Starting phenix.real_space_refine on Mon Mar 18 08:59:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezq_28748/03_2024/8ezq_28748.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezq_28748/03_2024/8ezq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezq_28748/03_2024/8ezq_28748.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezq_28748/03_2024/8ezq_28748.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezq_28748/03_2024/8ezq_28748.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezq_28748/03_2024/8ezq_28748.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Residue "A PHE 1158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 938": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1350": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 10.16, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 8.70 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 2.22 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: 7.40 Time building geometry restraints manager: 9.34 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: 99.80 - 106.64: 399 106.64 - 113.49: 11854 113.49 - 120.33: 7869 120.33 - 127.17: 7840 127.17 - 134.02: 133 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 2.520 nonbonded pdb=" OG1 THR B 798 " pdb=" OE1 GLU B 801 " model vdw 2.204 2.440 nonbonded pdb=" O ASN B1056 " pdb=" OG SER B1060 " model vdw 2.204 2.440 nonbonded pdb=" O PHE A1163 " pdb=" OG1 THR A1166 " model vdw 2.206 2.440 nonbonded pdb=" O GLN B1194 " pdb=" OG SER B1197 " model vdw 2.206 2.440 ... (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 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: 8.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 27.970 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 54.930 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.430 ------------------------------------------------------------------------------- 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= 0.214 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.016 0.002 TRP B 773 HIS 0.003 0.000 HIS A 713 PHE 0.017 0.001 PHE B1381 TYR 0.015 0.001 TYR A 138 ARG 0.005 0.000 ARG A 472 *********************** 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 fitting. rotamer outliers: 10 poor density : 769 time to evaluate : 2.323 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: 0.3409 time to fit residues: 395.8955 Evaluate side-chains 680 residues out of total 2365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 675 time to evaluate : 2.599 ------------------------------------------------------------------------------- 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 214 optimal weight: 0.9980 chunk 192 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 129 optimal weight: 0.2980 chunk 102 optimal weight: 0.1980 chunk 199 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 148 optimal weight: 4.9990 chunk 230 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 337 ASN A 602 ASN ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN A 919 GLN A1027 ASN A1319 ASN A1402 GLN B 204 ASN B 657 GLN B 709 ASN ** B1178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1194 GLN ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1250 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1237 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= 0.203 Angle : 0.647 12.517 28095 Z= 0.336 Chirality : 0.040 0.161 3318 Planarity : 0.004 0.051 3545 Dihedral : 4.956 49.583 2693 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.36 % Favored : 90.60 % Rotamer: Outliers : 3.09 % Allowed : 15.14 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2521 helix: 1.37 (0.13), residues: 1753 sheet: -2.79 (1.05), residues: 20 loop : -2.66 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 470 HIS 0.011 0.001 HIS A 617 PHE 0.026 0.002 PHE A 822 TYR 0.017 0.001 TYR B1062 ARG 0.006 0.000 ARG B 914 *********************** 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 763 residues out of total 2365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 690 time to evaluate : 2.368 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: A 18 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7333 (mm-30) REVERT: A 78 GLN cc_start: 0.7875 (tp40) cc_final: 0.7600 (tp40) REVERT: A 82 MET cc_start: 0.8025 (ttm) cc_final: 0.7633 (tmm) REVERT: A 91 ASN cc_start: 0.7643 (t0) cc_final: 0.7267 (t0) REVERT: A 154 PHE cc_start: 0.8435 (p90) cc_final: 0.8113 (p90) REVERT: A 155 GLU cc_start: 0.7589 (pt0) cc_final: 0.7261 (pt0) REVERT: A 184 LEU cc_start: 0.8152 (mt) cc_final: 0.7826 (mt) REVERT: A 199 SER cc_start: 0.8534 (t) cc_final: 0.8325 (t) REVERT: A 206 ARG cc_start: 0.7950 (tpp-160) cc_final: 0.7695 (tpp-160) REVERT: A 208 GLU cc_start: 0.7031 (mp0) cc_final: 0.6811 (mp0) REVERT: A 233 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7219 (mm-30) REVERT: A 240 ILE cc_start: 0.8840 (mt) cc_final: 0.8584 (mm) REVERT: A 253 LYS cc_start: 0.8087 (pttt) cc_final: 0.7588 (pttt) REVERT: A 368 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7461 (mt-10) REVERT: A 460 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7441 (tm-30) REVERT: A 492 ASP cc_start: 0.7160 (m-30) cc_final: 0.6856 (m-30) REVERT: A 555 LYS cc_start: 0.8748 (mmmm) cc_final: 0.8490 (mmmm) REVERT: A 559 ARG cc_start: 0.7829 (tpp80) cc_final: 0.7507 (tpp80) REVERT: A 562 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7068 (mt-10) REVERT: A 565 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7874 (mm-30) REVERT: A 593 LYS cc_start: 0.7689 (tptm) cc_final: 0.7085 (tptm) REVERT: A 600 PHE cc_start: 0.8549 (t80) cc_final: 0.8063 (t80) REVERT: A 626 GLU cc_start: 0.7828 (tp30) cc_final: 0.7273 (tp30) REVERT: A 656 GLN cc_start: 0.7249 (tm-30) cc_final: 0.6797 (tm-30) REVERT: A 659 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6865 (mt-10) REVERT: A 745 ASP cc_start: 0.8056 (t70) cc_final: 0.7847 (t0) REVERT: A 766 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7116 (tm-30) REVERT: A 802 LEU cc_start: 0.8125 (tp) cc_final: 0.7529 (tp) REVERT: A 806 ASP cc_start: 0.7662 (m-30) cc_final: 0.7144 (m-30) REVERT: A 830 ASP cc_start: 0.7412 (t70) cc_final: 0.7134 (t70) REVERT: A 837 MET cc_start: 0.7374 (mmm) cc_final: 0.7156 (mmt) REVERT: A 911 ARG cc_start: 0.7610 (tpp-160) cc_final: 0.7281 (mmt-90) REVERT: A 917 LYS cc_start: 0.7523 (mmtt) cc_final: 0.7028 (mttp) REVERT: A 931 ARG cc_start: 0.7861 (ttp-110) cc_final: 0.7642 (ttp-110) REVERT: A 956 ASP cc_start: 0.6836 (OUTLIER) cc_final: 0.6396 (p0) REVERT: A 1017 LYS cc_start: 0.8127 (ttmm) cc_final: 0.7847 (ttmm) REVERT: A 1020 MET cc_start: 0.7461 (tpp) cc_final: 0.7107 (tpp) REVERT: A 1021 GLU cc_start: 0.7787 (tp30) cc_final: 0.7086 (tp30) REVERT: A 1062 TYR cc_start: 0.7578 (p90) cc_final: 0.6934 (p90) REVERT: A 1071 ILE cc_start: 0.8392 (mm) cc_final: 0.8187 (mm) REVERT: A 1072 GLU cc_start: 0.8044 (tt0) cc_final: 0.7545 (tt0) REVERT: A 1087 LEU cc_start: 0.8545 (tp) cc_final: 0.8343 (tp) REVERT: A 1089 LYS cc_start: 0.8538 (ttmm) cc_final: 0.8129 (ttmm) REVERT: A 1093 GLN cc_start: 0.8575 (tp40) cc_final: 0.8227 (tp40) REVERT: A 1113 LEU cc_start: 0.8221 (tp) cc_final: 0.7919 (tp) REVERT: A 1116 LYS cc_start: 0.8710 (ttpt) cc_final: 0.8509 (ttmm) REVERT: A 1120 ILE cc_start: 0.9117 (mm) cc_final: 0.8751 (mm) REVERT: A 1126 GLN cc_start: 0.6925 (mm-40) cc_final: 0.6581 (mm-40) REVERT: A 1128 GLU cc_start: 0.7865 (tp30) cc_final: 0.7438 (tp30) REVERT: A 1132 LYS cc_start: 0.8383 (mmmm) cc_final: 0.7778 (mmmm) REVERT: A 1140 LYS cc_start: 0.7956 (mmmm) cc_final: 0.7528 (mmmm) REVERT: A 1157 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7242 (mt-10) REVERT: A 1163 PHE cc_start: 0.8172 (m-80) cc_final: 0.7842 (m-80) REVERT: A 1170 PHE cc_start: 0.7490 (m-10) cc_final: 0.7271 (m-10) REVERT: A 1187 LYS cc_start: 0.8574 (mmmm) cc_final: 0.8171 (mmmm) REVERT: A 1191 MET cc_start: 0.7370 (tpt) cc_final: 0.6620 (tpt) REVERT: A 1200 GLU cc_start: 0.7861 (tp30) cc_final: 0.7514 (tp30) REVERT: A 1219 MET cc_start: 0.8175 (mmm) cc_final: 0.7775 (mmm) REVERT: A 1263 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7499 (mt-10) REVERT: A 1267 LYS cc_start: 0.8510 (mttm) cc_final: 0.8110 (mtpp) REVERT: A 1305 ILE cc_start: 0.8559 (mm) cc_final: 0.8315 (mm) REVERT: A 1365 ASN cc_start: 0.8321 (m-40) cc_final: 0.8001 (m-40) REVERT: A 1366 VAL cc_start: 0.8553 (p) cc_final: 0.8303 (m) REVERT: A 1383 LYS cc_start: 0.8282 (mmtm) cc_final: 0.8039 (mmtm) REVERT: A 1399 LYS cc_start: 0.8551 (ptpp) cc_final: 0.8265 (pttm) REVERT: A 1400 LYS cc_start: 0.8801 (mmtm) cc_final: 0.8533 (mmtm) REVERT: B 10 ASP cc_start: 0.7984 (m-30) cc_final: 0.7628 (m-30) REVERT: B 91 ASN cc_start: 0.8101 (m110) cc_final: 0.7813 (m-40) REVERT: B 110 ILE cc_start: 0.8550 (pt) cc_final: 0.8146 (mm) REVERT: B 132 ASN cc_start: 0.8174 (p0) cc_final: 0.7784 (p0) REVERT: B 136 GLN cc_start: 0.8171 (mt0) cc_final: 0.7941 (mt0) REVERT: B 138 TYR cc_start: 0.8102 (p90) cc_final: 0.7887 (p90) REVERT: B 162 ASP cc_start: 0.7731 (m-30) cc_final: 0.7453 (p0) REVERT: B 174 ARG cc_start: 0.8208 (ttt180) cc_final: 0.7944 (ttt180) REVERT: B 191 TYR cc_start: 0.8208 (t80) cc_final: 0.7945 (t80) REVERT: B 205 ARG cc_start: 0.7832 (tpp80) cc_final: 0.7517 (mmm-85) REVERT: B 333 ARG cc_start: 0.7666 (mtt90) cc_final: 0.7256 (mtt90) REVERT: B 346 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7253 (mm-30) REVERT: B 361 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7495 (mt-10) REVERT: B 368 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7345 (mt-10) REVERT: B 397 GLN cc_start: 0.7629 (tt0) cc_final: 0.7400 (tt0) REVERT: B 499 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7946 (mtpp) REVERT: B 515 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7162 (tm-30) REVERT: B 547 GLN cc_start: 0.7251 (tp-100) cc_final: 0.6909 (tp-100) REVERT: B 580 MET cc_start: 0.7702 (tpp) cc_final: 0.7030 (tpp) REVERT: B 594 ASP cc_start: 0.7807 (m-30) cc_final: 0.7490 (m-30) REVERT: B 607 ASN cc_start: 0.6875 (t0) cc_final: 0.6579 (t0) REVERT: B 630 LEU cc_start: 0.8550 (mt) cc_final: 0.8216 (mt) REVERT: B 637 ARG cc_start: 0.6963 (mtp-110) cc_final: 0.6761 (mtp-110) REVERT: B 649 PHE cc_start: 0.7843 (p90) cc_final: 0.7552 (p90) REVERT: B 656 GLN cc_start: 0.7678 (mp10) cc_final: 0.7214 (mp-120) REVERT: B 707 MET cc_start: 0.7683 (tpp) cc_final: 0.7252 (tpp) REVERT: B 739 PHE cc_start: 0.7366 (OUTLIER) cc_final: 0.6620 (m-10) REVERT: B 775 ASN cc_start: 0.6275 (m-40) cc_final: 0.6057 (m-40) REVERT: B 803 LEU cc_start: 0.8228 (mt) cc_final: 0.7836 (mt) REVERT: B 807 ARG cc_start: 0.7878 (ttm170) cc_final: 0.7364 (ttp-170) REVERT: B 837 MET cc_start: 0.8106 (mmm) cc_final: 0.7455 (mmm) REVERT: B 912 PHE cc_start: 0.7418 (t80) cc_final: 0.7146 (t80) REVERT: B 919 GLN cc_start: 0.7530 (mt0) cc_final: 0.7251 (mt0) REVERT: B 1020 MET cc_start: 0.6842 (mmt) cc_final: 0.6572 (mmt) REVERT: B 1062 TYR cc_start: 0.7594 (p90) cc_final: 0.7036 (p90) REVERT: B 1063 PHE cc_start: 0.8102 (t80) cc_final: 0.7837 (t80) REVERT: B 1080 PHE cc_start: 0.7389 (t80) cc_final: 0.6851 (t80) REVERT: B 1096 PHE cc_start: 0.6809 (OUTLIER) cc_final: 0.6537 (m-10) REVERT: B 1106 LYS cc_start: 0.7500 (ttmt) cc_final: 0.6604 (ttmm) REVERT: B 1110 ARG cc_start: 0.7886 (ptp90) cc_final: 0.7625 (ptp-170) REVERT: B 1132 LYS cc_start: 0.8018 (mttt) cc_final: 0.7580 (mttp) REVERT: B 1148 LYS cc_start: 0.8600 (mtpp) cc_final: 0.8383 (mmmm) REVERT: B 1154 GLN cc_start: 0.8352 (tt0) cc_final: 0.8038 (tt0) REVERT: B 1163 PHE cc_start: 0.7581 (m-10) cc_final: 0.7253 (m-80) REVERT: B 1199 PHE cc_start: 0.8373 (t80) cc_final: 0.8149 (t80) REVERT: B 1200 GLU cc_start: 0.8164 (pt0) cc_final: 0.7783 (pt0) REVERT: B 1204 GLU cc_start: 0.7544 (pp20) cc_final: 0.7315 (pp20) REVERT: B 1231 MET cc_start: 0.6791 (mpp) cc_final: 0.6181 (mpp) REVERT: B 1263 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7973 (mt-10) REVERT: B 1266 LEU cc_start: 0.7883 (mt) cc_final: 0.7616 (mt) REVERT: B 1383 LYS cc_start: 0.8877 (pttm) cc_final: 0.8499 (pttm) outliers start: 73 outliers final: 49 residues processed: 720 average time/residue: 0.3409 time to fit residues: 372.6082 Evaluate