc_final: -0.0246 (mtt) REVERT: B 129 GLN cc_start: 0.5522 (tt0) cc_final: 0.4120 (tt0) REVERT: C 128 TYR cc_start: 0.7606 (m-10) cc_final: 0.7355 (m-10) outliers start: 49 outliers final: 34 residues processed: 180 average time/residue: 0.1083 time to fit residues: 29.1580 Evaluate side-chains 154 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1119 GLU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 179 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 102 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 80 optimal weight: 6.9990 chunk 116 optimal weight: 0.4980 chunk 144 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN A 912 GLN A1153 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.149260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.119721 restraints weight = 27671.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.115097 restraints weight = 31665.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.116626 restraints weight = 30633.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.117144 restraints weight = 17966.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.117765 restraints weight = 15889.415| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12790 Z= 0.117 Angle : 0.541 8.427 17353 Z= 0.279 Chirality : 0.040 0.142 2006 Planarity : 0.003 0.043 2156 Dihedral : 5.003 54.383 1771 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.70 % Allowed : 20.90 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.75 (0.21), residues: 1584 helix: 1.60 (0.19), residues: 783 sheet: 0.72 (0.33), residues: 273 loop : -1.33 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 113 TYR 0.013 0.001 TYR A 378 PHE 0.024 0.001 PHE A 200 TRP 0.014 0.001 TRP A 698 HIS 0.004 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (12785) covalent geometry : angle 0.53996 / 0.28 (17343) SS BOND : bond 0.00798 / 0.54 ( 5) SS BOND : angle 1.61684 / 0.95 ( 10) hydrogen bonds : bond 0.04572 / 2.98 ( 719) hydrogen bonds : angle 4.37736 / 3.23 ( 2085) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 155 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8553 (tt) REVERT: A 156 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8215 (mmp) REVERT: A 273 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7264 (mm-30) REVERT: A 309 SER cc_start: 0.7965 (p) cc_final: 0.7503 (t) REVERT: A 493 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6321 (mm-30) REVERT: A 514 MET cc_start: 0.5441 (mtm) cc_final: 0.4845 (tmm) REVERT: A 628 MET cc_start: -0.1041 (tpt) cc_final: -0.1322 (tpt) REVERT: A 891 GLU cc_start: 0.7345 (tt0) cc_final: 0.6549 (pp20) REVERT: A 949 MET cc_start: 0.8104 (tmm) cc_final: 0.7553 (tpt) REVERT: A 1270 MET cc_start: 0.0192 (tpt) cc_final: -0.0385 (mtt) outliers start: 36 outliers final: 23 residues processed: 164 average time/residue: 0.0986 time to fit residues: 24.8014 Evaluate side-chains 139 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1119 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 138 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 100 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1195 HIS B 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.148776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.119075 restraints weight = 27588.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.118677 restraints weight = 53216.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.119785 restraints weight = 39591.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.120066 restraints weight = 23820.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.120540 restraints weight = 20963.032| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12790 Z= 0.121 Angle : 0.546 10.535 17353 Z= 0.279 Chirality : 0.040 0.162 2006 Planarity : 0.003 0.043 2156 Dihedral : 4.891 54.166 1771 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.37 % Allowed : 21.35 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.84 (0.21), residues: 1584 helix: 1.66 (0.18), residues: 782 sheet: 0.78 (0.33), residues: 275 loop : -1.27 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 113 TYR 0.014 0.001 TYR A 326 PHE 0.025 0.001 PHE B 123 TRP 0.010 0.001 TRP A 708 HIS 0.002 0.001 HIS A1007 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (12785) covalent geometry : angle 0.54512 / 0.28 (17343) SS BOND : bond 0.00790 / 0.54 ( 5) SS BOND : angle 1.46441 / 0.84 ( 10) hydrogen bonds : bond 0.04535 / 2.95 ( 719) hydrogen bonds : angle 4.34038 / 3.19 ( 2085) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 128 time to evaluate : 0.513 Fit side-chains REVERT: A 155 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8518 (tt) REVERT: A 273 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7113 (mm-30) REVERT: A 309 SER cc_start: 0.7875 (p) cc_final: 