Starting phenix.real_space_refine on Wed Mar 4 10:01:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a65_11666/03_2026/7a65_11666.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a65_11666/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7a65_11666/03_2026/7a65_11666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a65_11666/03_2026/7a65_11666.map" model { file = "/net/cci-nas-00/data/ceres_data/7a65_11666/03_2026/7a65_11666.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a65_11666/03_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-5986/lib/python3.9/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: 2.86, per 1000 atoms: 0.23 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: 0.97 Conformation dependent library (CDL) restraints added in 478.8 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: 0.59 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: 2.01 Time building geometry restraints manager: 1.31 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: 7188 16.20 - 32.39: 536 32.39 - 48.59: 134 48.59 - 64.79: 34 64.79 - 80.98: 6 Dihedral angle restraints: 7898 sinusoidal: 3312 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 7895 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: 3.930 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.360 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 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 : 12.706 80.982 4943 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 covalent geometry : bond 0.00743 (12785) covalent geometry : angle 0.78791 (17343) SS BOND : bond 0.00773 ( 5) SS BOND : angle 1.62653 ( 10) hydrogen bonds : bond 0.17741 ( 719) hydrogen bonds : angle 7.19739 ( 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 : 0.402 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: 0.1363 time to fit residues: 55.3669 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 : 0.469 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.154917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.122967 restraints weight = 27635.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.124191 restraints weight = 45810.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.124914 restraints weight = 28348.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.125014 restraints weight = 19689.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.125395 restraints weight = 18737.819| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12790 Z= 0.159 Angle : 0.617 8.304 17353 Z= 0.321 Chirality : 0.042 0.168 2006 Planarity : 0.004 0.037 2156 Dihedral : 6.695 59.556 2131 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.07 % Allowed : 14.31 % Favored : 82.62 % 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: -0.60 (0.20), residues: 1584 helix: 0.50 (0.18), residues: 784 sheet: -0.03 (0.31), residues: 276 loop : -1.93 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 538 TYR 0.014 0.002 TYR C 95 PHE 0.018 0.002 PHE A 200 TRP 0.014 0.001 TRP A 698 HIS 0.004 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00341 (12785) covalent geometry : angle 0.61619 (17343) SS BOND : bond 0.00464 ( 5) SS BOND : angle 1.29017 ( 10) hydrogen bonds : bond 0.06236 ( 719) hydrogen bonds : angle 5.17853 ( 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 226 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.7618 (mmm) cc_final: 0.7195 (tpp) REVERT: A 232 TRP cc_start: 0.7814 (t60) cc_final: 0.7543 (t60) REVERT: A 514 MET cc_start: 0.4571 (mtm) cc_final: 0.4177 (tmm) REVERT: A 616 MET cc_start: 0.1313 (mmp) cc_final: 0.0673 (mmm) REVERT: A 832 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7682 (tpt-90) REVERT: A 948 MET cc_start: 0.7584 (tpt) cc_final: 0.7289 (tpp) REVERT: A 949 MET cc_start: 0.8147 (tmm) cc_final: 0.7645 (tpt) REVERT: A 973 ASP cc_start: 0.8054 (t0) cc_final: 0.7639 (m-30) REVERT: A 1270 MET cc_start: 0.0145 (tpt) cc_final: -0.0585 (mtt) REVERT: C 173 PRO cc_start: 0.7761 (Cg_endo) cc_final: 0.7438 (Cg_exo) outliers start: 41 outliers final: 21 residues processed: 210 average time/residue: 0.1053 time to fit residues: 32.2893 Evaluate side-chains 159 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 156 MET 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 832 ARG 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 182 SER Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 142 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 83 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1182 GLN B 18 GLN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.153766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.121988 restraints weight = 28102.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.119518 restraints weight = 47712.