side-chains 702 residues out of total 2365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 649 time to evaluate : 2.007 ------------------------------------------------------------------------------- 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 231 THR Chi-restraints excluded: chain A residue 242 ILE 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 727 SER Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1081 CYS Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1229 SER 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 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 611 ILE Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 750 SER 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 1028 ILE Chi-restraints excluded: chain B residue 1038 ASN 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 1117 ILE Chi-restraints excluded: chain B residue 1188 VAL 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 128 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 191 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 231 optimal weight: 0.3980 chunk 249 optimal weight: 0.9980 chunk 205 optimal weight: 0.9980 chunk 229 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 185 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 GLN B 709 ASN B 832 HIS ** B1178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1582 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= 0.227 Angle : 0.654 11.225 28095 Z= 0.341 Chirality : 0.040 0.169 3318 Planarity : 0.004 0.057 3545 Dihedral : 5.087 51.069 2693 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.44 % Favored : 90.44 % Rotamer: Outliers : 3.68 % Allowed : 17.12 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.17), residues: 2521 helix: 1.23 (0.12), residues: 1766 sheet: -2.86 (1.02), residues: 20 loop : -2.75 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 768 HIS 0.009 0.001 HIS A 617 PHE 0.028 0.002 PHE B 925 TYR 0.014 0.001 TYR A 138 ARG 0.005 0.000 ARG A1186 *********************** 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 762 residues out of total 2365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 675 time to evaluate : 2.483 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: 0.7631 (mm-30) cc_final: 0.7410 (mm-30) REVERT: A 78 GLN cc_start: 0.7911 (tp40) cc_final: 0.7635 (tp40) REVERT: A 82 MET cc_start: 0.8034 (ttm) cc_final: 0.7662 (tmm) REVERT: A 91 ASN cc_start: 0.7666 (t0) cc_final: 0.7270 (t0) REVERT: A 155 GLU cc_start: 0.7592 (pt0) cc_final: 0.7199 (pt0) REVERT: A 184 LEU cc_start: 0.8193 (mt) cc_final: 0.7862 (mt) REVERT: A 199 SER cc_start: 0.8551 (t) cc_final: 0.8319 (t) REVERT: A 206 ARG cc_start: 0.8047 (tpp-160) cc_final: 0.7833 (tpp-160) REVERT: A 233 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7246 (mm-30) REVERT: A 240 ILE cc_start: 0.8829 (mt) cc_final: 0.8541 (mm) REVERT: A 253 LYS cc_start: 0.8064 (pttt) cc_final: 0.7582 (pttt) REVERT: A 368 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7521 (mt-10) REVERT: A 460 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7429 (tm-30) REVERT: A 492 ASP cc_start: 0.7195 (m-30) cc_final: 0.6891 (m-30) REVERT: A 543 GLU cc_start: 0.7271 (mp0) cc_final: 0.7052 (mp0) REVERT: A 555 LYS cc_start: 0.8759 (mmmm) cc_final: 0.8493 (mmmm) REVERT: A 559 ARG cc_start: 0.7890 (tpp80) cc_final: 0.7327 (tpp80) REVERT: A 562 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7057 (mt-10) REVERT: A 565 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7871 (mm-30) REVERT: A 593 LYS cc_start: 0.7650 (tptm) cc_final: 0.7239 (tptm) REVERT: A 626 GLU cc_start: 0.7857 (tp30) cc_final: 0.7645 (tp30) REVERT: A 654 GLU cc_start: 0.7370 (pm20) cc_final: 0.6722 (pm20) REVERT: A 656 GLN cc_start: 0.7323 (tm-30) cc_final: 0.6798 (tm-30) REVERT: A 659 GLU cc_start: 0.7483 (mt-10) cc_final: 0.6613 (mp0) REVERT: A 745 ASP cc_start: 0.8126 (t70) cc_final: 0.7896 (t0) REVERT: A 802 LEU cc_start: 0.8141 (tp) cc_final: 0.7574 (tp) REVERT: A 806 ASP cc_start: 0.7683 (m-30) cc_final: 0.7144 (m-30) REVERT: A 830 ASP cc_start: 0.7387 (t70) cc_final: 0.7112 (t70) REVERT: A 866 LYS cc_start: 0.8068 (ptmm) cc_final: 0.7715 (ptmm) REVERT: A 911 ARG cc_start: 0.7627 (tpp-160) cc_final: 0.7271 (mmt-90) REVERT: A 917 LYS cc_start: 0.7535 (mmtt) cc_final: 0.7110 (mttp) REVERT: A 931 ARG cc_start: 0.7885 (ttp-110) cc_final: 0.7639 (ttp-110) REVERT: A 956 ASP cc_start: 0.6814 (OUTLIER) cc_final: 0.6290 (p0) REVERT: A 1017 LYS cc_start: 0.8132 (ttmm) cc_final: 0.7834 (ttmm) REVERT: A 1020 MET cc_start: 0.7500 (tpp) cc_final: 0.7131 (tpp) REVERT: A 1021 GLU cc_start: 0.7798 (tp30) cc_final: 0.7145 (tp30) REVERT: A 1062 TYR cc_start: 0.7577 (p90) cc_final: 0.6990 (p90) REVERT: A 1071 ILE cc_start: 0.8407 (mm) cc_final: 0.8193 (mm) REVERT: A 1072 GLU cc_start: 0.8091 (tt0) cc_final: 0.7524 (tt0) REVERT: A 1082 LYS cc_start: 0.7778 (mtpt) cc_final: 0.7398 (mtpt) REVERT: A 1089 LYS cc_start: 0.8532 (ttmm) cc_final: 0.8139 (ttmm) REVERT: A 1093 GLN cc_start: 0.8525 (tp40) cc_final: 0.8244 (tp40) REVERT: A 1113 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8030 (tp) REVERT: A 1116 LYS cc_start: 0.8740 (ttpt) cc_final: 0.8489 (ttmm) REVERT: A 1120 ILE cc_start: 0.9129 (mm) cc_final: 0.8765 (mm) REVERT: A 1126 GLN cc_start: 0.6961 (mm-40) cc_final: 0.6573 (mm-40) REVERT: A 1128 GLU cc_start: 0.7897 (tp30) cc_final: 0.7452 (tp30) REVERT: A 1132 LYS cc_start: 0.8380 (mmmm) cc_final: 0.7788 (mmmm) REVERT: A 1140 LYS cc_start: 0.7972 (mmmm) cc_final: 0.7539 (mmmm) REVERT: A 1157 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7374 (mm-30) REVERT: A 1186 ARG cc_start: 0.8132 (ttt90) cc_final: 0.7511 (ttm-80) REVERT: A 1187 LYS cc_start: 0.8512 (mmmm) cc_final: 0.8271 (mmmm) REVERT: A 1200 GLU cc_start: 0.7870 (tp30) cc_final: 0.7518 (tp30) REVERT: A 1219 MET cc_start: 0.8194 (mmm) cc_final: 0.7803 (mmm) REVERT: A 1263 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7503 (mt-10) REVERT: A 1267 LYS cc_start: 0.8534 (mttm) cc_final: 0.8187 (mtpp) REVERT: A 1336 GLU cc_start: 0.8091 (tp30) cc_final: 0.7711 (tp30) REVERT: A 1365 ASN cc_start: 0.8351 (m-40) cc_final: 0.8029 (m-40) REVERT: A 1366 VAL cc_start: 0.8591 (p) cc_final: 0.8355 (m) REVERT: A 1383 LYS cc_start: 0.8293 (mmtm) cc_final: 0.8049 (mmtm) REVERT: A 1399 LYS cc_start: 0.8559 (ptpp) cc_final: 0.8270 (pttm) REVERT: A 1400 LYS cc_start: 0.8794 (mmtm) cc_final: 0.8549 (mmtm) REVERT: A 1402 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8373 (mm-40) REVERT: A 1409 LYS cc_start: 0.8028 (mmmt) cc_final: 0.7748 (pttm) REVERT: B 10 ASP cc_start: 0.8016 (m-30) cc_final: 0.7629 (m-30) REVERT: B 82 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7528 (tmm) REVERT: B 91 ASN cc_start: 0.8088 (m110) cc_final: 0.7808 (m-40) REVERT: B 102 LEU cc_start: 0.8127 (mt) cc_final: 0.7855 (mt) REVERT: B 110 ILE cc_start: 0.8573 (pt) cc_final: 0.7249 (mm) REVERT: B 132 ASN cc_start: 0.8148 (p0) cc_final: 0.7702 (p0) REVERT: B 155 GLU cc_start: 0.7417 (pt0) cc_final: 0.6865 (pm20) REVERT: B 162 ASP cc_start: 0.7790 (m-30) cc_final: 0.7530 (p0) REVERT: B 191 TYR cc_start: 0.8188 (t80) cc_final: 0.7931 (t80) REVERT: B 205 ARG cc_start: 0.7872 (tpp80) cc_final: 0.7578 (mmm-85) REVERT: B 228 LYS cc_start: 0.8375 (tttm) cc_final: 0.8066 (tttp) REVERT: B 333 ARG cc_start: 0.7677 (mtt90) cc_final: 0.7253 (mtt90) REVERT: B 346 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7268 (mm-30) REVERT: B 361 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7499 (mt-10) REVERT: B 368 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7334 (mt-10) REVERT: B 397 GLN cc_start: 0.7657 (tt0) cc_final: 0.7415 (tt0) REVERT: B 428 GLU cc_start: 0.7495 (tt0) cc_final: 0.6976 (tm-30) REVERT: B 499 LYS cc_start: 0.8168 (mtpp) cc_final: 0.7628 (mppt) REVERT: B 503 LYS cc_start: 0.8534 (tttt) cc_final: 0.7892 (ttmm) REVERT: B 515 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7171 (tm-30) REVERT: B 547 GLN cc_start: 0.7304 (tp-100) cc_final: 0.6939 (tp-100) REVERT: B 580 MET cc_start: 0.7720 (tpp) cc_final: 0.7107 (tpp) REVERT: B 594 ASP cc_start: 0.7873 (m-30) cc_final: 0.7544 (m-30) REVERT: B 607 ASN cc_start: 0.6991 (t0) cc_final: 0.6492 (t0) REVERT: B 608 LYS cc_start: 0.8350 (mmmt) cc_final: 0.8121 (mmtp) REVERT: B 637 ARG cc_start: 0.7048 (mtp-110) cc_final: 0.6802 (mtp-110) REVERT: B 640 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7624 (mm-30) REVERT: B 649 PHE cc_start: 0.7829 (p90) cc_final: 0.7520 (p90) REVERT: B 739 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6571 (m-10) REVERT: B 775 ASN cc_start: 0.6431 (m-40) cc_final: 0.6200 (m-40) REVERT: B 803 LEU cc_start: 0.8239 (mt) cc_final: 0.7922 (mt) REVERT: B 807 ARG cc_start: 0.7912 (ttm170) cc_final: 0.7345 (ttp-170) REVERT: B 837 MET cc_start: 0.8148 (mmm) cc_final: 0.7763 (tpp) REVERT: B 1020 MET cc_start: 0.6815 (mmt) cc_final: 0.6511 (mmt) REVERT: B 1063 PHE cc_start: 0.8055 (t80) cc_final: 0.7801 (t80) REVERT: B 1066 GLU cc_start: 0.7952 (tt0) cc_final: 0.7637 (tt0) REVERT: B 1080 PHE cc_start: 0.7319 (t80) cc_final: 0.6765 (t80) REVERT: B 1096 PHE cc_start: 0.6827 (OUTLIER) cc_final: 0.6531 (m-10) REVERT: B 1106 LYS cc_start: 0.7497 (ttmt) cc_final: 0.6464 (ttmm) REVERT: B 1110 ARG cc_start: 0.7876 (ptp90) cc_final: 0.7598 (ptp-170) REVERT: B 1132 LYS cc_start: 0.8032 (mttt) cc_final: 0.7611 (mttm) REVERT: B 1148 LYS cc_start: 0.8635 (mtpp) cc_final: 0.8400 (mmmm) REVERT: B 1154 GLN cc_start: 0.8479 (tt0) cc_final: 0.8152 (tt0) REVERT: B 1163 PHE cc_start: 0.7567 (m-10) cc_final: 0.7277 (m-80) REVERT: B 1199 PHE cc_start: 0.8371 (t80) cc_final: 0.8134 (t80) REVERT: B 1200 GLU cc_start: 0.8185 (pt0) cc_final: 0.7794 (pt0) REVERT: B 1204 GLU cc_start: 0.7549 (pp20) cc_final: 0.7302 (pp20) REVERT: B 1219 MET cc_start: 0.7448 (mmp) cc_final: 0.6802 (mmp) REVERT: B 1224 LEU cc_start: 0.8379 (mt) cc_final: 0.8162 (mt) REVERT: B 1266 LEU cc_start: 0.7904 (mt) cc_final: 0.7643 (mt) REVERT: B 1383 LYS cc_start: 0.8867 (pttm) cc_final: 0.8438 (pttm) outliers start: 87 outliers final: 68 residues processed: 705 average time/residue: 0.3386 time to fit residues: 361.0985 Evaluate side-chains 727 residues out of total 2365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 654 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 73 LEU 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 231 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 372 ASP 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 702 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 901 THR Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1195 SER Chi-restraints excluded: chain A residue 1229 SER Chi-restraints excluded: chain B residue 22 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 98 LEU 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 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 817 ILE Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 1028 ILE Chi-restraints excluded: chain B residue 1046 THR Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1058 ASP 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 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 228 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 231 optimal weight: 0.5980 chunk 245 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 219 optimal weight: 0.9980 chunk 66 optimal weight: 0.0370 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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** A1285 ASN B 709 ASN ** B1178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20796 Z= 0.203 Angle : 0.658 11.699 28095 Z= 0.336 Chirality : 0.040 0.167 3318 Planarity : 0.004 0.060 3545 Dihedral : 5.105 52.266 2693 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.36 % Favored : 90.60 % Rotamer: Outliers : 3.93 % Allowed : 19.15 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.17), residues: 2521 helix: 1.27 (0.12), residues: 1762 sheet: -2.83 (1.02), residues: 20 loop : -2.70 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 470 HIS 0.009 0.001 HIS A 617 PHE 0.028 0.002 PHE B 925 TYR 0.031 0.001 TYR B 138 ARG 0.006 0.000 ARG A 174 *********************** 