Starting phenix.real_space_refine on Sun Aug 24 14:48:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ezq_28748/08_2025/8ezq_28748.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ezq_28748/08_2025/8ezq_28748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ezq_28748/08_2025/8ezq_28748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ezq_28748/08_2025/8ezq_28748.map" model { file = "/net/cci-nas-00/data/ceres_data/8ezq_28748/08_2025/8ezq_28748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ezq_28748/08_2025/8ezq_28748.cif" } resolution = 3.7 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= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 13124 2.51 5 N 3333 2.21 5 O 3925 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20456 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1273, 10223 Classifications: {'peptide': 1273} Link IDs: {'PTRANS': 39, 'TRANS': 1233} Chain breaks: 5 Chain: "B" Number of atoms: 10233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1272, 10233 Classifications: {'peptide': 1272} Link IDs: {'PTRANS': 39, 'TRANS': 1232} Chain breaks: 5 Time building chain proxies: 5.04, per 1000 atoms: 0.25 Number of scatterers: 20456 At special positions: 0 Unit cell: (120.888, 144.072, 303.048, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 3925 8.00 N 3333 7.00 C 13124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.97 Conformation dependent library (CDL) restraints added in 914.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4926 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 4 sheets defined 72.5% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 10 through 30 removed outlier: 3.770A pdb=" N ILE A 14 " --> pdb=" O ASP A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 94 through 107 Proline residue: A 100 - end of helix Processing helix chain 'A' and resid 111 through 128 Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.674A pdb=" N VAL A 146 " --> pdb=" O HIS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 178 removed outlier: 4.343A pdb=" N VAL A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 186 through 202 Processing helix chain 'A' and resid 208 through 231 removed outlier: 3.748A pdb=" N THR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 343 removed outlier: 3.762A pdb=" N VAL A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 371 Processing helix chain 'A' and resid 371 through 377 removed outlier: 3.879A pdb=" N TYR A 377 " --> pdb=" O ARG A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 386 Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 402 through 420 Processing helix chain 'A' and resid 423 through 439 Processing helix chain 'A' and resid 455 through 473 removed outlier: 3.782A pdb=" N LYS A 459 " --> pdb=" O PRO A 455 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 471 " --> pdb=" O SER A 467 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG A 472 " --> pdb=" O ILE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 485 Processing helix chain 'A' and resid 492 through 504 Processing helix chain 'A' and resid 506 through 511 Processing helix chain 'A' and resid 516 through 535 removed outlier: 3.759A pdb=" N ILE A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.582A pdb=" N PHE A 544 " --> pdb=" O ASP A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 559 through 573 Processing helix chain 'A' and resid 573 through 584 Proline residue: A 579 - end of helix removed outlier: 3.531A pdb=" N LYS A 584 " --> pdb=" O MET A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 607 through 616 removed outlier: 3.530A pdb=" N CYS A 616 " --> pdb=" O GLY A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 630 Processing helix chain 'A' and resid 638 through 648 removed outlier: 4.318A pdb=" N LYS A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 673 Processing helix chain 'A' and resid 694 through 713 Processing helix chain 'A' and resid 722 through 730 Processing helix chain 'A' and resid 733 through 737 Processing helix chain 'A' and resid 740 through 753 Processing helix chain 'A' and resid 767 through 778 Processing helix chain 'A' and resid 798 through 828 Proline residue: A 815 - end of helix Processing helix chain 'A' and resid 830 through 851 Processing helix chain 'A' and resid 853 through 868 Processing helix chain 'A' and resid 906 through 914 Processing helix chain 'A' and resid 915 through 932 Processing helix chain 'A' and resid 939 through 956 removed outlier: 3.775A pdb=" N ASP A 956 " --> pdb=" O THR A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 971 removed outlier: 4.039A pdb=" N GLN A 968 " --> pdb=" O PHE A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1026 Processing helix chain 'A' and resid 1027 through 1033 Processing helix chain 'A' and resid 1040 through 1050 removed outlier: 3.598A pdb=" N ILE A1044 " --> pdb=" O THR A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1061 removed outlier: 3.898A pdb=" N ARG A1061 " --> pdb=" O ALA A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1081 Processing helix chain 'A' and resid 1086 through 1100 Processing helix chain 'A' and resid 1105 through 1123 Processing helix chain 'A' and resid 1126 through 1140 removed outlier: 4.186A pdb=" N LEU A1130 " --> pdb=" O GLN A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1167 removed outlier: 3.577A pdb=" N LYS A1156 " --> pdb=" O THR A1152 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU A1157 " --> pdb=" O ASN A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1177 Processing helix chain 'A' and resid 1178 through 1190 Processing helix chain 'A' and resid 1194 through 1208 removed outlier: 3.676A pdb=" N ILE A1198 " --> pdb=" O GLN A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1247 removed outlier: 3.565A pdb=" N LYS A1244 " --> pdb=" O ILE A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1276 Processing helix chain 'A' and resid 1284 through 1299 Processing helix chain 'A' and resid 1302 through 1319 Processing helix chain 'A' and resid 1330 through 1345 removed outlier: 3.549A pdb=" N LEU A1334 " --> pdb=" O SER A1330 " (cutoff:3.500A) Proline residue: A1341 - end of helix Processing helix chain 'A' and resid 1351 through 1373 removed outlier: 3.582A pdb=" N LEU A1373 " --> pdb=" O HIS A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1391 Processing helix chain 'A' and resid 1395 through 1417 Processing helix chain 'B' and resid 10 through 30 removed outlier: 3.947A pdb=" N ILE B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 85 Processing helix chain 'B' and resid 93 through 107 removed outlier: 3.719A pdb=" N ILE B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Proline residue: B 100 - end of helix Processing helix chain 'B' and resid 111 through 128 Processing helix chain 'B' and resid 137 through 151 Processing helix chain 'B' and resid 158 through 178 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 186 through 203 Processing helix chain 'B' and resid 208 through 230 Processing helix chain 'B' and resid 328 through 344 Processing helix chain 'B' and resid 352 through 377 removed outlier: 3.736A pdb=" N ARG B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ASP B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG B 373 " --> pdb=" O ILE B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 386 Processing helix chain 'B' and resid 386 through 398 Processing helix chain 'B' and resid 401 through 420 Processing helix chain 'B' and resid 424 through 439 Processing helix chain 'B' and resid 456 through 471 removed outlier: 3.526A pdb=" N TRP B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 485 removed outlier: 3.688A pdb=" N PHE B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 506 removed outlier: 3.831A pdb=" N LEU B 506 " --> pdb=" O THR B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 Processing helix chain 'B' and resid 516 through 535 removed outlier: 3.830A pdb=" N ILE B 520 " --> pdb=" O SER B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.955A pdb=" N PHE B 544 " --> pdb=" O ASP B 540 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 558 Processing helix chain 'B' and resid 559 through 573 Processing helix chain 'B' and resid 573 through 584 removed outlier: 3.521A pdb=" N GLY B 577 " --> pdb=" O LYS B 573 " (cutoff:3.500A) Proline residue: B 579 - end of helix Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 607 through 615 removed outlier: 3.590A pdb=" N ILE B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 630 Processing helix chain 'B' and resid 637 through 647 Processing helix chain 'B' and resid 654 through 673 removed outlier: 3.594A pdb=" N GLN B 673 " --> pdb=" O TYR B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 713 Processing helix chain 'B' and resid 722 through 730 Processing helix chain 'B' and resid 740 through 754 removed outlier: 3.613A pdb=" N LEU B 744 " --> pdb=" O PRO B 740 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 777 Processing helix chain 'B' and resid 792 through 797 removed outlier: 3.636A pdb=" N ASP B 795 " --> pdb=" O SER B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 828 removed outlier: 3.710A pdb=" N LEU B 802 " --> pdb=" O THR B 798 " (cutoff:3.500A) Proline residue: B 815 - end of helix Processing helix chain 'B' and resid 830 through 851 Processing helix chain 'B' and resid 853 through 868 Processing helix chain 'B' and resid 907 through 915 Processing helix chain 'B' and resid 915 through 932 Processing helix chain 'B' and resid 939 through 956 removed outlier: 3.987A pdb=" N ASP B 956 " --> pdb=" O THR B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 971 removed outlier: 3.538A pdb=" N GLN B 968 " --> pdb=" O PHE B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1026 Processing helix chain 'B' and resid 1027 through 1033 Processing helix chain 'B' and resid 1040 through 1050 Processing helix chain 'B' and resid 1062 through 1080 Processing helix chain 'B' and resid 1085 through 1100 Processing helix chain 'B' and resid 1105 through 1123 Processing helix chain 'B' and resid 1126 through 1139 Processing helix chain 'B' and resid 1152 through 1167 Processing helix chain 'B' and resid 1178 through 1190 removed outlier: 3.813A pdb=" N TRP B1182 " --> pdb=" O ASN B1178 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B1190 " --> pdb=" O ARG B1186 " (cutoff:3.500A) Processing helix chain 'B' and resid 1191 through 1193 No H-bonds generated for 'chain 'B' and resid 1191 through 1193' Processing helix chain 'B' and resid 1194 through 1208 removed outlier: 3.658A pdb=" N ILE B1198 " --> pdb=" O GLN B1194 " (cutoff:3.500A) Processing helix chain 'B' and resid 1217 through 1247 removed outlier: 4.469A pdb=" N GLU B1241 " --> pdb=" O HIS B1237 " (cutoff:3.500A) Processing helix chain 'B' and resid 1258 through 1277 removed outlier: 3.705A pdb=" N ILE B1262 " --> pdb=" O TYR B1258 " (cutoff:3.500A) Processing helix chain 'B' and resid 1284 through 1300 Processing helix chain 'B' and resid 1302 through 1319 Processing helix chain 'B' and resid 1330 through 1344 Proline residue: B1341 - end of helix Processing helix chain 'B' and resid 1354 through 1372 Processing helix chain 'B' and resid 1378 through 1391 Processing helix chain 'B' and resid 1395 through 1413 removed outlier: 4.075A pdb=" N LYS B1399 " --> pdb=" O SER B1395 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B1401 " --> pdb=" O ILE B1397 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN B1402 " --> pdb=" O GLU B1398 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER B1410 " --> pdb=" O LEU B1406 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE B1411 " --> pdb=" O ASP B1407 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B1412 " --> pdb=" O LYS B1408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 241 through 242 removed outlier: 4.113A pdb=" N TYR A 241 " --> pdb=" O THR A 784 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A 784 " --> pdb=" O TYR A 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 903 through 905 removed outlier: 5.602A pdb=" N GLN A 893 " --> pdb=" O ILE A 985 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 241 through 242 removed outlier: 3.657A pdb=" N TYR B 241 " --> pdb=" O THR B 784 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 903 through 904 removed outlier: 3.750A pdb=" N GLN B 893 " --> pdb=" O ILE B 983 " (cutoff:3.500A) 1287 hydrogen bonds defined for protein. 3840 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.09 Time building geometry restraints manager: 2.53 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: 6469 1.34 - 1.45: 2407 1.45 - 1.57: 11806 1.57 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 20796 Sorted by residual: bond pdb=" N ASP A1394 " pdb=" CA ASP A1394 " ideal model delta sigma weight residual 1.457 1.501 -0.043 1.29e-02 6.01e+03 1.12e+01 bond pdb=" N ILE A1321 " pdb=" CA ILE A1321 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.15e-02 7.56e+03 1.03e+01 bond pdb=" N ILE A 958 " pdb=" CA ILE A 958 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.09e+00 bond pdb=" N ASP B 676 " pdb=" CA ASP B 676 " ideal model delta sigma weight residual 1.461 1.488 -0.027 9.20e-03 1.18e+04 8.68e+00 bond pdb=" N VAL A 691 " pdb=" CA VAL A 691 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.47e+00 ... (remaining 20791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 27438 1.79 - 3.57: 551 3.57 - 5.36: 84 5.36 - 7.15: 19 7.15 - 8.94: 3 Bond angle restraints: 28095 Sorted by residual: angle pdb=" N ILE B 777 " pdb=" CA ILE B 777 " pdb=" C ILE B 777 " ideal model delta sigma weight residual 112.29 108.57 3.72 9.40e-01 1.13e+00 1.57e+01 angle pdb=" N ILE B1354 " pdb=" CA ILE B1354 " pdb=" C ILE B1354 " ideal model delta sigma weight residual 112.96 109.02 3.94 1.00e+00 1.00e+00 1.55e+01 angle pdb=" N LYS A1320 " pdb=" CA LYS A1320 " pdb=" C LYS A1320 " ideal model delta sigma weight residual 113.23 108.46 4.77 1.22e+00 6.72e-01 1.53e+01 angle pdb=" N SER A1395 " pdb=" CA SER A1395 " pdb=" CB SER A1395 " ideal model delta sigma weight residual 114.17 109.76 4.41 1.14e+00 7.69e-01 1.50e+01 angle pdb=" CA GLN A 692 " pdb=" C GLN A 692 " pdb=" O GLN A 692 " ideal model delta sigma weight residual 121.34 117.91 3.43 9.40e-01 1.13e+00 1.33e+01 ... (remaining 28090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11903 17.97 - 35.93: 705 35.93 - 53.90: 139 53.90 - 71.87: 21 71.87 - 89.83: 5 Dihedral angle restraints: 12773 sinusoidal: 5250 harmonic: 7523 Sorted by residual: dihedral pdb=" CA ASP B1209 " pdb=" C ASP B1209 " pdb=" N SER B1210 " pdb=" CA SER B1210 " ideal model delta harmonic sigma weight residual 180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA THR A 781 " pdb=" C THR A 781 " pdb=" N VAL A 782 " pdb=" CA VAL A 782 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA LYS B1082 " pdb=" C LYS B1082 " pdb=" N GLU B1083 " pdb=" CA GLU B1083 " ideal model delta harmonic sigma weight residual 180.00 -161.17 -18.83 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 