Starting phenix.real_space_refine on Wed Nov 20 01:33:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezq_28748/11_2024/8ezq_28748.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezq_28748/11_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_28748/11_2024/8ezq_28748.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezq_28748/11_2024/8ezq_28748.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezq_28748/11_2024/8ezq_28748.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezq_28748/11_2024/8ezq_28748.cif" } 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. Time to flip 3 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 10.00, per 1000 atoms: 0.49 Number of scatterers: 20456 At special positions: 0 Unit cell: (120.888, 144.072, 303.048, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 3925 8.00 N 3333 7.00 C 13124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.95 Conformation dependent library (CDL) restraints added in 2.9 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: 1.96 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: 7.41 Time building geometry restraints manager: 5.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6469 1.34 - 1.45: 2407 1.45 - 1.57: 11806 1.57 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 20796 Sorted by residual: bond pdb=" N ASP A1394 " pdb=" CA ASP A1394 " ideal model delta sigma weight residual 1.457 1.501 -0.043 1.29e-02 6.01e+03 1.12e+01 bond pdb=" N ILE A1321 " pdb=" CA ILE A1321 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.15e-02 7.56e+03 1.03e+01 bond pdb=" N ILE A 958 " pdb=" CA ILE A 958 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.09e+00 bond pdb=" N ASP B 676 " pdb=" CA ASP B 676 " ideal model delta sigma weight residual 1.461 1.488 -0.027 9.20e-03 1.18e+04 8.68e+00 bond pdb=" N VAL A 691 " pdb=" CA VAL A 691 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.47e+00 ... (remaining 20791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 27438 1.79 - 3.57: 551 3.57 - 5.36: 84 5.36 - 7.15: 19 7.15 - 8.94: 3 Bond angle restraints: 28095 Sorted by residual: angle pdb=" N ILE B 777 " pdb=" CA ILE B 777 " pdb=" C ILE B 777 " ideal model delta sigma weight residual 112.29 108.57 3.72 9.40e-01 1.13e+00 1.57e+01 angle pdb=" N ILE B1354 " pdb=" CA ILE B1354 " pdb=" C ILE B1354 " ideal model delta sigma weight residual 112.96 109.02 3.94 1.00e+00 1.00e+00 1.55e+01 angle pdb=" N LYS A1320 " pdb=" CA LYS A1320 " pdb=" C LYS A1320 " ideal model delta sigma weight residual 113.23 108.46 4.77 1.22e+00 6.72e-01 1.53e+01 angle pdb=" N SER A1395 " pdb=" CA SER A1395 " pdb=" CB SER A1395 " ideal model delta sigma weight residual 114.17 109.76 4.41 1.14e+00 7.69e-01 1.50e+01 angle pdb=" CA GLN A 692 " pdb=" C GLN A 692 " pdb=" O GLN A 692 " ideal model delta sigma weight residual 121.34 117.91 3.43 9.40e-01 1.13e+00 1.33e+01 ... (remaining 28090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11903 17.97 - 35.93: 705 35.93 - 53.90: 139 53.90 - 71.87: 21 71.87 - 89.83: 5 Dihedral angle restraints: 12773 sinusoidal: 5250 harmonic: 7523 Sorted by residual: dihedral pdb=" CA ASP B1209 " pdb=" C ASP B1209 " pdb=" N SER B1210 " pdb=" CA SER B1210 " ideal model delta harmonic sigma weight residual 180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA THR A 781 " pdb=" C THR A 781 " pdb=" N VAL A 782 " pdb=" CA VAL A 782 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA LYS B1082 " pdb=" C LYS B1082 " pdb=" N GLU B1083 " pdb=" CA GLU B1083 " ideal model delta harmonic sigma weight residual 180.00 -161.17 -18.83 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 