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 768 residues out of total 2365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 675 time to evaluate : 2.042 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: A 17 LYS cc_start: 0.8441 (ttmt) cc_final: 0.8088 (ttmt) REVERT: A 18 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7392 (mm-30) REVERT: A 78 GLN cc_start: 0.7903 (tp40) cc_final: 0.7610 (tp40) REVERT: A 82 MET cc_start: 0.8035 (ttm) cc_final: 0.7645 (tmm) REVERT: A 91 ASN cc_start: 0.7648 (t0) cc_final: 0.7239 (t0) REVERT: A 155 GLU cc_start: 0.7618 (pt0) cc_final: 0.7181 (pt0) REVERT: A 184 LEU cc_start: 0.8216 (mt) cc_final: 0.7881 (mt) REVERT: A 199 SER cc_start: 0.8561 (t) cc_final: 0.8314 (t) REVERT: A 240 ILE cc_start: 0.8812 (mt) cc_final: 0.8523 (mm) REVERT: A 253 LYS cc_start: 0.8043 (pttt) cc_final: 0.7576 (pttt) REVERT: A 368 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7512 (mt-10) REVERT: A 460 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7408 (tm-30) REVERT: A 492 ASP cc_start: 0.7206 (m-30) cc_final: 0.6854 (m-30) REVERT: A 555 LYS cc_start: 0.8745 (mmmm) cc_final: 0.8472 (mmmm) REVERT: A 559 ARG cc_start: 0.7826 (tpp80) cc_final: 0.7182 (tpp80) REVERT: A 562 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7016 (mt-10) REVERT: A 565 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7842 (mm-30) REVERT: A 593 LYS cc_start: 0.7638 (tptm) cc_final: 0.7221 (tptm) REVERT: A 615 LEU cc_start: 0.7861 (mt) cc_final: 0.7477 (tp) REVERT: A 626 GLU cc_start: 0.7852 (tp30) cc_final: 0.7635 (tp30) REVERT: A 654 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6650 (pm20) REVERT: A 656 GLN cc_start: 0.7442 (tm-30) cc_final: 0.6836 (tm-30) REVERT: A 659 GLU cc_start: 0.7515 (mt-10) cc_final: 0.6465 (mp0) REVERT: A 663 GLU cc_start: 0.7531 (pt0) cc_final: 0.7086 (pt0) REVERT: A 745 ASP cc_start: 0.8121 (t70) cc_final: 0.7892 (t0) REVERT: A 802 LEU cc_start: 0.8105 (tp) cc_final: 0.7870 (tp) REVERT: A 911 ARG cc_start: 0.7595 (tpp-160) cc_final: 0.7247 (mmt-90) REVERT: A 917 LYS cc_start: 0.7506 (mmtt) cc_final: 0.7109 (mttp) REVERT: A 931 ARG cc_start: 0.7916 (ttp-110) cc_final: 0.7670 (ttp-110) REVERT: A 956 ASP cc_start: 0.6695 (OUTLIER) cc_final: 0.6290 (p0) REVERT: A 1017 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7809 (ttmm) REVERT: A 1020 MET cc_start: 0.7490 (tpp) cc_final: 0.7111 (tpp) REVERT: A 1021 GLU cc_start: 0.7834 (tp30) cc_final: 0.7178 (tp30) REVERT: A 1027 ASN cc_start: 0.6586 (p0) cc_final: 0.6307 (p0) REVERT: A 1062 TYR cc_start: 0.7520 (p90) cc_final: 0.6981 (p90) REVERT: A 1071 ILE cc_start: 0.8413 (mm) cc_final: 0.8201 (mm) REVERT: A 1072 GLU cc_start: 0.8073 (tt0) cc_final: 0.7529 (tt0) REVERT: A 1082 LYS cc_start: 0.7785 (mtpt) cc_final: 0.7382 (mtpt) REVERT: A 1089 LYS cc_start: 0.8495 (ttmm) cc_final: 0.7958 (ttmm) REVERT: A 1093 GLN cc_start: 0.8445 (tp40) cc_final: 0.8146 (tp40) REVERT: A 1112 MET cc_start: 0.7732 (mtp) cc_final: 0.6998 (ttm) REVERT: A 1113 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7911 (tp) REVERT: A 1116 LYS cc_start: 0.8755 (ttpt) cc_final: 0.8442 (ttmm) REVERT: A 1120 ILE cc_start: 0.9119 (mm) cc_final: 0.8744 (mm) REVERT: A 1126 GLN cc_start: 0.6954 (mm-40) cc_final: 0.6473 (mm-40) REVERT: A 1128 GLU cc_start: 0.7901 (tp30) cc_final: 0.7475 (tp30) REVERT: A 1132 LYS cc_start: 0.8366 (mmmm) cc_final: 0.7803 (mmmm) REVERT: A 1157 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7332 (mm-30) REVERT: A 1187 LYS cc_start: 0.8500 (mmmm) cc_final: 0.8227 (mmmm) REVERT: A 1200 GLU cc_start: 0.7850 (tp30) cc_final: 0.7511 (tp30) REVERT: A 1219 MET cc_start: 0.8184 (mmm) cc_final: 0.7792 (mmm) REVERT: A 1263 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7439 (mt-10) REVERT: A 1267 LYS cc_start: 0.8541 (mttm) cc_final: 0.8195 (mtpp) REVERT: A 1317 LEU cc_start: 0.8501 (mm) cc_final: 0.8251 (mt) REVERT: A 1336 GLU cc_start: 0.8092 (tp30) cc_final: 0.7711 (tp30) REVERT: A 1365 ASN cc_start: 0.8317 (m-40) cc_final: 0.7986 (m-40) REVERT: A 1366 VAL cc_start: 0.8571 (p) cc_final: 0.8320 (m) REVERT: A 1383 LYS cc_start: 0.8239 (mmtm) cc_final: 0.8007 (mmtm) REVERT: A 1399 LYS cc_start: 0.8557 (ptpp) cc_final: 0.8298 (pttm) REVERT: A 1400 LYS cc_start: 0.8788 (mmtm) cc_final: 0.8543 (mmtm) REVERT: B 10 ASP cc_start: 0.7995 (m-30) cc_final: 0.7598 (m-30) REVERT: B 18 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7546 (mm-30) REVERT: B 82 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7423 (tmm) REVERT: B 91 ASN cc_start: 0.8096 (m110) cc_final: 0.7808 (m-40) REVERT: B 102 LEU cc_start: 0.8116 (mt) cc_final: 0.7847 (mt) REVERT: B 110 ILE cc_start: 0.8572 (pt) cc_final: 0.7234 (mm) REVERT: B 132 ASN cc_start: 0.8154 (p0) cc_final: 0.7766 (p0) REVERT: B 155 GLU cc_start: 0.7379 (pt0) cc_final: 0.6839 (pm20) REVERT: B 162 ASP cc_start: 0.7751 (m-30) cc_final: 0.7517 (p0) REVERT: B 205 ARG cc_start: 0.7888 (tpp80) cc_final: 0.7580 (mmm-85) REVERT: B 228 LYS cc_start: 0.8346 (tttm) cc_final: 0.7784 (ttmm) REVERT: B 333 ARG cc_start: 0.7679 (mtt90) cc_final: 0.7246 (mtt90) REVERT: B 346 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7246 (mm-30) REVERT: B 361 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7524 (mt-10) REVERT: B 397 GLN cc_start: 0.7650 (tt0) cc_final: 0.7417 (tt0) REVERT: B 428 GLU cc_start: 0.7482 (tt0) cc_final: 0.7032 (tp30) REVERT: B 499 LYS cc_start: 0.8161 (mtpp) cc_final: 0.7857 (mmmm) REVERT: B 515 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7162 (tm-30) REVERT: B 547 GLN cc_start: 0.7292 (tp-100) cc_final: 0.6923 (tp-100) REVERT: B 580 MET cc_start: 0.7720 (tpp) cc_final: 0.7096 (tpp) REVERT: B 594 ASP cc_start: 0.7898 (m-30) cc_final: 0.7555 (m-30) REVERT: B 607 ASN cc_start: 0.6969 (t0) cc_final: 0.6430 (t0) REVERT: B 626 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8270 (mm-30) REVERT: B 637 ARG cc_start: 0.7093 (mtp-110) cc_final: 0.6846 (mtp-110) REVERT: B 649 PHE cc_start: 0.7793 (p90) cc_final: 0.7500 (p90) REVERT: B 674 ASP cc_start: 0.7781 (p0) cc_final: 0.7523 (p0) REVERT: B 707 MET cc_start: 0.7984 (tpp) cc_final: 0.7214 (tpp) REVERT: B 739 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.6501 (m-10) REVERT: B 775 ASN cc_start: 0.6453 (m-40) cc_final: 0.6185 (m-40) REVERT: B 803 LEU cc_start: 0.8198 (mt) cc_final: 0.7945 (mt) REVERT: B 807 ARG cc_start: 0.7935 (ttm170) cc_final: 0.7493 (ttp-170) REVERT: B 837 MET cc_start: 0.8168 (mmm) cc_final: 0.7783 (tpp) REVERT: B 1020 MET cc_start: 0.6801 (mmt) cc_final: 0.6535 (mmt) REVERT: B 1063 PHE cc_start: 0.7944 (t80) cc_final: 0.7690 (t80) REVERT: B 1066 GLU cc_start: 0.7843 (tt0) cc_final: 0.7349 (mm-30) REVERT: B 1096 PHE cc_start: 0.6797 (OUTLIER) cc_final: 0.6527 (m-10) REVERT: B 1106 LYS cc_start: 0.7556 (ttmt) cc_final: 0.7334 (ttmm) REVERT: B 1132 LYS cc_start: 0.8052 (mttt) cc_final: 0.7582 (mttp) REVERT: B 1148 LYS cc_start: 0.8627 (mtpp) cc_final: 0.8371 (mmmm) REVERT: B 1154 GLN cc_start: 0.8490 (tt0) cc_final: 0.8194 (tt0) REVERT: B 1163 PHE cc_start: 0.7599 (m-10) cc_final: 0.7237 (m-80) REVERT: B 1199 PHE cc_start: 0.8345 (t80) cc_final: 0.8119 (t80) REVERT: B 1200 GLU cc_start: 0.8152 (pt0) cc_final: 0.7709 (pt0) REVERT: B 1204 GLU cc_start: 0.7530 (pp20) cc_final: 0.7277 (pp20) REVERT: B 1219 MET cc_start: 0.7455 (mmp) cc_final: 0.6900 (mmp) REVERT: B 1263 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7836 (mt-10) REVERT: B 1266 LEU cc_start: 0.7875 (mt) cc_final: 0.7606 (mt) REVERT: B 1383 LYS cc_start: 0.8872 (pttm) cc_final: 0.8471 (pttm) REVERT: B 1399 LYS cc_start: 0.8731 (pptt) cc_final: 0.8310 (pptt) outliers start: 93 outliers final: 67 residues processed: 712 average time/residue: 0.3204 time to fit residues: 348.3917 Evaluate side-chains 731 residues out of total 2365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 658 time to evaluate : 2.716 ------------------------------------------------------------------------------- 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 231 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 501 LEU 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 654 GLU Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 844 CYS Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1195 SER 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 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 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 1046 THR 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 1252 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 204 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 101 optimal weight: 0.3980 chunk 209 optimal weight: 0.6980 chunk 169 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 220 optimal weight: 0.5980 chunk 61 optimal weight: 0.0060 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20796 Z= 0.204 Angle : 0.656 15.088 28095 Z= 0.336 Chirality : 0.040 0.157 3318 Planarity : 0.004 0.061 3545 Dihedral : 5.124 53.775 2693 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.48 % Favored : 90.48 % Rotamer: Outliers : 4.48 % Allowed : 20.59 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.17), residues: 2521 helix: 1.24 (0.12), residues: 1761 sheet: -2.78 (1.04), residues: 20 loop : -2.69 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 470 HIS 0.009 0.001 HIS A 617 PHE 0.028 0.002 PHE B 925 TYR 0.025 0.001 TYR B 138 ARG 0.006 0.000 ARG A 174 *********************** 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 778 residues out of total 2365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 672 time to evaluate : 2.554 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: A 17 LYS cc_start: 0.8419 (ttmt) cc_final: 0.8080 (ttmt) REVERT: A 18 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7404 (mm-30) REVERT: A 78 GLN cc_start: 0.7920 (tp40) cc_final: 0.7648 (tp40) REVERT: A 91 ASN cc_start: 0.7646 (t0) cc_final: 0.7228 (t0) REVERT: A 155 GLU cc_start: 0.7541 (pt0) cc_final: 0.7093 (pt0) REVERT: A 184 LEU cc_start: 0.8234 (mt) cc_final: 0.7900 (mt) REVERT: A 199 SER cc_start: 0.8565 (t) cc_final: 0.8316 (t) REVERT: A 240 ILE cc_start: 0.8805 (mt) cc_final: 0.8513 (mm) REVERT: A 253 LYS cc_start: 0.8036 (pttt) cc_final: 0.7573 (pttt) REVERT: A 368 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7498 (mt-10) REVERT: A 460 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7412 (tm-30) REVERT: A 543 GLU cc_start: 0.7320 (mp0) cc_final: 0.6950 (mp0) REVERT: A 555 LYS cc_start: 0.8738 (mmmm) cc_final: 0.8457 (mmmm) REVERT: A 559 ARG cc_start: 0.7824 (tpp80) cc_final: 0.7147 (tpp80) REVERT: A 562 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7064 (mt-10) REVERT: A 565 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7812 (mm-30) REVERT: A 593 LYS cc_start: 0.7634 (tptm) cc_final: 0.7208 (tptm) REVERT: A 626 GLU cc_start: 0.7847 (tp30) cc_final: 0.7633 (tp30) REVERT: A 654 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6623 (pm20) REVERT: A 656 GLN cc_start: 0.7446 (tm-30) cc_final: 0.6834 (tm-30) REVERT: A 659 GLU cc_start: 0.7533 (mt-10) cc_final: 0.6444 (mp0) REVERT: A 663 GLU cc_start: 0.7551 (pt0) cc_final: 0.7098 (pt0) REVERT: A 745 ASP cc_start: 0.8120 (t70) cc_final: 0.7902 (t0) REVERT: A 811 LYS cc_start: 0.8526 (tptp) cc_final: 0.8314 (tptm) REVERT: A 911 ARG cc_start: 0.7559 (tpp-160) cc_final: 0.7207 (mmt-90) REVERT: A 917 LYS cc_start: 0.7514 (mmtt) cc_final: 0.7127 (mttp) REVERT: A 931 ARG cc_start: 0.7927 (ttp-110) cc_final: 0.7654 (ttp-110) REVERT: A 956 ASP cc_start: 0.6621 (p0) cc_final: 0.6208 (p0) REVERT: A 978 LYS cc_start: 0.8321 (tptt) cc_final: 0.8088 (tptt) REVERT: A 1017 LYS cc_start: 0.8086 (ttmm) cc_final: 0.7800 (ttmm) REVERT: A 1020 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7098 (tpp) REVERT: A 1021 GLU cc_start: 0.7851 (tp30) cc_final: 0.7191 (tp30) REVERT: A 1027 ASN cc_start: 0.6545 (p0) cc_final: 0.6209 (p0) REVERT: A 1043 LEU cc_start: 0.8962 (tt) cc_final: 0.8727 (tp) REVERT: A 1062 TYR cc_start: 0.7528 (p90) cc_final: 0.6942 (p90) REVERT: A 1072 GLU cc_start: 0.8059 (tt0) cc_final: 0.7488 (tt0) REVERT: A 1082 LYS cc_start: 0.7876 (mtpt) cc_final: 0.7425 (mtpt) REVERT: A 1089 LYS cc_start: 0.8378 (ttmm) cc_final: 