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.121113 restraints weight = 38822.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.122258 restraints weight = 23245.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.122624 restraints weight = 21007.548| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12790 Z= 0.140 Angle : 0.571 8.832 17353 Z= 0.299 Chirality : 0.042 0.142 2006 Planarity : 0.004 0.040 2156 Dihedral : 5.885 56.651 2111 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.07 % Allowed : 16.55 % Favored : 80.37 % 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: 0.16 (0.21), residues: 1584 helix: 1.13 (0.18), residues: 785 sheet: 0.41 (0.32), residues: 275 loop : -1.63 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 538 TYR 0.015 0.001 TYR B 54 PHE 0.022 0.002 PHE A 200 TRP 0.016 0.001 TRP A 698 HIS 0.003 0.001 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00293 (12785) covalent geometry : angle 0.57023 (17343) SS BOND : bond 0.00805 ( 5) SS BOND : angle 1.37096 ( 10) hydrogen bonds : bond 0.05407 ( 719) hydrogen bonds : angle 4.73113 ( 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 202 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 TRP cc_start: 0.7838 (t60) cc_final: 0.6895 (t60) REVERT: A 514 MET cc_start: 0.4911 (mtm) cc_final: 0.4394 (tmm) REVERT: A 799 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7981 (tp40) REVERT: A 814 LEU cc_start: 0.8269 (mt) cc_final: 0.7920 (mt) REVERT: A 891 GLU cc_start: 0.7317 (tt0) cc_final: 0.6587 (pp20) REVERT: A 948 MET cc_start: 0.7549 (tpt) cc_final: 0.7275 (tpp) REVERT: A 949 MET cc_start: 0.8082 (tmm) cc_final: 0.7507 (tpt) REVERT: A 1010 MET cc_start: 0.5472 (ptt) cc_final: 0.4302 (ttp) REVERT: A 1119 GLU cc_start: 0.2923 (OUTLIER) cc_final: 0.2129 (pp20) REVERT: A 1270 MET cc_start: -0.0053 (tpt) cc_final: -0.0646 (mtt) REVERT: B 110 GLU cc_start: 0.7424 (tp30) cc_final: 0.6958 (tp30) REVERT: B 171 GLN cc_start: 0.7319 (tt0) cc_final: 0.6905 (tt0) outliers start: 41 outliers final: 22 residues processed: 193 average time/residue: 0.0969 time to fit residues: 28.2470 Evaluate side-chains 152 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 159 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 795 SER 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 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 B residue 83 VAL Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 142 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 0.0010 chunk 13 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 0.0470 chunk 148 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 145 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 overall best weight: 0.9488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 398 HIS ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 ASN B 142 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.153188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.121342 restraints weight = 27737.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.119049 restraints weight = 38777.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.120614 restraints weight = 31678.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.121343 restraints weight = 19383.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.121768 restraints weight = 17952.692| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12790 Z= 0.129 Angle : 0.552 8.697 17353 Z= 0.286 Chirality : 0.041 0.150 2006 Planarity : 0.003 0.045 2156 Dihedral : 5.493 59.299 2107 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.77 % Allowed : 18.35 % Favored : 78.88 % 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: 0.47 (0.21), residues: 1584 helix: 1.37 (0.18), residues: 785 sheet: 0.59 (0.32), residues: 273 loop : -1.48 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1085 TYR 0.013 0.001 TYR B 54 PHE 0.026 0.001 PHE A 200 TRP 0.024 0.002 TRP A 803 HIS 0.003 0.001 HIS A1007 Details of bonding type rmsd covalent geometry : bond 0.00273 (12785) covalent geometry : angle 0.55088 (17343) SS BOND : bond 0.00825 ( 5) SS BOND : angle 1.25730 ( 10) hydrogen bonds : bond 0.04958 ( 719) hydrogen bonds : angle 4.49759 ( 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 190 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 514 MET cc_start: 0.4939 (mtm) cc_final: 0.4554 (tmm) REVERT: A 891 GLU cc_start: 0.7307 (tt0) cc_final: 0.6616 (pp20) REVERT: A 948 MET cc_start: 0.7444 (tpt) cc_final: 0.7150 (tpp) REVERT: A 949 MET cc_start: 0.8118 (tmm) cc_final: 0.7716 (tpt) REVERT: A 1010 MET cc_start: 0.5752 (ptt) cc_final: 0.4704 (ttp) REVERT: A 1119 GLU cc_start: 0.3026 (OUTLIER) cc_final: 0.2230 (pp20) REVERT: A 1270 MET cc_start: 0.0042 (tpt) cc_final: -0.0597 (mtt) REVERT: B 110 GLU cc_start: 0.7384 (tp30) cc_final: 0.6971 (tp30) REVERT: C 103 GLU cc_start: 0.7368 (mp0) cc_final: 0.7038 (mp0) outliers start: 37 outliers final: 23 residues processed: 182 average time/residue: 0.0953 time to fit residues: 26.0696 Evaluate side-chains 152 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 1011 ILE 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 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 122 ILE Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 142 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 chunk 134 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 GLN B 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.151732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.122219 restraints weight = 28003.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.122800 restraints weight = 57002.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.123911 restraints weight = 36739.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.123635 restraints weight = 26610.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.124141 restraints weight = 22196.105| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12790 Z= 0.126 Angle : 0.547 8.285 17353 Z= 0.282 Chirality : 0.041 0.134 2006 Planarity : 0.003 0.044 2156 Dihedral : 5.290 54.053 2107 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.60 % Allowed : 18.35 % Favored : 78.05 % 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: 0.67 (0.21), residues: 1584 helix: 1.54 (0.18), residues: 787 sheet: 0.67 (0.33), residues: 273 loop : -1.40 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 699 TYR 0.013 0.001 TYR C 95 PHE 0.021 0.001 PHE A 200 TRP 0.020 0.001 TRP A 803 HIS 0.002 0.001 HIS A 936 Details of bonding type rmsd covalent geometry : bond 0.00267 (12785) covalent geometry : angle 0.54679 (17343) SS BOND : bond 0.00639 ( 5) SS BOND : angle 1.06955 ( 10) hydrogen bonds : bond 0.04736 ( 719) hydrogen bonds : angle 4.40307 ( 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 186 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 0.402 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 220 " (corrupted residue). Skipping it. REVERT: A 155 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8576 (tt) REVERT: A 514 MET cc_start: 0.4643 (mtm) cc_final: 0.4388 (tmm) REVERT: A 814 LEU cc_start: 0.8431 (mt) cc_final: 0.7813 (mt) REVERT: A 891 GLU cc_start: 0.7064 (tt0) cc_final: 0.6496 (pp20) REVERT: A 948 MET cc_start: 0.7558 (tpt) cc_final: 0.7234 (tpp) REVERT: A 949 MET cc_start: 0.8093 (tmm) cc_final: 0.7532 (tpt) REVERT: A 1010 MET cc_start: 0.5760 (ptt) cc_final: 0.4767 (ttp) REVERT: A 1119 GLU cc_start: 0.3053 (OUTLIER) cc_final: 0.2107 (pp20) REVERT: A 1270 MET cc_start: 0.0620 (tpt) cc_final: -0.0127 (mtt) outliers start: 48 outliers final: 29 residues processed: 176 average time/residue: 0.0935 time to fit residues: 25.3897 Evaluate side-chains 150 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 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 463 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 752 SER 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 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 1104 LEU Chi-restraints excluded: chain A residue 1119 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 138 THR 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: 0.2980 chunk 126 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.149827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.120565 restraints weight = 27862.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.122194 restraints weight = 50860.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.122289 restraints weight = 27274.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.122280 restraints weight = 20690.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.122564 restraints weight = 19037.105| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12790 Z= 0.138 Angle : 0.566 9.433 17353 Z= 0.291 Chirality : 0.041 0.187 2006 Planarity : 0.003 0.044 2156 Dihedral : 5.250 58.397 2107 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.52 % Allowed : 19.40 % Favored : 77.08 % 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: 0.65 (0.21), residues: 1584 helix: 1.52 (0.18), residues: 787 sheet: 0.73 (0.33), residues: 273 loop : -1.44 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 699 TYR 0.015 0.001 TYR B 54 PHE 0.021 0.001 PHE A 200 TRP 0.016 0.001 TRP A 708 HIS 0.004 0.001 HIS A 612 Details of bonding type rmsd covalent geometry : bond 0.00299 (12785) covalent geometry : angle 0.56220 (17343) SS BOND : bond 0.00879 ( 5) SS BOND : angle 2.68639 ( 10) hydrogen bonds : bond 0.04862 ( 719) hydrogen bonds : angle 