Starting phenix.real_space_refine on Fri Oct 23 20:35:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/23px_69160/10_2026/23px_69160.cif Found real_map, /net/cci-nas-00/data/ceres_data/23px_69160/10_2026/23px_69160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/23px_69160/10_2026/23px_69160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/23px_69160/10_2026/23px_69160.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/23px_69160/10_2026/23px_69160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/23px_69160/10_2026/23px_69160.map" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 42 5.16 5 C 6796 2.51 5 N 1828 2.21 5 O 2152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10819 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1391, 10818 Classifications: {'peptide': 1391} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 65, 'TRANS': 1323} Chain breaks: 4 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.33, per 1000 atoms: 0.22 Number of scatterers: 10819 At special positions: 0 Unit cell: (107.51, 109.991, 142.244, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 42 16.00 O 2152 8.00 N 1828 7.00 C 6796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 125 " distance=2.03 Simple disulfide: pdb=" SG CYS A1435 " - pdb=" SG CYS A1449 " 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: 0.70 Conformation dependent library (CDL) restraints added in 524.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1601 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A 236 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A1307 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A1303 " 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2562 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 20 sheets defined 30.8% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 164 through 178 removed outlier: 4.129A pdb=" N LYS A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER A 169 " --> pdb=" O ASP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 207 removed outlier: 3.711A pdb=" N SER A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 211 through 223 Processing helix chain 'A' and resid 223 through 229 removed outlier: 3.711A pdb=" N THR A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 341 through 356 Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 367 through 375 removed outlier: 4.006A pdb=" N ARG A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 406 through 414 removed outlier: 3.677A pdb=" N GLU A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE A 412 " --> pdb=" O PHE A 408 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 removed outlier: 3.574A pdb=" N ILE A 420 " --> pdb=" O GLN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.794A pdb=" N ILE A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 Processing helix chain 'A' and resid 568 through 575 removed outlier: 3.732A pdb=" N ILE A 572 " --> pdb=" O HIS A 568 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 573 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG A 574 " --> pdb=" O ASN A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 612 Processing helix chain 'A' and resid 706 through 720 Processing helix chain 'A' and resid 735 through 737 No H-bonds generated for 'chain 'A' and resid 735 through 737' Processing helix chain 'A' and resid 738 through 748 removed outlier: 3.924A pdb=" N ALA A 748 " --> pdb=" O LEU A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 810 removed outlier: 3.521A pdb=" N GLU A 809 " --> pdb=" O LYS A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 860 Processing helix chain 'A' and resid 903 through 911 removed outlier: 3.555A pdb=" N LYS A 908 " --> pdb=" O ALA A 904 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 911 " --> pdb=" O ALA A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 932 Processing helix chain 'A' and resid 941 through 957 removed outlier: 3.566A pdb=" N VAL A 954 " --> pdb=" O GLN A 950 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TRP A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 984 removed outlier: 3.704A pdb=" N PHE A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1006 removed outlier: 3.656A pdb=" N ASN A1006 " --> pdb=" O SER A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1041 Processing helix chain 'A' and resid 1209 through 1213 removed outlier: 3.701A pdb=" N ASN A1212 " --> pdb=" O LYS A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1238 removed outlier: 3.757A pdb=" N GLN A1222 " --> pdb=" O GLY A1218 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A1238 " --> pdb=" O MET A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1248 removed outlier: 4.176A pdb=" N HIS A1247 " --> pdb=" O ASP A1244 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG A1248 " --> pdb=" O GLY A1245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1244 through 1248' Processing helix chain 'A' and resid 1298 through 1309 removed outlier: 3.786A pdb=" N TRP A1302 " --> pdb=" O ASP A1298 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN A1308 " --> pdb=" O GLU A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1337 removed outlier: 3.682A pdb=" N ALA A1328 " --> pdb=" O ASN A1324 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY A1337 " --> pdb=" O ASP A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1356 Processing helix chain 'A' and resid 1365 through 1384 removed outlier: 3.913A pdb=" N LEU A1371 " --> pdb=" O GLY A1367 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET A1372 " --> pdb=" O ASP A1368 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR A1373 " --> pdb=" O ARG A1369 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS A1382 " --> pdb=" O GLU A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1385 through 1390 removed outlier: 4.204A pdb=" N TRP A1389 " --> pdb=" O ASP A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1419 removed outlier: 4.186A pdb=" N PHE A1412 " --> pdb=" O GLY A1408 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1430 removed outlier: 4.145A pdb=" N PHE A1429 " --> pdb=" O SER A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1455 removed outlier: 3.754A pdb=" N THR A1445 " --> pdb=" O ASN A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1466 Processing helix chain 'A' and resid 1487 through 1497 removed outlier: 3.526A pdb=" N TYR A1491 " --> pdb=" O SER A1487 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A1497 " --> pdb=" O THR A1493 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 117 removed outlier: 6.392A pdb=" N ASP A 113 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU A 94 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N THR A 91 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N PHE A 153 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR A 93 " --> pdb=" O PHE A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 117 removed outlier: 6.392A pdb=" N ASP A 113 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU A 94 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU A 94 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG A 101 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 Processing sheet with id=AA4, first strand: chain 'A' and resid 306 through 310 removed outlier: 8.904A pdb=" N ILE A 334 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ARG A 278 " --> pdb=" O ILE A 334 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 287 through 288 Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 300 removed outlier: 6.678A pdb=" N ILE A 319 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLU A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 468 through 471 Processing sheet with id=AA8, first strand: chain 'A' and resid 491 through 492 Processing sheet with id=AA9, first strand: chain 'A' and resid 498 through 504 removed outlier: 7.875A pdb=" N ILE A 551 " --> pdb=" O PRO A 499 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU A 501 " --> pdb=" O PRO A 549 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ALA A 503 " --> pdb=" O ASN A 547 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU A 676 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N MET A 726 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR A 625 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ILE A 677 " --> pdb=" O THR A 625 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY A 627 " --> pdb=" O ILE A 677 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 632 through 634 Processing sheet with id=AB2, first strand: chain 'A' and resid 681 through 683 removed outlier: 5.146A pdb=" N GLU A 682 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 819 through 820 removed outlier: 3.964A pdb=" N GLU A 782 " --> pdb=" O CYS A 877 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N CYS A 877 " --> pdb=" O GLU A 782 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 793 through 795 Processing sheet with id=AB5, first strand: chain 'A' and resid 822 through 827 Processing sheet with id=AB6, first strand: chain 'A' and resid 888 through 889 removed outlier: 3.731A pdb=" N VAL A 894 " --> pdb=" O THR A 889 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1009 through 1010 removed outlier: 3.752A pdb=" N MET A1019 " --> pdb=" O TYR A1010 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1063 through 1070 removed outlier: 4.730A pdb=" N GLN A1063 " --> pdb=" O GLY A1172 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A1172 " --> pdb=" O GLN A1063 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR A1086 " --> pdb=" O ILE A1156 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ILE A1156 " --> pdb=" O THR A1086 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LEU A1088 " --> pdb=" O ILE A1154 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A1152 " --> pdb=" O ALA A1090 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1063 through 1070 removed outlier: 4.730A pdb=" N GLN A1063 " --> pdb=" O GLY A1172 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A1172 " --> pdb=" O GLN A1063 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1183 through 1186 removed outlier: 6.442A pdb=" N PHE A1178 " --> pdb=" O LYS A1185 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR A1179 " --> pdb=" O GLU A1198 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1469 through 1472 354 hydrogen bonds defined for protein. 990 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: 2.58 Time building geometry restraints manager: 0.94 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: 3597 1.34 - 1.46: 2252 1.46 - 1.57: 5145 1.57 - 1.69: 0 1.69 - 1.81: 71 Bond restraints: 11065 Sorted by residual: bond pdb=" N GLY A 777 " pdb=" CA GLY A 777 " ideal model delta sigma weight residual 1.447 1.480 -0.033 1.08e-02 8.57e+03 9.49e+00 bond pdb=" CA SER A1275 " pdb=" CB SER A1275 " ideal model delta sigma weight residual 1.530 1.480 0.050 1.69e-02 3.50e+03 8.83e+00 bond pdb=" N VAL A1279 " pdb=" CA VAL A1279 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.25e-02 6.40e+03 8.46e+00 bond pdb=" N GLY A1276 " pdb=" CA GLY A1276 " ideal model delta sigma weight residual 1.448 1.472 -0.024 9.00e-03 1.23e+04 6.98e+00 bond pdb=" N TYR A1277 " pdb=" CA TYR A1277 " ideal model delta sigma weight residual 1.462 1.486 -0.025 9.50e-03 1.11e+04 6.74e+00 ... (remaining 11060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 14770 2.29 - 4.57: 224 4.57 - 6.86: 30 6.86 - 9.14: 5 9.14 - 11.43: 2 Bond angle restraints: 15031 Sorted by residual: angle pdb=" N PRO A 763 " pdb=" CA PRO A 763 " pdb=" CB PRO A 763 " ideal model delta sigma weight residual 103.25 91.82 11.43 1.05e+00 9.07e-01 1.18e+02 angle pdb=" CA GLY A1276 " pdb=" C GLY A1276 " pdb=" O GLY A1276 " ideal model delta sigma weight residual 122.45 117.57 4.88 7.20e-01 1.93e+00 4.60e+01 angle pdb=" N TYR A1277 " pdb=" CA TYR A1277 " pdb=" C TYR A1277 " ideal model delta sigma weight residual 113.25 105.62 7.63 1.30e+00 5.92e-01 3.44e+01 angle pdb=" N TYR A1277 " pdb=" CA TYR A1277 " pdb=" CB TYR A1277 " ideal model delta sigma weight residual 110.08 120.65 -10.57 1.89e+00 2.80e-01 3.13e+01 angle pdb=" C GLY A 777 " pdb=" N ILE A 778 " pdb=" CA ILE A 778 " ideal model delta sigma weight residual 121.71 115.08 6.63 1.20e+00 6.94e-01 3.05e+01 ... (remaining 15026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 6025 17.56 - 35.12: 475 35.12 - 52.69: 63 52.69 - 70.25: 13 70.25 - 87.81: 7 Dihedral angle restraints: 6583 sinusoidal: 2574 harmonic: 4009 Sorted by residual: dihedral pdb=" CB CYS A1435 " pdb=" SG CYS A1435 " pdb=" SG CYS A1449 " pdb=" CB CYS A1449 " ideal model delta sinusoidal sigma weight residual -86.00 -173.81 87.81 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" N PRO A 763 " pdb=" C PRO A 763 " pdb=" CA PRO A 763 " pdb=" CB PRO A 763 " ideal model delta harmonic sigma weight residual 115.10 104.96 10.14 0 2.50e+00 1.60e-01 1.65e+01 dihedral pdb=" CA LEU A 678 " pdb=" C LEU A 678 " pdb=" N ASN A 679 " pdb=" CA ASN A 679 " ideal model delta harmonic sigma weight residual 180.00 160.84 19.16 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 6580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1137 0.041 - 0.081: 352 0.081 - 0.121: 113 0.121 - 0.162: 19 0.162 - 0.202: 3 Chirality restraints: 1624 Sorted by residual: chirality pdb=" CA VAL A 759 " pdb=" N VAL A 759 " pdb=" C VAL A 759 " pdb=" CB VAL A 759 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA LEU A1396 " pdb=" N LEU A1396 " pdb=" C LEU A1396 " pdb=" CB LEU A1396 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" CA ASP A1181 " pdb=" N ASP A1181 " pdb=" C ASP A1181 " pdb=" CB ASP A1181 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 1621 not shown) Planarity restraints: 1986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 617 " 0.046 5.00e-02 4.00e+02 7.04e-02 7.92e+00 pdb=" N PRO A 618 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 618 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 618 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 823 " -0.020 2.00e-02 2.50e+03 1.63e-02 6.65e+00 pdb=" CG TRP A 823 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 823 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 823 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 823 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 823 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 823 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 823 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 823 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 823 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A1316 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PRO A1317 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A1317 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1317 " -0.031 5.00e-02 4.00e+02 ... (remaining 1983 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 25 2.31 - 2.96: 5180 2.96 - 3.60: 16133 3.60 - 4.25: 25262 4.25 - 4.90: 42502 Nonbonded interactions: 89102 Sorted by model distance: nonbonded pdb=" CD1 LEU A 524 " pdb=" OH TYR A 806 " model vdw 1.662 3.460 nonbonded pdb=" OE1 GLU A1321 " pdb="ZN ZN A1601 " model vdw 1.971 2.230 nonbonded pdb=" OE2 GLU A 825 " pdb=" NH2 ARG A 834 " model vdw 2.059 3.120 nonbonded pdb=" OG SER A 941 " pdb=" OD2 ASP A 944 " model vdw 2.110 3.040 nonbonded pdb=" O MET A1083 " pdb=" NH2 ARG A1261 " model vdw 2.137 3.120 ... (remaining 89097 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.300 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:1.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11070 Z= 0.228 Angle : 0.700 11.430 15035 Z= 0.415 Chirality : 0.045 0.202 1624 Planarity : 0.004 0.070 1986 Dihedral : 12.738 86.642 4015 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.20 % Favored : 95.66 % Rotamer: Outliers : 0.34 % Allowed : 0.43 % Favored : 99.23 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.99 % 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 (0.22), residues: 1381 helix: 0.10 (0.28), residues: 348 sheet: -0.30 (0.35), residues: 214 loop : -0.53 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 609 TYR 0.025 0.002 TYR A 873 PHE 0.025 0.002 PHE A1178 TRP 0.043 0.002 TRP A 823 HIS 0.004 0.001 HIS A1307 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.23 (11065) covalent geometry : angle 0.70008 / 0.41 (15031) SS BOND : bond 0.00272 / 0.13 ( 2) SS BOND : angle 0.68520 / 0.35 ( 4) hydrogen bonds : bond 0.15161 / 9.86 ( 344) hydrogen bonds : angle 6.42883 / 4.43 ( 990) metal coordination : bond 0.00615 / 0.