0.8068 (ttmm) REVERT: A 1093 GLN cc_start: 0.8439 (tp40) cc_final: 0.8134 (tp40) REVERT: A 1112 MET cc_start: 0.7719 (mtp) cc_final: 0.7117 (ttm) REVERT: A 1113 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7904 (tp) REVERT: A 1116 LYS cc_start: 0.8754 (ttpt) cc_final: 0.8441 (ttmm) REVERT: A 1120 ILE cc_start: 0.9131 (mm) cc_final: 0.8746 (mm) REVERT: A 1126 GLN cc_start: 0.6913 (mm-40) cc_final: 0.6479 (mm-40) REVERT: A 1128 GLU cc_start: 0.7916 (tp30) cc_final: 0.7540 (tp30) REVERT: A 1132 LYS cc_start: 0.8363 (mmmm) cc_final: 0.7818 (mmmm) REVERT: A 1152 THR cc_start: 0.8614 (t) cc_final: 0.8303 (p) REVERT: A 1157 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7214 (mt-10) REVERT: A 1175 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8042 (mm) REVERT: A 1187 LYS cc_start: 0.8513 (mmmm) cc_final: 0.8242 (mmmm) REVERT: A 1200 GLU cc_start: 0.7857 (tp30) cc_final: 0.7514 (tp30) REVERT: A 1219 MET cc_start: 0.8182 (mmm) cc_final: 0.7926 (mmm) REVERT: A 1227 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7209 (mt-10) REVERT: A 1231 MET cc_start: 0.8101 (mmt) cc_final: 0.7724 (mpp) REVERT: A 1263 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7424 (mt-10) REVERT: A 1267 LYS cc_start: 0.8548 (mttm) cc_final: 0.8199 (mtpp) REVERT: A 1336 GLU cc_start: 0.8073 (tp30) cc_final: 0.7692 (tp30) REVERT: A 1365 ASN cc_start: 0.8319 (m-40) cc_final: 0.7988 (m-40) REVERT: A 1366 VAL cc_start: 0.8582 (p) cc_final: 0.8337 (m) REVERT: A 1383 LYS cc_start: 0.8235 (mmtm) cc_final: 0.8026 (mmtm) REVERT: A 1399 LYS cc_start: 0.8608 (ptpp) cc_final: 0.8337 (pttm) REVERT: A 1400 LYS cc_start: 0.8790 (mmtm) cc_final: 0.8537 (mmtm) REVERT: B 18 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7530 (mm-30) REVERT: B 82 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7293 (tmm) REVERT: B 91 ASN cc_start: 0.8100 (m110) cc_final: 0.7812 (m-40) REVERT: B 102 LEU cc_start: 0.8119 (mt) cc_final: 0.7847 (mt) REVERT: B 110 ILE cc_start: 0.8565 (pt) cc_final: 0.7202 (mm) REVERT: B 132 ASN cc_start: 0.8178 (p0) cc_final: 0.7717 (p0) REVERT: B 154 PHE cc_start: 0.8132 (p90) cc_final: 0.7663 (p90) REVERT: B 155 GLU cc_start: 0.7421 (pt0) cc_final: 0.6851 (pm20) REVERT: B 191 TYR cc_start: 0.8183 (t80) cc_final: 0.7929 (t80) REVERT: B 205 ARG cc_start: 0.7897 (tpp80) cc_final: 0.7597 (mmm-85) REVERT: B 228 LYS cc_start: 0.8314 (tttm) cc_final: 0.7767 (ttmm) REVERT: B 333 ARG cc_start: 0.7689 (mtt90) cc_final: 0.7268 (mtt90) REVERT: B 346 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7232 (mm-30) REVERT: B 361 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7515 (mt-10) REVERT: B 397 GLN cc_start: 0.7662 (tt0) cc_final: 0.7422 (tt0) REVERT: B 428 GLU cc_start: 0.7473 (tt0) cc_final: 0.6975 (tp30) REVERT: B 499 LYS cc_start: 0.8145 (mtpp) cc_final: 0.7868 (mmmm) REVERT: B 503 LYS cc_start: 0.8479 (tttt) cc_final: 0.7868 (ttmm) REVERT: B 515 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7171 (tm-30) REVERT: B 547 GLN cc_start: 0.7266 (tp-100) cc_final: 0.6770 (tp-100) REVERT: B 580 MET cc_start: 0.7720 (tpp) cc_final: 0.7090 (tpp) REVERT: B 594 ASP cc_start: 0.7919 (m-30) cc_final: 0.7565 (m-30) REVERT: B 607 ASN cc_start: 0.6938 (t0) cc_final: 0.6392 (t0) REVERT: B 626 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8265 (mm-30) REVERT: B 637 ARG cc_start: 0.7113 (mtp-110) cc_final: 0.6824 (mtp-110) REVERT: B 640 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7672 (mm-30) REVERT: B 649 PHE cc_start: 0.7792 (p90) cc_final: 0.7470 (p90) REVERT: B 739 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6504 (m-10) REVERT: B 775 ASN cc_start: 0.6512 (m-40) cc_final: 0.6244 (m-40) REVERT: B 803 LEU cc_start: 0.8202 (mt) cc_final: 0.7960 (mt) REVERT: B 807 ARG cc_start: 0.7944 (ttm170) cc_final: 0.7406 (ttp-170) REVERT: B 837 MET cc_start: 0.8175 (mmm) cc_final: 0.7774 (tpp) REVERT: B 861 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7970 (mm) REVERT: B 919 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7314 (mt0) REVERT: B 973 LEU cc_start: 0.8389 (mm) cc_final: 0.7530 (mt) REVERT: B 1020 MET cc_start: 0.6773 (mmt) cc_final: 0.6520 (mmt) REVERT: B 1063 PHE cc_start: 0.7963 (t80) cc_final: 0.7689 (t80) REVERT: B 1066 GLU cc_start: 0.7930 (tt0) cc_final: 0.7395 (mm-30) REVERT: B 1096 PHE cc_start: 0.6788 (OUTLIER) cc_final: 0.6500 (m-10) REVERT: B 1106 LYS cc_start: 0.7484 (ttmt) cc_final: 0.7268 (ttmm) REVERT: B 1132 LYS cc_start: 0.8061 (mttt) cc_final: 0.7640 (mttm) REVERT: B 1148 LYS cc_start: 0.8616 (mtpp) cc_final: 0.8348 (mmmm) REVERT: B 1154 GLN cc_start: 0.8494 (tt0) cc_final: 0.8102 (tt0) REVERT: B 1163 PHE cc_start: 0.7581 (m-10) cc_final: 0.7254 (m-80) REVERT: B 1200 GLU cc_start: 0.8150 (pt0) cc_final: 0.7702 (pt0) REVERT: B 1204 GLU cc_start: 0.7494 (pp20) cc_final: 0.7239 (pp20) REVERT: B 1219 MET cc_start: 0.7461 (mmp) cc_final: 0.6900 (mmp) REVERT: B 1231 MET cc_start: 0.6846 (mpp) cc_final: 0.6625 (mpp) REVERT: B 1263 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7818 (mt-10) REVERT: B 1266 LEU cc_start: 0.7841 (mt) cc_final: 0.7571 (mt) REVERT: B 1383 LYS cc_start: 0.8868 (pttm) cc_final: 0.8458 (pttm) REVERT: B 1399 LYS cc_start: 0.8687 (pptt) cc_final: 0.8301 (pptt) outliers start: 106 outliers final: 74 residues processed: 717 average time/residue: 0.3386 time to fit residues: 368.4711 Evaluate side-chains 733 residues out of total 2365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 650 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 26 MET 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 150 THR Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 401 LYS 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 654 GLU Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 798 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 901 THR Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 986 ASN 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 1175 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1243 LYS Chi-restraints excluded: chain A residue 1297 GLN 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 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 741 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 861 LEU Chi-restraints excluded: chain B residue 919 GLN 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 1046 THR 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 1087 LEU Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1252 ILE 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 82 optimal weight: 0.7980 chunk 221 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 144 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 245 optimal weight: 0.9980 chunk 204 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 129 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 B 713 HIS ** B1178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20796 Z= 0.238 Angle : 0.677 11.770 28095 Z= 0.349 Chirality : 0.041 0.180 3318 Planarity : 0.004 0.062 3545 Dihedral : 5.188 55.287 2693 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.68 % Favored : 90.24 % Rotamer: Outliers : 4.36 % Allowed : 21.90 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2521 helix: 1.18 (0.12), residues: 1760 sheet: -2.77 (1.04), residues: 20 loop : -2.73 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 773 HIS 0.009 0.001 HIS A 617 PHE 0.035 0.002 PHE A1288 TYR 0.031 0.001 TYR B 138 ARG 0.006 0.000 ARG A 174 *********************** 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 781 residues out of total 2365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 678 time to evaluate : 2.216 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: A 78 GLN cc_start: 0.7893 (tp40) cc_final: 0.7621 (tp40) REVERT: A 82 MET cc_start: 0.8066 (ttm) cc_final: 0.7707 (tmm) REVERT: A 91 ASN cc_start: 0.7655 (t0) cc_final: 0.7235 (t0) REVERT: A 154 PHE cc_start: 0.8410 (p90) cc_final: 0.8085 (p90) REVERT: A 155 GLU cc_start: 0.7540 (pt0) cc_final: 0.7263 (pt0) REVERT: A 184 LEU cc_start: 0.8239 (mt) cc_final: 0.7890 (mt) REVERT: A 199 SER cc_start: 0.8557 (t) cc_final: 0.8295 (t) REVERT: A 240 ILE cc_start: 0.8808 (mt) cc_final: 0.8514 (mm) REVERT: A 253 LYS cc_start: 0.8026 (pttt) cc_final: 0.7574 (pttt) REVERT: A 368 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7528 (mt-10) REVERT: A 555 LYS cc_start: 0.8751 (mmmm) cc_final: 0.8483 (mmmm) REVERT: A 559 ARG cc_start: 0.7839 (tpp80) cc_final: 0.7114 (tpp80) REVERT: A 562 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7051 (mt-10) REVERT: A 565 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7822 (mm-30) REVERT: A 593 LYS cc_start: 0.7657 (tptm) cc_final: 0.7220 (tptm) REVERT: A 600 PHE cc_start: 0.8476 (t80) cc_final: 0.8167 (t80) REVERT: A 626 GLU cc_start: 0.7856 (tp30) cc_final: 0.7642 (tp30) REVERT: A 654 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6765 (pm20) REVERT: A 656 GLN cc_start: 0.7539 (tm-30) cc_final: 0.6927 (tm-30) REVERT: A 659 GLU cc_start: 0.7590 (mt-10) cc_final: 0.6489 (mp0) REVERT: A 663 GLU cc_start: 0.7573 (pt0) cc_final: 0.7128 (pt0) REVERT: A 745 ASP cc_start: 0.8158 (t70) cc_final: 0.7943 (t0) REVERT: A 777 ILE cc_start: 0.7514 (tp) cc_final: 0.7304 (tt) REVERT: A 811 LYS cc_start: 0.8553 (tptp) cc_final: 0.8331 (tptm) REVERT: A 911 ARG cc_start: 0.7549 (tpp-160) cc_final: 0.7208 (mmt-90) REVERT: A 931 ARG cc_start: 0.7955 (ttp-110) cc_final: 0.7692 (ttp-110) REVERT: A 956 ASP cc_start: 0.6564 (OUTLIER) cc_final: 0.6279 (p0) REVERT: A 978 LYS cc_start: 0.8311 (tptt) cc_final: 0.8101 (tptt) REVERT: A 1017 LYS cc_start: 0.8114 (ttmm) cc_final: 0.7838 (ttmm) REVERT: A 1020 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7108 (tpp) REVERT: A 1021 GLU cc_start: 0.7873 (tp30) cc_final: 0.7224 (tp30) REVERT: A 1027 ASN cc_start: 0.6575 (p0) cc_final: 0.6235 (p0) REVERT: A 1062 TYR cc_start: 0.7554 (p90) cc_final: 0.6962 (p90) REVERT: A 1072 GLU cc_start: 0.8105 (tt0) cc_final: 0.7538 (tt0) REVERT: A 1082 LYS cc_start: 0.7847 (mtpt) cc_final: 0.7426 (mtpt) REVERT: A 1089 LYS cc_start: 0.8500 (ttmm) cc_final: 0.8119 (ttmm) REVERT: A 1093 GLN cc_start: 0.8450 (tp40) cc_final: 0.8141 (tp40) REVERT: A 1113 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7916 (tp) REVERT: A 1116 LYS cc_start: 0.8739 (ttpt) cc_final: 0.8427 (ttmm) REVERT: A 1120 ILE cc_start: 0.9140 (mm) cc_final: 0.8749 (mm) REVERT: A 1126 GLN cc_start: 0.6945 (mm-40) cc_final: 0.6457 (mm-40) REVERT: A 1128 GLU cc_start: 0.7939 (tp30) cc_final: 0.7557 (tp30) REVERT: A 1132 LYS cc_start: 0.8369 (mmmm) cc_final: 0.7824 (mmmm) REVERT: A 1152 THR cc_start: 0.8654 (t) cc_final: 0.8281 (p) REVERT: A 1157 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7268 (mt-10) REVERT: A 1175 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8035 (mm) REVERT: A 1187 LYS cc_start: 0.8510 (mmmm) cc_final: 0.8199 (mmmm) REVERT: A 1191 MET cc_start: 0.7326 (tpt) cc_final: 0.6892 (tpt) REVERT: A 1200 GLU cc_start: 0.7862 (tp30) cc_final: 0.7518 (tp30) REVERT: A 1219 MET cc_start: 0.8181 (mmm) cc_final: 0.7925 (mmm) REVERT: A 1263 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7438 (mt-10) REVERT: A 1267 LYS cc_start: 0.8555 (mttm) cc_final: 0.8209 (mtpp) REVERT: A 1336 GLU cc_start: 0.8078 (tp30) cc_final: 0.7716 (tp30) REVERT: A 1365 ASN cc_start: 0.8358 (m-40) cc_final: 0.8038 (m-40) REVERT: A 1366 VAL cc_start: 0.8625 (p) cc_final: 0.8395 (m) REVERT: A 1383 LYS cc_start: 0.8243 (mmtm) cc_final: 0.8005 (mmtm) REVERT: A 1399 LYS cc_start: 0.8611 (ptpp) cc_final: 0.8314 (pttm) REVERT: A 1400 LYS cc_start: 0.8796 (mmtm) cc_final: 0.8534 (mmtm) REVERT: B 18 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7504 (mm-30) REVERT: B 81 LEU cc_start: 0.7960 (mt) cc_final: 0.7758 (mt) REVERT: B 82 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7314 (tmm) REVERT: B 91 ASN cc_start: 0.8114 (m110) cc_final: 0.7830 (m-40) REVERT: B 102 LEU cc_start: 0.8143 (mt) cc_final: 0.7875 (mt) REVERT: B 110 ILE cc_start: 0.8592 (pt) cc_final: 0.7252 (mm) REVERT: B 132 ASN cc_start: 0.8204 (p0) cc_final: 0.7762 (p0) REVERT: B 154 PHE cc_start: 0.8123 (p90) cc_final: 0.7771 (p90) REVERT: B 155 GLU cc_start: 0.7417 (pt0) cc_final: 0.6824 (pm20) REVERT: B 191 TYR cc_start: 0.8190 (t80) cc_final: 0.7949 (t80) REVERT: B 205 ARG cc_start: 0.7911 (tpp80) cc_final: 0.7639 (mmm-85) REVERT: B 228 LYS cc_start: 0.8328 (tttm) cc_final: 0.7769 (ttmm) REVERT: B 333 ARG cc_start: 0.7698 (mtt90) cc_final: 0.7277 (mtt90) REVERT: B 346 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7242 (mm-30) REVERT: B 361 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7520 (mt-10) REVERT: B 397 GLN cc_start: 0.7668 (tt0) cc_final: 0.7418 (tt0) REVERT: B 428 GLU cc_start: 0.7488 (tt0) cc_final: 0.7000 (tp30) REVERT: B 503 LYS cc_start: 0.8504 (tttt) cc_final: 0.7881 (ttmm) REVERT: B 515 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7194 (tm-30) REVERT: B 547 GLN cc_start: 0.7281 (tp-100) cc_final: 0.6810 (tp-100) REVERT: B 580 MET cc_start: 0.7748 (tpp) cc_final: 0.7113 (tpp) REVERT: B 594 ASP cc_start: 0.7940 (m-30) cc_final: 0.7575 (m-30) REVERT: B 607 ASN cc_start: 0.6939 (t0) cc_final: 0.6464 (t0) REVERT: B 626 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8192 (mm-30) REVERT: B 637 ARG cc_start: 0.7140 (mtp-110) cc_final: 0.6881 (mtp-110) REVERT: B 649 PHE cc_start: 0.7790 (p90) cc_final: 0.7471 (p90) REVERT: B 707 MET cc_start: 0.7985 (tpp) cc_final: 0.7253 (tpp) REVERT: B 739 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.6492 (m-10) REVERT: B 775 ASN cc_start: 0.6590 (m-40) cc_final: 0.6327 (m-40) REVERT: B 803 LEU cc_start: 0.8206 (mt) cc_final: 0.7970 (mt) REVERT: B 807 ARG cc_start: 0.7950 (ttm170) cc_final: 0.7446 (ttp-170) REVERT: B 837 MET cc_start: 0.8192 (mmm) cc_final: 0.7797 (tpp) REVERT: B 857 PHE cc_start: 0.7337 (t80) cc_final: 0.7118 (t80) REVERT: B 861 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8030 (mm) REVERT: B 919 GLN cc_start: 0.7730 (mt0) cc_final: 0.7517 (mt0) REVERT: B 1014 LYS cc_start: 0.8803 (pttp) cc_final: 0.8491 (pttp) REVERT: B 1020 MET cc_start: 0.6751 (mmt) cc_final: 0.6539 (mmt) REVERT: B 1063 PHE cc_start: 0.7924 (t80) cc_final: 0.7685 (t80) REVERT: B 1066 GLU cc_start: 0.7827 (tt0) cc_final: 0.7415 (mm-30) REVERT: B 1096 PHE cc_start: 0.6791 (OUTLIER) cc_final: 0.6502 (m-10) REVERT: B 1106 LYS cc_start: 0.7512 (ttmt) cc_final: 0.7264 (ttmm) REVERT: B 1112 MET cc_start: 0.8079 (mtp) cc_final: 0.7841 (mtm) REVERT: B 1132 LYS cc_start: 0.8091 (mttt) cc_final: 0.7607 (mttm) REVERT: B 1148 LYS cc_start: 0.8642 (mtpp) cc_final: 0.8365 (mmmm) REVERT: B 1154 GLN cc_start: 0.8547 (tt0) cc_final: 0.8261 (tt0) REVERT: B 1163 PHE cc_start: 0.7632 (m-10) cc_final: 0.7297 (m-80) REVERT: B 1200 GLU cc_start: 0.8133 (pt0) cc_final: 0.7712 (pt0) REVERT: B 1219 MET cc_start: 0.7517 (mmp) cc_final: 0.7020 (mmp) REVERT: B 1220 TRP cc_start: 0.7866 (m-10) cc_final: 0.7379 (m-90) REVERT: B 1263 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7806 (mt-10) REVERT: B 1266 LEU cc_start: 0.7829 (mt) cc_final: 0.7553 (mt) REVERT: B 1383 LYS cc_start: 0.8884 (pttm) cc_final: 0.8457 (pttm) REVERT: B 1399 LYS cc_start: 0.8658 (pptt) cc_final: 0.8351 (pptt) REVERT: B 1412 GLU cc_start: 0.5833 (OUTLIER) cc_final: 0.4070 (mm-30) outliers start: 103 outliers final: 77 residues processed: 715 average time/residue: 0.3359 time to fit residues: 364.5087 Evaluate side-chains 752 residues out of total 2365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 665 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 26 MET 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 150 THR Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 401 LYS 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 654 GLU Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 780 THR 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 838 ILE Chi-restraints excluded: chain A residue 844 CYS Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1012 GLU 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 1175 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1195 SER Chi-restraints excluded: chain A residue 1243 LYS Chi-restraints excluded: chain A residue 1297 GLN 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 98 LEU 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 240 ILE Chi-restraints excluded: chain B residue 385 SER 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 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 741 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 821 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 931 ARG Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 1028 ILE Chi-restraints excluded: chain B residue 1046 THR 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 1079 LEU Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1252 ILE 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 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 236 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 140 optimal weight: 0.5980 chunk 179 optimal weight: 0.5980 chunk 139 optimal weight: 0.5980 chunk 206 optimal weight: 0.5980 chunk 137 optimal weight: 0.8980 chunk 244 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 B 919 GLN ** B1178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2151 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= 0.229 Angle : 0.691 15.505 28095 Z= 0.353 Chirality : 0.042 0.290 3318 Planarity : 0.004 0.063 3545 Dihedral : 5.216 57.560 2693 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.44 % Favored : 90.44 % Rotamer: Outliers : 4.27 % Allowed : 22.41 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.17), residues: 2521 helix: 1.19 (0.12), residues: 1756 sheet: -3.07 (0.98), residues: 22 loop : -2.71 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 773 HIS 0.009 0.001 HIS A 617 PHE 0.036 0.002 PHE A1288 TYR 0.028 0.001 TYR B 138 ARG 0.006 0.000 ARG A 174 *********************** 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 782 residues out of total 2365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 681 time to evaluate : 2.467 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: A 17 LYS cc_start: 0.8373 (ttmt) cc_final: 0.8141 (ttmt) REVERT: A 78 GLN cc_start: 0.7901 (tp40) cc_final: 0.7627 (tp40) REVERT: A 91 ASN cc_start: 0.7663 (t0) cc_final: 0.7237 (t0) REVERT: A 154 PHE cc_start: 0.8399 (p90) cc_final: 0.8092 (p90) REVERT: A 155 GLU cc_start: 0.7526 (pt0) cc_final: 0.7111 (pt0) REVERT: A 184 LEU cc_start: 0.8244 (mt) cc_final: 0.7888 (mt) REVERT: A 199 SER cc_start: 0.8551 (t) cc_final: 0.8304 (t) REVERT: A 240 ILE cc_start: 0.8797 (mt) cc_final: 0.8512 (mm) REVERT: A 253 LYS cc_start: 0.7978 (pttt) cc_final: 0.7534 (pttt) REVERT: A 368 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7525 (mt-10) REVERT: A 555 LYS cc_start: 0.8745 (mmmm) cc_final: 0.8478 (mmmm) REVERT: A 559 ARG cc_start: 0.7829 (tpp80) cc_final: 0.7086 (tpp80) REVERT: A 562 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7039 (mt-10) REVERT: A 565 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7783 (mm-30) REVERT: A 593 LYS cc_start: 0.7661 (tptm) cc_final: 0.7217 (tptm) REVERT: A 600 PHE cc_start: 0.8485 (t80) cc_final: 0.8218 (t80) REVERT: A 606 MET cc_start: 0.7408 (mmm) cc_final: 0.7111 (tpp) REVERT: A 626 GLU cc_start: 0.7861 (tp30) cc_final: 0.7633 (tp30) REVERT: A 654 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6724 (pm20) REVERT: A 656 GLN cc_start: 0.7535 (tm-30) cc_final: 0.6926 (tm-30) REVERT: A 659 GLU cc_start: 0.7572 (mt-10) cc_final: 0.6489 (mp0) REVERT: A 663 GLU cc_start: 0.7586 (pt0) cc_final: 0.7147 (pt0) REVERT: A 745 ASP cc_start: 0.8155 (t70) cc_final: 0.7946 (t0) REVERT: A 811 LYS cc_start: 0.8534 (tptp) cc_final: 0.8305 (tptm) REVERT: A 819 SER cc_start: 0.8278 (m) cc_final: 0.7974 (p) REVERT: A 911 ARG cc_start: 0.7555 (tpp-160) cc_final: 0.7206 (mmt-90) REVERT: A 917 LYS cc_start: 0.7594 (mmtt) cc_final: 0.7063 (mttp) REVERT: A 931 ARG cc_start: 0.7948 (ttp-110) cc_final: 0.7674 (ttp-110) REVERT: A 956 ASP cc_start: 0.6646 (OUTLIER) cc_final: 0.6270 (p0) REVERT: A 1020 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7099 (tpp) REVERT: A 1021 GLU cc_start: 0.7888 (tp30) cc_final: 0.7254 (tp30) REVERT: A 1027 ASN cc_start: 0.6577 (p0) cc_final: 0.6202 (p0) REVERT: A 1062 TYR cc_start: 0.7568 (p90) cc_final: 0.6926 (p90) REVERT: A 1072 GLU cc_start: 0.8104 (tt0) cc_final: 0.7569 (tt0) REVERT: A 1082 LYS cc_start: 0.7809 (mtpt) cc_final: 0.7526 (mtpt) REVERT: A 1089 LYS cc_start: 0.8478 (ttmm) cc_final: 0.8092 (ttmm) REVERT: A 1093 GLN cc_start: 0.8392 (tp40) cc_final: 0.8148 (tp40) REVERT: A 1112 MET cc_start: 0.7703 (mtp) cc_final: 0.7056 (ttm) REVERT: A 1113 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7939 (tp) REVERT: A 1116 LYS cc_start: 0.8721 (ttpt) cc_final: 0.8376 (ttmm) REVERT: A 1120 ILE cc_start: 0.9145 (mm) cc_final: 0.8752 (mm) REVERT: A 1126 GLN cc_start: 0.6966 (mm-40) cc_final: 0.6456 (mm-40) REVERT: A 1128 GLU cc_start: 0.7946 (tp30) cc_final: 0.7565 (tp30) REVERT: A 1132 LYS cc_start: 0.8365 (mmmm) cc_final: 0.7827 (mmmm) REVERT: A 1157 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7259 (mt-10) REVERT: A 1175 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8041 (mm) REVERT: A 1187 LYS cc_start: 0.8506 (mmmm) cc_final: 0.8199 (mmmm) REVERT: A 1200 GLU cc_start: 0.7854 (tp30) cc_final: 0.7518 (tp30) REVERT: A 1219 MET cc_start: 0.8165 (mmm) cc_final: 0.7918 (mmm) REVERT: A 1231 MET cc_start: 0.8121 (mmt) cc_final: 0.7752 (mpp) REVERT: A 1263 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7439 (mt-10) REVERT: A 1267 LYS cc_start: 0.8544 (mttm) cc_final: 0.8200 (mtpp) REVERT: A 1336 GLU cc_start: 0.8077 (tp30) cc_final: 0.7735 (tp30) REVERT: A 1365 ASN cc_start: 0.8346 (m-40) cc_final: 0.8029 (m-40) REVERT: A 1366 VAL cc_start: 0.8628 (p) cc_final: 0.8391 (m) REVERT: A 1383 LYS cc_start: 0.8244 (mmtm) cc_final: 0.8014 (mmtm) REVERT: A 1385 LEU cc_start: 0.8255 (mm) cc_final: 0.7959 (mm) REVERT: A 1399 LYS cc_start: 0.8596 (ptpp) cc_final: 0.8289 (pttm) REVERT: A 1400 LYS cc_start: 0.8777 (mmtm) cc_final: 0.8516 (mmtm) REVERT: A 1409 LYS cc_start: 0.8103 (mmmt) cc_final: 0.7742 (pttm) REVERT: B 18 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7484 (mm-30) REVERT: B 81 LEU cc_start: 0.7996 (mt) cc_final: 0.7789 (mt) REVERT: B 82 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7294 (tmm) REVERT: B 91 ASN cc_start: 0.8111 (m110) cc_final: 0.7833 (m-40) REVERT: B 102 LEU cc_start: 0.8142 (mt) cc_final: 0.7867 (mt) REVERT: B 110 ILE cc_start: 0.8586 (pt) cc_final: 0.7236 (mm) REVERT: B 132 ASN cc_start: 0.8217 (p0) cc_final: 0.7759 (p0) REVERT: B 154 PHE cc_start: 0.8126 (p90) cc_final: 0.7706 (p90) REVERT: B 155 GLU cc_start: 0.7413 (pt0) cc_final: 0.6816 (pm20) REVERT: B 191 TYR cc_start: 0.8183 (t80) cc_final: 0.7942 (t80) REVERT: B 205 ARG cc_start: 0.7937 (tpp80) cc_final: 0.7676 (mmm-85) REVERT: B 333 ARG cc_start: 0.7711 (mtt90) cc_final: 0.7285 (mtt90) REVERT: B 346 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7247 (mm-30) REVERT: B 361 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7556 (mt-10) REVERT: B 397 GLN cc_start: 0.7665 (tt0) cc_final: 0.7328 (tt0) REVERT: B 428 GLU cc_start: 0.7480 (tt0) cc_final: 0.6988 (tp30) REVERT: B 503 LYS cc_start: 0.8505 (tttt) cc_final: 0.7880 (ttmm) REVERT: B 515 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7259 (tm-30) REVERT: B 547 GLN cc_start: 0.7290 (tp-100) cc_final: 0.6870 (tp-100) REVERT: B 580 MET cc_start: 0.7706 (tpp) cc_final: 0.7062 (tpp) REVERT: B 594 ASP cc_start: 0.7931 (m-30) cc_final: 0.7570 (m-30) REVERT: B 607 ASN cc_start: 0.6887 (t0) cc_final: 0.6361 (t0) REVERT: B 626 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8189 (mm-30) REVERT: B 637 ARG cc_start: 0.7132 (mtp-110) cc_final: 0.6713 (mtp-110) REVERT: B 640 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7696 (mm-30) REVERT: B 649 PHE cc_start: 0.7795 (p90) cc_final: 0.7460 (p90) REVERT: B 707 MET cc_start: 0.7978 (tpp) cc_final: 0.7236 (tpp) REVERT: B 739 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.6547 (m-10) REVERT: B 775 ASN cc_start: 0.6670 (m-40) cc_final: 0.6426 (m-40) REVERT: B 803 LEU cc_start: 0.8197 (mt) cc_final: 0.7927 (mt) REVERT: B 807 ARG cc_start: 0.7917 (ttm170) cc_final: 0.7533 (ttp-170) REVERT: B 861 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7894 (mm) REVERT: B 919 GLN cc_start: 0.7608 (mt0) cc_final: 0.7309 (mt0) REVERT: B 973 LEU cc_start: 0.8390 (mm) cc_final: 0.7530 (mt) REVERT: B 1020 MET cc_start: 0.6730 (mmt) cc_final: 0.6460 (mmt) REVERT: B 1059 ASN cc_start: 0.8340 (p0) cc_final: 0.8024 (p0) REVERT: B 1063 PHE cc_start: 0.7931 (t80) cc_final: 0.7687 (t80) REVERT: B 1066 GLU cc_start: 0.7808 (tt0) cc_final: 0.7466 (mm-30) REVERT: B 1080 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6904 (t80) REVERT: B 1096 PHE cc_start: 0.6771 (OUTLIER) cc_final: 0.6507 (m-10) REVERT: B 1106 LYS cc_start: 0.7525 (ttmt) cc_final: 0.7285 (ttmm) REVERT: B 1112 MET cc_start: 0.8062 (mtp) cc_final: 0.7817 (mtm) REVERT: B 1132 LYS cc_start: 0.8086 (mttt) cc_final: 0.7599 (mttm) REVERT: B 1150 PHE cc_start: 0.8496 (m-10) cc_final: 0.8272 (m-80) REVERT: B 1154 GLN cc_start: 0.8556 (tt0) cc_final: 0.8197 (tt0) REVERT: B 1200 GLU cc_start: 0.8097 (pt0) cc_final: 0.7818 (pt0) REVERT: B 1219 MET cc_start: 0.7529 (mmp) cc_final: 0.7041 (mmp) REVERT: B 1220 TRP cc_start: 0.7843 (m-10) cc_final: 0.7333 (m-90) REVERT: B 1231 MET cc_start: 0.6919 (mpp) cc_final: 0.6705 (mpp) REVERT: B 1266 LEU cc_start: 0.7802 (mt) cc_final: 0.7516 (mt) REVERT: B 1383 LYS cc_start: 0.8877 (pttm) cc_final: 0.8439 (pttm) REVERT: B 1399 LYS cc_start: 0.8668 (pptt) cc_final: 0.8337 (pptt) REVERT: B 1412 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.4185 (mm-30) outliers start: 101 outliers final: 78 residues processed: 718 average time/residue: 0.3325 time to fit residues: 362.0895 Evaluate side-chains 754 residues out of total 2365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 665 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 401 LYS 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 654 GLU Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 844 CYS Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1012 GLU 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 1175 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1195 SER Chi-restraints excluded: chain A residue 1297 GLN 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 192 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 385 SER 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 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 741 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 931 ARG 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 1046 THR 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 1079 LEU Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1194 GLN Chi-restraints excluded: chain B residue 1252 ILE Chi-restraints excluded: chain B residue 1290 ILE Chi-restraints excluded: chain B residue 1320 LYS 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 151 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 166 optimal weight: 0.5980 chunk 121 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 192 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** ** B1349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20796 Z= 0.239 Angle : 0.700 13.446 28095 Z= 0.356 Chirality : 0.042 0.363 3318 Planarity : 0.005 0.063 3545 Dihedral : 5.245 59.329 2693 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.52 % Favored : 90.40 % Rotamer: Outliers : 4.36 % Allowed : 22.92 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.17), residues: 2521 helix: 1.17 (0.12), residues: 1756 sheet: -3.05 (0.98), residues: 22 loop : -2.70 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 773 HIS 0.009 0.001 HIS A 617 PHE 0.037 0.002 PHE A1288 TYR 0.029 0.001 TYR B 138 ARG 0.007 0.000 ARG A 174 *********************** 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 791 residues out of total 2365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 688 time to evaluate : 2.644 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: 0.8380 (ttmt) cc_final: 0.8147 (ttmt) REVERT: A 78 GLN cc_start: 0.7893 (tp40) cc_final: 0.7638 (tp40) REVERT: A 91 ASN cc_start: 0.7666 (t0) cc_final: 0.7229 (t0) REVERT: A 154 PHE cc_start: 0.8401 (p90) cc_final: 0.8042 (p90) REVERT: A 155 GLU cc_start: 0.7533 (pt0) cc_final: 0.7119 (pt0) REVERT: A 184 LEU cc_start: 0.8244 (mt) cc_final: 0.7896 (mt) REVERT: A 199 SER cc_start: 0.8555 (t) cc_final: 0.8302 (t) REVERT: A 240 ILE cc_start: 0.8796 (mt) cc_final: 0.8512 (mm) REVERT: A 253 LYS cc_start: 0.7966 (pttt) cc_final: 0.7534 (pttt) REVERT: A 368 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7526 (mt-10) REVERT: A 555 LYS cc_start: 0.8744 (mmmm) cc_final: 0.8479 (mmmm) REVERT: A 559 ARG cc_start: 0.7827 (tpp80) cc_final: 0.7067 (tpp80) REVERT: A 562 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7032 (mt-10) REVERT: A 565 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7786 (mm-30) REVERT: A 593 LYS cc_start: 0.7625 (tptm) cc_final: 0.7185 (tptm) REVERT: A 597 GLU cc_start: 0.7670 (tm-30) cc_final: 0.6838 (tm-30) REVERT: A 600 PHE cc_start: 0.8497 (t80) cc_final: 0.8251 (t80) REVERT: A 626 GLU cc_start: 0.7862 (tp30) cc_final: 0.7627 (tp30) REVERT: A 654 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6681 (pm20) REVERT: A 656 GLN cc_start: 0.7542 (tm-30) cc_final: 0.6920 (tm-30) REVERT: A 659 GLU cc_start: 0.7571 (mt-10) cc_final: 0.6493 (mp0) REVERT: A 663 GLU cc_start: 0.7588 (pt0) cc_final: 0.7151 (pt0) REVERT: A 745 ASP cc_start: 0.8168 (t70) cc_final: 0.7960 (t0) REVERT: A 819 SER cc_start: 0.8280 (m) cc_final: 0.7967 (p) REVERT: A 852 ASP cc_start: 0.7455 (t0) cc_final: 0.7251 (t0) REVERT: A 911 ARG cc_start: 0.7555 (tpp-160) cc_final: 0.7214 (mmt-90) REVERT: A 917 LYS cc_start: 0.7597 (mmtt) cc_final: 0.7072 (mttp) REVERT: A 931 ARG cc_start: 0.7960 (ttp-110) cc_final: 0.7690 (ttp-110) REVERT: A 956 ASP cc_start: 0.6624 (OUTLIER) cc_final: 0.6220 (p0) REVERT: A 1020 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7084 (tpp) REVERT: A 1021 GLU cc_start: 0.7896 (tp30) cc_final: 0.7259 (tp30) REVERT: A 1027 ASN cc_start: 0.6623 (p0) cc_final: 0.6253 (p0) REVERT: A 1062 TYR cc_start: 0.7576 (p90) cc_final: 0.6888 (p90) REVERT: A 1072 GLU cc_start: 0.8116 (tt0) cc_final: 0.7339 (tt0) REVERT: A 1082 LYS cc_start: 0.7809 (mtpt) cc_final: 0.7512 (mtpt) REVERT: A 1089 LYS cc_start: 0.8447 (ttmm) cc_final: 0.8066 (ttmm) REVERT: A 1093 GLN cc_start: 0.8401 (tp40) cc_final: 0.8160 (tp40) REVERT: A 1113 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7939 (tp) REVERT: A 1116 LYS cc_start: 0.8712 (ttpt) cc_final: 0.8380 (ttmm) REVERT: A 1120 ILE cc_start: 0.9155 (mm) cc_final: 0.8761 (mm) REVERT: A 1126 GLN cc_start: 0.6972 (mm-40) cc_final: 0.6466 (mm-40) REVERT: A 1128 GLU cc_start: 0.7946 (tp30) cc_final: 0.7573 (tp30) REVERT: A 1132 LYS cc_start: 0.8361 (mmmm) cc_final: 0.7826 (mmmm) REVERT: A 1157 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7248 (mt-10) REVERT: A 1175 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8036 (mm) REVERT: A 1187 LYS cc_start: 0.8512 (mmmm) cc_final: 0.8212 (mmmm) REVERT: A 1200 GLU cc_start: 0.7850 (tp30) cc_final: 0.7517 (tp30) REVERT: A 1219 MET cc_start: 0.8174 (mmm) cc_final: 0.7783 (mmm) REVERT: A 1227 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7241 (mt-10) REVERT: A 1231 MET cc_start: 0.8125 (mmt) cc_final: 0.7823 (mpp) REVERT: A 1263 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7443 (mt-10) REVERT: A 1267 LYS cc_start: 0.8549 (mttm) cc_final: 0.8214 (mtpp) REVERT: A 1336 GLU cc_start: 0.8071 (tp30) cc_final: 0.7722 (tp30) REVERT: A 1365 ASN cc_start: 0.8323 (m-40) cc_final: 0.8003 (m-40) REVERT: A 1366 VAL cc_start: 0.8646 (p) cc_final: 0.8417 (m) REVERT: A 1383 LYS cc_start: 0.8233 (mmtm) cc_final: 0.8004 (mmtm) REVERT: A 1385 LEU cc_start: 0.8271 (mm) cc_final: 0.7993 (mm) REVERT: A 1399 LYS cc_start: 0.8567 (ptpp) cc_final: 0.8260 (pttm) REVERT: A 1400 LYS cc_start: 0.8776 (mmtm) cc_final: 0.8513 (mmtm) REVERT: A 1409 LYS cc_start: 0.8090 (mmmt) cc_final: 0.7754 (pttm) REVERT: B 81 LEU cc_start: 0.8009 (mt) cc_final: 0.7803 (mt) REVERT: B 82 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7300 (tmm) REVERT: B 91 ASN cc_start: 0.8112 (m110) cc_final: 0.7828 (m-40) REVERT: B 102 LEU cc_start: 0.8145 (mt) cc_final: 0.7873 (mt) REVERT: B 110 ILE cc_start: 0.8577 (pt) cc_final: 0.7216 (mm) REVERT: B 132 ASN cc_start: 0.8210 (p0) cc_final: 0.7774 (p0) REVERT: B 154 PHE cc_start: 0.8099 (p90) cc_final: 0.7581 (p90) REVERT: B 155 GLU cc_start: 0.7382 (pt0) cc_final: 0.6830 (pm20) REVERT: B 205 ARG cc_start: 0.7936 (tpp80) cc_final: 0.7685 (mmm-85) REVERT: B 333 ARG cc_start: 0.7706 (mtt90) cc_final: 0.7289 (mtt90) REVERT: B 346 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7248 (mm-30) REVERT: B 361 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7558 (mt-10) REVERT: B 397 GLN cc_start: 0.7666 (tt0) cc_final: 0.7337 (tt0) REVERT: B 428 GLU cc_start: 0.7478 (tt0) cc_final: 0.6976 (tp30) REVERT: B 499 LYS cc_start: 0.8097 (mmmm) cc_final: 0.7790 (mmmm) REVERT: B 503 LYS cc_start: 0.8512 (tttt) cc_final: 0.7878 (ttmm) REVERT: B 515 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7229 (tm-30) REVERT: B 547 GLN cc_start: 0.7288 (tp-100) cc_final: 0.6864 (tp-100) REVERT: B 580 MET cc_start: 0.7717 (tpp) cc_final: 0.7065 (tpp) REVERT: B 594 ASP cc_start: 0.7929 (m-30) cc_final: 0.7574 (m-30) REVERT: B 607 ASN cc_start: 0.6927 (t0) cc_final: 0.6431 (t0) REVERT: B 626 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8181 (mm-30) REVERT: B 637 ARG cc_start: 0.7141 (mtp-110) cc_final: 0.6778 (mtp-110) REVERT: B 707 MET cc_start: 0.7977 (tpp) cc_final: 0.7227 (tpp) REVERT: B 739 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.6458 (m-10) REVERT: B 775 ASN cc_start: 0.6711 (m-40) cc_final: 0.6470 (m-40) REVERT: B 803 LEU cc_start: 0.8175 (mt) cc_final: 0.7899 (mt) REVERT: B 807 ARG cc_start: 0.7910 (ttm170) cc_final: 0.7520 (ttp-170) REVERT: B 861 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7885 (mm) REVERT: B 919 GLN cc_start: 0.7636 (mt0) cc_final: 0.7387 (mt0) REVERT: B 972 LYS cc_start: 0.8437 (mttp) cc_final: 0.8143 (mtpt) REVERT: B 973 LEU cc_start: 0.8390 (mm) cc_final: 0.7494 (mt) REVERT: B 989 LYS cc_start: 0.6428 (pttt) cc_final: 0.5392 (pttm) REVERT: B 1020 MET cc_start: 0.6725 (mmt) cc_final: 0.6474 (mmt) REVERT: B 1059 ASN cc_start: 0.8354 (p0) cc_final: 0.8003 (p0) REVERT: B 1063 PHE cc_start: 0.7926 (t80) cc_final: 0.7671 (t80) REVERT: B 1066 GLU cc_start: 0.7916 (tt0) cc_final: 0.7500 (mm-30) REVERT: B 1080 PHE cc_start: 0.7236 (OUTLIER) cc_final: 0.6950 (t80) REVERT: B 1096 PHE cc_start: 0.6789 (OUTLIER) cc_final: 0.6539 (m-10) REVERT: B 1106 LYS cc_start: 0.7526 (ttmt) cc_final: 0.7293 (ttmm) REVERT: B 1112 MET cc_start: 0.8059 (mtp) cc_final: 0.7836 (mtm) REVERT: B 1132 LYS cc_start: 0.8085 (mttt) cc_final: 0.7592 (mttm) REVERT: B 1154 GLN cc_start: 0.8567 (tt0) cc_final: 0.8226 (tt0) REVERT: B 1200 GLU cc_start: 0.8080 (pt0) cc_final: 0.7796 (pt0) REVERT: B 1219 MET cc_start: 0.7562 (mmp) cc_final: 0.7037 (mmp) REVERT: B 1220 TRP cc_start: 0.7854 (m-10) cc_final: 0.7379 (m-90) REVERT: B 1231 MET cc_start: 0.6831 (mpp) cc_final: 0.6596 (mpp) REVERT: B 1263 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7842 (mt-10) REVERT: B 1266 LEU cc_start: 0.7816 (mt) cc_final: 0.7543 (mt) REVERT: B 1383 LYS cc_start: 0.8878 (pttm) cc_final: 0.8438 (pttm) REVERT: B 1399 LYS cc_start: 0.8660 (pptt) cc_final: 0.8353 (pptt) REVERT: B 1412 GLU cc_start: 0.5994 (OUTLIER) cc_final: 0.4151 (mm-30) outliers start: 103 outliers final: 81 residues processed: 725 average time/residue: 0.3511 time to fit residues: 388.2774 Evaluate side-chains 764 residues out of total 2365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 672 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 401 LYS 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 654 GLU Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 780 THR 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 832 HIS Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 844 CYS Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1012 GLU 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 1175 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1195 