12770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2627 0.047 - 0.094: 587 0.094 - 0.141: 95 0.141 - 0.188: 7 0.188 - 0.235: 2 Chirality restraints: 3318 Sorted by residual: chirality pdb=" CA ILE B 958 " pdb=" N ILE B 958 " pdb=" C ILE B 958 " pdb=" CB ILE B 958 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ILE A 983 " pdb=" N ILE A 983 " pdb=" C ILE A 983 " pdb=" CB ILE A 983 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE A1321 " pdb=" N ILE A1321 " pdb=" C ILE A1321 " pdb=" CB ILE A1321 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 3315 not shown) Planarity restraints: 3545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 477 " -0.019 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C PHE A 477 " 0.067 2.00e-02 2.50e+03 pdb=" O PHE A 477 " -0.025 2.00e-02 2.50e+03 pdb=" N THR A 478 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 402 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.34e+00 pdb=" C LEU A 402 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU A 402 " 0.016 2.00e-02 2.50e+03 pdb=" N SER A 403 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 814 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A 815 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 815 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 815 " -0.029 5.00e-02 4.00e+02 ... (remaining 3542 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 317 2.62 - 3.19: 20694 3.19 - 3.76: 32454 3.76 - 4.33: 42600 4.33 - 4.90: 68035 Nonbonded interactions: 164100 Sorted by model distance: nonbonded pdb=" OD1 ASP A 831 " pdb=" N HIS A 832 " model vdw 2.048 3.120 nonbonded pdb=" OG1 THR B 798 " pdb=" OE1 GLU B 801 " model vdw 2.204 3.040 nonbonded pdb=" O ASN B1056 " pdb=" OG SER B1060 " model vdw 2.204 3.040 nonbonded pdb=" O PHE A1163 " pdb=" OG1 THR A1166 " model vdw 2.206 3.040 nonbonded pdb=" O GLN B1194 " pdb=" OG SER B1197 " model vdw 2.206 3.040 ... (remaining 164095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 989 or resid 1004 through 1413)) selection = (chain 'B' and (resid 7 through 874 or resid 887 through 989 or resid 1004 throu \ gh 1413)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 21.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 45.600 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.520 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 10 poor density : 769 time to evaluate : 2.215 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: 0.3701 time to fit residues: 426.5621 Evaluate side-chains 680 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 675 time to evaluate : 2.309 ------------------------------------------------------------------------------- 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: 0.8980 chunk 192 optimal weight: 0.3980 chunk 106 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 199 optimal weight: 1.9990 chunk 77 optimal weight: 0.0970 chunk 121 optimal weight: 0.5980 chunk 148 optimal weight: 5.9990 chunk 230 optimal weight: 0.0770 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN A 132 ASN A 602 ASN ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN A 919 GLN A1027 ASN A1319 ASN A1402 GLN B 204 ASN B 709 ASN ** B1178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1250 HIS ** B1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 20796 Z= 0.201 Angle : 0.673 12.543 28095 Z= 0.349 Chirality : 0.041 0.179 3318 Planarity : 0.005 0.052 3545 Dihedral : 4.972 49.995 2693 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.73 % Favored : 91.19 % Rotamer: Outliers : 3.09 % Allowed : 14.50 % Favored : 82.41 % 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: 0.23 (0.17), residues: 2521 helix: 1.29 (0.12), residues: 1765 sheet: -2.84 (1.04), residues: 20 loop : -2.68 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 470 HIS 0.011 0.001 HIS A 617 PHE 0.026 0.002 PHE B 925 TYR 0.018 0.001 TYR A 627 ARG 0.006 0.000 ARG A 472 *********************** 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 767 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 694 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.7856 (tp40) cc_final: 0.7582 (tp40) REVERT: A 82 MET cc_start: 0.8007 (ttm) cc_final: 0.7612 (tmm) REVERT: A 91 ASN cc_start: 0.7628 (t0) cc_final: 0.7260 (t0) REVERT: A 120 ASP cc_start: 0.7597 (t0) cc_final: 0.7130 (m-30) REVERT: A 154 PHE cc_start: 0.8435 (p90) cc_final: 0.8169 (p90) REVERT: A 155 GLU cc_start: 0.7577 (pt0) cc_final: 0.7249 (pt0) REVERT: A 184 LEU cc_start: 0.8126 (mt) cc_final: 0.7800 (mt) REVERT: A 199 SER cc_start: 0.8542 (t) cc_final: 0.8340 (t) REVERT: A 206 ARG cc_start: 0.7901 (tpp-160) cc_final: 0.7671 (tpp-160) REVERT: A 233 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7487 (tp30) REVERT: A 240 ILE cc_start: 0.8829 (mt) cc_final: 0.8542 (mm) REVERT: A 253 LYS cc_start: 0.8092 (pttt) cc_final: 0.7587 (pttt) REVERT: A 368 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7510 (mt-10) REVERT: A 460 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7425 (tm-30) REVERT: A 523 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7495 (mm-30) REVERT: A 555 LYS cc_start: 0.8731 (mmmm) cc_final: 0.8465 (mmmm) REVERT: A 559 ARG cc_start: 0.7813 (tpp80) cc_final: 0.7488 (tpp80) REVERT: A 562 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7056 (mt-10) REVERT: A 565 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7848 (mm-30) REVERT: A 593 LYS cc_start: 0.7687 (tptm) cc_final: 0.7081 (tptm) REVERT: A 600 PHE cc_start: 0.8587 (t80) cc_final: 0.8108 (t80) REVERT: A 626 GLU cc_start: 0.7820 (tp30) cc_final: 0.7261 (tp30) REVERT: A 656 GLN cc_start: 0.7206 (tm-30) cc_final: 0.6825 (tm-30) REVERT: A 659 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6828 (mt-10) REVERT: A 745 ASP cc_start: 0.8029 (t70) cc_final: 0.7817 (t0) REVERT: A 765 ASN cc_start: 0.7642 (t0) cc_final: 0.6928 (t0) REVERT: A 830 ASP cc_start: 0.7363 (t70) cc_final: 0.7072 (t70) REVERT: A 837 MET cc_start: 0.7516 (mmm) cc_final: 0.7275 (mmt) REVERT: A 911 ARG cc_start: 0.7578 (tpp-160) cc_final: 0.7241 (mmt-90) REVERT: A 917 LYS cc_start: 0.7573 (mmtt) cc_final: 0.7074 (mttp) REVERT: A 931 ARG cc_start: 0.7831 (ttp-110) cc_final: 0.7601 (ttp-110) REVERT: A 956 ASP cc_start: 0.6756 (p0) cc_final: 0.6434 (p0) REVERT: A 1017 LYS cc_start: 0.8142 (ttmm) cc_final: 0.7847 (ttmm) REVERT: A 1020 MET cc_start: 0.7433 (tpp) cc_final: 0.7078 (tpp) REVERT: A 1021 GLU cc_start: 0.7783 (tp30) cc_final: 0.7071 (tp30) REVERT: A 1062 TYR cc_start: 0.7556 (p90) cc_final: 0.6891 (p90) REVERT: A 1071 ILE cc_start: 0.8402 (mm) cc_final: 0.8185 (mm) REVERT: A 1072 GLU cc_start: 0.8285 (tt0) cc_final: 0.7758 (tt0) REVERT: A 1087 LEU cc_start: 0.8560 (tp) cc_final: 0.8342 (tp) REVERT: A 1089 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8130 (ttmm) REVERT: A 1093 GLN cc_start: 0.8560 (tp40) cc_final: 0.8214 (tp40) REVERT: A 1112 MET cc_start: 0.7389 (ptm) cc_final: 0.7166 (mtp) REVERT: A 1113 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7870 (tp) REVERT: A 1116 LYS cc_start: 0.8691 (ttpt) cc_final: 0.8342 (ttmm) REVERT: A 1120 ILE cc_start: 0.9119 (mm) cc_final: 0.8725 (mm) REVERT: A 1126 GLN cc_start: 0.6865 (mm-40) cc_final: 