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 299 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 LYS cc_start: 0.8281 (ttmm) cc_final: 0.7906 (ttpp) REVERT: A 258 SER cc_start: 0.8274 (t) cc_final: 0.8029 (t) REVERT: A 272 ILE cc_start: 0.8731 (mt) cc_final: 0.7950 (mt) REVERT: A 303 GLU cc_start: 0.7283 (mp0) cc_final: 0.6972 (mp0) REVERT: A 418 LYS cc_start: 0.8009 (tppt) cc_final: 0.7724 (tptt) REVERT: A 450 GLN cc_start: 0.7754 (tm-30) cc_final: 0.7502 (tm-30) REVERT: A 468 LYS cc_start: 0.8112 (mtmm) cc_final: 0.7770 (mtmm) REVERT: A 507 LYS cc_start: 0.7879 (tptp) cc_final: 0.7669 (tptm) REVERT: A 515 GLU cc_start: 0.6870 (mp0) cc_final: 0.6430 (mp0) REVERT: A 600 MET cc_start: 0.7698 (mmm) cc_final: 0.7364 (mmm) REVERT: A 604 MET cc_start: 0.8075 (mmt) cc_final: 0.6730 (mmt) REVERT: A 613 ASP cc_start: 0.7179 (t0) cc_final: 0.6903 (t0) REVERT: A 641 VAL cc_start: 0.8598 (m) cc_final: 0.8310 (p) REVERT: A 704 LYS cc_start: 0.7754 (mtpt) cc_final: 0.7315 (mtpt) REVERT: A 732 ASN cc_start: 0.8106 (t0) cc_final: 0.7767 (t0) REVERT: A 781 TYR cc_start: 0.7299 (t80) cc_final: 0.6901 (t80) REVERT: A 819 GLU cc_start: 0.6920 (pm20) cc_final: 0.6646 (pm20) REVERT: A 850 LYS cc_start: 0.8454 (tmmt) cc_final: 0.8110 (ttmt) REVERT: A 876 ASN cc_start: 0.7779 (t0) cc_final: 0.7418 (t0) REVERT: A 908 LYS cc_start: 0.8503 (mtmm) cc_final: 0.8291 (mttp) REVERT: A 918 THR cc_start: 0.8344 (m) cc_final: 0.8107 (t) REVERT: A 952 MET cc_start: 0.7618 (tpp) cc_final: 0.6934 (mmm) REVERT: A 954 VAL cc_start: 0.8861 (t) cc_final: 0.8632 (m) REVERT: A 1044 ASP cc_start: 0.7585 (t0) cc_final: 0.7209 (t0) REVERT: A 1082 ASN cc_start: 0.7237 (p0) cc_final: 0.7004 (p0) REVERT: A 1148 VAL cc_start: 0.8641 (t) cc_final: 0.8280 (p) REVERT: A 1164 GLU cc_start: 0.7292 (pp20) cc_final: 0.6938 (pp20) REVERT: A 1196 GLU cc_start: 0.7165 (pt0) cc_final: 0.6822 (pt0) REVERT: A 1333 ASP cc_start: 0.7014 (m-30) cc_final: 0.6685 (m-30) REVERT: A 1338 LYS cc_start: 0.7617 (ptpt) cc_final: 0.7338 (ptmm) REVERT: A 1368 ASP cc_start: 0.7208 (t0) cc_final: 0.6944 (t70) REVERT: A 1483 GLU cc_start: 0.6620 (mp0) cc_final: 0.6406 (mp0) outliers start: 4 outliers final: 1 residues processed: 300 average time/residue: 0.1143 time to fit residues: 47.2097 Evaluate side-chains 266 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 776 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 ASN A 304 ASN A 353 HIS A 361 ASN ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 HIS A 872 HIS A 919 ASN A 958 ASN A1006 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.136004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.118378 restraints weight = 17253.397| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.62 r_work: 0.3447 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11070 Z= 0.154 Angle : 0.589 9.048 15035 Z= 0.306 Chirality : 0.043 0.147 1624 Planarity : 0.004 0.056 1986 Dihedral : 4.515 23.955 1493 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.20 % Allowed : 10.00 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.34 (0.22), residues: 1381 helix: 0.57 (0.28), residues: 356 sheet: -0.26 (0.34), residues: 215 loop : -0.53 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 328 TYR 0.013 0.001 TYR A 463 PHE 0.022 0.002 PHE A1178 TRP 0.017 0.001 TRP A 823 HIS 0.012 0.001 HIS A 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (11065) covalent geometry : angle 0.58881 / 0.31 (15031) SS BOND : bond 0.00286 / 0.14 ( 2) SS BOND : angle 0.70577 / 0.38 ( 4) hydrogen bonds : bond 0.03456 / 2.31 ( 344) hydrogen bonds : angle 4.84793 / 3.42 ( 990) metal coordination : bond 0.00630 / 0.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 274 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 LYS cc_start: 0.8509 (ttmm) cc_final: 0.8025 (ttpp) REVERT: A 258 SER cc_start: 0.8487 (t) cc_final: 0.8259 (t) REVERT: A 303 GLU cc_start: 0.7996 (mp0) cc_final: 0.7625 (mp0) REVERT: A 360 GLN cc_start: 0.7172 (pp30) cc_final: 0.6902 (pp30) REVERT: A 364 ARG cc_start: 0.8204 (mmm160) cc_final: 0.7875 (mmm160) REVERT: A 418 LYS cc_start: 0.8164 (tppt) cc_final: 0.7821 (tptt) REVERT: A 450 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7559 (tm-30) REVERT: A 468 LYS cc_start: 0.8421 (mtmm) cc_final: 0.8095 (mtmm) REVERT: A 507 LYS cc_start: 0.7984 (tptp) cc_final: 0.7749 (tptm) REVERT: A 515 GLU cc_start: 0.7115 (mp0) cc_final: 0.6795 (mp0) REVERT: A 521 LYS cc_start: 0.8350 (mttm) cc_final: 0.7977 (mttm) REVERT: A 562 MET cc_start: 0.8290 (ttm) cc_final: 0.8081 (ttm) REVERT: A 600 MET cc_start: 0.8024 (mmm) cc_final: 0.7708 (mmm) REVERT: A 613 ASP cc_start: 0.7692 (t0) cc_final: 0.7339 (t0) REVERT: A 641 VAL cc_start: 0.8761 (m) cc_final: 0.8452 (p) REVERT: A 704 LYS cc_start: 0.7964 (mtpt) cc_final: 0.7562 (mtpt) REVERT: A 722 SER cc_start: 0.8520 (m) cc_final: 0.8201 (p) REVERT: A 732 ASN cc_start: 0.8294 (t0) cc_final: 0.7917 (t0) REVERT: A 781 TYR cc_start: 0.7716 (t80) cc_final: 0.7265 (t80) REVERT: A 819 GLU cc_start: 0.7348 (pm20) cc_final: 0.6928 (pm20) REVERT: A 850 LYS cc_start: 0.8410 (tmmt) cc_final: 0.8068 (ttmt) REVERT: A 876 ASN cc_start: 0.8264 (t0) cc_final: 0.7826 (t0) REVERT: A 908 LYS cc_start: 0.8420 (mtmm) cc_final: 0.8213 (mtmm) REVERT: A 916 LEU cc_start: 0.8174 (mm) cc_final: 0.7956 (mp) REVERT: A 918 THR cc_start: 0.8491 (m) cc_final: 0.8242 (t) REVERT: A 1000 LYS cc_start: 0.8054 (ttpt) cc_final: 0.7771 (tppt) REVERT: A 1053 LYS cc_start: 0.8743 (mppt) cc_final: 0.8413 (mppt) REVERT: A 1148 VAL cc_start: 0.8696 (t) cc_final: 0.8287 (p) REVERT: A 1164 GLU cc_start: 0.7694 (pp20) cc_final: 0.7302 (pp20) REVERT: A 1165 SER cc_start: 0.8451 (m) cc_final: 0.7823 (m) REVERT: A 1187 ASP cc_start: 0.7778 (t70) cc_final: 0.7477 (t0) REVERT: A 1196 GLU cc_start: 0.7669 (pt0) cc_final: 0.7431 (pt0) REVERT: A 1282 SER cc_start: 0.8225 (m) cc_final: 0.7918 (p) REVERT: A 1311 GLU cc_start: 0.7208 (mm-30) cc_final: 0.7004 (mm-30) REVERT: A 1331 MET cc_start: 0.8383 (mmm) cc_final: 0.8062 (mmm) REVERT: A 1333 ASP cc_start: 0.7879 (m-30) cc_final: 0.7442 (m-30) REVERT: A 1338 LYS cc_start: 0.7856 (ptpt) cc_final: 0.7044 (ptmt) REVERT: A 1351 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7153 (pm20) REVERT: A 1357 ASN cc_start: 0.8479 (t0) cc_final: 0.8061 (t0) REVERT: A 1368 ASP cc_start: 0.7694 (t0) cc_final: 0.7400 (t70) REVERT: A 1389 TRP cc_start: 0.8625 (m100) cc_final: 0.7929 (m100) REVERT: A 1470 ASN cc_start: 0.7645 (m-40) cc_final: 0.7164 (m-40) REVERT: A 1483 GLU cc_start: 0.6954 (mp0) cc_final: 0.6725 (mp0) REVERT: A 1515 HIS cc_start: 0.8452 (t-170) cc_final: 0.8148 (t-170) outliers start: 14 outliers final: 8 residues processed: 280 average time/residue: 0.1135 time to fit residues: 43.9336 Evaluate side-chains 269 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 260 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 855 LYS Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1351 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [126, 12, 70, 69, 51, 44, 64, 131, 22, 27, 104] chunk 126 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN A 353 HIS A 411 GLN ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 ASN A 651 HIS A 919 ASN A 958 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.131834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.113799 restraints weight = 17388.713| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.66 r_work: 0.3394 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 11070 Z= 0.250 Angle : 0.612 8.275 15035 Z= 0.317 Chirality : 0.044 0.164 1624 Planarity : 0.004 0.058 1986 Dihedral : 4.631 18.646 1492 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.05 % Allowed : 13.33 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.36 (0.22), residues: 1381 helix: 0.46 (0.28), residues: 357 sheet: -0.31 (0.33), residues: 232 loop : -0.49 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 774 TYR 0.014 0.002 TYR A1204 PHE 0.022 0.002 PHE A1178 TRP 0.016 0.001 TRP A 457 HIS 0.014 0.002 HIS A 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.25 (11065) covalent geometry : angle 0.61187 / 0.32 (15031) SS BOND : bond 0.00442 / 0.21 ( 2) SS BOND : angle 0.87983 / 0.45 ( 4) hydrogen bonds : bond 0.03797 / 2.56 ( 344) hydrogen bonds : angle 4.77217 / 3.35 ( 990) metal coordination : bond 0.00951 / 0.42 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 273 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.7678 (tp) cc_final: 0.7260 (tp) REVERT: A 221 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.6006 (mp0) REVERT: A 231 LYS cc_start: 0.8542 (ttmm) cc_final: 0.8106 (ttpp) REVERT: A 258 SER cc_start: 0.8502 (t) cc_final: 0.8292 (t) REVERT: A 303 GLU cc_start: 0.8003 (mp0) cc_final: 0.7636 (mp0) REVERT: A 418 LYS cc_start: 0.8221 (tppt) cc_final: 0.7795 (tptt) REVERT: A 450 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7310 (tm-30) REVERT: A 507 LYS cc_start: 0.7977 (tptp) cc_final: 0.7740 (tptm) REVERT: A 515 GLU cc_start: 0.7227 (mp0) cc_final: 0.6865 (mp0) REVERT: A 521 LYS cc_start: 0.8425 (mttm) cc_final: 0.7972 (mttm) REVERT: A 562 MET cc_start: 0.8265 (ttm) cc_final: 0.8046 (ttm) REVERT: A 600 MET cc_start: 0.8152 (mmm) cc_final: 0.7678 (mmm) REVERT: A 613 ASP cc_start: 0.7728 (t0) cc_final: 0.7333 (t70) REVERT: A 699 ASP cc_start: 0.7734 (t70) cc_final: 0.7480 (t70) REVERT: A 722 SER cc_start: 0.8519 (m) cc_final: 0.8196 (p) REVERT: A 781 TYR cc_start: 0.7831 (t80) cc_final: 0.7288 (t80) REVERT: A 819 GLU cc_start: 0.7396 (pm20) cc_final: 0.7028 (pm20) REVERT: A 850 LYS cc_start: 0.8452 (tmmt) cc_final: 0.8097 (ttmt) REVERT: A 876 ASN cc_start: 0.8254 (t0) cc_final: 0.7720 (t0) REVERT: A 908 LYS cc_start: 0.8450 (mtmm) cc_final: 0.8222 (mtmm) REVERT: A 918 THR cc_start: 0.8528 (m) cc_final: 0.8280 (t) REVERT: A 938 GLU cc_start: 0.7496 (pp20) cc_final: 0.7141 (pp20) REVERT: A 946 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: A 952 MET cc_start: 0.8086 (mmm) cc_final: 0.7690 (mmm) REVERT: A 989 TYR cc_start: 0.8038 (m-10) cc_final: 0.7755 (m-80) REVERT: A 1028 TYR cc_start: 0.8450 (p90) cc_final: 0.8165 (p90) REVERT: A 1053 LYS cc_start: 0.8786 (mppt) cc_final: 0.8443 (mppt) REVERT: A 1082 ASN cc_start: 0.7933 (p0) cc_final: 0.7585 (p0) REVERT: A 1095 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7317 (tm-30) REVERT: A 1126 LEU cc_start: 0.8091 (tp) cc_final: 0.7877 (tp) REVERT: A 1164 GLU cc_start: 0.7710 (pp20) cc_final: 0.7304 (pp20) REVERT: A 1180 LYS cc_start: 0.7881 (mtpp) cc_final: 0.7643 (mttp) REVERT: A 1187 ASP cc_start: 0.7870 (t70) cc_final: 0.7540 (t0) REVERT: A 1196 GLU cc_start: 0.7775 (pt0) cc_final: 0.6900 (tt0) REVERT: A 1198 GLU cc_start: 0.7897 (tt0) cc_final: 0.7444 (tt0) REVERT: A 1204 TYR cc_start: 0.8257 (t80) cc_final: 0.7883 (t80) REVERT: A 1282 SER cc_start: 0.8218 (m) cc_final: 0.7924 (p) REVERT: A 1331 MET cc_start: 0.8480 (mmm) cc_final: 0.8158 (mmm) REVERT: A 1338 LYS cc_start: 0.7946 (ptpt) cc_final: 0.7454 (ptmt) REVERT: A 1348 VAL cc_start: 0.7699 (m) cc_final: 0.7496 (m) REVERT: A 1357 ASN cc_start: 0.8567 (t0) cc_final: 0.8089 (t0) REVERT: A 1368 ASP cc_start: 0.7778 (t0) cc_final: 0.7408 (t0) REVERT: A 1381 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7760 (tm-30) REVERT: A 1470 ASN cc_start: 0.7771 (m-40) cc_final: 0.7384 (m-40) outliers start: 24 outliers final: 14 residues processed: 286 average time/residue: 0.1081 time to fit residues: 42.6927 Evaluate side-chains 286 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 270 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 855 LYS Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1494 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [57, 51, 6, 34, 30, 95, 62, 103, 75, 135, 17] chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 95 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN A 353 HIS A 361 ASN ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 HIS A 760 ASN A 958 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.133601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.115568 restraints weight = 17364.417| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.68 r_work: 0.3415 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11070 Z= 0.144 Angle : 0.562 7.531 15035 Z= 0.292 Chirality : 0.042 0.166 1624 Planarity : 0.004 0.059 1986 Dihedral : 4.431 18.229 1492 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.14 % Allowed : 15.56 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.23 (0.22), residues: 1381 helix: 0.71 (0.29), residues: 355 sheet: -0.22 (0.33), residues: 232 loop : -0.48 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1261 TYR 0.012 0.001 TYR A 716 PHE 0.013 0.001 PHE A 681 TRP 0.012 0.001 TRP A 779 HIS 0.011 0.002 HIS A 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (11065) covalent geometry : angle 0.56202 / 0.29 (15031) SS BOND : bond 0.00214 / 0.10 ( 2) SS BOND : angle 0.60294 / 0.30 ( 4) hydrogen bonds : bond 0.03181 / 2.15 ( 344) hydrogen bonds : angle 4.55485 / 3.22 ( 990) metal coordination : bond 0.00484 / 0.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 273 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.7624 (tp) cc_final: 0.7216 (tp) REVERT: A 221 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6046 (mp0) REVERT: A 231 LYS cc_start: 0.8517 (ttmm) cc_final: 0.8132 (ttpp) REVERT: A 258 SER cc_start: 0.8488 (t) cc_final: 0.8226 (t) REVERT: A 303 GLU cc_start: 0.8025 (mp0) cc_final: 0.7652 (mp0) REVERT: A 360 GLN cc_start: 0.7223 (pp30) cc_final: 0.6958 (pp30) REVERT: A 364 ARG cc_start: 0.8274 (mmm160) cc_final: 0.7728 (mmm160) REVERT: A 418 LYS cc_start: 0.8199 (tppt) cc_final: 0.7990 (tppt) REVERT: A 450 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7314 (tm-30) REVERT: A 507 LYS cc_start: 0.7902 (tptp) cc_final: 0.7690 (tptm) REVERT: A 515 GLU cc_start: 0.7199 (mp0) cc_final: 0.6872 (mp0) REVERT: A 521 LYS cc_start: 0.8379 (mttm) cc_final: 0.7949 (mttm) REVERT: A 537 GLU cc_start: 0.8118 (pm20) cc_final: 0.7826 (pm20) REVERT: A 600 MET cc_start: 0.8079 (mmm) cc_final: 0.7694 (mmm) REVERT: A 613 ASP cc_start: 0.7756 (t0) cc_final: 0.7371 (t70) REVERT: A 665 TYR cc_start: 0.8544 (m-80) cc_final: 0.8260 (m-80) REVERT: A 671 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7501 (mm-40) REVERT: A 673 MET cc_start: 0.7732 (ttm) cc_final: 0.7399 (ttm) REVERT: A 704 LYS cc_start: 0.8078 (mttt) cc_final: 0.7877 (mtpp) REVERT: A 781 TYR cc_start: 0.7806 (t80) cc_final: 0.7296 (t80) REVERT: A 819 GLU cc_start: 0.7418 (pm20) cc_final: 0.6985 (pm20) REVERT: A 850 LYS cc_start: 0.8398 (tmmt) cc_final: 0.8043 (ttmt) REVERT: A 876 ASN cc_start: 0.8247 (t0) cc_final: 0.7671 (t0) REVERT: A 908 LYS cc_start: 0.8403 (mtmm) cc_final: 0.8169 (mtmm) REVERT: A 918 THR cc_start: 0.8460 (m) cc_final: 0.8206 (t) REVERT: A 936 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8314 (ptpp) REVERT: A 938 GLU cc_start: 0.7498 (pp20) cc_final: 0.7140 (pp20) REVERT: A 946 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: A 1028 TYR cc_start: 0.8438 (p90) cc_final: 0.8160 (p90) REVERT: A 1044 ASP cc_start: 0.7650 (t0) cc_final: 0.7377 (t0) REVERT: A 1053 LYS cc_start: 0.8803 (mppt) cc_final: 0.8450 (mppt) REVERT: A 1095 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7368 (tm-30) REVERT: A 1126 LEU cc_start: 0.7985 (tp) cc_final: 0.7687 (tp) REVERT: A 1164 GLU cc_start: 0.7708 (pp20) cc_final: 0.7381 (pp20) REVERT: A 1180 LYS cc_start: 0.7904 (mtpp) cc_final: 0.7696 (mttp) REVERT: A 1187 ASP cc_start: 0.7805 (t70) cc_final: 0.7455 (t0) REVERT: A 1282 SER cc_start: 0.8192 (m) cc_final: 0.7893 (p) REVERT: A 1331 MET cc_start: 0.8461 (mmm) cc_final: 0.8109 (mmm) REVERT: A 1338 LYS cc_start: 0.7793 (ptpt) cc_final: 0.7284 (ptmt) REVERT: A 1348 VAL cc_start: 0.7585 (m) cc_final: 0.6657 (m) REVERT: A 1351 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7146 (pm20) REVERT: A 1354 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6656 (mp0) REVERT: A 1357 ASN cc_start: 0.8567 (t0) cc_final: 0.8062 (t0) REVERT: A 1368 ASP cc_start: 0.7680 (t0) cc_final: 0.7330 (t0) REVERT: A 1470 ASN cc_start: 0.7673 (m-40) cc_final: 0.7073 (m-40) REVERT: A 1483 GLU cc_start: 0.7100 (mp0) cc_final: 0.6564 (mp0) outliers start: 25 outliers final: 13 residues processed: 286 average time/residue: 0.1093 time to fit residues: 43.2043 Evaluate side-chains 290 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 272 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 855 LYS Chi-restraints excluded: chain A residue 864 LYS Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1351 GLU Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1388 LYS Chi-restraints excluded: chain A residue 1494 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [39, 82, 133, 70, 78, 100, 77, 136, 89, 32, 85] chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 136 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 32 optimal weight: 0.0020 chunk 85 optimal weight: 0.5980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN A 353 HIS A 361 ASN ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN A 958 ASN A1084 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.134004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.115924 restraints weight = 17221.622| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.67 r_work: 0.3429 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11070 Z= 0.136 Angle : 0.553 7.375 15035 Z= 0.285 Chirality : 0.041 0.168 1624 Planarity : 0.004 0.059 1986 Dihedral : 4.323 18.359 1492 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.74 % Allowed : 16.07 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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 (0.23), residues: 1381 helix: 0.82 (0.29), residues: 355 sheet: -0.04 (0.34), residues: 225 loop : -0.47 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1261 TYR 0.011 0.001 TYR A 716 PHE 0.011 0.001 PHE A1462 TRP 0.014 0.001 TRP A 779 HIS 0.008 0.001 HIS A 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (11065) covalent geometry : angle 0.55278 / 0.29 (15031) SS BOND : bond 0.00205 / 0.10 ( 2) SS BOND : angle 0.54813 / 0.27 ( 4) hydrogen bonds : bond 0.03036 / 2.05 ( 344) hydrogen bonds : angle 4.41624 / 3.12 ( 990) metal coordination : bond 0.00520 / 0.