SER Chi-restraints excluded: chain A residue 1229 SER Chi-restraints excluded: chain A residue 1297 GLN Chi-restraints excluded: chain A residue 1313 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 193 VAL Chi-restraints excluded: chain B residue 385 SER 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 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 741 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 931 ARG 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 1046 THR 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 1080 PHE Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1215 ASN Chi-restraints excluded: chain B residue 1252 ILE Chi-restraints excluded: chain B residue 1290 ILE Chi-restraints excluded: chain B residue 1320 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 222 optimal weight: 0.7980 chunk 234 optimal weight: 2.9990 chunk 213 optimal weight: 0.0570 chunk 228 optimal weight: 0.3980 chunk 137 optimal weight: 0.9980 chunk 99 optimal weight: 0.0030 chunk 179 optimal weight: 0.8980 chunk 70 optimal weight: 0.3980 chunk 206 optimal weight: 0.5980 chunk 215 optimal weight: 0.6980 chunk 227 optimal weight: 0.5980 overall best weight: 0.2908 ------------------------------------------------------------------------------- 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 B 334 GLN ** B 692 GLN ** 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** ** B1349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20796 Z= 0.201 Angle : 0.713 14.086 28095 Z= 0.358 Chirality : 0.041 0.255 3318 Planarity : 0.004 0.063 3545 Dihedral : 5.177 58.938 2693 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.08 % Favored : 90.84 % Rotamer: Outliers : 3.93 % Allowed : 23.72 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.17), residues: 2521 helix: 1.24 (0.12), residues: 1753 sheet: -3.02 (1.00), residues: 22 loop : -2.72 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 470 HIS 0.009 0.001 HIS A 617 PHE 0.039 0.002 PHE A1288 TYR 0.019 0.001 TYR B 954 ARG 0.007 0.000 ARG A 174 *********************** 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 761 residues out of total 2365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 668 time to evaluate : 2.349 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 17 LYS cc_start: 0.8374 (ttmt) cc_final: 0.8117 (ttmt) REVERT: A 78 GLN cc_start: 0.7837 (tp40) cc_final: 0.7576 (tp40) REVERT: A 91 ASN cc_start: 0.7646 (t0) cc_final: 0.7202 (t0) REVERT: A 154 PHE cc_start: 0.8386 (p90) cc_final: 0.8040 (p90) REVERT: A 155 GLU cc_start: 0.7496 (pt0) cc_final: 0.7082 (pt0) REVERT: A 184 LEU cc_start: 0.8231 (mt) cc_final: 0.7893 (mt) REVERT: A 199 SER cc_start: 0.8570 (t) cc_final: 0.8316 (t) REVERT: A 240 ILE cc_start: 0.8792 (mt) cc_final: 0.8513 (mm) REVERT: A 253 LYS cc_start: 0.7965 (pttt) cc_final: 0.7534 (pttt) REVERT: A 368 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7491 (mt-10) REVERT: A 492 ASP cc_start: 0.7240 (m-30) cc_final: 0.6972 (m-30) REVERT: A 555 LYS cc_start: 0.8716 (mmmm) cc_final: 0.8445 (mmmm) REVERT: A 559 ARG cc_start: 0.7795 (tpp80) cc_final: 0.7036 (tpp80) REVERT: A 562 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6982 (mt-10) REVERT: A 565 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7733 (mm-30) REVERT: A 593 LYS cc_start: 0.7572 (tptm) cc_final: 0.6910 (tptm) REVERT: A 597 GLU cc_start: 0.7609 (tm-30) cc_final: 0.6794 (tm-30) REVERT: A 600 PHE cc_start: 0.8483 (t80) cc_final: 0.8226 (t80) REVERT: A 626 GLU cc_start: 0.7835 (tp30) cc_final: 0.7193 (tp30) REVERT: A 654 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6937 (pt0) REVERT: A 656 GLN cc_start: 0.7487 (tm-30) cc_final: 0.6938 (tm-30) REVERT: A 657 GLN cc_start: 0.7479 (mp10) cc_final: 0.6667 (mp10) REVERT: A 659 GLU cc_start: 0.7507 (mt-10) cc_final: 0.6442 (mp0) REVERT: A 663 GLU cc_start: 0.7594 (pt0) cc_final: 0.7146 (pt0) REVERT: A 745 ASP cc_start: 0.8084 (t70) cc_final: 0.7880 (t0) REVERT: A 819 SER cc_start: 0.8258 (m) cc_final: 0.7965 (p) REVERT: A 911 ARG cc_start: 0.7510 (tpp-160) cc_final: 0.7175 (mmt-90) REVERT: A 917 LYS cc_start: 0.7567 (mmtt) cc_final: 0.7013 (mttp) REVERT: A 931 ARG cc_start: 0.7818 (ttp-110) cc_final: 0.7553 (ttp-110) REVERT: A 956 ASP cc_start: 0.6583 (OUTLIER) cc_final: 0.6197 (p0) REVERT: A 1020 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.7035 (tpp) REVERT: A 1021 GLU cc_start: 0.7878 (tp30) cc_final: 0.7226 (tp30) REVERT: A 1027 ASN cc_start: 0.6643 (p0) cc_final: 0.6260 (p0) REVERT: A 1072 GLU cc_start: 0.8060 (tt0) cc_final: 0.7597 (tt0) REVERT: A 1082 LYS cc_start: 0.7750 (mtpt) cc_final: 0.7421 (mtpt) REVERT: A 1089 LYS cc_start: 0.8443 (ttmm) cc_final: 0.8050 (ttmm) REVERT: A 1093 GLN cc_start: 0.8300 (tp40) cc_final: 0.8030 (tp40) REVERT: A 1112 MET cc_start: 0.7658 (ttp) cc_final: 0.7028 (ttp) REVERT: A 1113 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7889 (tp) REVERT: A 1116 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8340 (ttmm) REVERT: A 1117 ILE cc_start: 0.8866 (tt) cc_final: 0.8662 (tp) REVERT: A 1120 ILE cc_start: 0.9137 (mm) cc_final: 0.8746 (mm) REVERT: A 1126 GLN cc_start: 0.6957 (mm-40) cc_final: 0.6473 (mm-40) REVERT: A 1128 GLU cc_start: 0.7945 (tp30) cc_final: 0.7570 (tp30) REVERT: A 1132 LYS cc_start: 0.8324 (mmmm) cc_final: 0.7794 (mmmm) REVERT: A 1152 THR cc_start: 0.8606 (t) cc_final: 0.8222 (p) REVERT: A 1157 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7199 (mt-10) REVERT: A 1175 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8037 (mm) REVERT: A 1184 PHE cc_start: 0.8692 (t80) cc_final: 0.8419 (t80) REVERT: A 1186 ARG cc_start: 0.8157 (ttt90) cc_final: 0.7134 (ttm-80) REVERT: A 1187 LYS cc_start: 0.8528 (mmmm) cc_final: 0.8194 (mmmm) REVERT: A 1191 MET cc_start: 0.7239 (tpt) cc_final: 0.6701 (tpt) REVERT: A 1200 GLU cc_start: 0.7828 (tp30) cc_final: 0.7493 (tp30) REVERT: A 1219 MET cc_start: 0.8168 (mmm) cc_final: 0.7856 (mmm) REVERT: A 1227 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7195 (mm-30) REVERT: A 1263 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7427 (mt-10) REVERT: A 1267 LYS cc_start: 0.8530 (mttm) cc_final: 0.8196 (mtpp) REVERT: A 1336 GLU cc_start: 0.8057 (tp30) cc_final: 0.7702 (tp30) REVERT: A 1365 ASN cc_start: 0.8271 (m-40) cc_final: 0.7950 (m-40) REVERT: A 1366 VAL cc_start: 0.8550 (p) cc_final: 0.8322 (m) REVERT: A 1383 LYS cc_start: 0.8222 (mmtm) cc_final: 0.8002 (mmtm) REVERT: A 1385 LEU cc_start: 0.8249 (mm) cc_final: 0.7968 (mm) REVERT: A 1399 LYS cc_start: 0.8558 (ptpp) cc_final: 0.8244 (pttm) REVERT: A 1400 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8497 (mmtm) REVERT: A 1409 LYS cc_start: 0.8073 (mmmt) cc_final: 0.7773 (pttm) REVERT: B 18 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7463 (mm-30) REVERT: B 81 LEU cc_start: 0.7968 (mt) cc_final: 0.7766 (mt) REVERT: B 82 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7273 (tmm) REVERT: B 91 ASN cc_start: 0.8094 (m110) cc_final: 0.7798 (m-40) REVERT: B 102 LEU cc_start: 0.8090 (mt) cc_final: 0.7825 (mt) REVERT: B 110 ILE cc_start: 0.8540 (pt) cc_final: 0.7156 (mm) REVERT: B 120 ASP cc_start: 0.7121 (m-30) cc_final: 0.6826 (m-30) REVERT: B 132 ASN cc_start: 0.8193 (p0) cc_final: 0.7703 (p0) REVERT: B 154 PHE cc_start: 0.8073 (p90) cc_final: 0.7655 (p90) REVERT: B 155 GLU cc_start: 0.7309 (pt0) cc_final: 0.6721 (pm20) REVERT: B 205 ARG cc_start: 0.7941 (tpp80) cc_final: 0.7667 (mmm-85) REVERT: B 228 LYS cc_start: 0.8285 (tttm) cc_final: 0.7902 (tttp) REVERT: B 333 ARG cc_start: 0.7714 (mtt90) cc_final: 0.7290 (mtt90) REVERT: B 346 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7211 (mm-30) REVERT: B 361 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7529 (mt-10) REVERT: B 397 GLN cc_start: 0.7661 (tt0) cc_final: 0.7362 (tt0) REVERT: B 499 LYS cc_start: 0.8105 (mmmm) cc_final: 0.7783 (mmmm) REVERT: B 503 LYS cc_start: 0.8465 (tttt) cc_final: 0.7821 (ttmm) REVERT: B 515 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7203 (tm-30) REVERT: B 547 GLN cc_start: 0.7252 (tp-100) cc_final: 0.6890 (tp40) REVERT: B 580 MET cc_start: 0.7700 (tpp) cc_final: 0.7041 (tpp) REVERT: B 594 ASP cc_start: 0.7917 (m-30) cc_final: 0.7568 (m-30) REVERT: B 607 ASN cc_start: 0.6874 (t0) cc_final: 0.6328 (t0) REVERT: B 626 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8134 (tp30) REVERT: B 637 ARG cc_start: 0.7111 (mtp180) cc_final: 0.6677 (mtp-110) REVERT: B 640 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7687 (mm-30) REVERT: B 707 MET cc_start: 0.7964 (tpp) cc_final: 0.7160 (tpp) REVERT: B 739 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6440 (m-10) REVERT: B 775 ASN cc_start: 0.6652 (m-40) cc_final: 0.6436 (m-40) REVERT: B 803 LEU cc_start: 0.8135 (mt) cc_final: 0.7913 (mt) REVERT: B 807 ARG cc_start: 0.7962 (ttm170) cc_final: 0.7608 (ttp-170) REVERT: B 857 PHE cc_start: 0.7400 (t80) cc_final: 0.7156 (t80) REVERT: B 861 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7985 (mm) REVERT: B 919 GLN cc_start: 0.7515 (mt0) cc_final: 0.7252 (mt0) REVERT: B 972 LYS cc_start: 0.8425 (mttp) cc_final: 0.8114 (mtpt) REVERT: B 973 LEU cc_start: 0.8392 (mm) cc_final: 0.7447 (mt) REVERT: B 989 LYS cc_start: 0.6346 (pttt) cc_final: 0.5320 (pttm) REVERT: B 1014 LYS cc_start: 0.8779 (pttp) cc_final: 0.8463 (pttp) REVERT: B 1020 MET cc_start: 0.6685 (mmt) cc_final: 0.6432 (mmt) REVERT: B 1059 ASN cc_start: 0.8289 (p0) cc_final: 0.7927 (p0) REVERT: B 1063 PHE cc_start: 0.7869 (t80) cc_final: 0.7609 (t80) REVERT: B 1066 GLU cc_start: 0.7914 (tt0) cc_final: 0.7489 (mm-30) REVERT: B 1096 PHE cc_start: 0.6766 (OUTLIER) cc_final: 0.6481 (m-10) REVERT: B 1106 LYS cc_start: 0.7509 (ttmt) cc_final: 0.7199 (ttmm) REVERT: B 1110 ARG cc_start: 0.7796 (ptp90) cc_final: 0.7101 (mtm-85) REVERT: B 1112 MET cc_start: 0.8012 (mtp) cc_final: 0.7782 (mtm) REVERT: B 1132 LYS cc_start: 0.8045 (mttt) cc_final: 0.7540 (mttm) REVERT: B 1154 GLN cc_start: 0.8532 (tt0) cc_final: 0.8193 (tt0) REVERT: B 1200 GLU cc_start: 0.8047 (pt0) cc_final: 0.7741 (pt0) REVERT: B 1219 MET cc_start: 0.7526 (mmp) cc_final: 0.6976 (mmp) REVERT: B 1220 TRP cc_start: 0.7820 (m-10) cc_final: 0.7294 (m-90) REVERT: B 1231 MET cc_start: 0.6747 (mpp) cc_final: 0.6484 (mpp) REVERT: B 1263 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7799 (mt-10) REVERT: B 1266 LEU cc_start: 0.7813 (mt) cc_final: 0.7537 (mt) REVERT: B 1383 LYS cc_start: 0.8843 (pttm) cc_final: 0.8407 (pttm) REVERT: B 1399 LYS cc_start: 0.8645 (pptt) cc_final: 0.8334 (pptt) REVERT: B 1403 GLN cc_start: 0.7713 (tp40) cc_final: 0.7401 (tp40) REVERT: B 1412 GLU cc_start: 0.5872 (OUTLIER) cc_final: 0.4236 (mm-30) outliers start: 93 outliers final: 73 residues processed: 702 average time/residue: 0.3301 time to fit residues: 351.2779 Evaluate side-chains 737 residues out of total 2365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 654 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 401 LYS 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 654 GLU Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 844 CYS Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1012 GLU 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 1175 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1195 SER Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1297 GLN Chi-restraints excluded: chain A residue 1313 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 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 240 ILE Chi-restraints excluded: chain B residue 385 SER 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 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 678 SER Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 741 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 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 1072 GLU Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1143 ASP Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1215 ASN Chi-restraints excluded: chain B residue 1252 ILE Chi-restraints excluded: chain B residue 1290 ILE 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 149 optimal weight: 0.8980 chunk 241 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 