0.6450 (mm-40) REVERT: A 1128 GLU cc_start: 0.7883 (tp30) cc_final: 0.7461 (tp30) REVERT: A 1132 LYS cc_start: 0.8358 (mmmm) cc_final: 0.7766 (mmmm) REVERT: A 1140 LYS cc_start: 0.7953 (mmmm) cc_final: 0.7524 (mmmm) REVERT: A 1157 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7241 (mt-10) REVERT: A 1170 PHE cc_start: 0.7435 (m-10) cc_final: 0.7233 (m-10) REVERT: A 1186 ARG cc_start: 0.8178 (tpt-90) cc_final: 0.7907 (ttt90) REVERT: A 1187 LYS cc_start: 0.8555 (mmmm) cc_final: 0.8186 (mmmm) REVERT: A 1191 MET cc_start: 0.7285 (tpt) cc_final: 0.6430 (tpt) REVERT: A 1200 GLU cc_start: 0.7850 (tp30) cc_final: 0.7496 (tp30) REVERT: A 1219 MET cc_start: 0.8158 (mmm) cc_final: 0.7754 (mmm) REVERT: A 1224 LEU cc_start: 0.8297 (mt) cc_final: 0.7772 (mt) REVERT: A 1227 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7144 (mt-10) REVERT: A 1259 LYS cc_start: 0.8299 (mppt) cc_final: 0.7686 (mppt) REVERT: A 1263 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7503 (mt-10) REVERT: A 1267 LYS cc_start: 0.8498 (mttm) cc_final: 0.8164 (mtpp) REVERT: A 1365 ASN cc_start: 0.8293 (m-40) cc_final: 0.8048 (m-40) REVERT: A 1366 VAL cc_start: 0.8549 (p) cc_final: 0.8307 (m) REVERT: A 1383 LYS cc_start: 0.8333 (mmtm) cc_final: 0.8071 (mmtm) REVERT: A 1399 LYS cc_start: 0.8613 (ptpp) cc_final: 0.8376 (pttm) REVERT: A 1400 LYS cc_start: 0.8803 (mmtm) cc_final: 0.8533 (mmtm) REVERT: B 10 ASP cc_start: 0.7978 (m-30) cc_final: 0.7618 (m-30) REVERT: B 90 ASP cc_start: 0.7889 (t0) cc_final: 0.7358 (t70) REVERT: B 91 ASN cc_start: 0.8102 (m110) cc_final: 0.7137 (m-40) REVERT: B 110 ILE cc_start: 0.8542 (pt) cc_final: 0.7218 (mm) REVERT: B 132 ASN cc_start: 0.8163 (p0) cc_final: 0.7710 (p0) REVERT: B 136 GLN cc_start: 0.8199 (mt0) cc_final: 0.7981 (mt0) REVERT: B 138 TYR cc_start: 0.8095 (p90) cc_final: 0.7883 (p90) REVERT: B 151 HIS cc_start: 0.8103 (m170) cc_final: 0.7895 (m90) REVERT: B 154 PHE cc_start: 0.8100 (p90) cc_final: 0.7813 (p90) REVERT: B 155 GLU cc_start: 0.7509 (pt0) cc_final: 0.7175 (pm20) REVERT: B 162 ASP cc_start: 0.7730 (m-30) cc_final: 0.7455 (p0) REVERT: B 174 ARG cc_start: 0.8179 (ttt180) cc_final: 0.7905 (ttt180) REVERT: B 178 ASP cc_start: 0.7729 (t70) cc_final: 0.7295 (t0) REVERT: B 191 TYR cc_start: 0.8209 (t80) cc_final: 0.7982 (t80) REVERT: B 205 ARG cc_start: 0.7848 (tpp80) cc_final: 0.7540 (mmm-85) REVERT: B 333 ARG cc_start: 0.7646 (mtt90) cc_final: 0.7243 (mtt90) REVERT: B 346 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7241 (mm-30) REVERT: B 361 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7520 (mt-10) REVERT: B 364 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: B 499 LYS cc_start: 0.8233 (mtpp) cc_final: 0.8022 (mtpp) REVERT: B 515 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7134 (tm-30) REVERT: B 547 GLN cc_start: 0.7209 (tp-100) cc_final: 0.6872 (tp-100) REVERT: B 580 MET cc_start: 0.7870 (tpp) cc_final: 0.7181 (tpp) REVERT: B 594 ASP cc_start: 0.7864 (m-30) cc_final: 0.7537 (m-30) REVERT: B 597 GLU cc_start: 0.7703 (tp30) cc_final: 0.7388 (tp30) REVERT: B 607 ASN cc_start: 0.7297 (t0) cc_final: 0.6879 (t0) REVERT: B 630 LEU cc_start: 0.8539 (mt) cc_final: 0.8200 (mt) REVERT: B 637 ARG cc_start: 0.7141 (mtp-110) cc_final: 0.6914 (mtp-110) REVERT: B 646 LEU cc_start: 0.8756 (mp) cc_final: 0.8542 (mp) REVERT: B 649 PHE cc_start: 0.7847 (p90) cc_final: 0.7578 (p90) REVERT: B 656 GLN cc_start: 0.7798 (mp10) cc_final: 0.7024 (mp-120) REVERT: B 707 MET cc_start: 0.7680 (tpp) cc_final: 0.7220 (tpp) REVERT: B 739 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6615 (m-10) REVERT: B 803 