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 275 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.7671 (tp) cc_final: 0.7224 (tp) REVERT: A 221 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.6021 (mp0) REVERT: A 231 LYS cc_start: 0.8514 (ttmm) cc_final: 0.8129 (ttpp) REVERT: A 249 LYS cc_start: 0.8239 (mtmm) cc_final: 0.7952 (mttp) REVERT: A 258 SER cc_start: 0.8447 (t) cc_final: 0.8220 (t) REVERT: A 303 GLU cc_start: 0.7994 (mp0) cc_final: 0.7612 (mp0) REVERT: A 360 GLN cc_start: 0.7222 (pp30) cc_final: 0.6955 (pp30) REVERT: A 364 ARG cc_start: 0.8258 (mmm160) cc_final: 0.7746 (mmm160) REVERT: A 418 LYS cc_start: 0.8197 (tppt) cc_final: 0.7981 (tppt) REVERT: A 450 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7251 (tm-30) REVERT: A 463 TYR cc_start: 0.7543 (m-10) cc_final: 0.7288 (m-10) REVERT: A 507 LYS cc_start: 0.7859 (tptp) cc_final: 0.7632 (tptm) REVERT: A 515 GLU cc_start: 0.7180 (mp0) cc_final: 0.6901 (mp0) REVERT: A 521 LYS cc_start: 0.8283 (mttm) cc_final: 0.7866 (mttm) REVERT: A 537 GLU cc_start: 0.8079 (pm20) cc_final: 0.7863 (pm20) REVERT: A 600 MET cc_start: 0.8099 (mmm) cc_final: 0.7782 (mmm) REVERT: A 613 ASP cc_start: 0.7720 (t0) cc_final: 0.7307 (t70) REVERT: A 615 LYS cc_start: 0.8488 (mtmm) cc_final: 0.8087 (mttt) REVERT: A 665 TYR cc_start: 0.8548 (m-80) cc_final: 0.8314 (m-80) REVERT: A 671 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7440 (mm-40) REVERT: A 673 MET cc_start: 0.7706 (ttm) cc_final: 0.7376 (ttm) REVERT: A 699 ASP cc_start: 0.7807 (t0) cc_final: 0.7500 (t70) REVERT: A 726 MET cc_start: 0.8101 (mtt) cc_final: 0.7652 (mtm) REVERT: A 781 TYR cc_start: 0.7799 (t80) cc_final: 0.7310 (t80) REVERT: A 819 GLU cc_start: 0.7408 (pm20) cc_final: 0.6952 (pm20) REVERT: A 850 LYS cc_start: 0.8384 (tmmt) cc_final: 0.8021 (ttmt) REVERT: A 876 ASN cc_start: 0.8241 (t0) cc_final: 0.7677 (t0) REVERT: A 908 LYS cc_start: 0.8407 (mtmm) cc_final: 0.8175 (mtmm) REVERT: A 918 THR cc_start: 0.8451 (m) cc_final: 0.8185 (t) REVERT: A 936 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8299 (ptpp) REVERT: A 938 GLU cc_start: 0.7393 (pp20) cc_final: 0.6991 (pp20) REVERT: A 946 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: A 1028 TYR cc_start: 0.8431 (p90) cc_final: 0.8159 (p90) REVERT: A 1044 ASP cc_start: 0.7463 (t0) cc_final: 0.7093 (t0) REVERT: A 1053 LYS cc_start: 0.8812 (mppt) cc_final: 0.8435 (mppt) REVERT: A 1095 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7384 (tm-30) REVERT: A 1126 LEU cc_start: 0.8010 (tp) cc_final: 0.7721 (tp) REVERT: A 1164 GLU cc_start: 0.7725 (pp20) cc_final: 0.7394 (pp20) REVERT: A 1165 SER cc_start: 0.8525 (m) cc_final: 0.7912 (m) REVERT: A 1187 ASP cc_start: 0.7755 (t70) cc_final: 0.7389 (t0) REVERT: A 1200 ASP cc_start: 0.7650 (t0) cc_final: 0.7227 (t0) REVERT: A 1282 SER cc_start: 0.8199 (m) cc_final: 0.7883 (p) REVERT: A 1304 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7298 (tp30) REVERT: A 1331 MET cc_start: 0.8442 (mmm) cc_final: 0.8099 (mmm) REVERT: A 1338 LYS cc_start: 0.7595 (ptpt) cc_final: 0.7303 (ptmt) REVERT: A 1348 VAL cc_start: 0.7593 (m) cc_final: 0.6666 (m) REVERT: A 1351 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7087 (pm20) REVERT: A 1354 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: A 1357 ASN cc_start: 0.8563 (t0) cc_final: 0.8036 (t0) REVERT: A 1368 ASP cc_start: 0.7636 (t0) cc_final: 0.7292 (t0) REVERT: A 1470 ASN cc_start: 0.7650 (m-40) cc_final: 0.7278 (m-40) REVERT: A 1494 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8646 (tp) REVERT: A 1513 THR cc_start: 0.8417 (m) cc_final: 0.8174 (p) outliers start: 32 outliers final: 18 residues processed: 291 average time/residue: 0.1104 time to fit residues: 44.3759 Evaluate side-chains 290 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 266 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 855 LYS Chi-restraints excluded: chain A residue 864 LYS Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1351 GLU Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1388 LYS Chi-restraints excluded: chain A residue 1472 TYR Chi-restraints excluded: chain A residue 1480 MET Chi-restraints excluded: chain A residue 1494 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [96, 5, 10, 6, 17, 16, 94, 12, 130, 115, 40] chunk 96 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 40 optimal weight: 0.0670 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN A 353 HIS A 361 ASN ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN A 872 HIS A 958 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.133372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.115396 restraints weight = 17326.902| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.66 r_work: 0.3423 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11070 Z= 0.159 Angle : 0.573 12.168 15035 Z= 0.292 Chirality : 0.042 0.173 1624 Planarity : 0.004 0.069 1986 Dihedral : 4.325 18.846 1492 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.16 % Allowed : 16.15 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.20 (0.22), residues: 1381 helix: 0.68 (0.28), residues: 369 sheet: -0.02 (0.35), residues: 213 loop : -0.51 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1261 TYR 0.012 0.001 TYR A 716 PHE 0.012 0.001 PHE A 307 TRP 0.011 0.001 TRP A 779 HIS 0.010 0.002 HIS A 872 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (11065) covalent geometry : angle 0.57324 / 0.29 (15031) SS BOND : bond 0.00241 / 0.12 ( 2) SS BOND : angle 0.58916 / 0.29 ( 4) hydrogen bonds : bond 0.03076 / 2.08 ( 344) hydrogen bonds : angle 4.40776 / 3.12 ( 990) metal coordination : bond 0.00641 / 0.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.7689 (tp) cc_final: 0.7257 (tp) REVERT: A 221 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.6033 (mp0) REVERT: A 231 LYS cc_start: 0.8514 (ttmm) cc_final: 0.8128 (ttpp) REVERT: A 258 SER cc_start: 0.8463 (t) cc_final: 0.8231 (t) REVERT: A 283 GLN cc_start: 0.7613 (mt0) cc_final: 0.7231 (pt0) REVERT: A 303 GLU cc_start: 0.8022 (mp0) cc_final: 0.7635 (mp0) REVERT: A 338 GLU cc_start: 0.7792 (pt0) cc_final: 0.7408 (pp20) REVERT: A 418 LYS cc_start: 0.8202 (tppt) cc_final: 0.7811 (tptm) REVERT: A 450 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7311 (tm-30) REVERT: A 507 LYS cc_start: 0.7862 (tptp) cc_final: 0.7650 (tptm) REVERT: A 515 GLU cc_start: 0.7214 (mp0) cc_final: 0.6915 (mp0) REVERT: A 521 LYS cc_start: 0.8341 (mttm) cc_final: 0.7928 (mttm) REVERT: A 560 LYS cc_start: 0.8478 (ptpt) cc_final: 0.8090 (mtmm) REVERT: A 600 MET cc_start: 0.8125 (mmm) cc_final: 0.7803 (mmm) REVERT: A 613 ASP cc_start: 0.7774 (t0) cc_final: 0.7371 (t70) REVERT: A 615 LYS cc_start: 0.8464 (mtmm) cc_final: 0.8082 (mttt) REVERT: A 671 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7458 (mm-40) REVERT: A 673 MET cc_start: 0.7690 (ttm) cc_final: 0.7436 (ttm) REVERT: A 699 ASP cc_start: 0.7828 (t0) cc_final: 0.7503 (t70) REVERT: A 726 MET cc_start: 0.8082 (mtt) cc_final: 0.7645 (mtm) REVERT: A 781 TYR cc_start: 0.7813 (t80) cc_final: 0.7316 (t80) REVERT: A 793 TYR cc_start: 0.8620 (p90) cc_final: 0.8139 (p90) REVERT: A 819 GLU cc_start: 0.7431 (pm20) cc_final: 0.6962 (pm20) REVERT: A 835 TYR cc_start: 0.7950 (m-80) cc_final: 0.7580 (m-80) REVERT: A 850 LYS cc_start: 0.8385 (tmmt) cc_final: 0.8017 (ttmt) REVERT: A 876 ASN cc_start: 0.8287 (t0) cc_final: 0.7657 (t0) REVERT: A 908 LYS cc_start: 0.8419 (mtmm) cc_final: 0.8193 (mttp) REVERT: A 918 THR cc_start: 0.8464 (m) cc_final: 0.8204 (t) REVERT: A 936 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8327 (ptpp) REVERT: A 938 GLU cc_start: 0.7429 (pp20) cc_final: 0.7043 (pp20) REVERT: A 946 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: A 1028 TYR cc_start: 0.8467 (p90) cc_final: 0.8188 (p90) REVERT: A 1044 ASP cc_start: 0.7544 (t0) cc_final: 0.7175 (t0) REVERT: A 1053 LYS cc_start: 0.8814 (mppt) cc_final: 0.8427 (mppt) REVERT: A 1095 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7399 (tm-30) REVERT: A 1126 LEU