12770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2627 0.047 - 0.094: 587 0.094 - 0.141: 95 0.141 - 0.188: 7 0.188 - 0.235: 2 Chirality restraints: 3318 Sorted by residual: chirality pdb=" CA ILE B 958 " pdb=" N ILE B 958 " pdb=" C ILE B 958 " pdb=" CB ILE B 958 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ILE A 983 " pdb=" N ILE A 983 " pdb=" C ILE A 983 " pdb=" CB ILE A 983 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE A1321 " pdb=" N ILE A1321 " pdb=" C ILE A1321 " pdb=" CB ILE A1321 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 3315 not shown) Planarity restraints: 3545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 477 " -0.019 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C PHE A 477 " 0.067 2.00e-02 2.50e+03 pdb=" O PHE A 477 " -0.025 2.00e-02 2.50e+03 pdb=" N THR A 478 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 402 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.34e+00 pdb=" C LEU A 402 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU A 402 " 0.016 2.00e-02 2.50e+03 pdb=" N SER A 403 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 814 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A 815 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 815 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 815 " -0.029 5.00e-02 4.00e+02 ... (remaining 3542 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 317 2.62 - 3.19: 20694 3.19 - 3.76: 32454 3.76 - 4.33: 42600 4.33 - 4.90: 68035 Nonbonded interactions: 164100 Sorted by model distance: nonbonded pdb=" OD1 ASP A 831 " pdb=" N HIS A 832 " model vdw 2.048 3.120 nonbonded pdb=" OG1 THR B 798 " pdb=" OE1 GLU B 801 " model vdw 2.204 3.040 nonbonded pdb=" O ASN B1056 " pdb=" OG SER B1060 " model vdw 2.204 3.040 nonbonded pdb=" O PHE A1163 " pdb=" OG1 THR A1166 " model vdw 2.206 3.040 nonbonded pdb=" O GLN B1194 " pdb=" OG SER B1197 " model vdw 2.206 3.040 ... (remaining 164095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 989 or resid 1004 through 1413)) selection = (chain 'B' and (resid 7 through 874 or resid 887 through 989 or resid 1004 throu \ gh 1413)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.140 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.550 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 20796 Z= 0.192 Angle : 0.613 8.937 28095 Z= 0.352 Chirality : 0.040 0.235 3318 Planarity : 0.004 0.052 3545 Dihedral : 11.914 89.832 7847 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 0.42 % Allowed : 9.43 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.17), residues: 2521 helix: 1.40 (0.13), residues: 1743 sheet: -2.66 (1.04), residues: 20 loop : -2.68 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 472 TYR 0.015 0.001 TYR A 138 PHE 0.017 0.001 PHE B1381 TRP 0.016 0.002 TRP B 773 HIS 0.003 0.000 HIS A 713 Details of bonding type rmsd covalent geometry : bond 0.00343 (20796) covalent geometry : angle 0.61264 (28095) hydrogen bonds : bond 0.11452 ( 1287) hydrogen bonds : angle 5.26209 ( 3840) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 769 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7452 (mm-30) REVERT: A 29 TYR cc_start: 0.7433 (t80) cc_final: 0.7217 (t80) REVERT: A 78 GLN cc_start: 0.7895 (tp40) cc_final: 0.7618 (tp40) REVERT: A 82 MET cc_start: 0.7963 (ttm) cc_final: 0.7635 (tmm) REVERT: A 91 ASN cc_start: 0.7649 (t0) cc_final: 0.7269 (t0) REVERT: A 155 GLU cc_start: 0.7527 (pt0) cc_final: 0.7166 (pt0) REVERT: A 184 LEU cc_start: 0.8097 (mt) cc_final: 0.7752 (mt) REVERT: A 206 ARG cc_start: 0.7893 (tpp-160) cc_final: 0.7626 (tpp-160) REVERT: A 208 GLU cc_start: 0.7017 (mp0) cc_final: 0.6815 (mp0) REVERT: A 233 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7185 (mm-30) REVERT: A 240 ILE cc_start: 0.8829 (mt) cc_final: 0.8514 (mm) REVERT: A 253 LYS cc_start: 0.8063 (pttt) cc_final: 0.7532 (pttt) REVERT: A 368 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7427 (mt-10) REVERT: A 460 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7429 (tm-30) REVERT: A 461 LEU cc_start: 0.7978 (tp) cc_final: 0.7726 (tt) REVERT: A 471 THR cc_start: 0.7862 (m) cc_final: 0.7619 (t) REVERT: A 555 LYS cc_start: 0.8751 (mmmm) cc_final: 0.8512 (mmmm) REVERT: A 559 ARG cc_start: 0.7820 (tpp80) cc_final: 0.7561 (tpp80) REVERT: A 562 GLU cc_start: 0.7297 (mt-10) cc_final: 0.7032 (mt-10) REVERT: A 565 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7715 (mm-30) REVERT: A 572 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7193 (tm-30) REVERT: A 593 LYS cc_start: 0.7713 (tptm) cc_final: 0.7062 (tptm) REVERT: A 600 PHE cc_start: 0.8444 (t80) cc_final: 0.8162 (t80) REVERT: A 626 GLU cc_start: 0.7897 (tp30) cc_final: 0.7363 (tp30) REVERT: A 657 GLN cc_start: 0.7350 (mp10) cc_final: 0.7089 (mp10) REVERT: A 802 LEU cc_start: 0.8098 (tp) cc_final: 0.7332 (tp) REVERT: A 806 ASP cc_start: 0.7558 (m-30) cc_final: 0.7033 (m-30) REVERT: A 830 ASP cc_start: 0.7418 (t70) cc_final: 0.7169 (t70) REVERT: A 837 MET cc_start: 0.7513 (mmm) cc_final: 0.7283 (mmt) REVERT: A 864 ILE cc_start: 0.7612 (mt) cc_final: 0.7306 (mt) REVERT: A 1017 LYS cc_start: 0.8126 (ttmm) cc_final: 0.7852 (ttmm) REVERT: A 1020 MET cc_start: 0.7335 (tpp) cc_final: 0.6928 (tpp) REVERT: A 1021 GLU cc_start: 0.7795 (tp30) cc_final: 0.7144 (tp30) REVERT: A 1063 PHE cc_start: 0.7752 (t80) cc_final: 0.7522 (t80) REVERT: A 1071 ILE cc_start: 0.8461 (mm) cc_final: 0.8156 (mm) REVERT: A 1072 GLU cc_start: 0.8132 (tt0) cc_final: 0.7552 (tt0) REVERT: A 1073 LEU cc_start: 0.8375 (tp) cc_final: 0.8155 (tp) REVERT: A 1074 THR cc_start: 0.8377 (t) cc_final: 0.8013 (p) REVERT: A 1082 LYS cc_start: 0.7763 (mtpt) cc_final: 0.7355 (mtpt) REVERT: A 1087 LEU cc_start: 0.8634 (tp) cc_final: 0.8292 (tp) REVERT: A 1089 LYS cc_start: 0.8505 (ttmm) cc_final: 0.8103 (ttmm) REVERT: A 1093 GLN cc_start: 0.8596 (tp40) cc_final: 0.8283 (tp40) REVERT: A 1112 MET cc_start: 0.7433 (ptm) cc_final: 0.7140 (mtp) REVERT: A 1113 LEU cc_start: 0.8222 (tp) cc_final: 0.7943 (tp) REVERT: A 1120 ILE cc_start: 0.9109 (mm) cc_final: 0.8781 (mm) REVERT: A 1126 GLN cc_start: 0.6962 (mm-40) cc_final: 0.6643 (mm-40) REVERT: A 1128 GLU cc_start: 0.7896 (tp30) cc_final: 0.7534 (tp30) REVERT: A 1132 LYS cc_start: 0.8379 (mmmm) cc_final: 0.7853 (mmmm) REVERT: A 1139 LEU cc_start: 0.7947 (mm) cc_final: 0.7670 (mm) REVERT: A 1140 LYS cc_start: 0.8081 (mmmm) cc_final: 0.7654 (mmmm) REVERT: A 1152 THR cc_start: 0.8619 (t) cc_final: 0.8124 (p) REVERT: A 1156 LYS cc_start: 0.8011 (mttm) cc_final: 0.7807 (mttm) REVERT: A 1157 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7359 (mm-30) REVERT: A 1160 LYS cc_start: 0.8421 (tttm) cc_final: 0.8192 (tttm) REVERT: A 1167 GLU cc_start: 0.7722 (pp20) cc_final: 0.7521 (tm-30) REVERT: A 1170 PHE cc_start: 0.7436 (m-10) cc_final: 0.7183 (m-10) REVERT: A 1175 LEU cc_start: 0.8354 (mm) cc_final: 0.7978 (mm) REVERT: A 1184 PHE cc_start: 0.8675 (t80) cc_final: 0.8421 (t80) REVERT: A 1186 ARG cc_start: 0.8274 (tpt-90) cc_final: 0.7661 (tpp80) REVERT: A 1187 LYS cc_start: 0.8686 (mmmm) cc_final: 0.8324 (mmmm) REVERT: A 1200 GLU cc_start: 0.7869 (tp30) cc_final: 0.7542 (tp30) REVERT: A 1219 MET cc_start: 0.8148 (mmm) cc_final: 0.7732 (mmm) REVERT: A 1227 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7050 (mm-30) REVERT: A 1243 LYS cc_start: 0.8308 (ttmt) cc_final: 0.8081 (ttmt) REVERT: A 1263 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7493 (mt-10) REVERT: A 1267 LYS cc_start: 0.8512 (mttm) cc_final: 0.8185 (mtpp) REVERT: A 1365 ASN cc_start: 0.8322 (m-40) cc_final: 0.8008 (m-40) REVERT: A 1366 VAL cc_start: 0.8561 (p) cc_final: 0.8315 (m) REVERT: A 1383 LYS cc_start: 0.8270 (mmtm) cc_final: 0.8030 (mmtm) REVERT: A 1399 LYS cc_start: 0.8554 (ptpp) cc_final: 0.8305 (pttm) REVERT: A 1400 LYS cc_start: 0.8803 (mmtm) cc_final: 0.8534 (mmtm) REVERT: B 9 VAL cc_start: 0.7021 (m) cc_final: 0.6275 (t) REVERT: B 10 ASP cc_start: 0.8070 (m-30) cc_final: 0.7681 (m-30) REVERT: B 19 CYS cc_start: 0.8081 (m) cc_final: 0.7851 (m) REVERT: B 91 ASN cc_start: 0.8093 (m110) cc_final: 0.7832 (m-40) REVERT: B 110 ILE cc_start: 0.8442 (pt) cc_final: 0.7168 (mm) REVERT: B 132 ASN cc_start: 0.8148 (p0) cc_final: 0.7728 (p0) REVERT: B 136 GLN cc_start: 0.8212 (mt0) cc_final: 0.7968 (mt0) REVERT: B 138 TYR cc_start: 0.8105 (p90) cc_final: 0.7900 (p90) REVERT: B 154 PHE cc_start: 0.8071 (p90) cc_final: 0.7826 (p90) REVERT: B 155 GLU cc_start: 0.7434 (pt0) cc_final: 0.7097 (pm20) REVERT: B 174 ARG cc_start: 0.8172 (ttt180) cc_final: 0.7933 (ttt180) REVERT: B 178 ASP cc_start: 0.7821 (t70) cc_final: 0.7424 (t0) REVERT: B 191 TYR cc_start: 0.8222 (t80) cc_final: 0.7970 (t80) REVERT: B 205 ARG cc_start: 0.7876 (tpp80) cc_final: 0.7522 (mmm-85) REVERT: B 218 MET cc_start: 0.7998 (mmm) cc_final: 0.7721 (mmm) REVERT: B 333 ARG cc_start: 0.7700 (mtt90) cc_final: 0.7215 (mtt90) REVERT: B 361 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7518 (mt-10) REVERT: B 368 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7433 (mt-10) REVERT: B 397 GLN cc_start: 0.7686 (tt0) cc_final: 0.7399 (tt0) REVERT: B 428 GLU cc_start: 0.7502 (tt0) cc_final: 0.7101 (tp30) REVERT: B 499 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7865 (mtpp) REVERT: B 515 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7185 (tm-30) REVERT: B 547 GLN cc_start: 0.7067 (tp-100) cc_final: 0.6698 (tp-100) REVERT: B 580 MET cc_start: 0.7711 (tpp) cc_final: 0.7008 (tpp) REVERT: B 597 GLU cc_start: 0.7776 (tp30) cc_final: 0.7457 (tp30) REVERT: B 607 ASN cc_start: 0.6942 (t0) cc_final: 0.6469 (t0) REVERT: B 608 LYS cc_start: 0.8324 (mmtp) cc_final: 0.8016 (mmtp) REVERT: B 630 LEU cc_start: 0.8587 (mt) cc_final: 0.8278 (mt) REVERT: B 646 LEU cc_start: 0.8759 (mp) cc_final: 0.8534 (mp) REVERT: B 649 PHE cc_start: 0.7830 (p90) cc_final: 0.7593 (p90) REVERT: B 656 GLN cc_start: 0.7630 (mp10) cc_final: 0.6860 (mp10) REVERT: B 707 MET cc_start: 0.7657 (tpp) cc_final: 0.7277 (tpp) REVERT: B 758 MET cc_start: 0.8353 (mmm) cc_final: 0.7738 (mmm) REVERT: B 775 ASN cc_start: 0.6255 (m-40) cc_final: 0.5997 (m-40) REVERT: B 807 ARG cc_start: 0.7909 (ttm170) cc_final: 0.7623 (ttp-170) REVERT: B 822 PHE cc_start: 0.8397 (m-80) cc_final: 0.8175 (m-80) REVERT: B 850 PHE cc_start: 0.8284 (t80) cc_final: 0.7992 (t80) REVERT: B 912 PHE cc_start: 0.7568 (t80) cc_final: 0.7293 (t80) REVERT: B 919 GLN cc_start: 0.7744 (mt0) cc_final: 0.7317 (mt0) REVERT: B 954 TYR cc_start: 0.7600 (t80) cc_final: 0.6856 (t80) REVERT: B 969 LYS cc_start: 0.8194 (ttmm) cc_final: 0.7844 (ttpp) REVERT: B 1020 MET cc_start: 0.6765 (mmt) cc_final: 0.6431 (mmt) REVERT: B 1063 PHE cc_start: 0.8147 (t80) cc_final: 0.7834 (t80) REVERT: B 1066 GLU cc_start: 0.8026 (tp30) cc_final: 0.6962 (tp30) REVERT: B 1071 ILE cc_start: 0.8496 (mm) cc_final: 0.8295 (mt) REVERT: B 1080 PHE cc_start: 0.7468 (t80) cc_final: 0.6973 (t80) REVERT: B 1096 PHE cc_start: 0.6859 (OUTLIER) cc_final: 0.6556 (m-10) REVERT: B 1106 LYS cc_start: 0.7553 (ttmt) cc_final: 0.6710 (ttmm) REVERT: B 1110 ARG cc_start: 0.7922 (ptp90) cc_final: 0.7608 (ptp-170) REVERT: B 1132 LYS cc_start: 0.8030 (mttt) cc_final: 0.7676 (mttm) REVERT: B 1148 LYS cc_start: 0.8578 (mtpp) cc_final: 0.8353 (mmmm) REVERT: B 1154 GLN cc_start: 0.8285 (tt0) cc_final: 0.8002 (tt0) REVERT: B 1159 LEU cc_start: 0.8633 (mm) cc_final: 0.8425 (mm) REVERT: B 1163 PHE cc_start: 0.7521 (m-10) cc_final: 0.7317 (m-80) REVERT: B 1200 GLU cc_start: 0.8130 (pt0) cc_final: 0.7758 (pt0) REVERT: B 1204 GLU cc_start: 0.7495 (pp20) cc_final: 0.7295 (pp20) REVERT: B 1219 MET cc_start: 0.7394 (mmp) cc_final: 0.7120 (mmp) REVERT: B 1228 ILE cc_start: 0.8032 (mm) cc_final: 0.7456 (mm) REVERT: B 1231 MET cc_start: 0.6872 (mpp) cc_final: 0.6254 (mpp) REVERT: B 1263 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7774 (mt-10) REVERT: B 1266 LEU cc_start: 0.7896 (mt) cc_final: 0.7573 (mt) REVERT: B 1305 ILE cc_start: 0.7972 (mt) cc_final: 0.7769 (mt) REVERT: B 1383 LYS cc_start: 0.8891 (pttm) cc_final: 0.8551 (pttm) outliers start: 10 outliers final: 4 residues processed: 774 average time/residue: 0.1731 time to fit residues: 200.4436 Evaluate side-chains 680 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 675 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 1096 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 247 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN A 132 ASN A 602 ASN ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 GLN A1402 GLN B 204 ASN B 709 ASN ** B1178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1250 HIS ** B1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.118152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.101680 restraints weight = 48823.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.104945 restraints weight = 25121.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.107065 restraints weight = 15341.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.108519 restraints weight = 10524.