LEU cc_start: 0.8221 (mt) cc_final: 0.7826 (mt) REVERT: B 807 ARG cc_start: 0.7876 (ttm170) cc_final: 0.7222 (ttp-170) REVERT: B 837 MET cc_start: 0.8130 (mmm) cc_final: 0.7482 (mmm) REVERT: B 912 PHE cc_start: 0.7371 (t80) cc_final: 0.7122 (t80) REVERT: B 919 GLN cc_start: 0.7569 (mt0) cc_final: 0.7260 (mt0) REVERT: B 1020 MET cc_start: 0.6816 (mmt) cc_final: 0.6537 (mmt) REVERT: B 1062 TYR cc_start: 0.7583 (p90) cc_final: 0.7088 (p90) REVERT: B 1063 PHE cc_start: 0.8071 (t80) cc_final: 0.7799 (t80) REVERT: B 1080 PHE cc_start: 0.7370 (t80) cc_final: 0.6840 (t80) REVERT: B 1096 PHE cc_start: 0.6750 (OUTLIER) cc_final: 0.6447 (m-10) REVERT: B 1110 ARG cc_start: 0.7866 (ptp90) cc_final: 0.7517 (ptp-170) REVERT: B 1132 LYS cc_start: 0.8043 (mttt) cc_final: 0.7601 (mttm) REVERT: B 1154 GLN cc_start: 0.8366 (tt0) cc_final: 0.8048 (tt0) REVERT: B 1157 GLU cc_start: 0.7440 (tp30) cc_final: 0.6664 (tp30) REVERT: B 1163 PHE cc_start: 0.7641 (m-10) cc_final: 0.7339 (m-80) REVERT: B 1199 PHE cc_start: 0.8350 (t80) cc_final: 0.8111 (t80) REVERT: B 1200 GLU cc_start: 0.8134 (pt0) cc_final: 0.7757 (pt0) REVERT: B 1231 MET cc_start: 0.6772 (mpp) cc_final: 0.6162 (mpp) REVERT: B 1263 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7979 (mt-10) REVERT: B 1266 LEU cc_start: 0.7895 (mt) cc_final: 0.7613 (mt) REVERT: B 1383 LYS cc_start: 0.8864 (pttm) cc_final: 0.8484 (pttm) outliers start: 73 outliers final: 47 residues processed: 724 average time/residue: 0.3531 time to fit residues: 384.4726 Evaluate side-chains 698 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 647 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 737 LYS 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 985 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 817 ILE Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 1028 ILE 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 1250 HIS Chi-restraints excluded: chain B residue 1252 ILE Chi-restraints excluded: chain B residue 1290 ILE Chi-restraints excluded: chain B residue 1367 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 128 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 191 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 231 optimal weight: 0.7980 chunk 249 optimal weight: 1.9990 chunk 205 optimal weight: 0.7980 chunk 229 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 185 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 832 HIS ** B1178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1194 GLN ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1647 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= 0.261 Angle : 0.683 10.724 28095 Z= 0.361 Chirality : 0.042 0.164 3318 Planarity : 0.005 0.060 3545 Dihedral : 5.165 51.721 2693 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.20 % Favored : 90.64 % Rotamer: Outliers : 3.21 % Allowed : 17.63 % Favored : 79.15 % 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: 0.05 (0.17), residues: 2521 helix: 1.16 (0.12), residues: 1763 sheet: -2.99 (0.98), residues: 20 loop : -2.74 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 768 HIS 0.011 0.001 HIS B1250 PHE 0.037 0.002 PHE A1288 TYR 0.015 0.001 TYR A 138 ARG 0.006 0.000 ARG A 174 *********************** 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 756 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 680 time to evaluate : 2.