4.45021 ( 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 171 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 124 time to evaluate : 0.473 Fit side-chains REVERT: A 155 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8595 (tt) REVERT: A 462 ASN cc_start: 0.2143 (OUTLIER) cc_final: 0.1684 (m110) REVERT: A 493 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.6104 (mm-30) REVERT: A 514 MET cc_start: 0.4752 (mtm) cc_final: 0.4457 (tmm) REVERT: A 616 MET cc_start: 0.3401 (mpp) cc_final: 0.2987 (mpp) REVERT: A 891 GLU cc_start: 0.7039 (tt0) cc_final: 0.6513 (pp20) REVERT: A 948 MET cc_start: 0.7545 (tpt) cc_final: 0.7183 (tpp) REVERT: A 949 MET cc_start: 0.8162 (tmm) cc_final: 0.7580 (tpt) REVERT: A 1270 MET cc_start: 0.0600 (tpt) cc_final: -0.0151 (mtt) outliers start: 47 outliers final: 33 residues processed: 163 average time/residue: 0.0871 time to fit residues: 21.8335 Evaluate side-chains 150 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER 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 165 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain A residue 463 VAL 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 770 PHE 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 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 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 1104 LEU Chi-restraints excluded: chain A residue 1115 ILE 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 122 ILE Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 189 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 107 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1195 HIS ** 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 = 0.4049 r_free = 0.4049 target = 0.143994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.113144 restraints weight = 27871.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.112554 restraints weight = 45021.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.113726 restraints weight = 31876.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.114522 restraints weight = 19686.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.115029 restraints weight = 17247.205| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12790 Z= 0.211 Angle : 0.696 13.541 17353 Z= 0.359 Chirality : 0.046 0.279 2006 Planarity : 0.004 0.051 2156 Dihedral : 5.726 43.073 2107 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.19 % Allowed : 18.80 % 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: 0.13 (0.21), residues: 1584 helix: 1.07 (0.18), residues: 780 sheet: 0.57 (0.33), residues: 267 loop : -1.64 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 459 TYR 0.020 0.002 TYR C 95 PHE 0.020 0.002 PHE A 200 TRP 0.011 0.002 TRP B 168 HIS 0.009 0.002 HIS A1007 Details of bonding type rmsd covalent geometry : bond 0.00478 (12785) covalent geometry : angle 0.69493 (17343) SS BOND : bond 0.01034 ( 5) SS BOND : angle 1.85857 ( 10) hydrogen bonds : bond 0.05934 ( 719) hydrogen bonds : angle 4.97556 ( 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 177 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 121 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 258 LEU cc_start: 0.8457 (mm) cc_final: 0.8250 (mm) REVERT: A 273 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7207 (mm-30) REVERT: A 514 MET cc_start: 0.5308 (mtm) cc_final: 0.4958 (tmm) REVERT: A 814 LEU cc_start: 0.8435 (mt) cc_final: 0.7955 (mt) REVERT: A 891 GLU cc_start: 0.7185 (tt0) cc_final: 0.6543 (pp20) REVERT: A 948 MET cc_start: 0.7820 (tpt) cc_final: 0.7533 (tpp) REVERT: A 1270 MET cc_start: 0.0269 (tpt) cc_final: -0.0441 (mtt) outliers start: 56 outliers final: 37 residues processed: 167 average time/residue: 0.0863 time to fit residues: 22.8542 Evaluate side-chains 143 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 134 SER 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 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 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 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 1080 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 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 189 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 169 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 GLN ** 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 = 0.4079 r_free = 0.4079 target = 0.146665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.116557 restraints weight = 27665.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.115378 restraints weight = 52043.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.116665 restraints weight = 39317.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.117466 restraints weight = 24070.