cc_start: 0.8049 (tp) cc_final: 0.7772 (tp) REVERT: A 1141 SER cc_start: 0.8720 (m) cc_final: 0.8379 (p) REVERT: A 1164 GLU cc_start: 0.7724 (pp20) cc_final: 0.7430 (pp20) REVERT: A 1165 SER cc_start: 0.8548 (m) cc_final: 0.7958 (m) REVERT: A 1180 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7529 (mttp) REVERT: A 1187 ASP cc_start: 0.7768 (t70) cc_final: 0.7380 (t0) REVERT: A 1200 ASP cc_start: 0.7688 (t0) cc_final: 0.7231 (t0) REVERT: A 1282 SER cc_start: 0.8200 (m) cc_final: 0.7883 (p) REVERT: A 1331 MET cc_start: 0.8451 (mmm) cc_final: 0.8130 (mmm) REVERT: A 1338 LYS cc_start: 0.7679 (ptpt) cc_final: 0.7369 (ptmt) REVERT: A 1348 VAL cc_start: 0.7694 (m) cc_final: 0.6759 (m) REVERT: A 1351 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7090 (pm20) REVERT: A 1354 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: A 1357 ASN cc_start: 0.8612 (t0) cc_final: 0.8075 (t0) REVERT: A 1368 ASP cc_start: 0.7626 (t0) cc_final: 0.7328 (t0) REVERT: A 1470 ASN cc_start: 0.7691 (m-40) cc_final: 0.7265 (m-40) REVERT: A 1483 GLU cc_start: 0.7119 (mp0) cc_final: 0.6782 (mp0) REVERT: A 1494 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8672 (tp) REVERT: A 1513 THR cc_start: 0.8432 (m) cc_final: 0.8169 (p) outliers start: 37 outliers final: 19 residues processed: 295 average time/residue: 0.1031 time to fit residues: 42.0476 Evaluate side-chains 303 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 277 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 864 LYS Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1120 GLU Chi-restraints excluded: chain A residue 1180 LYS Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1351 GLU Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1388 LYS Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1472 TYR Chi-restraints excluded: chain A residue 1480 MET Chi-restraints excluded: chain A residue 1494 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [77, 87, 71, 79, 25, 43, 99, 96, 9, 121, 135] chunk 77 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 96 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN A 353 HIS A 361 ASN ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN A 958 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.135095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.117620 restraints weight = 17283.170| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.61 r_work: 0.3431 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11070 Z= 0.143 Angle : 0.571 10.803 15035 Z= 0.291 Chirality : 0.041 0.175 1624 Planarity : 0.004 0.059 1986 Dihedral : 4.261 18.988 1492 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.98 % Favored : 95.94 % Rotamer: Outliers : 2.65 % Allowed : 16.15 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.21 (0.23), residues: 1381 helix: 0.73 (0.28), residues: 369 sheet: -0.06 (0.34), residues: 219 loop : -0.53 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.011 0.001 TYR A 716 PHE 0.011 0.001 PHE A1170 TRP 0.012 0.001 TRP A 779 HIS 0.005 0.001 HIS A1307 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (11065) covalent geometry : angle 0.57138 / 0.29 (15031) SS BOND : bond 0.00206 / 0.10 ( 2) SS BOND : angle 0.55687 / 0.28 ( 4) hydrogen bonds : bond 0.03000 / 2.01 ( 344) hydrogen bonds : angle 4.36861 / 3.10 ( 990) metal coordination : bond 0.00520 / 0.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 275 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.7733 (tp) cc_final: 0.7269 (tp) REVERT: A 221 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.6020 (mp0) REVERT: A 231 LYS cc_start: 0.8498 (ttmm) cc_final: 0.8115 (ttpp) REVERT: A 249 LYS cc_start: 0.8272 (mtmm) cc_final: 0.7981 (mttp) REVERT: A 258 SER cc_start: 0.8445 (t) cc_final: 0.8208 (t) REVERT: A 303 GLU cc_start: 0.7990 (mp0) cc_final: 0.7604 (mp0) REVERT: A 360 GLN cc_start: 0.7199 (pp30) cc_final: 0.6928 (pp30) REVERT: A 418 LYS cc_start: 0.8197 (tppt) cc_final: 0.7797 (tptm) REVERT: A 450 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7285 (tm-30) REVERT: A 515 GLU cc_start: 0.7208 (mp0) cc_final: 0.6929 (mp0) REVERT: A 521 LYS cc_start: 0.8313 (mttm) cc_final: 0.7899 (mttm) REVERT: A 560 LYS cc_start: 0.8473 (ptpt) cc_final: 0.8095 (mtmm) REVERT: A 600 MET cc_start: 0.8102 (mmm) cc_final: 0.7778 (mmm) REVERT: A 613 ASP cc_start: 0.7729 (t0) cc_final: 0.7332 (t70) REVERT: A 615 LYS cc_start: 0.8445 (mtmm) cc_final: 0.8068 (mttt) REVERT: A 671 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7445 (mm-40) REVERT: A 673 MET cc_start: 0.7672 (ttm) cc_final: 0.7445 (ttm) REVERT: A 699 ASP cc_start: 0.7849 (t0) cc_final: 0.7548 (t70) REVERT: A 726 MET cc_start: 0.8046 (mtt) cc_final: 0.7632 (mtm) REVERT: A 727 GLU cc_start: 0.7656 (tp30) cc_final: 0.7365 (tm-30) REVERT: A 793 TYR cc_start: 0.8598 (p90) cc_final: 0.8214 (p90) REVERT: A 819 GLU cc_start: 0.7432 (pm20) cc_final: 0.6799 (pm20) REVERT: A 835 TYR cc_start: 0.7939 (m-80) cc_final: 0.7535 (m-80) REVERT: A 850 LYS cc_start: 0.8394 (tmmt) cc_final: 0.8018 (ttmt) REVERT: A 876 ASN cc_start: 0.8298 (t0) cc_final: 0.7699 (t0) REVERT: A 908 LYS cc_start: 0.8418 (mtmm) cc_final: 0.8180 (mttp) REVERT: A 918 THR cc_start: 0.8460 (m) cc_final: 0.8201 (t) REVERT: A 936 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8342 (ptpp) REVERT: A 938 GLU cc_start: 0.7488 (pp20) cc_final: 0.7109 (pp20) REVERT: A 946 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: A 1028 TYR cc_start: 0.8447 (p90) cc_final: 0.8171 (p90) REVERT: A 1044 ASP cc_start: 0.7515 (t0) cc_final: 0.7111 (t0) REVERT: A 1053 LYS cc_start: 0.8798 (mppt) cc_final: 0.8401 (mppt) REVERT: A 1095 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7410 (tm-30) REVERT: A 1126 LEU cc_start: 0.8049 (tp) cc_final: 0.7764 (tp) REVERT: A 1141 SER cc_start: 0.8707 (m) cc_final: 0.8364 (p) REVERT: A 1164 GLU cc_start: 0.7722 (pp20) cc_final: 0.7387 (pp20) REVERT: A 1165 SER cc_start: 0.8529 (m) cc_final: 0.7910 (m) REVERT: A 1180 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7544 (mttp) REVERT: A 1187 ASP cc_start: 0.7742 (t70) cc_final: 0.7350 (t0) REVERT: A 1200 ASP cc_start: 0.7682 (t0) cc_final: 0.7224 (t0) REVERT: A 1282 SER cc_start: 0.8175 (m) cc_final: 0.7852 (p) REVERT: A 1304 GLU cc_start: 0.7489 (tp30) cc_final: 0.7182 (tp30) REVERT: A 1331 MET cc_start: 0.8431 (mmm) cc_final: 0.8084 (mmm) REVERT: A 1338 LYS cc_start: 0.7662 (ptpt) cc_final: 0.7355 (ptmt) REVERT: A 1348 VAL cc_start: 0.7689 (m) cc_final: 0.6826 (m) REVERT: A 1351 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7081 (pm20) REVERT: A 1354 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6681 (mp0) REVERT: A 1357 ASN cc_start: 0.8628 (t0) cc_final: 0.8125 (t0) REVERT: A 1368 ASP cc_start: 0.7624 (t0) cc_final: 0.7323 (t0) REVERT: A 1470 ASN cc_start: 0.7655 (m-40) cc_final: 0.7214 (m-40) REVERT: A 1483 GLU cc_start: 0.7103 (mp0) cc_final: 0.6776 (mp0) REVERT: A 1513 THR cc_start: 0.8407 (m) cc_final: 0.8156 (p) outliers start: 31 outliers final: 19 residues processed: 288 average time/residue: 0.1044 time to fit residues: 41.5282 Evaluate side-chains 292 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 267 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1180 LYS Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1351 GLU Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1388 LYS Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1472 TYR Chi-restraints excluded: chain A residue 1480 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [68, 69, 124, 59, 22, 91, 21, 26, 20, 31, 62] chunk 68 optimal weight: 5.9990 chunk 69 optimal weight: 0.4980 chunk 124 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN A1007 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.134014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116169 restraints weight = 17290.451| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.64 r_work: 0.3416 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11070 Z= 0.179 Angle : 0.595 10.600 15035 Z= 0.303 Chirality : 0.042 0.176 1624 Planarity : 0.004 0.059 1986 Dihedral : 4.311 19.858 1492 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.91 % Favored : 96.02 % Rotamer: Outliers : 2.82 % Allowed : 16.67 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.22 (0.23), residues: 1381 helix: 0.69 (0.28), residues: 369 sheet: -0.05 (0.35), residues: 213 loop : -0.53 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 774 TYR 0.012 0.001 TYR A1472 PHE 0.013 0.001 PHE A1170 TRP 0.010 0.001 TRP A1389 HIS 0.011 0.001 HIS A1515 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (11065) covalent geometry : angle 0.59529 / 0.30 (15031) SS BOND : bond 0.00266 / 0.13 ( 2) SS BOND : angle 0.66467 / 0.33 ( 4) hydrogen bonds : bond 0.03134 / 2.10 ( 344) hydrogen bonds : angle 4.41220 / 3.13 ( 990) metal coordination : bond 0.00709 / 0.