167 optimal weight: 0.0000 chunk 253 optimal weight: 0.6980 chunk 232 optimal weight: 0.9980 chunk 201 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 155 optimal weight: 0.0980 chunk 123 optimal weight: 0.5980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN A 617 HIS B 692 GLN B 709 ASN B 968 GLN B1126 GLN B1147 GLN ** B1178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2384 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= 0.219 Angle : 0.721 13.857 28095 Z= 0.365 Chirality : 0.042 0.212 3318 Planarity : 0.005 0.068 3545 Dihedral : 5.061 57.471 2691 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.20 % Favored : 90.68 % Rotamer: Outliers : 3.76 % Allowed : 24.36 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.17), residues: 2521 helix: 1.20 (0.12), residues: 1751 sheet: -2.67 (1.07), residues: 20 loop : -2.72 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 773 HIS 0.013 0.001 HIS A 617 PHE 0.029 0.002 PHE A 850 TYR 0.025 0.001 TYR B1201 ARG 0.010 0.000 ARG B 931 ********************** 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 747 residues out of total 2365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 658 time to evaluate : 2.370 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: A 17 LYS cc_start: 0.8368 (ttmt) cc_final: 0.8122 (ttmt) REVERT: A 27 ARG cc_start: 0.8092 (ttm170) cc_final: 0.7563 (mtm110) REVERT: A 78 GLN cc_start: 0.7837 (tp40) cc_final: 0.7578 (tp40) REVERT: A 91 ASN cc_start: 0.7646 (t0) cc_final: 0.7195 (t0) REVERT: A 154 PHE cc_start: 0.8391 (p90) cc_final: 0.8042 (p90) REVERT: A 155 GLU cc_start: 0.7513 (pt0) cc_final: 0.7083 (pt0) REVERT: A 167 LEU cc_start: 0.8473 (tp) cc_final: 0.8206 (tp) REVERT: A 184 LEU cc_start: 0.8223 (mt) cc_final: 0.7937 (mt) REVERT: A 199 SER cc_start: 0.8564 (t) cc_final: 0.8313 (t) REVERT: A 240 ILE cc_start: 0.8799 (mt) cc_final: 0.8518 (mm) REVERT: A 253 LYS cc_start: 0.7974 (pttt) cc_final: 0.7541 (pttt) REVERT: A 368 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7479 (mt-10) REVERT: A 459 LYS cc_start: 0.8133 (mttp) cc_final: 0.7889 (mtmm) REVERT: A 559 ARG cc_start: 0.7793 (tpp80) cc_final: 0.7046 (tpp80) REVERT: A 562 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6968 (mt-10) REVERT: A 565 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7747 (mm-30) REVERT: A 593 LYS cc_start: 0.7578 (tptm) cc_final: 0.6912 (tptm) REVERT: A 597 GLU cc_start: 0.7632 (tm-30) cc_final: 0.6788 (tm-30) REVERT: A 600 PHE cc_start: 0.8482 (t80) cc_final: 0.8236 (t80) REVERT: A 606 MET cc_start: 0.7355 (mmm) cc_final: 0.7099 (tpp) REVERT: A 626 GLU cc_start: 0.7861 (tp30) cc_final: 0.7198 (tp30) REVERT: A 656 GLN cc_start: 0.7519 (tm-30) cc_final: 0.7273 (tm-30) REVERT: A 663 GLU cc_start: 0.7604 (pt0) cc_final: 0.7155 (pt0) REVERT: A 819 SER cc_start: 0.8265 (m) cc_final: 0.7962 (p) REVERT: A 866 LYS cc_start: 0.7997 (ptmm) cc_final: 0.7781 (ptmm) REVERT: A 911 ARG cc_start: 0.7533 (tpp-160) cc_final: 0.7195 (mmt-90) REVERT: A 917 LYS cc_start: 0.7533 (mmtt) cc_final: 0.6990 (mttp) REVERT: A 931 ARG cc_start: 0.7849 (ttp-110) cc_final: 0.7560 (ttp-110) REVERT: A 956 ASP cc_start: 0.6575 (OUTLIER) cc_final: 0.6149 (p0) REVERT: A 1020 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7030 (tpp) REVERT: A 1021 GLU cc_start: 0.7881 (tp30) cc_final: 0.7227 (tp30) REVERT: A 1027 ASN cc_start: 0.6639 (p0) cc_final: 0.6252 (p0) REVERT: A 1072 GLU cc_start: 0.8082 (tt0) cc_final: 0.7632 (tt0) REVERT: A 1082 LYS cc_start: 0.7716 (mtpt) cc_final: 0.7353 (mtpt) REVERT: A 1089 LYS cc_start: 0.8428 (ttmm) cc_final: 0.8053 (ttmm) REVERT: A 1093 GLN cc_start: 0.8346 (tp40) cc_final: 0.8095 (tp40) REVERT: A 1112 MET cc_start: 0.7610 (ttp) cc_final: 0.6988 (ttp) REVERT: A 1113 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7932 (tp) REVERT: A 1116 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8347 (ttmm) REVERT: A 1120 ILE cc_start: 0.9145 (mm) cc_final: 0.8754 (mm) REVERT: A 1126 GLN cc_start: 0.6949 (mm-40) cc_final: 0.6467 (mm-40) REVERT: A 1128 GLU cc_start: 0.7940 (tp30) cc_final: 0.7574 (tp30) REVERT: A 1132 LYS cc_start: 0.8329 (mmmm) cc_final: 0.7798 (mmmm) REVERT: A 1152 THR cc_start: 0.8607 (t) cc_final: 0.8230 (p) REVERT: A 1157 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7230 (mt-10) REVERT: A 1175 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8036 (mm) REVERT: A 1184 PHE cc_start: 0.8689 (t80) cc_final: 0.8406 (t80) REVERT: A 1187 LYS cc_start: 0.8521 (mmmm) cc_final: 0.8211 (mmmm) REVERT: A 1191 MET cc_start: 0.7162 (tpt) cc_final: 0.6746 (tpt) REVERT: A 1200 GLU cc_start: 0.7844 (tp30) cc_final: 0.7528 (tp30) REVERT: A 1219 MET cc_start: 0.8189 (mmm) cc_final: 0.7885 (mmm) REVERT: A 1231 MET cc_start: 0.8056 (mmt) cc_final: 0.7784 (mpp) REVERT: A 1263 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7428 (mt-10) REVERT: A 1267 LYS cc_start: 0.8536 (mttm) cc_final: 0.8203 (mtpp) REVERT: A 1336 GLU cc_start: 0.8065 (tp30) cc_final: 0.7715 (tp30) REVERT: A 1365 ASN cc_start: 0.8298 (m-40) cc_final: 0.7972 (m-40) REVERT: A 1366 VAL cc_start: 0.8584 (p) cc_final: 0.8361 (m) REVERT: A 1383 LYS cc_start: 0.8238 (mmtm) cc_final: 0.8028 (mmtm) REVERT: A 1385 LEU cc_start: 0.8257 (mm) cc_final: 0.7989 (mm) REVERT: A 1399 LYS cc_start: 0.8549 (ptpp) cc_final: 0.8236 (pttm) REVERT: A 1400 LYS cc_start: 0.8766 (mmtm) cc_final: 0.8500 (mmtm) REVERT: A 1409 LYS cc_start: 0.8079 (mmmt) cc_final: 0.7790 (pttm) REVERT: B 77 ILE cc_start: 0.8143 (mt) cc_final: 0.7854 (mm) REVERT: B 81 LEU cc_start: 0.7990 (mt) cc_final: 0.7776 (mt) REVERT: B 82 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7281 (tmm) REVERT: B 91 ASN cc_start: 0.8094 (m110) cc_final: 0.7803 (m-40) REVERT: B 102 LEU cc_start: 0.8101 (mt) cc_final: 0.7831 (mt) REVERT: B 110 ILE cc_start: 0.8548 (pt) cc_final: 0.7185 (mm) REVERT: B 120 ASP cc_start: 0.7072 (m-30) cc_final: 0.6813 (m-30) REVERT: B 132 ASN cc_start: 0.8196 (p0) cc_final: 0.7725 (p0) REVERT: B 154 PHE cc_start: 0.8190 (p90) cc_final: 0.7753 (p90) REVERT: B 155 GLU cc_start: 0.7319 (pt0) cc_final: 0.6750 (pm20) REVERT: B 205 ARG cc_start: 0.7957 (tpp80) cc_final: 0.7681 (mmm-85) REVERT: B 228 LYS cc_start: 0.8332 (tttm) cc_final: 0.7931 (tttp) REVERT: B 232 ILE cc_start: 0.8280 (mt) cc_final: 0.7927 (tt) REVERT: B 333 ARG cc_start: 0.7716 (mtt90) cc_final: 0.7295 (mtt90) REVERT: B 346 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7231 (mm-30) REVERT: B 361 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7526 (mt-10) REVERT: B 397 GLN cc_start: 0.7643 (tt0) cc_final: 0.7335 (tt0) REVERT: B 428 GLU cc_start: 0.7475 (tt0) cc_final: 0.6962 (tp30) REVERT: B 499 LYS cc_start: 0.8103 (mmmm) cc_final: 0.7789 (mmmm) REVERT: B 515 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7219 (tm-30) REVERT: B 547 GLN cc_start: 0.7220 (tp-100) cc_final: 0.6860 (tp40) REVERT: B 580 MET cc_start: 0.7703 (tpp) cc_final: 0.7012 (tpp) REVERT: B 594 ASP cc_start: 0.7924 (m-30) cc_final: 0.7572 (m-30) REVERT: B 606 MET cc_start: 0.7102 (tpt) cc_final: 0.6613 (tpt) REVERT: B 607 ASN cc_start: 0.6882 (t0) cc_final: 0.6148 (t0) REVERT: B 626 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8120 (tp30) REVERT: B 637 ARG cc_start: 0.7119 (mtp180) cc_final: 0.6690 (mtp-110) REVERT: B 640 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7706 (mm-30) REVERT: B 739 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.6474 (m-10) REVERT: B 775 ASN cc_start: 0.6725 (m-40) cc_final: 0.6471 (m-40) REVERT: B 803 LEU cc_start: 0.8139 (mt) cc_final: 0.7928 (mt) REVERT: B 807 ARG cc_start: 0.7963 (ttm170) cc_final: 0.7615 (ttp-170) REVERT: B 857 PHE cc_start: 0.7399 (t80) cc_final: 0.7123 (t80) REVERT: B 861 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7849 (mm) REVERT: B 972 LYS cc_start: 0.8435 (mttp) cc_final: 0.8119 (mtpt) REVERT: B 973 LEU cc_start: 0.8404 (mm) cc_final: 0.7468 (mt) REVERT: B 989 LYS cc_start: 0.6286 (pttt) cc_final: 0.5274 (pttm) REVERT: B 1014 LYS cc_start: 0.8790 (pttp) cc_final: 0.8464 (pttp) REVERT: B 1020 MET cc_start: 0.6677 (mmt) cc_final: 0.6476 (mmt) REVERT: B 1059 ASN cc_start: 0.8318 (p0) cc_final: 0.7953 (p0) REVERT: B 1063 PHE cc_start: 0.7885 (t80) cc_final: 0.7625 (t80) REVERT: B 1066 GLU cc_start: 0.7924 (tt0) cc_final: 0.7495 (mm-30) REVERT: B 1080 PHE cc_start: 0.7716 (t80) cc_final: 0.7374 (t80) REVERT: B 1096 PHE cc_start: 0.6786 (OUTLIER) cc_final: 0.6499 (m-10) REVERT: B 1106 LYS cc_start: 0.7498 (ttmt) cc_final: 0.7243 (ttmm) REVERT: B 1110 ARG cc_start: 0.7791 (ptp90) cc_final: 0.7093 (mtm-85) REVERT: B 1112 MET cc_start: 0.8020 (mtp) cc_final: 0.7790 (mtm) REVERT: B 1132 LYS cc_start: 0.8052 (mttt) cc_final: 0.7559 (mttm) REVERT: B 1154 GLN cc_start: 0.8557 (tt0) cc_final: 0.8208 (tt0) REVERT: B 1200 GLU cc_start: 0.8057 (pt0) cc_final: 0.7762 (pt0) REVERT: B 1219 MET cc_start: 0.7538 (mmp) cc_final: 0.6998 (mmp) REVERT: B 1220 TRP cc_start: 0.7862 (m-10) cc_final: 0.7329 (m-90) REVERT: B 1231 MET cc_start: 0.6744 (mpp) cc_final: 0.6471 (mpp) REVERT: B 1263 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7786 (mt-10) REVERT: B 1266 LEU cc_start: 0.7835 (mt) cc_final: 0.7558 (mt) REVERT: B 1383 LYS cc_start: 0.8851 (pttm) cc_final: 0.8413 (pttm) REVERT: B 1399 LYS cc_start: 0.8630 (pptt) cc_final: 0.8329 (pptt) REVERT: B 1412 GLU cc_start: 0.5930 (OUTLIER) cc_final: 0.4263 (mm-30) outliers start: 89 outliers final: 76 residues processed: 689 average time/residue: 0.3392 time to fit residues: 353.0205 Evaluate side-chains 734 residues out of total 2365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 649 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 401 LYS 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 702 SER Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 844 CYS Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1012 GLU 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 1175 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1195 SER Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1297 GLN Chi-restraints excluded: chain A residue 1313 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 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 229 LEU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 523 GLU 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 678 SER Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 741 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 1072 GLU Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1194 GLN Chi-restraints excluded: chain B residue 1215 ASN Chi-restraints excluded: chain B residue 1252 ILE Chi-restraints excluded: chain B residue 1279 ASN Chi-restraints excluded: chain B residue 1290 ILE 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 160 optimal weight: 0.7980 chunk 214 optimal weight: 0.5980 chunk 61 optimal weight: 0.0060 chunk 185 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 207 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 B 709 ASN B1126 GLN ** B1178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1349 GLN ** 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 = 0.3763 r_free = 0.3763 target = 0.119316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.102888 restraints weight = 48383.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.106156 restraints weight = 25108.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.108284 restraints weight = 15400.135| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20796 Z= 0.231 Angle : 0.730 13.904 28095 Z= 0.371 Chirality : 0.042 0.209 3318 Planarity : 0.005 0.070 3545 Dihedral : 5.073 56.134 2691 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.68 % Favored : 90.20 % Rotamer: Outliers : 3.76 % Allowed : 24.57 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2521 helix: 1.14 (0.12), residues: 1759 sheet: -2.66 (1.07), residues: 20 loop : -2.70 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1238 HIS 0.012 0.001 HIS A 617 PHE 0.043 0.002 PHE A1288 TYR 0.029 0.001 TYR B1201 ARG 0.009 0.000 ARG B 931 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6519.16 seconds wall clock time: 117 minutes 59.39 seconds (7079.39 seconds total)