0.7437 (t) REVERT: A 493 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6185 (mm-30) REVERT: A 514 MET cc_start: 0.4996 (mtm) cc_final: 0.4665 (tmm) REVERT: A 543 ARG cc_start: 0.6932 (ttp-170) cc_final: 0.6504 (ttt-90) REVERT: A 701 MET cc_start: 0.6296 (ptt) cc_final: 0.6002 (ptm) REVERT: A 891 GLU cc_start: 0.6990 (tt0) cc_final: 0.6257 (pp20) REVERT: A 949 MET cc_start: 0.8120 (tmm) cc_final: 0.7607 (tpt) REVERT: A 1270 MET cc_start: 0.0362 (tpt) cc_final: -0.0475 (mtt) REVERT: B 181 SER cc_start: 0.8352 (p) cc_final: 0.8019 (m) REVERT: C 34 MET cc_start: 0.9062 (mmm) cc_final: 0.8747 (mmm) outliers start: 45 outliers final: 33 residues processed: 164 average time/residue: 0.1040 time to fit residues: 25.7217 Evaluate side-chains 154 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1119 GLU Chi-restraints excluded: chain A residue 1182 GLN Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 138 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.144373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.114508 restraints weight = 27800.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.113234 restraints weight = 53777.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.114573 restraints weight = 39908.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.115102 restraints weight = 24090.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.115446 restraints weight = 22303.087| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12790 Z= 0.165 Angle : 0.618 11.148 17353 Z= 0.316 Chirality : 0.042 0.177 2006 Planarity : 0.004 0.039 2156 Dihedral : 5.119 50.509 1771 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.30 % Allowed : 21.65 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.56 (0.21), residues: 1584 helix: 1.40 (0.18), residues: 789 sheet: 0.72 (0.33), residues: 265 loop : -1.39 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 547 TYR 0.022 0.002 TYR A 326 PHE 0.023 0.002 PHE A 200 TRP 0.010 0.001 TRP C 105 HIS 0.008 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (12785) covalent geometry : angle 0.61715 / 0.32 (17343) SS BOND : bond 0.00926 / 0.64 ( 5) SS BOND : angle 1.68129 / 0.93 ( 10) hydrogen bonds : bond 0.05174 / 3.38 ( 719) hydrogen bonds : angle 4.61021 / 3.39 ( 2085) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 0.471 Fit side-chains REVERT: A 155 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8676 (tt) REVERT: A 514 MET cc_start: 0.5095 (mtm) cc_final: 0.4858 (tmm) REVERT: A 543 ARG cc_start: 0.7149 (ttp-170) cc_final: 0.6626 (ttt180) REVERT: A 948 MET cc_start: 0.7474 (tpp) cc_final: 0.7088 (tpp) REVERT: A 1270 MET cc_start: 0.0314 (tpt) cc_final: -0.0523 (mtt) outliers start: 44 outliers final: 37 residues processed: 159 average time/residue: 0.0994 time to fit residues: 24.2356 Evaluate side-chains 147 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1119 GLU Chi-restraints excluded: chain A residue 1182 GLN Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 138 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 5 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.145851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.116656 restraints weight = 27704.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.112563 restraints weight = 47552.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.114308 restraints weight = 38793.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.115053 restraints weight = 22484.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.115499 restraints weight = 20551.745| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12790 Z= 0.132 Angle : 0.585 11.516 17353 Z= 0.296 Chirality : 0.041 0.147 2006 Planarity : 0.004 0.075 2156 Dihedral : 4.978 52.357 1771 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.55 % Allowed : 22.85 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.72 (0.21), residues: 1584 helix: 1.57 (0.18), residues: 792 sheet: 0.74 (0.33), residues: 262 loop : -1.35 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 174 TYR 0.014 0.001 TYR B 54 PHE 0.027 0.001 PHE A 200 TRP 0.052 0.002 TRP B 153 HIS 0.002 0.001 HIS A 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (12785) covalent geometry : angle 0.58353 / 0.30 (17343) SS BOND : bond 0.00879 / 0.61 ( 5) SS BOND : angle 1.62786 / 0.97 ( 10) hydrogen bonds : bond 0.04761 / 3.12 ( 719) hydrogen bonds : angle 4.43762 / 3.26 ( 2085) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.475 Fit side-chains REVERT: A 155 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8586 (tt) REVERT: A 273 GLU cc_start: 0.7406 (mm-30) cc_final: 0.6950 (mm-30) REVERT: A 470 ILE cc_start: 0.8250 (tp) cc_final: 0.8023 (mt) REVERT: A 493 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6218 (mm-30) REVERT: A 514 MET cc_start: 0.5315 (mtm) cc_final: 0.4802 (tmm) REVERT: A 920 TYR cc_start: 0.7767 (t80) cc_final: 0.7269 (t80) REVERT: A 1088 ASP cc_start: 0.7307 (m-30) cc_final: 0.6775 (t0) REVERT: A 1270 MET cc_start: 0.0338 (tpt) cc_final: -0.0415 (mtt) REVERT: C 34 MET cc_start: 0.9068 (mmm) cc_final: 0.8854 (mmm) outliers start: 34 outliers final: 27 residues processed: 156 average time/residue: 0.0990 time to fit residues: 24.0308 Evaluate side-chains 145 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1119 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 138 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 139 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 39 optimal weight: 20.0000 chunk 152 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.146805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.117217 restraints weight = 27787.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.116588 restraints weight = 52055.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.117927 restraints weight = 37836.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.117963 restraints weight = 22651.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.118479 restraints weight = 20615.593| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12790 Z= 0.122 Angle : 0.581 10.843 17353 Z= 0.292 Chirality : 0.041 0.206 2006 Planarity : 0.004 0.059 2156 Dihedral : 4.825 53.905 1771 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.32 % Allowed : 22.77 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.85 (0.21), residues: 1584 helix: 1.75 (0.18), residues: 784 sheet: 0.72 (0.33), residues: 264 loop : -1.34 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 547 TYR 0.014 0.001 TYR B 54 PHE 0.026 0.001 PHE A 200 TRP 0.073 0.002 TRP B 153 HIS 0.002 0.001 HIS A1007 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (12785) covalent geometry : angle 0.58019 / 0.29 (17343) SS BOND : bond 0.00781 / 0.54 ( 5) SS BOND : angle 1.43832 / 0.84 ( 10) hydrogen bonds : bond 0.04461 / 2.91 ( 719) hydrogen bonds : angle 4.32942 / 3.18 ( 2085) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.475 Fit side-chains REVERT: A 155 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8531 (tt) REVERT: A 273 GLU cc_start: 0.7321 (mm-30) cc_final: 0.6836 (mm-30) REVERT: A 514 MET cc_start: 0.4889 (mtm) cc_final: 0.4588 (tmm) REVERT: A 543 ARG cc_start: 0.6901 (ttp-170) cc_final: 0.6503 (ttt-90) REVERT: A 701 MET cc_start: 0.6175 (ptt) cc_final: 0.5851 (ptm) REVERT: A 891 GLU cc_start: 0.7023 (tt0) cc_final: 0.6368 (pp20) REVERT: A 920 TYR cc_start: 0.7626 (t80) cc_final: 0.7182 (t80) REVERT: A 949 MET cc_start: 0.8135 (tmm) cc_final: 0.7606 (tpt) REVERT: A 1088 ASP cc_start: 0.7126 (m-30) cc_final: 0.6763 (t0) REVERT: A 1270 MET cc_start: 0.0280 (tpt) cc_final: -0.0324 (tpt) outliers start: 31 outliers final: 26 residues processed: 152 average time/residue: 0.1098 time to fit residues: 25.1921 Evaluate side-chains 147 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1119 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 138 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 10 optimal weight: 4.9990 chunk 116 optimal weight: 0.2980 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 31 optimal weight: 0.0980 chunk 133 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** A1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.145816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.116918 restraints weight = 27715.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.117652 restraints weight = 49945.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.118458 restraints weight = 31259.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.118285 restraints weight = 23104.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.118784 restraints weight = 19596.853| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12790 Z= 0.129 Angle : 0.592 11.772 17353 Z= 0.296 Chirality : 0.040 0.155 2006 Planarity : 0.003 0.050 2156 Dihedral : 4.817 53.449 1771 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.25 % Allowed : 23.30 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.86 (0.21), residues: 1584 helix: 1.74 (0.18), residues: 785 sheet: 0.75 (0.33), residues: 262 loop : -1.32 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 547 TYR 0.015 0.001 TYR B 54 PHE 0.026 0.001 PHE A 200 TRP 0.071 0.002 TRP B 153 HIS 0.004 0.001 HIS A1155 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (12785) covalent geometry : angle 0.59115 / 0.30 (17343) SS BOND : bond 0.00814 / 0.56 ( 5) SS BOND : angle 1.50665 / 0.88 ( 10) hydrogen bonds : bond 0.04541 / 2.97 ( 719) hydrogen bonds : angle 4.37510 / 3.22 ( 2085) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1978.09 seconds wall clock time: 35 minutes 15.70 seconds (2115.70 seconds total)