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.117786 restraints weight = 21306.955| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12790 Z= 0.131 Angle : 0.590 10.773 17353 Z= 0.298 Chirality : 0.041 0.188 2006 Planarity : 0.003 0.043 2156 Dihedral : 5.157 46.368 2107 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.32 % Allowed : 20.90 % Favored : 76.78 % 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: 0.55 (0.21), residues: 1584 helix: 1.43 (0.18), residues: 787 sheet: 0.74 (0.34), residues: 265 loop : -1.48 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 547 TYR 0.014 0.001 TYR C 95 PHE 0.029 0.001 PHE A 200 TRP 0.010 0.001 TRP A 708 HIS 0.002 0.001 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00275 (12785) covalent geometry : angle 0.58879 (17343) SS BOND : bond 0.00785 ( 5) SS BOND : angle 1.50645 ( 10) hydrogen bonds : bond 0.04874 ( 719) hydrogen bonds : angle 4.56517 ( 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 157 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.513 Fit side-chains REVERT: A 75 MET cc_start: 0.7527 (tmm) cc_final: 0.7282 (tmm) REVERT: A 273 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7093 (mm-30) REVERT: A 450 MET cc_start: 0.6894 (mmp) cc_final: 0.6679 (mmt) REVERT: A 514 MET cc_start: 0.5163 (mtm) cc_final: 0.4895 (tmm) REVERT: A 814 LEU cc_start: 0.8357 (mt) cc_final: 0.7878 (mt) REVERT: A 891 GLU cc_start: 0.6985 (tt0) cc_final: 0.6274 (pp20) REVERT: A 920 TYR cc_start: 0.7841 (t80) cc_final: 0.7508 (t80) REVERT: A 924 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7897 (mt) REVERT: A 948 MET cc_start: 0.7551 (tpt) cc_final: 0.7183 (tpp) REVERT: A 1270 MET cc_start: 0.0533 (tpt) cc_final: -0.0355 (mtt) REVERT: C 25 SER cc_start: 0.8517 (p) cc_final: 0.8201 (t) outliers start: 31 outliers final: 25 residues processed: 153 average time/residue: 0.1005 time to fit residues: 23.4896 Evaluate side-chains 143 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER 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 512 PHE Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 801 VAL 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 924 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 1119 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 5 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.142773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.112941 restraints weight = 28200.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.112387 restraints weight = 58240.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.113826 restraints weight = 38763.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.114052 restraints weight = 23162.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.114441 restraints weight = 21373.307| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12790 Z= 0.199 Angle : 0.678 12.696 17353 Z= 0.344 Chirality : 0.044 0.206 2006 Planarity : 0.004 0.082 2156 Dihedral : 5.541 49.080 2107 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.70 % Allowed : 20.82 % Favored : 76.48 % 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: 0.32 (0.21), residues: 1584 helix: 1.25 (0.18), residues: 783 sheet: 0.59 (0.33), residues: 265 loop : -1.56 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 174 TYR 0.022 0.002 TYR B 54 PHE 0.024 0.002 PHE A 200 TRP 0.013 0.002 TRP A 232 HIS 0.005 0.001 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00450 (12785) covalent geometry : angle 0.67657 (17343) SS BOND : bond 0.01040 ( 5) SS BOND : angle 1.91189 ( 10) hydrogen bonds : bond 0.05501 ( 719) hydrogen bonds : angle 4.81995 ( 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 164 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 514 MET cc_start: 0.5219 (mtm) cc_final: 0.4869 (tmm) REVERT: A 814 LEU cc_start: 0.8468 (mt) cc_final: 0.8011 (mt) REVERT: A 891 GLU cc_start: 0.7060 (tt0) cc_final: 0.6407 (pp20) REVERT: A 920 TYR cc_start: 0.7958 (t80) cc_final: 0.7444 (t80) REVERT: A 948 MET cc_start: 0.7751 (tpt) cc_final: 0.7488 (tpp) REVERT: A 1270 MET cc_start: 0.0272 (tpt) cc_final: -0.0550 (mtt) REVERT: B 180 MET cc_start: 0.7528 (tmm) cc_final: 0.6911 (tmm) REVERT: C 25 SER cc_start: 0.8631 (p) cc_final: 0.8317 (t) outliers start: 36 outliers final: 31 residues processed: 158 average time/residue: 0.0870 time to fit residues: 21.2955 Evaluate side-chains 144 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER 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 512 PHE Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 801 VAL 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 924 LEU 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 B residue 22 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 122 ILE 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 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 139 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 39 optimal weight: 0.0870 chunk 152 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 GLN ** 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 = 0.4070 r_free = 0.4070 target = 0.145842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.115718 restraints weight = 27755.