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.109503 restraints weight = 7849.786| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20796 Z= 0.184 Angle : 0.688 12.200 28095 Z= 0.361 Chirality : 0.042 0.168 3318 Planarity : 0.005 0.051 3545 Dihedral : 5.089 50.397 2693 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.24 % Favored : 90.68 % Rotamer: Outliers : 3.09 % Allowed : 14.59 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.17), residues: 2521 helix: 1.18 (0.12), residues: 1768 sheet: -2.97 (1.00), residues: 20 loop : -2.75 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 914 TYR 0.019 0.001 TYR A 138 PHE 0.027 0.002 PHE B 925 TRP 0.016 0.002 TRP A 470 HIS 0.012 0.001 HIS A 617 Details of bonding type rmsd covalent geometry : bond 0.00381 (20796) covalent geometry : angle 0.68775 (28095) hydrogen bonds : bond 0.05064 ( 1287) hydrogen bonds : angle 4.93179 ( 3840) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 702 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7271 (mm-30) REVERT: A 78 GLN cc_start: 0.7850 (tp40) cc_final: 0.7565 (tp40) REVERT: A 82 MET cc_start: 0.8027 (ttm) cc_final: 0.7661 (tmm) REVERT: A 91 ASN cc_start: 0.7624 (t0) cc_final: 0.7248 (t0) REVERT: A 154 PHE cc_start: 0.8474 (p90) cc_final: 0.8204 (p90) REVERT: A 155 GLU cc_start: 0.7582 (pt0) cc_final: 0.7271 (pt0) REVERT: A 184 LEU cc_start: 0.8171 (mt) cc_final: 0.7847 (mt) REVERT: A 199 SER cc_start: 0.8600 (t) cc_final: 0.8385 (t) REVERT: A 208 GLU cc_start: 0.7049 (mp0) cc_final: 0.6840 (mp0) REVERT: A 240 ILE cc_start: 0.8801 (mt) cc_final: 0.8531 (mm) REVERT: A 253 LYS cc_start: 0.8095 (pttt) cc_final: 0.7605 (pttt) REVERT: A 368 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7479 (mt-10) REVERT: A 523 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7498 (mm-30) REVERT: A 555 LYS cc_start: 0.8688 (mmmm) cc_final: 0.8451 (mmmm) REVERT: A 559 ARG cc_start: 0.7833 (tpp80) cc_final: 0.7508 (tpp80) REVERT: A 562 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7044 (mt-10) REVERT: A 565 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7855 (mm-30) REVERT: A 593 LYS cc_start: 0.7681 (tptm) cc_final: 0.7281 (tptm) REVERT: A 600 PHE cc_start: 0.8622 (t80) cc_final: 0.8092 (t80) REVERT: A 626 GLU cc_start: 0.7821 (tp30) cc_final: 0.7615 (tp30) REVERT: A 656 GLN cc_start: 0.7273 (tm-30) cc_final: 0.6808 (tm-30) REVERT: A 659 GLU cc_start: 0.7414 (mt-10) cc_final: 0.6634 (mt-10) REVERT: A 663 GLU cc_start: 0.7607 (pt0) cc_final: 0.7161 (pt0) REVERT: A 745 ASP cc_start: 0.8056 (t70) cc_final: 0.7838 (t0) REVERT: A 765 ASN cc_start: 0.7521 (t0) cc_final: 0.6875 (t0) REVERT: A 802 LEU cc_start: 0.8107 (tp) cc_final: 0.7873 (tp) REVERT: A 830 ASP cc_start: 0.7377 (t70) cc_final: 0.7092 (t70) REVERT: A 837 MET cc_start: 0.7469 (mmm) cc_final: 0.7237 (mmt) REVERT: A 852 ASP cc_start: 0.7346 (t0) cc_final: 0.7126 (t0) REVERT: A 908 ASP cc_start: 0.7714 (p0) cc_final: 0.7323 (p0) REVERT: A 911 ARG cc_start: 0.7612 (tpp-160) cc_final: 0.7251 (mmt-90) REVERT: A 917 LYS cc_start: 0.7572 (mmtt) cc_final: 0.7126 (mttp) REVERT: A 956 ASP cc_start: 0.6739 (p0) cc_final: 0.6379 (p0) REVERT: A 1017 LYS cc_start: 0.8131 (ttmm) cc_final: 0.7813 (ttmm) REVERT: A 1020 MET cc_start: 0.7294 (tpp) cc_final: 0.6968 (tpp) REVERT: A 1021 GLU cc_start: 0.7728 (tp30) cc_final: 0.7029 (tp30) REVERT: A 1035 ASN cc_start: 0.6598 (t0) cc_final: 0.6388 (t0) REVERT: A 1071 ILE cc_start: 0.8475 (mm) cc_final: 0.8236 (mm) REVERT: A 1072 GLU cc_start: 0.8210 (tt0) cc_final: 0.7695 (tt0) REVERT: A 1089 LYS cc_start: 0.8535 (ttmm) cc_final: 0.8132 (ttmm) REVERT: A 1093 GLN cc_start: 0.8572 (tp40) cc_final: 0.8237 (tp40) REVERT: A 1112 MET cc_start: 0.7373 (ptm) cc_final: 0.7169 (mtp) REVERT: A 1113 LEU cc_start: 0.8232 (tp) cc_final: 0.7928 (tp) REVERT: A 1116 LYS cc_start: 0.8723 (ttpt) cc_final: 0.8381 (ttmm) REVERT: A 1120 ILE cc_start: 0.9125 (mm) cc_final: 0.8756 (mm) REVERT: A 1126 GLN cc_start: 0.6835 (mm-40) cc_final: 0.6455 (mm-40) REVERT: A 1128 GLU cc_start: 0.7910 (tp30) cc_final: 0.7491 (tp30) REVERT: A 1132 LYS cc_start: 0.8392 (mmmm) cc_final: 0.7820 (mmmm) REVERT: A 1139 LEU cc_start: 0.7952 (mm) cc_final: 0.7701 (mm) REVERT: A 1140 LYS cc_start: 0.8001 (mmmm) cc_final: 0.7573 (mmmm) REVERT: A 1157 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7258 (mt-10) REVERT: A 1170 PHE cc_start: 0.7452 (m-10) cc_final: 0.7249 (m-10) REVERT: A 1187 LYS cc_start: 0.8583 (mmmm) cc_final: 0.8186 (mmmm) REVERT: A 1191 MET cc_start: 0.7110 (tpt) cc_final: 0.6359 (tpt) REVERT: A 1200 GLU cc_start: 0.7814 (tp30) cc_final: 0.7462 (tp30) REVERT: A 1219 MET cc_start: 0.8166 (mmm) cc_final: 0.7770 (mmm) REVERT: A 1259 LYS cc_start: 0.8359 (mppt) cc_final: 0.7743 (mppt) REVERT: A 1263 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7493 (mt-10) REVERT: A 1267 LYS cc_start: 0.8505 (mttm) cc_final: 0.8180 (mtpp) REVERT: A 1305 ILE cc_start: 0.8508 (mm) cc_final: 0.8294 (mm) REVERT: A 1336 GLU cc_start: 0.8101 (tp30) cc_final: 0.7708 (tp30) REVERT: A 1366 VAL cc_start: 0.8677 (p) cc_final: 0.8430 (m) REVERT: A 1383 LYS cc_start: 0.8370 (mmtm) cc_final: 0.8093 (mmtm) REVERT: A 1399 LYS cc_start: 0.8573 (ptpp) cc_final: 0.8332 (pttm) REVERT: A 1400 LYS cc_start: 0.8781 (mmtm) cc_final: 0.8512 (mmtm) REVERT: B 10 ASP cc_start: 0.7949 (m-30) cc_final: 0.7592 (m-30) REVERT: B 90 ASP cc_start: 0.7853 (t0) cc_final: 0.7276 (t0) REVERT: B 91 ASN cc_start: 0.8088 (m110) cc_final: 0.7000 (m-40) REVERT: B 110 ILE cc_start: 0.8604 (pt) cc_final: 0.7307 (mm) REVERT: B 132 ASN cc_start: 0.8204 (p0) cc_final: 0.7796 (p0) REVERT: B 136 GLN cc_start: 0.8221 (mt0) cc_final: 0.8021 (mt0) REVERT: B 138 TYR cc_start: 0.8112 (p90) cc_final: 0.7911 (p90) REVERT: B 151 HIS cc_start: 0.8156 (m170) cc_final: 0.7956 (m90) REVERT: B 154 PHE cc_start: 0.8140 (p90) cc_final: 0.7778 (p90) REVERT: B 155 GLU cc_start: 0.7525 (pt0) cc_final: 0.7243 (pm20) REVERT: B 174 ARG cc_start: 0.8226 (ttt180) cc_final: 0.7981 (ttt180) REVERT: B 191 TYR cc_start: 0.8180 (t80) cc_final: 0.7897 (t80) REVERT: B 205 ARG cc_start: 0.7787 (tpp80) cc_final: 0.7481 (mmm-85) REVERT: B 228 LYS cc_start: 0.8368 (tttm) cc_final: 0.7766 (ttmm) REVERT: B 333 ARG cc_start: 0.7655 (mtt90) cc_final: 0.7240 (mtt90) REVERT: B 346 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7239 (mm-30) REVERT: B 361 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7489 (mt-10) REVERT: B 364 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7088 (tm-30) REVERT: B 368 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7000 (mt-10) REVERT: B 428 GLU cc_start: 0.7527 (tt0) cc_final: 0.6959 (tm-30) REVERT: B 499 LYS cc_start: 0.8237 (mtpp) cc_final: 0.8009 (mtpp) REVERT: B 515 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7100 (tm-30) REVERT: B 547 GLN cc_start: 0.7174 (tp-100) cc_final: 0.6890 (tp-100) REVERT: B 580 MET cc_start: 0.7867 (tpp) cc_final: 0.7197 (tpp) REVERT: B 594 ASP cc_start: 0.7850 (m-30) cc_final: 0.7512 (m-30) REVERT: B 597 GLU cc_start: 0.7703 (tp30) cc_final: 0.7395 (tp30) REVERT: B 607 ASN cc_start: 0.7311 (t0) cc_final: 0.6872 (t0) REVERT: B 630 LEU cc_start: 0.8578 (mt) cc_final: 0.8267 (mt) REVERT: B 649 PHE cc_start: 0.7814 (p90) cc_final: 0.7521 (p90) REVERT: B 656 GLN cc_start: 0.7756 (mp10) cc_final: 0.6917 (mp10) REVERT: B 707 MET cc_start: 0.7638 (tpp) cc_final: 0.7240 (tpp) REVERT: B 739 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.6576 (m-10) REVERT: B 775 ASN cc_start: 0.6332 (m-40) cc_final: 0.6112 (m-40) REVERT: B 803 LEU cc_start: 0.8234 (mt) cc_final: 0.7839 (mt) REVERT: B 807 ARG cc_start: 0.7851 (ttm170) cc_final: 0.7202 (ttp-170) REVERT: B 837 MET cc_start: 0.8081 (mmm) cc_final: 0.7383 (mmm) REVERT: B 912 PHE cc_start: 0.7421 (t80) cc_final: 0.7160 (t80) REVERT: B 919 GLN cc_start: 0.7582 (mt0) cc_final: 0.7299 (mt0) REVERT: B 958 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7183 (mm) REVERT: B 1020 MET cc_start: 0.6593 (mmt) cc_final: 0.6369 (mmt) REVERT: B 1062 TYR cc_start: 0.7596 (p90) cc_final: 0.7105 (p90) REVERT: B 1063 PHE cc_start: 0.8063 (t80) cc_final: 0.7799 (t80) REVERT: B 1080 PHE cc_start: 0.7376 (t80) cc_final: 0.6864 (t80) REVERT: B 1096 PHE cc_start: 0.6754 (OUTLIER) cc_final: 0.6425 (m-10) REVERT: B 1106 LYS cc_start: 0.7515 (ttmt) cc_final: 0.6628 (ttmm) REVERT: B 1110 ARG cc_start: 0.7842 (ptp90) cc_final: 0.7565 (ptp-170) REVERT: B 1132 LYS cc_start: 0.8056 (mttt) cc_final: 0.7611 (mttm) REVERT: B 1148 LYS cc_start: 0.8679 (mtpp) cc_final: 0.8448 (mmmm) REVERT: B 1154 GLN cc_start: 0.8374 (tt0) cc_final: 0.8051 (tt0) REVERT: B 1157 GLU cc_start: 0.7428 (tp30) cc_final: 0.6639 (tp30) REVERT: B 1159 LEU cc_start: 0.8636 (mm) cc_final: 0.8390 (mm) REVERT: B 1199 PHE cc_start: 0.8362 (t80) cc_final: 0.8155 (t80) REVERT: B 1200 GLU cc_start: 0.8128 (pt0) cc_final: 0.7777 (pt0) REVERT: B 1201 TYR cc_start: 0.8358 (t80) cc_final: 0.7603 (t80) REVERT: B 1231 MET cc_start: 0.6739 (mpp) cc_final: 0.6148 (mpp) REVERT: B 1263 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8046 (mt-10) REVERT: B 1266 LEU cc_start: 0.7933 (mt) cc_final: 0.7644 (mt) REVERT: B 1383 LYS cc_start: 0.8883 (pttm) cc_final: 0.8510 (pttm) outliers start: 73 outliers final: 44 residues processed: 735 average time/residue: 0.1658 time to fit residues: 184.2806 Evaluate side-chains 708 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 660 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 844 CYS Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 817 ILE Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 1028 ILE Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1250 HIS Chi-restraints excluded: chain B residue 1252 ILE Chi-restraints excluded: chain B residue 1290 ILE Chi-restraints excluded: chain B residue 1367 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 51 optimal weight: 0.8980 chunk 157 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 235 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 11 optimal weight: 0.0170 chunk 156 optimal weight: 0.4980 chunk 183 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 33 optimal weight: 0.0470 chunk 236 optimal weight: 0.9980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1285 ASN B 709 ASN B 832 HIS B1147 GLN B1178 ASN B1194 GLN ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.119606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.103049 restraints weight = 48627.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.106337 restraints weight = 25046.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.108493 restraints weight = 15291.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.109924 restraints weight = 10476.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.110929 restraints weight = 7849.522| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20796 Z= 0.146 Angle : 0.664 10.759 28095 Z= 0.346 Chirality : 0.040 0.173 3318 Planarity : 0.005 0.058 3545 Dihedral : 5.100 51.505 2693 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.69 % Favored : 91.19 % Rotamer: Outliers : 3.51 % Allowed : 17.46 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.17), residues: 2521 helix: 1.21 (0.12), residues: 1768 sheet: -2.95 (1.00), residues: 20 loop : -2.74 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 174 TYR 0.028 0.001 TYR B1258 PHE 0.027 0.002 PHE B 925 TRP 0.026 0.002 TRP B 768 HIS 0.008 0.001 HIS A 617 Details of bonding type rmsd covalent geometry : bond 0.00309 (20796) covalent geometry : angle 0.66376 (28095) hydrogen bonds : bond 0.04654 ( 1287) hydrogen bonds : angle 4.81029 ( 3840) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 677 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7207 (mm-30) REVERT: A 78 GLN cc_start: 0.7834 (tp40) cc_final: 0.7560 (tp40) REVERT: A 82 MET cc_start: 0.8022 (ttm) cc_final: 0.7648 (tmm) REVERT: A 91 ASN cc_start: 0.7631 (t0) cc_final: 0.7228 (t0) REVERT: A 120 ASP cc_start: 0.7569 (t70) cc_final: 0.7110 (m-30) REVERT: A 155 GLU cc_start: 0.7588 (pt0) cc_final: 0.7211 (pt0) REVERT: A 184 LEU cc_start: 0.8227 (mt) cc_final: 0.7890 (mt) REVERT: A 199 SER cc_start: 0.8632 (t) cc_final: 0.8398 (t) REVERT: A 240 ILE cc_start: 0.8794 (mt) cc_final: 0.8518 (mm) REVERT: A 253 LYS cc_start: 0.8099 (pttt) cc_final: 0.7610 (pttt) REVERT: A 368 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7439 (mt-10) REVERT: A 523 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7455 (mm-30) REVERT: A 555 LYS cc_start: 0.8666 (mmmm) cc_final: 0.8413 (mmmm) REVERT: A 558 ASP cc_start: 0.7936 (t0) cc_final: 0.7736 (t0) REVERT: A 559 ARG cc_start: 0.7785 (tpp80) cc_final: 0.7229 (tpp80) REVERT: A 562 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6960 (mt-10) REVERT: A 565 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7868 (mm-30) REVERT: A 593 LYS cc_start: 0.7648 (tptm) cc_final: 0.7228 (tptm) REVERT: A 597 GLU cc_start: 0.7654 (tm-30) cc_final: 0.6761 (tm-30) REVERT: A 626 GLU cc_start: 0.7816 (tp30) cc_final: 0.7607 (tp30) REVERT: A 656 GLN cc_start: 0.7274 (tm-30) cc_final: 0.6638 (tm-30) REVERT: A 657 GLN cc_start: 0.7466 (mp10) cc_final: 0.6669 (mp10) REVERT: A 659 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6332 (mp0) REVERT: A 663 GLU cc_start: 0.7570 (pt0) cc_final: 0.7115 (pt0) REVERT: A 745 ASP cc_start: 0.8064 (t70) cc_final: 0.7825 (t0) REVERT: A 830 ASP cc_start: 0.7354 (t70) cc_final: 0.7101 (t70) REVERT: A 859 ASP cc_start: 0.6290 (m-30) cc_final: 0.5596 (m-30) REVERT: A 911 ARG cc_start: 0.7550 (tpp-160) cc_final: 0.7186 (mmt-90) REVERT: A 917 LYS cc_start: 0.7515 (mmtt) cc_final: 0.7084 (mttp) REVERT: A 956 ASP cc_start: 0.6727 (p0) cc_final: 0.6454 (p0) REVERT: A 1017 LYS cc_start: 0.8086 (ttmm) cc_final: 0.7785 (ttmm) REVERT: A 1020 MET cc_start: 0.7308 (tpp) cc_final: 0.6964 (tpp) REVERT: A 1021 GLU cc_start: 0.7758 (tp30) cc_final: 0.7073 (tp30) REVERT: A 1062 TYR cc_start: 0.7542 (p90) cc_final: 0.7044 (p90) REVERT: A 1072 GLU cc_start: 0.8191 (tt0) cc_final: 0.7682 (tt0) REVERT: A 1082 LYS cc_start: 0.7839 (mtpt) cc_final: 0.7386 (mtpt) REVERT: A 1086 GLU cc_start: 0.6040 (tm-30) cc_final: 0.5806 (tm-30) REVERT: A 1089 LYS cc_start: 0.8495 (ttmm) cc_final: 0.7941 (ttmm) REVERT: A 1093 GLN cc_start: 0.8527 (tp40) cc_final: 0.8237 (tp40) REVERT: A 1113 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7801 (tp) REVERT: A 1116 LYS cc_start: 0.8661 (ttpt) cc_final: 0.8300 (ttmm) REVERT: A 1120 ILE cc_start: 0.9134 (mm) cc_final: 0.8716 (mm) REVERT: A 1126 GLN cc_start: 0.6848 (mm-40) cc_final: 0.6430 (mm-40) REVERT: A 1128 GLU cc_start: 0.7902 (tp30) cc_final: 0.7470 (tp30) REVERT: A 1132 LYS cc_start: 0.8366 (mmmm) cc_final: 0.7779 (mmmm) REVERT: A 1140 LYS cc_start: 0.7968 (mmmm) cc_final: 0.7534 (mmmm) REVERT: A 1157 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7277 (mm-30) REVERT: A 1186 ARG cc_start: 0.8119 (ttt90) cc_final: 0.7573 (ttm-80) REVERT: A 1187 LYS cc_start: 0.8523 (mmmm) cc_final: 0.8278 (mmmm) REVERT: A 1200 GLU cc_start: 0.7795 (tp30) cc_final: 0.7447 (tp30) REVERT: A 1219 MET cc_start: 0.8170 (mmm) cc_final: 0.7903 (mmm) REVERT: A 1231 MET cc_start: 0.7978 (mmt) cc_final: 0.7652 (mpp) REVERT: A 1259 LYS cc_start: 0.8337 (mppt) cc_final: 0.7785 (mppt) REVERT: A 1263 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7496 (mt-10) REVERT: A 1267 LYS cc_start: 0.8497 (mttm) cc_final: 0.8161 (mtpp) REVERT: A 1336 GLU cc_start: 0.8098 (tp30) cc_final: 0.7703 (tp30) REVERT: A 1365 ASN cc_start: 0.8340 (m-40) cc_final: 0.7974 (m-40) REVERT: A 1366 VAL cc_start: 0.8633 (p) cc_final: 0.8391 (m) REVERT: A 1383 LYS cc_start: 0.8339 (mmtm) cc_final: 0.8079 (mmtm) REVERT: A 1399 LYS cc_start: 0.8600 (ptpp) cc_final: 0.8282 (pttm) REVERT: A 1400 LYS cc_start: 0.8789 (mmtm) cc_final: 0.8544 (mmtm) REVERT: A 1402 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8378 (mm-40) REVERT: A 1409 LYS cc_start: 0.8039 (mmmt) cc_final: 0.7717 (pttm) REVERT: B 10 ASP cc_start: 0.7974 (m-30) cc_final: 0.7607 (m-30) REVERT: B 82 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7486 (tmm) REVERT: B 90 ASP cc_start: 0.7838 (t0) cc_final: 0.7248 (t0) REVERT: B 91 ASN cc_start: 0.8059 (m110) cc_final: 0.6929 (m-40) REVERT: B 102 LEU cc_start: 0.8128 (mt) cc_final: 0.7838 (mt) REVERT: B 110 ILE cc_start: 0.8611 (pt) cc_final: 0.7267 (mm) REVERT: B 132 ASN cc_start: 0.8214 (p0) cc_final: 0.7798 (p0) REVERT: B 136 GLN cc_start: 0.8189 (mt0) cc_final: 0.7955 (mt0) REVERT: B 154 PHE cc_start: 0.8116 (p90) cc_final: 0.7756 (p90) REVERT: B 155 GLU cc_start: 0.7469 (pt0) cc_final: 0.7201 (pm20) REVERT: B 174 ARG cc_start: 0.8179 (ttt180) cc_final: 0.7954 (ttt180) REVERT: B 191 TYR cc_start: 0.8145 (t80) cc_final: 0.7902 (t80) REVERT: B 205 ARG cc_start: 0.7811 (tpp80) cc_final: 0.7529 (mmm-85) REVERT: B 228 LYS cc_start: 0.8337 (tttm) cc_final: 0.7781 (ttmm) REVERT: B 333 ARG cc_start: 0.7656 (mtt90) cc_final: 0.7250 (mtt90) REVERT: B 346 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7199 (mm-30) REVERT: B 361 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7482 (mt-10) REVERT: B 368 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7333 (mt-10) REVERT: B 499 LYS cc_start: 0.8223 (mtpp) cc_final: 0.7667 (mppt) REVERT: B 515 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7057 (tm-30) REVERT: B 547 GLN cc_start: 0.7183 (tp-100) cc_final: 0.6855 (tp-100) REVERT: B 580 MET cc_start: 0.7868 (tpp) cc_final: 0.7184 (tpp) REVERT: B 594 ASP cc_start: 0.7880 (m-30) cc_final: 0.7544 (m-30) REVERT: B 597 GLU cc_start: 0.7672 (tp30) cc_final: 0.7218 (tp30) REVERT: B 607 ASN cc_start: 0.7445 (t0) cc_final: 0.6761 (t0) REVERT: B 649 PHE cc_start: 0.7796 (p90) cc_final: 0.7516 (p90) REVERT: B 656 GLN cc_start: 0.7727 (mp10) cc_final: 0.7298 (mp10) REVERT: B 739 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.6589 (m-10) REVERT: B 807 ARG cc_start: 0.7850 (ttm170) cc_final: 0.7265 (ttp-170) REVERT: B 837 MET cc_start: 0.8082 (mmm) cc_final: 0.7728 (tpp) REVERT: B 851 PHE cc_start: 0.6984 (m-80) cc_final: 0.6783 (m-80) REVERT: B 1020 MET cc_start: 0.6516 (mmt) cc_final: 0.6265 (mmt) REVERT: B 1063 PHE cc_start: 0.8019 (t80) cc_final: 0.7697 (t80) REVERT: B 1066 GLU cc_start: 0.7780 (tt0) cc_final: 0.7241 (mm-30) REVERT: B 1080 PHE cc_start: 0.7304 (t80) cc_final: 0.6849 (t80) REVERT: B 1096 PHE cc_start: 0.6699 (OUTLIER) cc_final: 0.6392 (m-10) REVERT: B 1106 LYS cc_start: 0.7518 (ttmt) cc_final: 0.7212 (ttmm) REVERT: B 1132 LYS cc_start: 0.8000 (mttt) cc_final: 0.7547 (mttm) REVERT: B 1154 GLN cc_start: 0.8348 (tt0) cc_final: 0.8060 (tt0) REVERT: B 1157 GLU cc_start: 0.7367 (tp30) cc_final: 0.6543 (tp30) REVERT: B 1200 GLU cc_start: 0.8111 (pt0) cc_final: 0.7880 (pt0) REVERT: B 1219 MET cc_start: 0.7386 (mmp) cc_final: 0.6732 (mmp) REVERT: B 1263 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7773 (mt-10) REVERT: B 1266 LEU cc_start: 0.7885 (mt) cc_final: 0.7611 (mt) REVERT: B 1383 LYS cc_start: 0.8849 (pttm) cc_final: 0.8424 (pttm) REVERT: B 1399 LYS cc_start: 0.8723 (pptt) cc_final: 0.8176 (pttm) outliers start: 83 outliers final: 61 residues processed: 707 average time/residue: 0.1661 time to fit residues: 177.3827 Evaluate side-chains 716 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 651 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 844 CYS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 1028 ILE Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1250 HIS Chi-restraints excluded: chain B residue 1252 ILE Chi-restraints excluded: chain B residue 1290 ILE Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1367 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 221 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 224 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 138 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 229 optimal weight: 0.7980 chunk 189 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 709 ASN ** B1178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1250 HIS ** B1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.117915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.101380 restraints weight = 48950.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.104673 restraints weight = 25167.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.106821 restraints weight = 15370.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.108174 restraints weight = 10524.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.109207 restraints weight = 7947.802| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20796 Z= 0.180 Angle : 0.691 11.473 28095 Z= 0.358 Chirality : 0.042 0.213 3318 Planarity : 0.005 0.062 3545 Dihedral : 5.221 52.896 2693 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.04 % Favored : 90.80 % Rotamer: Outliers : 4.14 % Allowed : 18.73 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.17), residues: 2521 helix: 1.14 (0.12), residues: 1763 sheet: -3.00 (0.99), residues: 20 loop : -2.77 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 174 TYR 0.033 0.002 TYR B 138 PHE 0.028 0.002 PHE B 925 TRP 0.012 0.002 TRP B 773 HIS 0.010 0.001 HIS A 617 Details of bonding type rmsd covalent geometry : bond 0.00379 (20796) covalent geometry : angle 0.69055 (28095) hydrogen bonds : bond 0.04838 ( 1287) hydrogen bonds : angle 4.92219 ( 3840) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 678 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7295 (mm-30) REVERT: A 78 GLN cc_start: 0.7875 (tp40) cc_final: 0.7589 (tp40) REVERT: A 82 MET cc_start: 0.8026 (ttm) cc_final: 0.7673 (tmm) REVERT: A 91 ASN cc_start: 0.7659 (t0) cc_final: 0.7293 (t0) REVERT: A 155 GLU cc_start: 0.7565 (pt0) cc_final: 0.7135 (pt0) REVERT: A 184 LEU cc_start: 0.8229 (mt) cc_final: 0.7903 (mt) REVERT: A 199 SER cc_start: 0.8582 (t) cc_final: 0.8355 (t) REVERT: A 240 ILE cc_start: 0.8786 (mt) cc_final: 0.8526 (mm) REVERT: A 253 LYS cc_start: 0.8077 (pttt) cc_final: 0.7598 (pttt) REVERT: A 368 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7498 (mt-10) REVERT: A 459 LYS cc_start: 0.8160 (mtmm) cc_final: 0.7910 (mttp) REVERT: A 523 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7489 (mm-30) REVERT: A 555 LYS cc_start: 0.8684 (mmmm) cc_final: 0.8262 (mmmm) REVERT: A 559 ARG cc_start: 0.7778 (tpp80) cc_final: 0.7132 (tpp80) REVERT: A 562 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6930 (mt-10) REVERT: A 565 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7828 (mm-30) REVERT: A 593 LYS cc_start: 0.7673 (tptm) cc_final: 0.7239 (tptm) REVERT: A 597 GLU cc_start: 0.7720 (tm-30) cc_final: 0.6851 (tm-30) REVERT: A 615 LEU cc_start: 0.7905 (mt) cc_final: 0.7584 (tp) REVERT: A 626 GLU cc_start: 0.7832 (tp30) cc_final: 0.7626 (tp30) REVERT: A 656 GLN cc_start: 0.7364 (tm-30) cc_final: 0.6665 (tm-30) REVERT: A 657 GLN cc_start: 0.7522 (mp10) cc_final: 0.7199 (mp10) REVERT: A 659 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6408 (mp0) REVERT: A 663 GLU cc_start: 0.7593 (pt0) cc_final: 0.7127 (pt0) REVERT: A 745 ASP cc_start: 0.8124 (t70) cc_final: 0.7882 (t0) REVERT: A 830 ASP cc_start: 0.7274 (t70) cc_final: 0.7068 (t70) REVERT: A 911 ARG cc_start: 0.7506 (tpp-160) cc_final: 0.7165 (mmt-90) REVERT: A 917 LYS cc_start: 0.7577 (mmtt) cc_final: 0.7353 (mttt) REVERT: A 956 ASP cc_start: 0.6574 (p0) cc_final: 0.6206 (p0) REVERT: A 1017 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7804 (ttmm) REVERT: A 1020 MET cc_start: 0.7318 (tpp) cc_final: 0.6976 (tpp) REVERT: A 1021 GLU cc_start: 0.7784 (tp30) cc_final: 0.7094 (tp30) REVERT: A 1062 TYR cc_start: 0.7535 (p90) cc_final: 0.7017 (p90) REVERT: A 1072 GLU cc_start: 0.8210 (tt0) cc_final: 0.7758 (tt0) REVERT: A 1082 LYS cc_start: 0.7797 (mtpt) cc_final: 0.7380 (mtpt) REVERT: A 1089 LYS cc_start: 0.8469 (ttmm) cc_final: 0.8098 (ttmm) REVERT: A 1093 GLN cc_start: 0.8422 (tp40) cc_final: 0.8151 (tp40) REVERT: A 1113 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7906 (tp) REVERT: A 1116 LYS cc_start: 0.8691 (ttpt) cc_final: 0.8294 (ttmm) REVERT: A 1120 ILE cc_start: 0.9121 (mm) cc_final: 0.8701 (mm) REVERT: A 1126 GLN cc_start: 0.6866 (mm-40) cc_final: 0.6416 (mm-40) REVERT: A 1128 GLU cc_start: 0.7926 (tp30) cc_final: 0.7563 (tp30) REVERT: A 1132 LYS cc_start: 0.8385 (mmmm) cc_final: 0.7846 (mmmm) REVERT: A 1157 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7228 (mt-10) REVERT: A 1187 LYS cc_start: 0.8529 (mmmm) cc_final: 0.8234 (mmmm) REVERT: A 1200 GLU cc_start: 0.7809 (tp30) cc_final: 0.7461 (tp30) REVERT: A 1219 MET cc_start: 0.8201 (mmm) cc_final: 0.7950 (mmm) REVERT: A 1258 TYR cc_start: 0.7386 (m-80) cc_final: 0.7183 (m-80) REVERT: A 1259 LYS cc_start: 0.8355 (mppt) cc_final: 0.7784 (mppt) REVERT: A 1263 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7508 (mt-10) REVERT: A 1267 LYS cc_start: 0.8530 (mttm) cc_final: 0.8200 (mtpp) REVERT: A 1317 LEU cc_start: 0.8540 (mm) cc_final: 0.8322 (mt) REVERT: A 1336 GLU cc_start: 0.8088 (tp30) cc_final: 0.7711 (tp30) REVERT: A 1366 VAL cc_start: 0.8689 (p) cc_final: 0.8434 (m) REVERT: A 1383 LYS cc_start: 0.8332 (mmtm) cc_final: 0.8066 (mmtm) REVERT: A 1400 LYS cc_start: 0.8764 (mmtm) cc_final: 0.8425 (mmtm) REVERT: A 1409 LYS cc_start: 0.8057 (mmmt) cc_final: 0.7838 (pttm) REVERT: B 10 ASP cc_start: 0.7977 (m-30) cc_final: 0.7602 (m-30) REVERT: B 82 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7323 (tmm) REVERT: B 90 ASP cc_start: 0.7847 (t0) cc_final: 0.7275 (t0) REVERT: B 91 ASN cc_start: 0.8090 (m110) cc_final: 0.6856 (m-40) REVERT: B 110 ILE cc_start: 0.8628 (pt) cc_final: 0.7245 (mm) REVERT: B 124 LYS cc_start: 0.8364 (ttmt) cc_final: 0.8064 (ttpt) REVERT: B 132 ASN cc_start: 0.8218 (p0) cc_final: 0.7806 (p0) REVERT: B 154 PHE cc_start: 0.8066 (p90) cc_final: 0.7635 (p90) REVERT: B 155 GLU cc_start: 0.7485 (pt0) cc_final: 0.7210 (pm20) REVERT: B 191 TYR cc_start: 0.8188 (t80) cc_final: 0.7946 (t80) REVERT: B 205 ARG cc_start: 0.7824 (tpp80) cc_final: 0.7531 (mmm-85) REVERT: B 228 LYS cc_start: 0.8335 (tttm) cc_final: 0.7793 (ttmm) REVERT: B 333 ARG cc_start: 0.7688 (mtt90) cc_final: 0.7263 (mtt90) REVERT: B 346 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7208 (mm-30) REVERT: B 361 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7512 (mt-10) REVERT: B 428 GLU cc_start: 0.7574 (tt0) cc_final: 0.6997 (tp30) REVERT: B 503 LYS cc_start: 0.8621 (tttt) cc_final: 0.7979 (ttmm) REVERT: B 515 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7139 (tm-30) REVERT: B 547 GLN cc_start: 0.7256 (tp-100) cc_final: 0.6861 (tp-100) REVERT: B 580 MET cc_start: 0.7866 (tpp) cc_final: 0.7177 (tpp) REVERT: B 594 ASP cc_start: 0.7887 (m-30) cc_final: 0.7534 (m-30) REVERT: B 597 GLU cc_start: 0.7700 (tp30) cc_final: 0.7247 (tp30) REVERT: B 607 ASN cc_start: 0.7471 (t0) cc_final: 0.6839 (t0) REVERT: B 640 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7666 (mm-30) REVERT: B 649 PHE cc_start: 0.7774 (p90) cc_final: 0.7493 (p90) REVERT: B 656 GLN cc_start: 0.7753 (mp10) cc_final: 0.7282 (mp10) REVERT: B 692 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7265 (mm110) REVERT: B 707 MET cc_start: 0.7931 (tpp) cc_final: 0.7199 (tpp) REVERT: B 739 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.6559 (m-10) REVERT: B 803 LEU cc_start: 0.8228 (mt) cc_final: 0.7882 (mt) REVERT: B 807 ARG cc_start: 0.7859 (ttm170) cc_final: 0.7361 (ttp-170) REVERT: B 837 MET cc_start: 0.8124 (mmm) cc_final: 0.7774 (tpp) REVERT: B 851 PHE cc_start: 0.7048 (m-80) cc_final: 0.6827 (m-80) REVERT: B 1020 MET cc_start: 0.6579 (mmt) cc_final: 0.6329 (mmt) REVERT: B 1063 PHE cc_start: 0.7989 (t80) cc_final: 0.7686 (t80) REVERT: B 1066 GLU cc_start: 0.7732 (tt0) cc_final: 0.7257 (mm-30) REVERT: B 1096 PHE cc_start: 0.6729 (OUTLIER) cc_final: 0.6418 (m-10) REVERT: B 1106 LYS cc_start: 0.7494 (ttmt) cc_final: 0.6884 (ttmm) REVERT: B 1110 ARG cc_start: 0.7823 (ptp90) cc_final: 0.7391 (mtt180) REVERT: B 1132 LYS cc_start: 0.8064 (mttt) cc_final: 0.7650 (mttm) REVERT: B 1154 GLN cc_start: 0.8429 (tt0) cc_final: 0.8098 (tt0) REVERT: B 1157 GLU cc_start: 0.7377 (tp30) cc_final: 0.6612 (tp30) REVERT: B 1200 GLU cc_start: 0.8106 (pt0) cc_final: 0.7770 (pt0) REVERT: B 1201 TYR cc_start: 0.8247 (t80) cc_final: 0.7808 (t80) REVERT: B 1204 GLU cc_start: 0.7514 (pp20) cc_final: 0.7292 (pp20) REVERT: B 1219 MET cc_start: 0.7484 (mmp) cc_final: 0.6884 (mmp) REVERT: B 1263 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7774 (mt-10) REVERT: B 1266 LEU cc_start: 0.7869 (mt) cc_final: 0.7579 (mt) REVERT: B 1383 LYS cc_start: 0.8858 (pttm) cc_final: 0.8424 (pttm) outliers start: 98 outliers final: 64 residues processed: 721 average time/residue: 0.1626 time to fit residues: 177.0706 Evaluate side-chains 716 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 648 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 844 CYS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 560 LYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 1028 ILE Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1250 HIS Chi-restraints excluded: chain B residue 1252 ILE Chi-restraints excluded: chain B residue 1290 ILE Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1367 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 230 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 69 optimal weight: 0.0870 chunk 65 optimal weight: 0.3980 chunk 142 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 205 optimal weight: 0.3980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN B 919 GLN ** B1178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1344 ASN ** 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 = 0.3760 r_free = 0.3760 target = 0.119035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.102460 restraints weight = 48533.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.105746 restraints weight = 25119.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.107897 restraints weight = 15354.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.109360 restraints weight = 10530.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.110282 restraints weight = 7868.989| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20796 Z= 0.151 Angle : 0.677 12.003 28095 Z= 0.350 Chirality : 0.041 0.175 3318 Planarity : 0.005 0.062 3545 Dihedral : 5.224 54.558 2693 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.16 % Favored : 90.68 % Rotamer: Outliers : 4.06 % Allowed : 20.68 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.17), residues: 2521 helix: 1.18 (0.12), residues: 1764 sheet: -2.96 (1.00), residues: 20 loop : -2.78 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 174 TYR 0.030 0.001 TYR B1258 PHE 0.028 0.002 PHE B 925 TRP 0.012 0.002 TRP B 470 HIS 0.015 0.001 HIS B1250 Details of bonding type rmsd covalent geometry : bond 0.00321 (20796) covalent geometry : angle 0.67733 (28095) hydrogen bonds : bond 0.04544 ( 1287) hydrogen bonds : angle 4.84741 ( 3840) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 673 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8426 (ttmt) cc_final: 0.8131 (ttmt) REVERT: A 18 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7289 (mm-30) REVERT: A 78 GLN cc_start: 0.7855 (tp40) cc_final: 0.7561 (tp-100) REVERT: A 91 ASN cc_start: 0.7645 (t0) cc_final: 0.7272 (t0) REVERT: A 120 ASP cc_start: 0.7599 (t70) cc_final: 0.7161 (m-30) REVERT: A 155 GLU cc_start: 0.7517 (pt0) cc_final: 0.7234 (pt0) REVERT: A 184 LEU cc_start: 0.8238 (mt) cc_final: 0.7891 (mt) REVERT: A 199 SER cc_start: 0.8598 (t) cc_final: 0.8362 (t) REVERT: A 240 ILE cc_start: 0.8767 (mt) cc_final: 0.8515 (mm) REVERT: A 253 LYS cc_start: 0.8067 (pttt) cc_final: 0.7591 (pttt) REVERT: A 368 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7480 (mt-10) REVERT: A 523 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7453 (mm-30) REVERT: A 559 ARG cc_start: 0.7739 (tpp80) cc_final: 0.7058 (tpp80) REVERT: A 562 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6977 (mt-10) REVERT: A 565 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7821 (mm-30) REVERT: A 593 LYS cc_start: 0.7638 (tptm) cc_final: 0.7204 (tptm) REVERT: A 597 GLU cc_start: 0.7724 (tm-30) cc_final: 0.6840 (tm-30) REVERT: A 615 LEU cc_start: 0.8034 (mt) cc_final: 0.7725 (tp) REVERT: A 626 GLU cc_start: 0.7821 (tp30) cc_final: 0.7609 (tp30) REVERT: A 656 GLN cc_start: 0.7401 (tm-30) cc_final: 0.6712 (tm-30) REVERT: A 657 GLN cc_start: 0.7587 (mp10) cc_final: 0.7251 (mp10) REVERT: A 659 GLU cc_start: 0.7528 (mt-10) cc_final: 0.6421 (mp0) REVERT: A 663 GLU cc_start: 0.7595 (pt0) cc_final: 0.7137 (pt0) REVERT: A 745 ASP cc_start: 0.8070 (t70) cc_final: 0.7859 (t0) REVERT: A 777 ILE cc_start: 0.7462 (tp) cc_final: 0.7237 (tt) REVERT: A 859 ASP cc_start: 0.6323 (m-30) cc_final: 0.5652 (m-30) REVERT: A 911 ARG cc_start: 0.7505 (tpp-160) cc_final: 0.7155 (mmt-90) REVERT: A 917 LYS cc_start: 0.7522 (mmtt) cc_final: 0.7311 (mttt) REVERT: A 956 ASP cc_start: 0.6486 (p0) cc_final: 0.6155 (p0) REVERT: A 1017 LYS cc_start: 0.8088 (ttmm) cc_final: 0.7800 (ttmm) REVERT: A 1020 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6924 (tpp) REVERT: A 1021 GLU cc_start: 0.7797 (tp30) cc_final: 0.7107 (tp30) REVERT: A 1062 TYR cc_start: 0.7538 (p90) cc_final: 0.6958 (p90) REVERT: A 1072 GLU cc_start: 0.8187 (tt0) cc_final: 0.7571 (tt0) REVERT: A 1082 LYS cc_start: 0.7730 (mtpt) cc_final: 0.7311 (mtpt) REVERT: A 1089 LYS cc_start: 0.8478 (ttmm) cc_final: 0.8102 (ttmm) REVERT: A 1093 GLN cc_start: 0.8437 (tp40) cc_final: 0.8165 (tp40) REVERT: A 1113 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7850 (tp) REVERT: A 1116 LYS cc_start: 0.8669 (ttpt) cc_final: 0.8307 (ttmm) REVERT: A 1120 ILE cc_start: 0.9129 (mm) cc_final: 0.8712 (mm) REVERT: A 1126 GLN cc_start: 0.6864 (mm-40) cc_final: 0.6338 (mm-40) REVERT: A 1128 GLU cc_start: 0.7931 (tp30) cc_final: 0.7567 (tp30) REVERT: A 1132 LYS cc_start: 0.8355 (mmmm) cc_final: 0.7810 (mmmm) REVERT: A 1150 PHE cc_start: 0.8710 (m-80) cc_final: 0.8364 (m-80) REVERT: A 1152 THR cc_start: 0.8583 (t) cc_final: 0.8141 (p) REVERT: A 1157 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7169 (mt-10) REVERT: A 1187 LYS cc_start: 0.8539 (mmmm) cc_final: 0.8247 (mmmm) REVERT: A 1200 GLU cc_start: 0.7788 (tp30) cc_final: 0.7433 (tp30) REVERT: A 1219 MET cc_start: 0.8189 (mmm) cc_final: 0.7939 (mmm) REVERT: A 1243 LYS cc_start: 0.7891 (mmmt) cc_final: 0.7624 (mmmt) REVERT: A 1258 TYR cc_start: 0.7396 (m-80) cc_final: 0.7103 (m-80) REVERT: A 1259 LYS cc_start: 0.8349 (mppt) cc_final: 0.7517 (mppt) REVERT: A 1263 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7419 (mt-10) REVERT: A 1267 LYS cc_start: 0.8524 (mttm) cc_final: 0.8188 (mtpp) REVERT: A 1336 GLU cc_start: 0.8103 (tp30) cc_final: 0.7718 (tp30) REVERT: A 1366 VAL cc_start: 0.8677 (p) cc_final: 0.8436 (m) REVERT: A 1383 LYS cc_start: 0.8322 (mmtm) cc_final: 0.8086 (mmtm) REVERT: A 1400 LYS cc_start: 0.8768 (mmtm) cc_final: 0.8424 (mmtm) REVERT: A 1409 LYS cc_start: 0.8072 (mmmt) cc_final: 0.7864 (pttm) REVERT: B 18 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7171 (mm-30) REVERT: B 81 LEU cc_start: 0.7957 (mt) cc_final: 0.7752 (mt) REVERT: B 90 ASP cc_start: 0.7848 (t0) cc_final: 0.7260 (t0) REVERT: B 91 ASN cc_start: 0.8097 (m110) cc_final: 0.6857 (m-40) REVERT: B 110 ILE cc_start: 0.8628 (pt) cc_final: 0.7226 (mm) REVERT: B 124 LYS cc_start: 0.8362 (ttmt) cc_final: 0.7992 (ttpt) REVERT: B 132 ASN cc_start: 0.8219 (p0) cc_final: 0.7790 (p0) REVERT: B 154 PHE cc_start: 0.8053 (p90) cc_final: 0.7633 (p90) REVERT: B 155 GLU cc_start: 0.7499 (pt0) cc_final: 0.7191 (pm20) REVERT: B 191 TYR cc_start: 0.8149 (t80) cc_final: 0.7912 (t80) REVERT: B 205 ARG cc_start: 0.7844 (tpp80) cc_final: 0.7569 (mmm-85) REVERT: B 333 ARG cc_start: 0.7696 (mtt90) cc_final: 0.7276 (mtt90) REVERT: B 346 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7190 (mm-30) REVERT: B 361 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7501 (mt-10) REVERT: B 485 ASP cc_start: 0.6739 (m-30) cc_final: 0.6296 (m-30) REVERT: B 515 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7101 (tm-30) REVERT: B 547 GLN cc_start: 0.7230 (tp-100) cc_final: 0.6862 (tp-100) REVERT: B 580 MET cc_start: 0.7865 (tpp) cc_final: 0.7172 (tpp) REVERT: B 594 ASP cc_start: 0.7887 (m-30) cc_final: 0.7537 (m-30) REVERT: B 597 GLU cc_start: 0.7688 (tp30) cc_final: 0.7213 (tp30) REVERT: B 607 ASN cc_start: 0.7458 (t0) cc_final: 0.6839 (t0) REVERT: B 649 PHE cc_start: 0.7787 (p90) cc_final: 0.7476 (p90) REVERT: B 656 GLN cc_start: 0.7753 (mp10) cc_final: 0.7292 (mp10) REVERT: B 692 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7475 (mp-120) REVERT: B 707 MET cc_start: 0.7934 (tpp) cc_final: 0.7191 (tpp) REVERT: B 739 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.6544 (m-10) REVERT: B 803 LEU cc_start: 0.8213 (mt) cc_final: 0.7821 (mt) REVERT: B 807 ARG cc_start: 0.7873 (ttm170) cc_final: 0.7397 (ttp-170) REVERT: B 851 PHE cc_start: 0.6928 (m-80) cc_final: 0.6711 (m-80) REVERT: B 861 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8001 (mm) REVERT: B 919 GLN cc_start: 0.7449 (mt0) cc_final: 0.7206 (mt0) REVERT: B 1014 LYS cc_start: 0.8764 (pttp) cc_final: 0.8466 (pttp) REVERT: B 1020 MET cc_start: 0.6473 (mmt) cc_final: 0.6234 (mmt) REVERT: B 1063 PHE cc_start: 0.8028 (t80) cc_final: 0.7757 (t80) REVERT: B 1066 GLU cc_start: 0.7810 (tt0) cc_final: 0.7417 (mm-30) REVERT: B 1096 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.6384 (m-10) REVERT: B 1106 LYS cc_start: 0.7433 (ttmt) cc_final: 0.7175 (ttmm) REVERT: B 1132 LYS cc_start: 0.8053 (mttt) cc_final: 0.7628 (mttm) REVERT: B 1148 LYS cc_start: 0.8648 (mmmm) cc_final: 0.8417 (mmmm) REVERT: B 1154 GLN cc_start: 0.8472 (tt0) cc_final: 0.8171 (tt0) REVERT: B 1156 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6820 (mmtp) REVERT: B 1157 GLU cc_start: 0.7398 (tp30) cc_final: 0.6609 (tp30) REVERT: B 1200 GLU cc_start: 0.8065 (pt0) cc_final: 0.7678 (pt0) REVERT: B 1201 TYR cc_start: 0.8270 (t80) cc_final: 0.7682 (t80) REVERT: B 1204 GLU cc_start: 0.7544 (pp20) cc_final: 0.7284 (pp20) REVERT: B 1219 MET cc_start: 0.7447 (mmp) cc_final: 0.6994 (mmp) REVERT: B 1231 MET cc_start: 0.6806 (mpp) cc_final: 0.6583 (mpp) REVERT: B 1263 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7742 (mt-10) REVERT: B 1266 LEU cc_start: 0.7865 (mt) cc_final: 0.7571 (mt) REVERT: B 1383 LYS cc_start: 0.8841 (pttm) cc_final: 0.8430 (pttm) REVERT: B 1399 LYS cc_start: 0.8708 (pptt) cc_final: 0.8365 (pptt) outliers start: 96 outliers final: 66 residues processed: 716 average time/residue: 0.1437 time to fit residues: 155.8559 Evaluate side-chains 724 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 652 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 844 CYS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 560 LYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 1028 ILE Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1156 LYS Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1290 ILE Chi-restraints excluded: chain B residue 1325 THR Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1367 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 16 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 221 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN B 713 HIS ** B1178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1250 HIS ** B1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.117405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.100932 restraints weight = 48438.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.104196 restraints weight = 25013.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.106332 restraints weight = 15320.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.107756 restraints weight = 10495.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.108747 restraints weight = 7856.113| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20796 Z= 0.193 Angle : 0.704 12.302 28095 Z= 0.366 Chirality : 0.043 0.178 3318 Planarity : 0.005 0.063 3545 Dihedral : 5.329 56.906 2693 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.68 % Favored : 90.16 % Rotamer: Outliers : 3.89 % Allowed : 21.69 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.17), residues: 2521 helix: 1.07 (0.12), residues: 1761 sheet: -2.99 (0.99), residues: 20 loop : -2.73 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 174 TYR 0.030 0.002 TYR B 138 PHE 0.033 0.002 PHE A1288 TRP 0.012 0.002 TRP B 773 HIS 0.010 0.001 HIS A 617 Details of bonding type rmsd covalent geometry : bond 0.00405 (20796) covalent geometry : angle 0.70396 (28095) hydrogen bonds : bond 0.04875 ( 1287) hydrogen bonds : angle 4.97046 ( 3840) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 677 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8425 (ttmt) cc_final: 0.8142 (ttmt) REVERT: A 78 GLN cc_start: 0.7852 (tp40) cc_final: 0.7598 (tp40) REVERT: A 91 ASN cc_start: 0.7676 (t0) cc_final: 0.7277 (t0) REVERT: A 154 PHE cc_start: 0.8403 (p90) cc_final: 0.8184 (p90) REVERT: A 155 GLU cc_start: 0.7505 (pt0) cc_final: 0.7234 (pt0) REVERT: A 184 LEU cc_start: 0.8255 (mt) cc_final: 0.7901 (mt) REVERT: A 199 SER cc_start: 0.8577 (t) cc_final: 0.8329 (t) REVERT: A 240 ILE cc_start: 0.8760 (mt) cc_final: 0.8503 (mm) REVERT: A 253 LYS cc_start: 0.8016 (pttt) cc_final: 0.7561 (pttt) REVERT: A 368 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7518 (mt-10) REVERT: A 460 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7262 (tm-30) REVERT: A 523 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7491 (mm-30) REVERT: A 559 ARG cc_start: 0.7757 (tpp80) cc_final: 0.7019 (tpp80) REVERT: A 562 GLU cc_start: 0.7412 (mt-10) cc_final: 0.6979 (mt-10) REVERT: A 565 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7801 (mm-30) REVERT: A 593 LYS cc_start: 0.7658 (tptm) cc_final: 0.7222 (tptm) REVERT: A 597 GLU cc_start: 0.7764 (tm-30) cc_final: 0.6909 (tm-30) REVERT: A 615 LEU cc_start: 0.8360 (mt) cc_final: 0.8116 (tp) REVERT: A 626 GLU cc_start: 0.7840 (tp30) cc_final: 0.7623 (tp30) REVERT: A 656 GLN cc_start: 0.7485 (tm-30) cc_final: 0.6776 (tm-30) REVERT: A 659 GLU cc_start: 0.7563 (mt-10) cc_final: 0.6463 (mp0) REVERT: A 663 GLU cc_start: 0.7621 (pt0) cc_final: 0.7169 (pt0) REVERT: A 725 ASP cc_start: 0.8039 (m-30) cc_final: 0.7827 (m-30) REVERT: A 745 ASP cc_start: 0.8150 (t70) cc_final: 0.7927 (t0) REVERT: A 766 GLU cc_start: 0.7696 (mp0) cc_final: 0.7443 (mp0) REVERT: A 858 ASN cc_start: 0.7420 (p0) cc_final: 0.7123 (p0) REVERT: A 859 ASP cc_start: 0.6358 (m-30) cc_final: 0.5674 (m-30) REVERT: A 908 ASP cc_start: 0.7467 (p0) cc_final: 0.7082 (p0) REVERT: A 911 ARG cc_start: 0.7537 (tpp-160) cc_final: 0.7213 (mmt-90) REVERT: A 956 ASP cc_start: 0.6376 (p0) cc_final: 0.6050 (p0) REVERT: A 978 LYS cc_start: 0.8319 (tptt) cc_final: 0.8107 (tptt) REVERT: A 1017 LYS cc_start: 0.8109 (ttmm) cc_final: 0.7836 (ttmm) REVERT: A 1020 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6953 (tpp) REVERT: A 1021 GLU cc_start: 0.7812 (tp30) cc_final: 0.7143 (tp30) REVERT: A 1062 TYR cc_start: 0.7540 (p90) cc_final: 0.6953 (p90) REVERT: A 1072 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: A 1082 LYS cc_start: 0.7703 (mtpt) cc_final: 0.7436 (mtpt) REVERT: A 1089 LYS cc_start: 0.8475 (ttmm) cc_final: 0.8080 (ttmm) REVERT: A 1093 GLN cc_start: 0.8431 (tp40) cc_final: 0.8149 (tp40) REVERT: A 1113 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7954 (tp) REVERT: A 1116 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8332 (ttmm) REVERT: A 1120 ILE cc_start: 0.9143 (mm) cc_final: 0.8722 (mm) REVERT: A 1122 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8668 (mm) REVERT: A 1126 GLN cc_start: 0.6877 (mm-40) cc_final: 0.6341 (mm-40) REVERT: A 1128 GLU cc_start: 0.7962 (tp30) cc_final: 0.7606 (tp30) REVERT: A 1132 LYS cc_start: 0.8391 (mmmm) cc_final: 0.7846 (mmmm) REVERT: A 1152 THR cc_start: 0.8604 (t) cc_final: 0.8177 (p) REVERT: A 1157 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7226 (mt-10) REVERT: A 1175 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8078 (mm) REVERT: A 1187 LYS cc_start: 0.8559 (mmmm) cc_final: 0.8279 (mmmm) REVERT: A 1200 GLU cc_start: 0.7805 (tp30) cc_final: 0.7460 (tp30) REVERT: A 1219 MET cc_start: 0.8195 (mmm) cc_final: 0.7896 (mmm) REVERT: A 1227 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7248 (mt-10) REVERT: A 1242 TYR cc_start: 0.7485 (m-10) cc_final: 0.7278 (m-10) REVERT: A 1259 LYS cc_start: 0.8387 (mppt) cc_final: 0.7573 (mppt) REVERT: A 1263 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7453 (mt-10) REVERT: A 1267 LYS cc_start: 0.8526 (mttm) cc_final: 0.8199 (mtpp) REVERT: A 1336 GLU cc_start: 0.8104 (tp30) cc_final: 0.7764 (tp30) REVERT: A 1366 VAL cc_start: 0.8715 (p) cc_final: 0.8484 (m) REVERT: A 1383 LYS cc_start: 0.8376 (mmtm) cc_final: 0.8121 (mmtm) REVERT: A 1399 LYS cc_start: 0.8600 (ptpp) cc_final: 0.8341 (pttm) REVERT: B 91 ASN cc_start: 0.8111 (m110) cc_final: 0.7856 (m-40) REVERT: B 110 ILE cc_start: 0.8659 (pt) cc_final: 0.7278 (mm) REVERT: B 124 LYS cc_start: 0.8388 (ttmt) cc_final: 0.8093 (ttpt) REVERT: B 132 ASN cc_start: 0.8226 (p0) cc_final: 0.7796 (p0) REVERT: B 154 PHE cc_start: 0.8055 (p90) cc_final: 0.7565 (p90) REVERT: B 155 GLU cc_start: 0.7489 (pt0) cc_final: 0.7142 (pm20) REVERT: B 205 ARG cc_start: 0.7848 (tpp80) cc_final: 0.7554 (mmm-85) REVERT: B 228 LYS cc_start: 0.8301 (ttmm) cc_final: 0.8028 (tttp) REVERT: B 333 ARG cc_start: 0.7716 (mtt90) cc_final: 0.7296 (mtt90) REVERT: B 346 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7200 (mm-30) REVERT: B 361 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7511 (mt-10) REVERT: B 428 GLU cc_start: 0.7561 (tt0) cc_final: 0.6943 (tp30) REVERT: B 433 ARG cc_start: 0.8377 (tpp80) cc_final: 0.8017 (mmm160) REVERT: B 485 ASP cc_start: 0.6797 (m-30) cc_final: 0.6313 (m-30) REVERT: B 515 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7176 (tm-30) REVERT: B 547 GLN cc_start: 0.7254 (tp-100) cc_final: 0.6867 (tp-100) REVERT: B 580 MET cc_start: 0.7856 (tpp) cc_final: 0.7158 (tpp) REVERT: B 594 ASP cc_start: 0.7907 (m-30) cc_final: 0.7541 (m-30) REVERT: B 597 GLU cc_start: 0.7708 (tp30) cc_final: 0.7215 (tp30) REVERT: B 607 ASN cc_start: 0.7527 (t0) cc_final: 0.6943 (t0) REVERT: B 649 PHE cc_start: 0.7786 (p90) cc_final: 0.7461 (p90) REVERT: B 692 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7562 (mp10) REVERT: B 707 MET cc_start: 0.7890 (tpp) cc_final: 0.7153 (tpp) REVERT: B 739 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.6536 (m-10) REVERT: B 803 LEU cc_start: 0.8220 (mt) cc_final: 0.7801 (mt) REVERT: B 807 ARG cc_start: 0.7880 (ttm170) cc_final: 0.7165 (ttp-170) REVERT: B 851 PHE cc_start: 0.6963 (m-80) cc_final: 0.6707 (m-80) REVERT: B 861 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8039 (mm) REVERT: B 1063 PHE cc_start: 0.8019 (t80) cc_final: 0.7802 (t80) REVERT: B 1066 GLU cc_start: 0.7806 (tt0) cc_final: 0.7437 (mm-30) REVERT: B 1072 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7260 (tp30) REVERT: B 1096 PHE cc_start: 0.6688 (OUTLIER) cc_final: 0.6404 (m-10) REVERT: B 1106 LYS cc_start: 0.7449 (ttmt) cc_final: 0.6256 (ttmm) REVERT: B 1110 ARG cc_start: 0.7794 (ptp90) cc_final: 0.7534 (ptp-170) REVERT: B 1132 LYS cc_start: 0.8083 (mttt) cc_final: 0.7598 (mttm) REVERT: B 1154 GLN cc_start: 0.8550 (tt0) cc_final: 0.8158 (tt0) REVERT: B 1157 GLU cc_start: 0.7408 (tp30) cc_final: 0.6589 (tp30) REVERT: B 1201 TYR cc_start: 0.8285 (t80) cc_final: 0.7689 (t80) REVERT: B 1204 GLU cc_start: 0.7564 (pp20) cc_final: 0.7304 (pp20) REVERT: B 1219 MET cc_start: 0.7544 (mmp) cc_final: 0.7033 (mmp) REVERT: B 1239 GLU cc_start: 0.6751 (tm-30) cc_final: 0.6526 (tm-30) REVERT: B 1263 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7959 (mt-10) REVERT: B 1266 LEU cc_start: 0.7863 (mt) cc_final: 0.7578 (mt) REVERT: B 1383 LYS cc_start: 0.8845 (pttm) cc_final: 0.8431 (pttm) REVERT: B 1399 LYS cc_start: 0.8706 (pptt) cc_final: 0.8364 (pptt) REVERT: B 1412 GLU cc_start: 0.6136 (OUTLIER) cc_final: 0.4144 (mm-30) outliers start: 92 outliers final: 61 residues processed: 717 average time/residue: 0.1568 time to fit residues: 170.5625 Evaluate side-chains 727 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 656 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 844 CYS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 560 LYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 1028 ILE Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1250 HIS Chi-restraints excluded: chain B residue 1290 ILE Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1325 THR Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1367 TYR Chi-restraints excluded: chain B residue 1412 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 13 optimal weight: 2.9990 chunk 226 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 243 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 133 optimal weight: 0.4980 chunk 4 optimal weight: 0.8980 chunk 176 optimal weight: 0.0980 chunk 43 optimal weight: 0.9990 chunk 167 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN ** B1178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.118386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.101795 restraints weight = 48441.