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 278 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.7726 (tp) cc_final: 0.7285 (tp) REVERT: A 221 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.6009 (mp0) REVERT: A 231 LYS cc_start: 0.8506 (ttmm) cc_final: 0.8121 (ttpp) REVERT: A 249 LYS cc_start: 0.8285 (mtmm) cc_final: 0.8000 (mttp) REVERT: A 258 SER cc_start: 0.8456 (t) cc_final: 0.8223 (t) REVERT: A 283 GLN cc_start: 0.7628 (mt0) cc_final: 0.7259 (pt0) REVERT: A 303 GLU cc_start: 0.7999 (mp0) cc_final: 0.7613 (mp0) REVERT: A 338 GLU cc_start: 0.7779 (pt0) cc_final: 0.7398 (pp20) REVERT: A 360 GLN cc_start: 0.7212 (pp30) cc_final: 0.6941 (pp30) REVERT: A 418 LYS cc_start: 0.8210 (tppt) cc_final: 0.7796 (tptm) REVERT: A 450 GLN cc_start: 0.7922 (tm-30) cc_final: 0.7254 (tm-30) REVERT: A 515 GLU cc_start: 0.7204 (mp0) cc_final: 0.6933 (mp0) REVERT: A 521 LYS cc_start: 0.8337 (mttm) cc_final: 0.8135 (mttm) REVERT: A 560 LYS cc_start: 0.8469 (ptpt) cc_final: 0.8083 (mtmm) REVERT: A 600 MET cc_start: 0.8128 (mmm) cc_final: 0.7802 (mmm) REVERT: A 613 ASP cc_start: 0.7738 (t0) cc_final: 0.7343 (t70) REVERT: A 615 LYS cc_start: 0.8465 (mtmm) cc_final: 0.8129 (mttt) REVERT: A 665 TYR cc_start: 0.8511 (m-80) cc_final: 0.7888 (m-80) REVERT: A 672 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7672 (mm-30) REVERT: A 673 MET cc_start: 0.7705 (ttm) cc_final: 0.7479 (ttm) REVERT: A 699 ASP cc_start: 0.7868 (t0) cc_final: 0.7548 (t70) REVERT: A 704 LYS cc_start: 0.7992 (mtpp) cc_final: 0.7604 (mtpp) REVERT: A 726 MET cc_start: 0.8063 (mtt) cc_final: 0.7650 (mtm) REVERT: A 727 GLU cc_start: 0.7676 (tp30) cc_final: 0.7376 (tm-30) REVERT: A 793 TYR cc_start: 0.8620 (p90) cc_final: 0.8200 (p90) REVERT: A 819 GLU cc_start: 0.7430 (pm20) cc_final: 0.6964 (pm20) REVERT: A 850 LYS cc_start: 0.8411 (tmmt) cc_final: 0.8039 (ttmt) REVERT: A 876 ASN cc_start: 0.8322 (t0) cc_final: 0.7692 (t0) REVERT: A 908 LYS cc_start: 0.8445 (mtmm) cc_final: 0.8208 (mttp) REVERT: A 918 THR cc_start: 0.8468 (m) cc_final: 0.8203 (t) REVERT: A 936 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8368 (ptpp) REVERT: A 938 GLU cc_start: 0.7501 (pp20) cc_final: 0.7130 (pp20) REVERT: A 946 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: A 1028 TYR cc_start: 0.8470 (p90) cc_final: 0.8179 (p90) REVERT: A 1044 ASP cc_start: 0.7603 (t0) cc_final: 0.7182 (t0) REVERT: A 1053 LYS cc_start: 0.8798 (mppt) cc_final: 0.8412 (mppt) REVERT: A 1095 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7402 (tm-30) REVERT: A 1126 LEU cc_start: 0.8103 (tp) cc_final: 0.7827 (tp) REVERT: A 1141 SER cc_start: 0.8731 (m) cc_final: 0.8400 (p) REVERT: A 1164 GLU cc_start: 0.7729 (pp20) cc_final: 0.7425 (pp20) REVERT: A 1165 SER cc_start: 0.8570 (m) cc_final: 0.7944 (m) REVERT: A 1180 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7552 (mttp) REVERT: A 1187 ASP cc_start: 0.7759 (t70) cc_final: 0.7375 (t0) REVERT: A 1200 ASP cc_start: 0.7690 (t0) cc_final: 0.7236 (t0) REVERT: A 1282 SER cc_start: 0.8183 (m) cc_final: 0.7848 (p) REVERT: A 1331 MET cc_start: 0.8434 (mmm) cc_final: 0.8081 (mmm) REVERT: A 1338 LYS cc_start: 0.7741 (ptpt) cc_final: 0.7427 (ptmt) REVERT: A 1348 VAL cc_start: 0.7807 (m) cc_final: 0.6964 (m) REVERT: A 1351 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7110 (pm20) REVERT: A 1354 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: A 1357 ASN cc_start: 0.8655 (t0) cc_final: 0.8159 (t0) REVERT: A 1368 ASP cc_start: 0.7662 (t0) cc_final: 0.7352 (t0) REVERT: A 1470 ASN cc_start: 0.7701 (m-40) cc_final: 0.7170 (m-40) REVERT: A 1483 GLU cc_start: 0.7123 (mp0) cc_final: 0.6690 (mp0) REVERT: A 1513 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8162 (p) outliers start: 33 outliers final: 21 residues processed: 291 average time/residue: 0.1057 time to fit residues: 42.6126 Evaluate side-chains 303 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 275 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain A residue 864 LYS Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1180 LYS Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1351 GLU Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1388 LYS Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1472 TYR Chi-restraints excluded: chain A residue 1480 MET Chi-restraints excluded: chain A residue 1513 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [61, 37, 22, 126, 99, 134, 9, 76, 92, 121, 17] chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 126 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN A 958 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.133562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.115671 restraints weight = 17127.314| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.66 r_work: 0.3425 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11070 Z= 0.154 Angle : 0.599 10.132 15035 Z= 0.304 Chirality : 0.042 0.174 1624 Planarity : 0.004 0.060 1986 Dihedral : 4.291 19.461 1492 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.98 % Favored : 95.94 % Rotamer: Outliers : 2.65 % Allowed : 17.09 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.24 (0.23), residues: 1381 helix: 0.73 (0.28), residues: 369 sheet: -0.06 (0.37), residues: 192 loop : -0.57 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 774 TYR 0.011 0.001 TYR A 716 PHE 0.012 0.001 PHE A 681 TRP 0.013 0.001 TRP A 779 HIS 0.007 0.001 HIS A1307 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (11065) covalent geometry : angle 0.59921 / 0.30 (15031) SS BOND : bond 0.00207 / 0.10 ( 2) SS BOND : angle 0.60197 / 0.30 ( 4) hydrogen bonds : bond 0.03010 / 2.01 ( 344) hydrogen bonds : angle 4.34895 / 3.09 ( 990) metal coordination : bond 0.00606 / 0.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 279 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.7687 (tp) cc_final: 0.7230 (tp) REVERT: A 221 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.6000 (mp0) REVERT: A 231 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8125 (ttpp) REVERT: A 249 LYS cc_start: 0.8284 (mtmm) cc_final: 0.8003 (mttp) REVERT: A 258 SER cc_start: 0.8444 (t) cc_final: 0.8205 (t) REVERT: A 283 GLN cc_start: 0.7646 (mt0) cc_final: 0.7109 (pt0) REVERT: A 303 GLU cc_start: 0.7985 (mp0) cc_final: 0.7613 (mp0) REVERT: A 360 GLN cc_start: 0.7203 (pp30) cc_final: 0.6931 (pp30) REVERT: A 418 LYS cc_start: 0.8202 (tppt) cc_final: 0.7783 (tptm) REVERT: A 450 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7239 (tm-30) REVERT: A 515 GLU cc_start: 0.7199 (mp0) cc_final: 0.6929 (mp0) REVERT: A 521 LYS cc_start: 0.8322 (mttm) cc_final: 0.8114 (mttm) REVERT: A 560 LYS cc_start: 0.8464 (ptpt) cc_final: 0.8050 (mtmm) REVERT: A 562 MET cc_start: 0.8236 (ttm) cc_final: 0.8035 (ttt) REVERT: A 600 MET cc_start: 0.8098 (mmm) cc_final: 0.7773 (mmm) REVERT: A 613 ASP cc_start: 0.7756 (t0) cc_final: 0.7359 (t70) REVERT: A 615 LYS cc_start: 0.8453 (mtmm) cc_final: 0.8119 (mttt) REVERT: A 665 TYR cc_start: 0.8502 (m-80) cc_final: 0.7943 (m-80) REVERT: A 671 GLN cc_start: 0.7919 (mm-40) cc_final: 0.7529 (mm-40) REVERT: A 672 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7682 (mm-30) REVERT: A 673 MET cc_start: 0.7669 (ttm) cc_final: 0.7456 (ttm) REVERT: A 726 MET cc_start: 0.8051 (mtt) cc_final: 0.7632 (mtm) REVERT: A 793 TYR cc_start: 0.8605 (p90) cc_final: 0.8196 (p90) REVERT: A 819 GLU cc_start: 0.7430 (pm20) cc_final: 0.6961 (pm20) REVERT: A 850 LYS cc_start: 0.8408 (tmmt) cc_final: 0.8037 (ttmt) REVERT: A 876 ASN cc_start: 0.8325 (t0) cc_final: 0.7684 (t0) REVERT: A 918 THR cc_start: 0.8451 (m) cc_final: 0.8183 (t) REVERT: A 936 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8348 (ptpp) REVERT: A 938 GLU cc_start: 0.7499 (pp20) cc_final: 0.7130 (pp20) REVERT: A 946 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: A 1044 ASP cc_start: 0.7602 (t0) cc_final: 0.7186 (t0) REVERT: A 1053 LYS cc_start: 0.8803 (mppt) cc_final: 0.8399 (mppt) REVERT: A 1095 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7408 (tm-30) REVERT: A 1126 LEU cc_start: 0.8090 (tp) cc_final: 0.7809 (tp) REVERT: A 1141 SER cc_start: 0.8712 (m) cc_final: 0.8359 (p) REVERT: A 1164 GLU cc_start: 0.7738 (pp20) cc_final: 0.7424 (pp20) REVERT: A 1165 SER cc_start: 0.8543 (m) cc_final: 0.7922 (m) REVERT: A 1180 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7553 (mttp) REVERT: A 1187 ASP cc_start: 0.7746 (t70) cc_final: 0.7350 (t0) REVERT: A 1282 SER cc_start: 0.8155 (m) cc_final: 0.7854 (p) REVERT: A 1304 GLU cc_start: 0.7399 (tt0) cc_final: 0.7183 (mm-30) REVERT: A 1331 MET cc_start: 0.8438 (mmm) cc_final: 0.8095 (mmm) REVERT: A 1338 LYS cc_start: 0.7718 (ptpt) cc_final: 0.7402 (ptmt) REVERT: A 1348 VAL cc_start: 0.7759 (m) cc_final: 0.6919 (m) REVERT: A 1351 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7121 (pm20) REVERT: A 1354 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6656 (mp0) REVERT: A 1357 ASN cc_start: 0.8655 (t0) cc_final: 0.8181 (t0) REVERT: A 1368 ASP cc_start: 0.7698 (t0) cc_final: 0.7388 (t0) REVERT: A 1372 MET cc_start: 0.8491 (ttm) cc_final: 0.8220 (ttp) REVERT: A 1470 ASN cc_start: 0.7685 (m-40) cc_final: 0.7135 (m-40) REVERT: A 1483 GLU cc_start: 0.7135 (mp0) cc_final: 0.6709 (mp0) REVERT: A 1513 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8157 (p) outliers start: 31 outliers final: 18 residues processed: 292 average time/residue: 0.1044 time to fit residues: 42.4528 Evaluate side-chains 300 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 275 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 864 LYS Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1180 LYS Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1351 GLU Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1472 TYR Chi-restraints excluded: chain A residue 1480 MET Chi-restraints excluded: chain A residue 1513 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [2, 1, 119, 79, 0, 65, 27, 55, 30, 60, 102] chunk 2 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 119 optimal weight: 0.0270 chunk 79 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 GLN ** A1515 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 = 0.3818 r_free = 0.3818 target = 0.135242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.117602 restraints weight = 17205.235| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.64 r_work: 0.3437 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11070 Z= 0.141 Angle : 0.599 9.945 15035 Z= 0.304 Chirality : 0.041 0.172 1624 Planarity : 0.004 0.060 1986 Dihedral : 4.258 18.423 1492 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.91 % Favored : 96.02 % Rotamer: Outliers : 2.31 % Allowed : 17.86 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.22 (0.23), residues: 1381 helix: 0.78 (0.28), residues: 369 sheet: -0.06 (0.37), residues: 192 loop : -0.57 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1261 TYR 0.018 0.001 TYR A1028 PHE 0.011 0.001 PHE A 307 TRP 0.016 0.001 TRP A 779 HIS 0.010 0.001 HIS A1515 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (11065) covalent geometry : angle 0.59880 / 0.30 (15031) SS BOND : bond 0.00183 / 0.09 ( 2) SS BOND : angle 0.54796 / 0.27 ( 4) hydrogen bonds : bond 0.02914 / 1.95 ( 344) hydrogen bonds : angle 4.30458 / 3.06 ( 990) metal coordination : bond 0.00492 / 0.22 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 274 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.6194 (tm-30) cc_final: 0.5891 (tm-30) REVERT: A 218 LEU cc_start: 0.7667 (tp) cc_final: 0.7202 (tp) REVERT: A 221 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.6005 (mp0) REVERT: A 231 LYS cc_start: 0.8500 (ttmm) cc_final: 0.8115 (ttpp) REVERT: A 249 LYS cc_start: 0.8293 (mtmm) cc_final: 0.8022 (mttp) REVERT: A 258 SER cc_start: 0.8426 (t) cc_final: 0.8184 (t) REVERT: A 303 GLU cc_start: 0.7962 (mp0) cc_final: 0.7586 (mp0) REVERT: A 338 GLU cc_start: 0.7733 (pt0) cc_final: 0.7378 (pp20) REVERT: A 418 LYS cc_start: 0.8201 (tppt) cc_final: 0.7780 (tptm) REVERT: A 450 GLN cc_start: 0.7910 (tm-30) cc_final: 0.7233 (tm-30) REVERT: A 515 GLU cc_start: 0.7167 (mp0) cc_final: 0.6927 (mp0) REVERT: A 521 LYS cc_start: 0.8327 (mttm) cc_final: 0.8106 (mttm) REVERT: A 560 LYS cc_start: 0.8455 (ptpt) cc_final: 0.8060 (mtmm) REVERT: A 600 MET cc_start: 0.8091 (mmm) cc_final: 0.7770 (mmm) REVERT: A 613 ASP cc_start: 0.7723 (t0) cc_final: 0.7339 (t0) REVERT: A 615 LYS cc_start: 0.8441 (mtmm) cc_final: 0.8124 (mttt) REVERT: A 665 TYR cc_start: 0.8486 (m-80) cc_final: 0.8012 (m-80) REVERT: A 671 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7514 (mm-40) REVERT: A 672 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7674 (mm-30) REVERT: A 673 MET cc_start: 0.7688 (ttm) cc_final: 0.7472 (ttm) REVERT: A 726 MET cc_start: 0.8067 (mtt) cc_final: 0.7647 (mtm) REVERT: A 793 TYR cc_start: 0.8606 (p90) cc_final: 0.8187 (p90) REVERT: A 819 GLU cc_start: 0.7411 (pm20) cc_final: 0.6940 (pm20) REVERT: A 850 LYS cc_start: 0.8401 (tmmt) cc_final: 0.8028 (ttmt) REVERT: A 876 ASN cc_start: 0.8326 (t0) cc_final: 0.7674 (t0) REVERT: A 918 THR cc_start: 0.8451 (m) cc_final: 0.8187 (t) REVERT: A 936 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8339 (ptpp) REVERT: A 938 GLU cc_start: 0.7458 (pp20) cc_final: 0.7084 (pp20) REVERT: A 946 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: A 1044 ASP cc_start: 0.7623 (t0) cc_final: 0.7210 (t0) REVERT: A 1053 LYS cc_start: 0.8804 (mppt) cc_final: 0.8427 (mppt) REVERT: A 1095 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7395 (tm-30) REVERT: A 1126 LEU cc_start: 0.8086 (tp) cc_final: 0.7819 (tp) REVERT: A 1141 SER cc_start: 0.8698 (m) cc_final: 0.8338 (p) REVERT: A 1164 GLU cc_start: 0.7738 (pp20) cc_final: 0.7427 (pp20) REVERT: A 1165 SER cc_start: 0.8538 (m) cc_final: 0.7916 (m) REVERT: A 1180 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7569 (mttp) REVERT: A 1187 ASP cc_start: 0.7736 (t70) cc_final: 0.7345 (t0) REVERT: A 1202 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8495 (t80) REVERT: A 1282 SER cc_start: 0.8165 (m) cc_final: 0.7862 (p) REVERT: A 1304 GLU cc_start: 0.7430 (tt0) cc_final: 0.7207 (mm-30) REVERT: A 1331 MET cc_start: 0.8431 (mmm) cc_final: 0.8090 (mmm) REVERT: A 1338 LYS cc_start: 0.7699 (ptpt) cc_final: 0.7381 (ptmt) REVERT: A 1348 VAL cc_start: 0.7713 (m) cc_final: 0.6903 (m) REVERT: A 1351 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7113 (pm20) REVERT: A 1354 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6633 (mp0) REVERT: A 1357 ASN cc_start: 0.8629 (t0) cc_final: 0.8172 (t0) REVERT: A 1368 ASP cc_start: 0.7656 (t0) cc_final: 0.7336 (t0) REVERT: A 1372 MET cc_start: 0.8503 (ttm) cc_final: 0.8234 (ttp) REVERT: A 1389 TRP cc_start: 0.8656 (m100) cc_final: 0.8042 (m100) REVERT: A 1457 ASP cc_start: 0.7555 (t0) cc_final: 0.7164 (t0) REVERT: A 1470 ASN cc_start: 0.7647 (m-40) cc_final: 0.7295 (m-40) REVERT: A 1513 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8142 (p) outliers start: 27 outliers final: 16 residues processed: 286 average time/residue: 0.1051 time to fit residues: 41.6474 Evaluate side-chains 300 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 276 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 864 LYS Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1180 LYS Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1351 GLU Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1472 TYR Chi-restraints excluded: chain A residue 1480 MET Chi-restraints excluded: chain A residue 1513 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [25, 7, 41, 119, 48, 1, 99, 42, 71, 26, 106] chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.131238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.113263 restraints weight = 17441.233| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.67 r_work: 0.3393 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11070 Z= 0.262 Angle : 0.657 10.080 15035 Z= 0.336 Chirality : 0.045 0.180 1624 Planarity : 0.004 0.060 1986 Dihedral : 4.558 21.968 1492 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.00 % Favored : 94.93 % Rotamer: Outliers : 2.14 % Allowed : 17.86 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.37 (0.23), residues: 1381 helix: 0.53 (0.28), residues: 370 sheet: -0.16 (0.36), residues: 203 loop : -0.60 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 364 TYR 0.021 0.002 TYR A1028 PHE 0.017 0.002 PHE A1170 TRP 0.011 0.001 TRP A1389 HIS 0.011 0.001 HIS A1307 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.26 (11065) covalent geometry : angle 0.65709 / 0.34 (15031) SS BOND : bond 0.00411 / 0.20 ( 2) SS BOND : angle 0.94047 / 0.48 ( 4) hydrogen bonds : bond 0.03438 / 2.32 ( 344) hydrogen bonds : angle 4.51897 / 3.19 ( 990) metal coordination : bond 0.01000 / 0.45 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2436.56 seconds wall clock time: 42 minutes 42.53 seconds (2562.53 seconds total)