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.111375 restraints weight = 29336.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.112769 restraints weight = 27089.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.113725 restraints weight = 17004.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.113978 restraints weight = 14762.424| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12790 Z= 0.123 Angle : 0.586 10.957 17353 Z= 0.296 Chirality : 0.041 0.216 2006 Planarity : 0.004 0.065 2156 Dihedral : 5.097 53.837 2107 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.57 % Allowed : 22.32 % Favored : 76.10 % 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: 0.67 (0.21), residues: 1584 helix: 1.59 (0.19), residues: 788 sheet: 0.68 (0.33), residues: 263 loop : -1.45 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 547 TYR 0.013 0.001 TYR C 95 PHE 0.029 0.001 PHE A 200 TRP 0.017 0.001 TRP C 160 HIS 0.002 0.001 HIS A1007 Details of bonding type rmsd covalent geometry : bond 0.00258 (12785) covalent geometry : angle 0.58547 (17343) SS BOND : bond 0.00764 ( 5) SS BOND : angle 1.53201 ( 10) hydrogen bonds : bond 0.04643 ( 719) hydrogen bonds : angle 4.47026 ( 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 146 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.7543 (tmm) cc_final: 0.7343 (tmm) REVERT: A 258 LEU cc_start: 0.8473 (mm) cc_final: 0.8230 (mm) REVERT: A 514 MET cc_start: 0.5433 (mtm) cc_final: 0.4843 (tmm) REVERT: A 701 MET cc_start: 0.6316 (ptt) cc_final: 0.5980 (ptm) REVERT: A 814 LEU cc_start: 0.8366 (mt) cc_final: 0.8000 (mt) REVERT: A 891 GLU cc_start: 0.7296 (tt0) cc_final: 0.6493 (pp20) REVERT: A 920 TYR cc_start: 0.7854 (t80) cc_final: 0.7344 (t80) REVERT: A 948 MET cc_start: 0.7606 (tpt) cc_final: 0.7254 (tpp) REVERT: A 1270 MET cc_start: 0.0123 (tpt) cc_final: -0.0258 (tpt) REVERT: B 180 MET cc_start: 0.7466 (tmm) cc_final: 0.6811 (tmm) REVERT: C 25 SER cc_start: 0.8605 (p) cc_final: 0.8265 (t) outliers start: 21 outliers final: 21 residues processed: 141 average time/residue: 0.0987 time to fit residues: 21.8018 Evaluate side-chains 138 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 MET 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 512 PHE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 801 VAL 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 1041 VAL Chi-restraints excluded: chain A residue 1060 VAL 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 84 GLU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 10 optimal weight: 0.6980 chunk 116 optimal weight: 0.0570 chunk 58 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 31 optimal weight: 0.4980 chunk 133 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 GLN ** 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 = 0.4052 r_free = 0.4052 target = 0.144406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.115537 restraints weight = 27826.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.110921 restraints weight = 39695.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.112539 restraints weight = 36546.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.113580 restraints weight = 22083.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.113837 restraints weight = 20309.424| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.6141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12790 Z= 0.141 Angle : 0.603 10.369 17353 Z= 0.304 Chirality : 0.041 0.170 2006 Planarity : 0.004 0.058 2156 Dihedral : 5.108 59.452 2107 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.02 % Allowed : 21.65 % Favored : 76.33 % 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: 0.67 (0.21), residues: 1584 helix: 1.58 (0.18), residues: 788 sheet: 0.64 (0.33), residues: 263 loop : -1.41 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 547 TYR 0.016 0.002 TYR B 54 PHE 0.028 0.002 PHE A 200 TRP 0.018 0.001 TRP C 160 HIS 0.003 0.001 HIS A 518 Details of bonding type rmsd covalent geometry : bond 0.00312 (12785) covalent geometry : angle 0.60152 (17343) SS BOND : bond 0.00838 ( 5) SS BOND : angle 1.62943 ( 10) hydrogen bonds : bond 0.04786 ( 719) hydrogen bonds : angle 4.48792 ( 2085) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1847.04 seconds wall clock time: 32 minutes 53.06 seconds (1973.06 seconds total)