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.105080 restraints weight = 25106.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.107209 restraints weight = 15386.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.108677 restraints weight = 10572.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.109595 restraints weight = 7893.311| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20796 Z= 0.156 Angle : 0.720 11.898 28095 Z= 0.367 Chirality : 0.042 0.193 3318 Planarity : 0.005 0.064 3545 Dihedral : 5.316 58.641 2693 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.28 % Favored : 90.60 % Rotamer: Outliers : 4.06 % Allowed : 22.24 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.17), residues: 2521 helix: 1.11 (0.12), residues: 1761 sheet: -3.26 (0.94), residues: 22 loop : -2.83 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 174 TYR 0.030 0.001 TYR B1258 PHE 0.038 0.002 PHE A1288 TRP 0.012 0.002 TRP B 470 HIS 0.012 0.001 HIS A 617 Details of bonding type rmsd covalent geometry : bond 0.00337 (20796) covalent geometry : angle 0.71974 (28095) hydrogen bonds : bond 0.04560 ( 1287) hydrogen bonds : angle 4.88997 ( 3840) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 668 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8379 (ttmt) cc_final: 0.8130 (ttmt) REVERT: A 78 GLN cc_start: 0.7801 (tp40) cc_final: 0.7552 (tp40) REVERT: A 91 ASN cc_start: 0.7643 (t0) cc_final: 0.7237 (t0) REVERT: A 120 ASP cc_start: 0.7613 (t70) cc_final: 0.7165 (m-30) REVERT: A 154 PHE cc_start: 0.8384 (p90) cc_final: 0.8181 (p90) REVERT: A 155 GLU cc_start: 0.7520 (pt0) cc_final: 0.7236 (pt0) REVERT: A 184 LEU cc_start: 0.8249 (mt) cc_final: 0.7891 (mt) REVERT: A 199 SER cc_start: 0.8598 (t) cc_final: 0.8344 (t) REVERT: A 240 ILE cc_start: 0.8747 (mt) cc_final: 0.8510 (mm) REVERT: A 253 LYS cc_start: 0.8042 (pttt) cc_final: 0.7572 (pttt) REVERT: A 368 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7503 (mt-10) REVERT: A 459 LYS cc_start: 0.8179 (mttp) cc_final: 0.7867 (mtmm) REVERT: A 460 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7208 (tm-30) REVERT: A 523 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7438 (mm-30) REVERT: A 559 ARG cc_start: 0.7715 (tpp80) cc_final: 0.7029 (tpp80) REVERT: A 562 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6944 (mt-10) REVERT: A 565 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7767 (mm-30) REVERT: A 593 LYS cc_start: 0.7587 (tptm) cc_final: 0.7153 (tptm) REVERT: A 597 GLU cc_start: 0.7715 (tm-30) cc_final: 0.6841 (tm-30) REVERT: A 606 MET cc_start: 0.7452 (mmm) cc_final: 0.7236 (tpt) REVERT: A 615 LEU cc_start: 0.8196 (mt) cc_final: 0.7949 (tp) REVERT: A 626 GLU cc_start: 0.7829 (tp30) cc_final: 0.7591 (tp30) REVERT: A 656 GLN cc_start: 0.7542 (tm-30) cc_final: 0.6584 (tm-30) REVERT: A 657 GLN cc_start: 0.7793 (mp10) cc_final: 0.7159 (mp10) REVERT: A 659 GLU cc_start: 0.7517 (mt-10) cc_final: 0.6429 (mp0) REVERT: A 663 GLU cc_start: 0.7606 (pt0) cc_final: 0.7144 (pt0) REVERT: A 745 ASP cc_start: 0.8113 (t70) cc_final: 0.7901 (t0) REVERT: A 765 ASN cc_start: 0.7102 (t0) cc_final: 0.6735 (t0) REVERT: A 766 GLU cc_start: 0.7473 (mp0) cc_final: 0.7206 (mp0) REVERT: A 819 SER cc_start: 0.8291 (m) cc_final: 0.7961 (p) REVERT: A 859 ASP cc_start: 0.6305 (m-30) cc_final: 0.5676 (m-30) REVERT: A 911 ARG cc_start: 0.7530 (tpp-160) cc_final: 0.7193 (mmt-90) REVERT: A 917 LYS cc_start: 0.7570 (mmtt) cc_final: 0.6992 (mttp) REVERT: A 956 ASP cc_start: 0.6408 (p0) cc_final: 0.6174 (p0) REVERT: A 978 LYS cc_start: 0.8301 (tptt) cc_final: 0.8085 (tptt) REVERT: A 1017 LYS cc_start: 0.8103 (ttmm) cc_final: 0.7836 (ttmm) REVERT: A 1020 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.6937 (tpp) REVERT: A 1021 GLU cc_start: 0.7824 (tp30) cc_final: 0.7171 (tp30) REVERT: A 1072 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7477 (tt0) REVERT: A 1082 LYS cc_start: 0.7671 (mtpt) cc_final: 0.7227 (mtpt) REVERT: A 1089 LYS cc_start: 0.8428 (ttmm) cc_final: 0.8045 (ttmm) REVERT: A 1093 GLN cc_start: 0.8422 (tp40) cc_final: 0.8154 (tp40) REVERT: A 1113 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7984 (tp) REVERT: A 1116 LYS cc_start: 0.8654 (ttpt) cc_final: 0.8309 (ttmm) REVERT: A 1120 ILE cc_start: 0.9137 (mm) cc_final: 0.8718 (mm) REVERT: A 1122 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8641 (mm) REVERT: A 1126 GLN cc_start: 0.6875 (mm-40) cc_final: 0.6340 (mm-40) REVERT: A 1128 GLU cc_start: 0.7974 (tp30) cc_final: 0.7630 (tp30) REVERT: A 1132 LYS cc_start: 0.8353 (mmmm) cc_final: 0.7811 (mmmm) REVERT: A 1152 THR cc_start: 0.8595 (t) cc_final: 0.8152 (p) REVERT: A 1157 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7166 (mt-10) REVERT: A 1187 LYS cc_start: 0.8558 (mmmm) cc_final: 0.8249 (mmmm) REVERT: A 1191 MET cc_start: 0.6965 (tpt) cc_final: 0.6606 (tpt) REVERT: A 1200 GLU cc_start: 0.7806 (tp30) cc_final: 0.7451 (tp30) REVERT: A 1219 MET cc_start: 0.8207 (mmm) cc_final: 0.7844 (mmm) REVERT: A 1243 LYS cc_start: 0.7927 (mmmt) cc_final: 0.7595 (mmmt) REVERT: A 1256 ASN cc_start: 0.7005 (p0) cc_final: 0.6513 (p0) REVERT: A 1259 LYS cc_start: 0.8363 (mppt) cc_final: 0.7398 (mppt) REVERT: A 1263 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7430 (mt-10) REVERT: A 1267 LYS cc_start: 0.8515 (mttm) cc_final: 0.8188 (mtpp) REVERT: A 1336 GLU cc_start: 0.8114 (tp30) cc_final: 0.7778 (tp30) REVERT: A 1365 ASN cc_start: 0.8366 (m-40) cc_final: 0.7816 (p0) REVERT: A 1366 VAL cc_start: 0.8699 (p) cc_final: 0.8260 (m) REVERT: A 1383 LYS cc_start: 0.8339 (mmtm) cc_final: 0.8100 (mmtm) REVERT: A 1385 LEU cc_start: 0.8291 (mm) cc_final: 0.7969 (mm) REVERT: A 1399 LYS cc_start: 0.8584 (ptpp) cc_final: 0.8300 (pttm) REVERT: B 18 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7136 (mm-30) REVERT: B 90 ASP cc_start: 0.7858 (t0) cc_final: 0.7328 (t0) REVERT: B 91 ASN cc_start: 0.8109 (m110) cc_final: 0.6855 (m-40) REVERT: B 110 ILE cc_start: 0.8635 (pt) cc_final: 0.7221 (mm) REVERT: B 124 LYS cc_start: 0.8370 (ttmt) cc_final: 0.8016 (ttpt) REVERT: B 132 ASN cc_start: 0.8205 (p0) cc_final: 0.7785 (p0) REVERT: B 154 PHE cc_start: 0.8031 (p90) cc_final: 0.7540 (p90) REVERT: B 155 GLU cc_start: 0.7470 (pt0) cc_final: 0.7136 (pm20) REVERT: B 205 ARG cc_start: 0.7853 (tpp80) cc_final: 0.7569 (mmm-85) REVERT: B 228 LYS cc_start: 0.8318 (ttmm) cc_final: 0.8048 (tttp) REVERT: B 333 ARG cc_start: 0.7725 (mtt90) cc_final: 0.7313 (mtt90) REVERT: B 346 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7204 (mm-30) REVERT: B 361 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7529 (mt-10) REVERT: B 485 ASP cc_start: 0.6766 (m-30) cc_final: 0.6255 (m-30) REVERT: B 503 LYS cc_start: 0.8623 (tttt) cc_final: 0.8395 (tttt) REVERT: B 515 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7101 (tm-30) REVERT: B 547 GLN cc_start: 0.7195 (tp-100) cc_final: 0.6841 (tp-100) REVERT: B 580 MET cc_start: 0.7846 (tpp) cc_final: 0.7141 (tpp) REVERT: B 594 ASP cc_start: 0.7893 (m-30) cc_final: 0.7540 (m-30) REVERT: B 597 GLU cc_start: 0.7684 (tp30) cc_final: 0.7196 (tp30) REVERT: B 607 ASN cc_start: 0.7505 (t0) cc_final: 0.6936 (t0) REVERT: B 640 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7703 (mm-30) REVERT: B 692 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7490 (mp10) REVERT: B 707 MET cc_start: 0.7966 (tpp) cc_final: 0.7186 (tpp) REVERT: B 739 PHE cc_start: 0.7447 (OUTLIER) cc_final: 0.6557 (m-10) REVERT: B 807 ARG cc_start: 0.7856 (ttm170) cc_final: 0.7089 (ttp-170) REVERT: B 851 PHE cc_start: 0.6924 (m-80) cc_final: 0.6685 (m-80) REVERT: B 861 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8033 (mm) REVERT: B 1020 MET cc_start: 0.6433 (mmt) cc_final: 0.6173 (mmt) REVERT: B 1063 PHE cc_start: 0.8043 (t80) cc_final: 0.7765 (t80) REVERT: B 1066 GLU cc_start: 0.7779 (tt0) cc_final: 0.7419 (mm-30) REVERT: B 1072 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7282 (tp30) REVERT: B 1096 PHE cc_start: 0.6621 (OUTLIER) cc_final: 0.6339 (m-10) REVERT: B 1106 LYS cc_start: 0.7454 (ttmt) cc_final: 0.6207 (ttmm) REVERT: B 1110 ARG cc_start: 0.7753 (ptp90) cc_final: 0.7490 (ptp-170) REVERT: B 1112 MET cc_start: 0.7800 (mtm) cc_final: 0.7592 (mtp) REVERT: B 1126 GLN cc_start: 0.7313 (tp40) cc_final: 0.6843 (tp40) REVERT: B 1132 LYS cc_start: 0.8025 (mttt) cc_final: 0.7547 (mttm) REVERT: B 1154 GLN cc_start: 0.8514 (tt0) cc_final: 0.8233 (tt0) REVERT: B 1157 GLU cc_start: 0.7374 (tp30) cc_final: 0.6570 (tp30) REVERT: B 1200 GLU cc_start: 0.8036 (pt0) cc_final: 0.7646 (pt0) REVERT: B 1201 TYR cc_start: 0.8301 (t80) cc_final: 0.7588 (t80) REVERT: B 1204 GLU cc_start: 0.7528 (pp20) cc_final: 0.7209 (pp20) REVERT: B 1219 MET cc_start: 0.7500 (mmp) cc_final: 0.6978 (mmp) REVERT: B 1231 MET cc_start: 0.6839 (mpp) cc_final: 0.6631 (mpp) REVERT: B 1266 LEU cc_start: 0.7826 (mt) cc_final: 0.7541 (mt) REVERT: B 1383 LYS cc_start: 0.8820 (pttm) cc_final: 0.8397 (pttm) REVERT: B 1399 LYS cc_start: 0.8696 (pptt) cc_final: 0.8357 (pptt) REVERT: B 1412 GLU cc_start: 0.5998 (OUTLIER) cc_final: 0.4168 (mm-30) outliers start: 96 outliers final: 73 residues processed: 708 average time/residue: 0.1438 time to fit residues: 154.0452 Evaluate side-chains 733 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 651 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 844 CYS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1297 GLN Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 560 LYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 1028 ILE Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1290 ILE Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1313 LEU Chi-restraints excluded: chain B residue 1320 LYS Chi-restraints excluded: chain B residue 1325 THR Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1367 TYR Chi-restraints excluded: chain B residue 1412 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 48 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 210 optimal weight: 0.2980 chunk 193 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1344 ASN ** 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 = 0.3739 r_free = 0.3739 target = 0.117712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.101233 restraints weight = 48490.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.104479 restraints weight = 25105.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.106637 restraints weight = 15395.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.108057 restraints weight = 10559.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.109054 restraints weight = 7919.022| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20796 Z= 0.178 Angle : 0.732 15.949 28095 Z= 0.376 Chirality : 0.043 0.211 3318 Planarity : 0.005 0.065 3545 Dihedral : 5.335 59.840 2693 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.52 % Favored : 90.36 % Rotamer: Outliers : 4.40 % Allowed : 22.75 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.17), residues: 2521 helix: 1.05 (0.12), residues: 1757 sheet: -3.30 (0.93), residues: 22 loop : -2.78 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 174 TYR 0.032 0.002 TYR B1258 PHE 0.039 0.002 PHE A1288 TRP 0.013 0.002 TRP B 470 HIS 0.013 0.001 HIS A 617 Details of bonding type rmsd covalent geometry : bond 0.00381 (20796) covalent geometry : angle 0.73238 (28095) hydrogen bonds : bond 0.04716 ( 1287) hydrogen bonds : angle 4.93753 ( 3840) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 667 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8390 (ttmt) cc_final: 0.8139 (ttmt) REVERT: A 78 GLN cc_start: 0.7818 (tp40) cc_final: 0.7559 (tp40) REVERT: A 91 ASN cc_start: 0.7663 (t0) cc_final: 0.7260 (t0) REVERT: A 154 PHE cc_start: 0.8395 (p90) cc_final: 0.8184 (p90) REVERT: A 155 GLU cc_start: 0.7520 (pt0) cc_final: 0.7243 (pt0) REVERT: A 199 SER cc_start: 0.8588 (t) cc_final: 0.8326 (t) REVERT: A 240 ILE cc_start: 0.8747 (mt) cc_final: 0.8511 (mm) REVERT: A 253 LYS cc_start: 0.8010 (pttt) cc_final: 0.7546 (pttt) REVERT: A 368 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7528 (mt-10) REVERT: A 459 LYS cc_start: 0.8209 (mttp) cc_final: 0.7898 (mtmm) REVERT: A 460 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7229 (tm-30) REVERT: A 523 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7451 (mm-30) REVERT: A 559 ARG cc_start: 0.7703 (tpp80) cc_final: 0.7006 (tpp80) REVERT: A 562 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6946 (mt-10) REVERT: A 565 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7773 (mm-30) REVERT: A 593 LYS cc_start: 0.7613 (tptm) cc_final: 0.7169 (tptm) REVERT: A 597 GLU cc_start: 0.7744 (tm-30) cc_final: 0.6887 (tm-30) REVERT: A 600 PHE cc_start: 0.8585 (t80) cc_final: 0.8317 (t80) REVERT: A 615 LEU cc_start: 0.8325 (mt) cc_final: 0.8098 (tp) REVERT: A 626 GLU cc_start: 0.7842 (tp30) cc_final: 0.7609 (tp30) REVERT: A 656 GLN cc_start: 0.7564 (tm-30) cc_final: 0.6685 (tm-30) REVERT: A 657 GLN cc_start: 0.7797 (mp10) cc_final: 0.7237 (mp10) REVERT: A 659 GLU cc_start: 0.7517 (mt-10) cc_final: 0.6449 (mp0) REVERT: A 663 GLU cc_start: 0.7622 (pt0) cc_final: 0.7158 (pt0) REVERT: A 745 ASP cc_start: 0.8135 (t70) cc_final: 0.7916 (t0) REVERT: A 765 ASN cc_start: 0.7059 (t0) cc_final: 0.6634 (t0) REVERT: A 766 GLU cc_start: 0.7472 (mp0) cc_final: 0.7077 (mp0) REVERT: A 819 SER cc_start: 0.8304 (m) cc_final: 0.7960 (p) REVERT: A 908 ASP cc_start: 0.7460 (p0) cc_final: 0.7020 (p0) REVERT: A 911 ARG cc_start: 0.7554 (tpp-160) cc_final: 0.7224 (mmt-90) REVERT: A 917 LYS cc_start: 0.7533 (mmtt) cc_final: 0.6961 (mttp) REVERT: A 956 ASP cc_start: 0.6372 (p0) cc_final: 0.5974 (p0) REVERT: A 978 LYS cc_start: 0.8327 (tptt) cc_final: 0.8091 (tptt) REVERT: A 1017 LYS cc_start: 0.8109 (ttmm) cc_final: 0.7839 (ttmm) REVERT: A 1020 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6942 (tpp) REVERT: A 1021 GLU cc_start: 0.7835 (tp30) cc_final: 0.7183 (tp30) REVERT: A 1072 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: A 1082 LYS cc_start: 0.7634 (mtpt) cc_final: 0.7239 (mtpt) REVERT: A 1089 LYS cc_start: 0.8434 (ttmm) cc_final: 0.8051 (ttmm) REVERT: A 1093 GLN cc_start: 0.8438 (tp40) cc_final: 0.8160 (tp40) REVERT: A 1113 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.8014 (tp) REVERT: A 1116 LYS cc_start: 0.8662 (ttpt) cc_final: 0.8312 (ttmm) REVERT: A 1120 ILE cc_start: 0.9107 (mm) cc_final: 0.8687 (mm) REVERT: A 1122 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8681 (mm) REVERT: A 1126 GLN cc_start: 0.6894 (mm-40) cc_final: 0.6339 (mm-40) REVERT: A 1128 GLU cc_start: 0.7970 (tp30) cc_final: 0.7603 (tp30) REVERT: A 1132 LYS cc_start: 0.8366 (mmmm) cc_final: 0.7822 (mmmm) REVERT: A 1152 THR cc_start: 0.8614 (t) cc_final: 0.8158 (p) REVERT: A 1157 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7174 (mt-10) REVERT: A 1187 LYS cc_start: 0.8516 (mmmm) cc_final: 0.8247 (mmmm) REVERT: A 1191 MET cc_start: 0.6993 (tpt) cc_final: 0.6734 (tpt) REVERT: A 1200 GLU cc_start: 0.7826 (tp30) cc_final: 0.7476 (tp30) REVERT: A 1219 MET cc_start: 0.8202 (mmm) cc_final: 0.7839 (mmm) REVERT: A 1227 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7420 (mt-10) REVERT: A 1256 ASN cc_start: 0.7004 (p0) cc_final: 0.6534 (p0) REVERT: A 1259 LYS cc_start: 0.8404 (mppt) cc_final: 0.7509 (mppt) REVERT: A 1263 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7466 (mt-10) REVERT: A 1267 LYS cc_start: 0.8531 (mttm) cc_final: 0.8209 (mtpp) REVERT: A 1336 GLU cc_start: 0.8120 (tp30) cc_final: 0.7778 (tp30) REVERT: A 1366 VAL cc_start: 0.8700 (p) cc_final: 0.8473 (m) REVERT: A 1383 LYS cc_start: 0.8364 (mmtm) cc_final: 0.8115 (mmtm) REVERT: A 1385 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7978 (mm) REVERT: A 1409 LYS cc_start: 0.8095 (mmmt) cc_final: 0.7795 (pttm) REVERT: B 91 ASN cc_start: 0.8110 (m110) cc_final: 0.7842 (m-40) REVERT: B 110 ILE cc_start: 0.8638 (pt) cc_final: 0.7241 (mm) REVERT: B 124 LYS cc_start: 0.8378 (ttmt) cc_final: 0.8082 (ttpt) REVERT: B 132 ASN cc_start: 0.8217 (p0) cc_final: 0.7791 (p0) REVERT: B 154 PHE cc_start: 0.8032 (p90) cc_final: 0.7538 (p90) REVERT: B 155 GLU cc_start: 0.7452 (pt0) cc_final: 0.6999 (pm20) REVERT: B 205 ARG cc_start: 0.7860 (tpp80) cc_final: 0.7601 (mmm-85) REVERT: B 228 LYS cc_start: 0.8330 (ttmm) cc_final: 0.8043 (tttp) REVERT: B 333 ARG cc_start: 0.7722 (mtt90) cc_final: 0.7310 (mtt90) REVERT: B 346 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7221 (mm-30) REVERT: B 361 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7545 (mt-10) REVERT: B 485 ASP cc_start: 0.6805 (m-30) cc_final: 0.6310 (m-30) REVERT: B 499 LYS cc_start: 0.8152 (mmmm) cc_final: 0.7842 (mtpp) REVERT: B 515 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7135 (tm-30) REVERT: B 547 GLN cc_start: 0.7180 (tp-100) cc_final: 0.6836 (tp-100) REVERT: B 580 MET cc_start: 0.7848 (tpp) cc_final: 0.7144 (tpp) REVERT: B 594 ASP cc_start: 0.7909 (m-30) cc_final: 0.7547 (m-30) REVERT: B 597 GLU cc_start: 0.7689 (tp30) cc_final: 0.7220 (tp30) REVERT: B 607 ASN cc_start: 0.7513 (t0) cc_final: 0.6900 (t0) REVERT: B 707 MET cc_start: 0.7985 (tpp) cc_final: 0.7219 (tpp) REVERT: B 739 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.6455 (m-10) REVERT: B 807 ARG cc_start: 0.7869 (ttm170) cc_final: 0.7191 (ttp-170) REVERT: B 851 PHE cc_start: 0.6946 (m-80) cc_final: 0.6717 (m-80) REVERT: B 861 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.7928 (mm) REVERT: B 973 LEU cc_start: 0.8431 (mm) cc_final: 0.8217 (mp) REVERT: B 1014 LYS cc_start: 0.8674 (pttp) cc_final: 0.8009 (pttm) REVERT: B 1017 LYS cc_start: 0.7654 (mtmt) cc_final: 0.7373 (mtmt) REVERT: B 1020 MET cc_start: 0.6456 (mmt) cc_final: 0.6210 (mmt) REVERT: B 1066 GLU cc_start: 0.7802 (tt0) cc_final: 0.7415 (mm-30) REVERT: B 1072 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7250 (tp30) REVERT: B 1096 PHE cc_start: 0.6655 (OUTLIER) cc_final: 0.6367 (m-10) REVERT: B 1106 LYS cc_start: 0.7462 (ttmt) cc_final: 0.6176 (ttmm) REVERT: B 1110 ARG cc_start: 0.7765 (ptp90) cc_final: 0.7541 (ptp-170) REVERT: B 1112 MET cc_start: 0.7780 (mtm) cc_final: 0.7528 (mtp) REVERT: B 1132 LYS cc_start: 0.8031 (mttt) cc_final: 0.7598 (mttm) REVERT: B 1154 GLN cc_start: 0.8538 (tt0) cc_final: 0.8311 (tt0) REVERT: B 1157 GLU cc_start: 0.7389 (tp30) cc_final: 0.6556 (tp30) REVERT: B 1191 MET cc_start: 0.7170 (tpp) cc_final: 0.6610 (tmm) REVERT: B 1200 GLU cc_start: 0.8074 (pt0) cc_final: 0.7655 (pt0) REVERT: B 1201 TYR cc_start: 0.8325 (t80) cc_final: 0.7566 (t80) REVERT: B 1204 GLU cc_start: 0.7558 (pp20) cc_final: 0.7240 (pp20) REVERT: B 1219 MET cc_start: 0.7538 (mmp) cc_final: 0.7016 (mmp) REVERT: B 1231 MET cc_start: 0.6824 (mpp) cc_final: 0.6610 (mpp) REVERT: B 1262 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7654 (pt) REVERT: B 1263 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7815 (mt-10) REVERT: B 1266 LEU cc_start: 0.7844 (mt) cc_final: 0.7563 (mt) REVERT: B 1383 LYS cc_start: 0.8812 (pttm) cc_final: 0.8390 (pttm) REVERT: B 1399 LYS cc_start: 0.8695 (pptt) cc_final: 0.8356 (pptt) REVERT: B 1412 GLU cc_start: 0.6099 (OUTLIER) cc_final: 0.4180 (mm-30) outliers start: 104 outliers final: 80 residues processed: 711 average time/residue: 0.1460 time to fit residues: 158.2969 Evaluate side-chains 747 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 656 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 844 CYS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1297 GLN Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 560 LYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 1028 ILE Chi-restraints excluded: chain B residue 1039 ILE Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1213 LEU Chi-restraints excluded: chain B residue 1262 ILE Chi-restraints excluded: chain B residue 1290 ILE Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1313 LEU Chi-restraints excluded: chain B residue 1320 LYS Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1333 GLU Chi-restraints excluded: chain B residue 1367 TYR Chi-restraints excluded: chain B residue 1412 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 73 optimal weight: 0.8980 chunk 24 optimal weight: 0.0170 chunk 210 optimal weight: 0.0270 chunk 47 optimal weight: 0.8980 chunk 150 optimal weight: 0.6980 chunk 220 optimal weight: 0.5980 chunk 93 optimal weight: 0.3980 chunk 104 optimal weight: 0.3980 chunk 213 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN B 709 ASN B1236 ASN ** B1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.119681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.103142 restraints weight = 48229.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.106443 restraints weight = 25078.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.108611 restraints weight = 15366.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.110084 restraints weight = 10548.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.111080 restraints weight = 7865.191| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20796 Z= 0.147 Angle : 0.735 13.430 28095 Z= 0.374 Chirality : 0.042 0.196 3318 Planarity : 0.005 0.067 3545 Dihedral : 5.262 57.409 2693 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.89 % Favored : 91.00 % Rotamer: Outliers : 3.81 % Allowed : 23.64 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.17), residues: 2521 helix: 1.11 (0.12), residues: 1762 sheet: -3.33 (0.94), residues: 22 loop : -2.72 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 174 TYR 0.029 0.001 TYR B1258 PHE 0.039 0.002 PHE A1288 TRP 0.017 0.002 TRP B 470 HIS 0.012 0.001 HIS A 617 Details of bonding type rmsd covalent geometry : bond 0.00317 (20796) covalent geometry : angle 0.73497 (28095) hydrogen bonds : bond 0.04315 ( 1287) hydrogen bonds : angle 4.80872 ( 3840) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 669 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8384 (ttmt) cc_final: 0.8122 (ttmt) REVERT: A 78 GLN cc_start: 0.7774 (tp40) cc_final: 0.7524 (tp40) REVERT: A 91 ASN cc_start: 0.7638 (t0) cc_final: 0.7215 (t0) REVERT: A 120 ASP cc_start: 0.7595 (t70) cc_final: 0.7121 (m-30) REVERT: A 154 PHE cc_start: 0.8375 (p90) cc_final: 0.8095 (p90) REVERT: A 155 GLU cc_start: 0.7521 (pt0) cc_final: 0.7261 (pt0) REVERT: A 199 SER cc_start: 0.8604 (t) cc_final: 0.8371 (t) REVERT: A 239 GLN cc_start: 0.7802 (mt0) cc_final: 0.7179 (mt0) REVERT: A 240 ILE cc_start: 0.8741 (mt) cc_final: 0.8499 (mm) REVERT: A 253 LYS cc_start: 0.8042 (pttt) cc_final: 0.7572 (pttt) REVERT: A 368 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7502 (mt-10) REVERT: A 459 LYS cc_start: 0.8134 (mttp) cc_final: 0.7818 (mtmm) REVERT: A 460 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7195 (tm-30) REVERT: A 523 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7410 (mm-30) REVERT: A 559 ARG cc_start: 0.7662 (tpp80) cc_final: 0.6952 (tpp80) REVERT: A 562 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6926 (mt-10) REVERT: A 565 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7731 (mm-30) REVERT: A 593 LYS cc_start: 0.7552 (tptm) cc_final: 0.6900 (tptm) REVERT: A 597 GLU cc_start: 0.7671 (tm-30) cc_final: 0.6833 (tm-30) REVERT: A 600 PHE cc_start: 0.8579 (t80) cc_final: 0.8308 (t80) REVERT: A 626 GLU cc_start: 0.7813 (tp30) cc_final: 0.7145 (tp30) REVERT: A 637 ARG cc_start: 0.7852 (ttp-110) cc_final: 0.7635 (ttp80) REVERT: A 656 GLN cc_start: 0.7498 (tm-30) cc_final: 0.6640 (tm-30) REVERT: A 657 GLN cc_start: 0.7755 (mp10) cc_final: 0.7337 (mp10) REVERT: A 659 GLU cc_start: 0.7483 (mt-10) cc_final: 0.6347 (mp0) REVERT: A 663 GLU cc_start: 0.7594 (pt0) cc_final: 0.7130 (pt0) REVERT: A 745 ASP cc_start: 0.8104 (t70) cc_final: 0.7878 (t0) REVERT: A 765 ASN cc_start: 0.6945 (t0) cc_final: 0.6462 (t0) REVERT: A 766 GLU cc_start: 0.7431 (mp0) cc_final: 0.6849 (mp0) REVERT: A 819 SER cc_start: 0.8308 (m) cc_final: 0.7962 (p) REVERT: A 837 MET cc_start: 0.7414 (mmm) cc_final: 0.7015 (mmm) REVERT: A 908 ASP cc_start: 0.7431 (p0) cc_final: 0.6996 (p0) REVERT: A 911 ARG cc_start: 0.7493 (tpp-160) cc_final: 0.7179 (mmt-90) REVERT: A 917 LYS cc_start: 0.7551 (mmtt) cc_final: 0.6987 (mttp) REVERT: A 956 ASP cc_start: 0.6380 (p0) cc_final: 0.6015 (p0) REVERT: A 978 LYS cc_start: 0.8305 (tptt) cc_final: 0.8083 (tptt) REVERT: A 1020 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6907 (tpp) REVERT: A 1021 GLU cc_start: 0.7834 (tp30) cc_final: 0.7175 (tp30) REVERT: A 1027 ASN cc_start: 0.6678 (p0) cc_final: 0.6408 (p0) REVERT: A 1072 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7584 (tt0) REVERT: A 1082 LYS cc_start: 0.7578 (mtpt) cc_final: 0.7212 (mtpt) REVERT: A 1089 LYS cc_start: 0.8377 (ttmm) cc_final: 0.7992 (ttmm) REVERT: A 1093 GLN cc_start: 0.8370 (tp40) cc_final: 0.8087 (tp40) REVERT: A 1113 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7836 (tp) REVERT: A 1116 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8270 (ttmm) REVERT: A 1120 ILE cc_start: 0.9113 (mm) cc_final: 0.8677 (mm) REVERT: A 1122 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8664 (mm) REVERT: A 1126 GLN cc_start: 0.6870 (mm-40) cc_final: 0.6353 (mm-40) REVERT: A 1128 GLU cc_start: 0.7957 (tp30) cc_final: 0.7607 (tp30) REVERT: A 1132 LYS cc_start: 0.8331 (mmmm) cc_final: 0.7776 (mmmm) REVERT: A 1152 THR cc_start: 0.8604 (t) cc_final: 0.8157 (p) REVERT: A 1157 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7176 (mt-10) REVERT: A 1187 LYS cc_start: 0.8502 (mmmm) cc_final: 0.8216 (mmmm) REVERT: A 1191 MET cc_start: 0.6976 (tpt) cc_final: 0.6742 (tpt) REVERT: A 1200 GLU cc_start: 0.7775 (tp30) cc_final: 0.7418 (tp30) REVERT: A 1219 MET cc_start: 0.8218 (mmm) cc_final: 0.7853 (mmm) REVERT: A 1227 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7310 (mt-10) REVERT: A 1243 LYS cc_start: 0.7906 (mmmt) cc_final: 0.7446 (mmmt) REVERT: A 1256 ASN cc_start: 0.6915 (p0) cc_final: 0.6384 (p0) REVERT: A 1259 LYS cc_start: 0.8354 (mppt) cc_final: 0.7403 (mppt) REVERT: A 1263 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7419 (mt-10) REVERT: A 1267 LYS cc_start: 0.8527 (mttm) cc_final: 0.8202 (mtpp) REVERT: A 1336 GLU cc_start: 0.8087 (tp30) cc_final: 0.7746 (tp30) REVERT: A 1366 VAL cc_start: 0.8665 (p) cc_final: 0.8426 (m) REVERT: A 1383 LYS cc_start: 0.8324 (mmtm) cc_final: 0.8077 (mmtm) REVERT: A 1385 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7946 (mm) REVERT: A 1409 LYS cc_start: 0.8101 (mmmt) cc_final: 0.7863 (pttm) REVERT: B 18 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7133 (mm-30) REVERT: B 90 ASP cc_start: 0.7879 (t0) cc_final: 0.7412 (t70) REVERT: B 91 ASN cc_start: 0.8101 (m110) cc_final: 0.6948 (m-40) REVERT: B 110 ILE cc_start: 0.8602 (pt) cc_final: 0.8102 (mm) REVERT: B 124 LYS cc_start: 0.8371 (ttmt) cc_final: 0.8014 (ttpt) REVERT: B 132 ASN cc_start: 0.8229 (p0) cc_final: 0.7789 (p0) REVERT: B 205 ARG cc_start: 0.7873 (tpp80) cc_final: 0.7599 (mmm-85) REVERT: B 228 LYS cc_start: 0.8305 (ttmm) cc_final: 0.7604 (ttmm) REVERT: B 327 TYR cc_start: 0.8095 (p90) cc_final: 0.7844 (p90) REVERT: B 333 ARG cc_start: 0.7722 (mtt90) cc_final: 0.7336 (mtt90) REVERT: B 346 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7217 (mm-30) REVERT: B 361 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7503 (mt-10) REVERT: B 503 LYS cc_start: 0.8505 (tttt) cc_final: 0.7933 (ttmm) REVERT: B 515 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7075 (tm-30) REVERT: B 547 GLN cc_start: 0.7147 (tp-100) cc_final: 0.6843 (tp-100) REVERT: B 580 MET cc_start: 0.7816 (tpp) cc_final: 0.7060 (tpp) REVERT: B 594 ASP cc_start: 0.7895 (m-30) cc_final: 0.7591 (m-30) REVERT: B 597 GLU cc_start: 0.7685 (tp30) cc_final: 0.7209 (tp30) REVERT: B 607 ASN cc_start: 0.7452 (t0) cc_final: 0.6855 (t0) REVERT: B 640 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7706 (mm-30) REVERT: B 707 MET cc_start: 0.7972 (tpp) cc_final: 0.7144 (tpp) REVERT: B 739 PHE cc_start: 0.7415 (OUTLIER) cc_final: 0.6492 (m-10) REVERT: B 807 ARG cc_start: 0.7849 (ttm170) cc_final: 0.6996 (ttp80) REVERT: B 851 PHE cc_start: 0.6835 (m-80) cc_final: 0.6592 (m-80) REVERT: B 861 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8017 (mm) REVERT: B 973 LEU cc_start: 0.8454 (mm) cc_final: 0.7715 (mt) REVERT: B 1014 LYS cc_start: 0.8654 (pttp) cc_final: 0.7819 (pttp) REVERT: B 1017 LYS cc_start: 0.7634 (mtmt) cc_final: 0.7402 (mtmt) REVERT: B 1020 MET cc_start: 0.6401 (mmt) cc_final: 0.6186 (mmt) REVERT: B 1049 ASP cc_start: 0.8107 (m-30) cc_final: 0.7826 (m-30) REVERT: B 1066 GLU cc_start: 0.7747 (tt0) cc_final: 0.7379 (mm-30) REVERT: B 1072 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7250 (tp30) REVERT: B 1080 PHE cc_start: 0.7696 (t80) cc_final: 0.7388 (t80) REVERT: B 1096 PHE cc_start: 0.6597 (OUTLIER) cc_final: 0.6307 (m-10) REVERT: B 1106 LYS cc_start: 0.7475 (ttmt) cc_final: 0.6213 (ttmm) REVERT: B 1110 ARG cc_start: 0.7726 (ptp90) cc_final: 0.7493 (ptp-170) REVERT: B 1132 LYS cc_start: 0.8020 (mttt) cc_final: 0.7555 (mttm) REVERT: B 1154 GLN cc_start: 0.8472 (tt0) cc_final: 0.8117 (tt0) REVERT: B 1156 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6800 (mmtp) REVERT: B 1157 GLU cc_start: 0.7347 (tp30) cc_final: 0.6500 (tp30) REVERT: B 1200 GLU cc_start: 0.8039 (pt0) cc_final: 0.7606 (pt0) REVERT: B 1201 TYR cc_start: 0.8302 (t80) cc_final: 0.7532 (t80) REVERT: B 1204 GLU cc_start: 0.7505 (pp20) cc_final: 0.7176 (pp20) REVERT: B 1219 MET cc_start: 0.7469 (mmp) cc_final: 0.6921 (mmp) REVERT: B 1231 MET cc_start: 0.6734 (mpp) cc_final: 0.6057 (mpp) REVERT: B 1263 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7802 (mt-10) REVERT: B 1266 LEU cc_start: 0.7860 (mt) cc_final: 0.7570 (mt) REVERT: B 1383 LYS cc_start: 0.8795 (pttm) cc_final: 0.8366 (pttm) REVERT: B 1399 LYS cc_start: 0.8684 (pptt) cc_final: 0.8342 (pptt) REVERT: B 1412 GLU cc_start: 0.5933 (OUTLIER) cc_final: 0.4082 (mm-30) outliers start: 90 outliers final: 71 residues processed: 705 average time/residue: 0.1594 time to fit residues: 169.9859 Evaluate side-chains 738 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 656 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 844 CYS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1297 GLN Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 560 LYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 1028 ILE Chi-restraints excluded: chain B residue 1039 ILE Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1156 LYS Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1194 GLN Chi-restraints excluded: chain B residue 1213 LEU Chi-restraints excluded: chain B residue 1218 PHE Chi-restraints excluded: chain B residue 1290 ILE Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1320 LYS Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1333 GLU Chi-restraints excluded: chain B residue 1367 TYR Chi-restraints excluded: chain B residue 1412 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 198 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 175 optimal weight: 0.0770 chunk 173 optimal weight: 0.0570 chunk 228 optimal weight: 0.9980 chunk 249 optimal weight: 0.7980 chunk 80 optimal weight: 0.4980 chunk 178 optimal weight: 0.7980 chunk 140 optimal weight: 0.0770 chunk 88 optimal weight: 0.0370 chunk 55 optimal weight: 3.9990 overall best weight: 0.1492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1217 ASN A1402 GLN B 709 ASN ** B1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.120945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.104335 restraints weight = 48240.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.107641 restraints weight = 25105.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.109826 restraints weight = 15377.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.111286 restraints weight = 10544.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.112301 restraints weight = 7874.803| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20796 Z= 0.148 Angle : 0.759 15.200 28095 Z= 0.385 Chirality : 0.042 0.210 3318 Planarity : 0.005 0.066 3545 Dihedral : 5.209 53.085 2693 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.65 % Favored : 91.23 % Rotamer: Outliers : 3.38 % Allowed : 24.99 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.17), residues: 2521 helix: 1.12 (0.12), residues: 1764 sheet: -3.24 (0.97), residues: 22 loop : -2.77 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 174 TYR 0.035 0.001 TYR B1258 PHE 0.032 0.002 PHE A 925 TRP 0.016 0.002 TRP B 470 HIS 0.012 0.001 HIS A 617 Details of bonding type rmsd covalent geometry : bond 0.00322 (20796) covalent geometry : angle 0.75944 (28095) hydrogen bonds : bond 0.04208 ( 1287) hydrogen bonds : angle 4.77198 ( 3840) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 664 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8392 (ttmt) cc_final: 0.8115 (ttmt) REVERT: A 27 ARG cc_start: 0.8093 (ttm170) cc_final: 0.7583 (mtm110) REVERT: A 78 GLN cc_start: 0.7741 (tp40) cc_final: 0.7506 (tp40) REVERT: A 91 ASN cc_start: 0.7614 (t0) cc_final: 0.7186 (t0) REVERT: A 120 ASP cc_start: 0.7560 (t70) cc_final: 0.7109 (m-30) REVERT: A 154 PHE cc_start: 0.8362 (p90) cc_final: 0.8091 (p90) REVERT: A 155 GLU cc_start: 0.7526 (pt0) cc_final: 0.7260 (pt0) REVERT: A 199 SER cc_start: 0.8639 (t) cc_final: 0.8407 (t) REVERT: A 240 ILE cc_start: 0.8769 (mt) cc_final: 0.8505 (mm) REVERT: A 250 ASP cc_start: 0.6661 (m-30) cc_final: 0.6446 (m-30) REVERT: A 253 LYS cc_start: 0.8045 (pttt) cc_final: 0.7573 (pttt) REVERT: A 368 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7436 (mt-10) REVERT: A 459 LYS cc_start: 0.8119 (mttp) cc_final: 0.7786 (mtmm) REVERT: A 460 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7152 (tm-30) REVERT: A 523 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7394 (mm-30) REVERT: A 559 ARG cc_start: 0.7631 (tpp80) cc_final: 0.6929 (tpp80) REVERT: A 562 GLU cc_start: 0.7312 (mt-10) cc_final: 0.6879 (mt-10) REVERT: A 565 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7715 (mm-30) REVERT: A 593 LYS cc_start: 0.7506 (tptm) cc_final: 0.6857 (tptm) REVERT: A 597 GLU cc_start: 0.7659 (tm-30) cc_final: 0.6778 (tm-30) REVERT: A 600 PHE cc_start: 0.8588 (t80) cc_final: 0.8350 (t80) REVERT: A 615 LEU cc_start: 0.8066 (tp) cc_final: 0.7546 (tt) REVERT: A 626 GLU cc_start: 0.7779 (tp30) cc_final: 0.7113 (tp30) REVERT: A 637 ARG cc_start: 0.7850 (ttp-110) cc_final: 0.7623 (ttp80) REVERT: A 656 GLN cc_start: 0.7477 (tm-30) cc_final: 0.7188 (tm-30) REVERT: A 657 GLN cc_start: 0.7852 (mp10) cc_final: 0.7379 (mp10) REVERT: A 663 GLU cc_start: 0.7570 (pt0) cc_final: 0.7106 (pt0) REVERT: A 745 ASP cc_start: 0.8081 (t70) cc_final: 0.7864 (t0) REVERT: A 750 SER cc_start: 0.8120 (p) cc_final: 0.7857 (p) REVERT: A 819 SER cc_start: 0.8304 (m) cc_final: 0.7975 (p) REVERT: A 837 MET cc_start: 0.7311 (mmm) cc_final: 0.6954 (mmm) REVERT: A 908 ASP cc_start: 0.7408 (p0) cc_final: 0.6989 (p0) REVERT: A 911 ARG cc_start: 0.7447 (tpp-160) cc_final: 0.7141 (mmt-90) REVERT: A 917 LYS cc_start: 0.7511 (mmtt) cc_final: 0.6919 (mttp) REVERT: A 956 ASP cc_start: 0.6364 (p0) cc_final: 0.5983 (p0) REVERT: A 978 LYS cc_start: 0.8317 (tptt) cc_final: 0.8072 (tptt) REVERT: A 1020 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6874 (tpp) REVERT: A 1021 GLU cc_start: 0.7810 (tp30) cc_final: 0.7161 (tp30) REVERT: A 1027 ASN cc_start: 0.6671 (p0) cc_final: 0.6390 (p0) REVERT: A 1072 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: A 1082 LYS cc_start: 0.7585 (mtpt) cc_final: 0.7170 (mtpt) REVERT: A 1089 LYS cc_start: 0.8351 (ttmm) cc_final: 0.7968 (ttmm) REVERT: A 1093 GLN cc_start: 0.8328 (tp40) cc_final: 0.8086 (tp40) REVERT: A 1113 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7802 (tp) REVERT: A 1116 LYS cc_start: 0.8587 (ttpt) cc_final: 0.8138 (ttmm) REVERT: A 1120 ILE cc_start: 0.9064 (mm) cc_final: 0.8642 (mm) REVERT: A 1122 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8642 (mm) REVERT: A 1126 GLN cc_start: 0.6886 (mm-40) cc_final: 0.6368 (mm-40) REVERT: A 1128 GLU cc_start: 0.7971 (tp30) cc_final: 0.7628 (tp30) REVERT: A 1132 LYS cc_start: 0.8321 (mmmm) cc_final: 0.7764 (mmmm) REVERT: A 1152 THR cc_start: 0.8585 (t) cc_final: 0.8121 (p) REVERT: A 1157 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7128 (mt-10) REVERT: A 1183 LYS cc_start: 0.7909 (tptp) cc_final: 0.7698 (mtmm) REVERT: A 1186 ARG cc_start: 0.8154 (ttt90) cc_final: 0.7589 (ttm-80) REVERT: A 1187 LYS cc_start: 0.8514 (mmmm) cc_final: 0.8223 (mmmm) REVERT: A 1191 MET cc_start: 0.6870 (tpt) cc_final: 0.6663 (tpt) REVERT: A 1200 GLU cc_start: 0.7728 (tp30) cc_final: 0.7402 (tp30) REVERT: A 1219 MET cc_start: 0.8220 (mmm) cc_final: 0.7942 (mmm) REVERT: A 1243 LYS cc_start: 0.7875 (mmmt) cc_final: 0.7420 (mmmt) REVERT: A 1256 ASN cc_start: 0.6903 (p0) cc_final: 0.6343 (p0) REVERT: A 1259 LYS cc_start: 0.8342 (mppt) cc_final: 0.7393 (mppt) REVERT: A 1263 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7420 (mt-10) REVERT: A 1267 LYS cc_start: 0.8518 (mttm) cc_final: 0.8184 (mtpp) REVERT: A 1270 GLN cc_start: 0.7868 (tm-30) cc_final: 0.7179 (tm-30) REVERT: A 1336 GLU cc_start: 0.8073 (tp30) cc_final: 0.7736 (tp30) REVERT: A 1366 VAL cc_start: 0.8619 (p) cc_final: 0.8383 (m) REVERT: A 1383 LYS cc_start: 0.8312 (mmtm) cc_final: 0.8062 (mmtm) REVERT: A 1385 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7941 (mm) REVERT: A 1409 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7852 (pttm) REVERT: B 18 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7549 (mm-30) REVERT: B 90 ASP cc_start: 0.7867 (t0) cc_final: 0.7399 (t70) REVERT: B 91 ASN cc_start: 0.8051 (m110) cc_final: 0.6950 (m-40) REVERT: B 110 ILE cc_start: 0.8523 (pt) cc_final: 0.8075 (mm) REVERT: B 132 ASN cc_start: 0.8229 (p0) cc_final: 0.7813 (p0) REVERT: B 205 ARG cc_start: 0.7883 (tpp80) cc_final: 0.7623 (mmm-85) REVERT: B 228 LYS cc_start: 0.8271 (ttmm) cc_final: 0.7581 (ttmm) REVERT: B 327 TYR cc_start: 0.8080 (p90) cc_final: 0.7815 (p90) REVERT: B 333 ARG cc_start: 0.7698 (mtt90) cc_final: 0.7332 (mtt90) REVERT: B 346 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7215 (mm-30) REVERT: B 361 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7486 (mt-10) REVERT: B 503 LYS cc_start: 0.8476 (tttt) cc_final: 0.7904 (ttmm) REVERT: B 515 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7070 (tm-30) REVERT: B 547 GLN cc_start: 0.7062 (tp-100) cc_final: 0.6834 (tp40) REVERT: B 580 MET cc_start: 0.7788 (tpp) cc_final: 0.7019 (tpp) REVERT: B 591 SER cc_start: 0.8443 (OUTLIER) cc_final: 0.8065 (t) REVERT: B 597 GLU cc_start: 0.7649 (tp30) cc_final: 0.7211 (tp30) REVERT: B 607 ASN cc_start: 0.7419 (t0) cc_final: 0.6797 (t0) REVERT: B 640 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7715 (mm-30) REVERT: B 707 MET cc_start: 0.7988 (tpp) cc_final: 0.7133 (tpp) REVERT: B 739 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6473 (m-10) REVERT: B 807 ARG cc_start: 0.7868 (ttm170) cc_final: 0.7037 (ttp-170) REVERT: B 846 TYR cc_start: 0.8682 (t80) cc_final: 0.8468 (t80) REVERT: B 861 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.7873 (mm) REVERT: B 938 PHE cc_start: 0.7241 (m-80) cc_final: 0.6919 (m-10) REVERT: B 973 LEU cc_start: 0.8466 (mm) cc_final: 0.7673 (mt) REVERT: B 1014 LYS cc_start: 0.8642 (pttp) cc_final: 0.7824 (pttp) REVERT: B 1017 LYS cc_start: 0.7628 (mtmt) cc_final: 0.7403 (mtmt) REVERT: B 1020 MET cc_start: 0.6388 (mmt) cc_final: 0.6170 (mmt) REVERT: B 1066 GLU cc_start: 0.7738 (tt0) cc_final: 0.7348 (mm-30) REVERT: B 1072 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7254 (tp30) REVERT: B 1080 PHE cc_start: 0.7575 (t80) cc_final: 0.7138 (t80) REVERT: B 1096 PHE cc_start: 0.6570 (OUTLIER) cc_final: 0.6286 (m-10) REVERT: B 1106 LYS cc_start: 0.7461 (ttmt) cc_final: 0.6354 (ttmm) REVERT: B 1126 GLN cc_start: 0.7059 (tp40) cc_final: 0.6843 (tp40) REVERT: B 1132 LYS cc_start: 0.8006 (mttt) cc_final: 0.7541 (mttm) REVERT: B 1154 GLN cc_start: 0.8468 (tt0) cc_final: 0.8108 (tt0) REVERT: B 1156 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6812 (mmtp) REVERT: B 1157 GLU cc_start: 0.7349 (tp30) cc_final: 0.6463 (tp30) REVERT: B 1200 GLU cc_start: 0.8008 (pt0) cc_final: 0.7586 (pt0) REVERT: B 1201 TYR cc_start: 0.8296 (t80) cc_final: 0.7561 (t80) REVERT: B 1204 GLU cc_start: 0.7509 (pp20) cc_final: 0.7169 (pp20) REVERT: B 1219 MET cc_start: 0.7435 (mmp) cc_final: 0.7041 (mmp) REVERT: B 1231 MET cc_start: 0.6682 (mpp) cc_final: 0.6019 (mpp) REVERT: B 1263 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7790 (mt-10) REVERT: B 1266 LEU cc_start: 0.7814 (mt) cc_final: 0.7529 (mt) REVERT: B 1383 LYS cc_start: 0.8769 (pttm) cc_final: 0.8326 (pttm) REVERT: B 1399 LYS cc_start: 0.8670 (pptt) cc_final: 0.8333 (pptt) REVERT: B 1412 GLU cc_start: 0.5824 (OUTLIER) cc_final: 0.4209 (mm-30) outliers start: 80 outliers final: 58 residues processed: 699 average time/residue: 0.1425 time to fit residues: 150.8221 Evaluate side-chains 720 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 650 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 844 CYS Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1231 MET Chi-restraints excluded: chain A residue 1297 GLN Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 560 LYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 1028 ILE Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1156 LYS Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1218 PHE Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1320 LYS Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1333 GLU Chi-restraints excluded: chain B residue 1367 TYR Chi-restraints excluded: chain B residue 1412 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 97 optimal weight: 0.9990 chunk 189 optimal weight: 0.0670 chunk 68 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 118 optimal weight: 0.0270 chunk 134 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN B1194 GLN ** B1349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.119877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.103284 restraints weight = 48311.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.106574 restraints weight = 25183.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.108713 restraints weight = 15460.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.110182 restraints weight = 10630.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.111154 restraints weight = 7935.394| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20796 Z= 0.159 Angle : 0.775 14.895 28095 Z= 0.394 Chirality : 0.043 0.213 3318 Planarity : 0.005 0.066 3545 Dihedral : 5.216 50.256 2693 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.04 % Favored : 90.88 % Rotamer: Outliers : 3.09 % Allowed : 26.00 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.17), residues: 2521 helix: 1.08 (0.12), residues: 1763 sheet: -2.92 (1.04), residues: 20 loop : -2.71 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1107 TYR 0.036 0.001 TYR B1258 PHE 0.043 0.002 PHE A1288 TRP 0.013 0.002 TRP B 470 HIS 0.013 0.001 HIS A 617 Details of bonding type rmsd covalent geometry : bond 0.00349 (20796) covalent geometry : angle 0.77456 (28095) hydrogen bonds : bond 0.04368 ( 1287) hydrogen bonds : angle 4.82856 ( 3840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4708.37 seconds wall clock time: 81 minutes 57.44 seconds (4917.44 seconds total)