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.7931 (tp40) cc_final: 0.7644 (tp40) REVERT: A 82 MET cc_start: 0.8052 (ttm) cc_final: 0.7658 (tmm) REVERT: A 91 ASN cc_start: 0.7688 (t0) cc_final: 0.7333 (t0) REVERT: A 155 GLU cc_start: 0.7566 (pt0) cc_final: 0.7123 (pt0) REVERT: A 184 LEU cc_start: 0.8194 (mt) cc_final: 0.7877 (mt) REVERT: A 199 SER cc_start: 0.8535 (t) cc_final: 0.8303 (t) REVERT: A 206 ARG cc_start: 0.8074 (tpp-160) cc_final: 0.7871 (tpp-160) REVERT: A 236 ASN cc_start: 0.7105 (m-40) cc_final: 0.6779 (m-40) REVERT: A 239 GLN cc_start: 0.7844 (mt0) cc_final: 0.7427 (mt0) REVERT: A 240 ILE cc_start: 0.8834 (mt) cc_final: 0.8523 (mm) REVERT: A 253 LYS cc_start: 0.8073 (pttt) cc_final: 0.7583 (pttt) REVERT: A 368 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7535 (mt-10) REVERT: A 523 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7517 (mm-30) REVERT: A 532 MET cc_start: 0.8261 (mtt) cc_final: 0.8020 (mtt) REVERT: A 555 LYS cc_start: 0.8765 (mmmm) cc_final: 0.8505 (mmmm) REVERT: A 559 ARG cc_start: 0.7901 (tpp80) cc_final: 0.7340 (tpp80) REVERT: A 562 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7067 (mt-10) REVERT: A 565 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7866 (mm-30) REVERT: A 593 LYS cc_start: 0.7682 (tptm) cc_final: 0.7259 (tptm) REVERT: A 597 GLU cc_start: 0.7740 (tm-30) cc_final: 0.6873 (tm-30) REVERT: A 606 MET cc_start: 0.7446 (mmm) cc_final: 0.7240 (tpp) REVERT: A 656 GLN cc_start: 0.7314 (tm-30) cc_final: 0.6561 (tm-30) REVERT: A 659 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6438 (mp0) REVERT: A 663 GLU cc_start: 0.7618 (pt0) cc_final: 0.7162 (pt0) REVERT: A 745 ASP cc_start: 0.8123 (t70) cc_final: 0.7885 (t0) REVERT: A 830 ASP cc_start: 0.7352 (t70) cc_final: 0.7152 (t70) REVERT: A 852 ASP cc_start: 0.7405 (t0) cc_final: 0.7185 (t0) REVERT: A 908 ASP cc_start: 0.7682 (p0) cc_final: 0.7325 (p0) REVERT: A 911 ARG cc_start: 0.7532 (tpp-160) cc_final: 0.7186 (mmt-90) REVERT: A 917 LYS cc_start: 0.7568 (mmtt) cc_final: 0.7143 (mttp) REVERT: A 931 ARG cc_start: 0.7953 (ttp-110) cc_final: 0.7713 (ttp-110) REVERT: A 956 ASP cc_start: 0.6687 (p0) cc_final: 0.6347 (p0) REVERT: A 1017 LYS cc_start: 0.8139 (ttmm) cc_final: 0.7843 (ttmm) REVERT: A 1020 MET cc_start: 0.7500 (tpp) cc_final: 0.7141 (tpp) REVERT: A 1021 GLU cc_start: 0.7842 (tp30) cc_final: 0.7162 (tp30) REVERT: A 1062 TYR cc_start: 0.7539 (p90) cc_final: 0.6905 (p90) REVERT: A 1071 ILE cc_start: 0.8503 (mm) cc_final: 0.8262 (mm) REVERT: A 1072 GLU cc_start: 0.8312 (tt0) cc_final: 0.7816 (tt0) REVERT: A 1082 LYS cc_start: 0.7840 (mtpt) cc_final: 0.7400 (mtpt) REVERT: A 1089 LYS cc_start: 0.8525 (ttmm) cc_final: 0.8138 (ttmm) REVERT: A 1093 GLN cc_start: 0.8543 (tp40) cc_final: 0.8220 (tp40) REVERT: A 1113 LEU cc_start: 0.8228 (tp) cc_final: 0.8003 (tp) REVERT: A 1116 LYS cc_start: 0.8728 (ttpt) cc_final: 0.8358 (ttmm) REVERT: A 1120 ILE cc_start: 0.9134 (mm) cc_final: 0.8758 (mm) REVERT: A 1126 GLN cc_start: 0.6902 (mm-40) cc_final: 0.6487 (mm-40) REVERT: A 1128 GLU cc_start: 0.7917 (tp30) cc_final: 0.7556 (tp30) REVERT: A 1132 LYS cc_start: 0.8393 (mmmm) cc_final: 0.7833 (mmmm) REVERT: A 1140 LYS cc_start: 0.7997 (mmmm) cc_final: 0.7549 (mmmm) REVERT: A 1157 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7268 (mt-10) REVERT: A 1184 PHE cc_start: 0.8761 (t80) cc_final: 0.8549 (t80) REVERT: A 1187 LYS cc_start: 0.8567 (mmmm) cc_final: 0.8208 (mmmm) REVERT: A 1200 GLU cc_start: 0.7890 (tp30) cc_final: 0.7533 (tp30) REVERT: A 1219 MET cc_start: 0.8185 (mmm) cc_final: 0.7788 (mmm) REVERT: A 1258 TYR cc_start: 0.7049 (m-80) cc_final: 0.6812 (m-10) REVERT: A 1259 LYS cc_start: 0.8360 (mppt) cc_final: 0.7729 (mppt) REVERT: A 1263 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7514 (mt-10) REVERT: A 1267 LYS cc_start: 0.8529 (mttm) cc_final: 0.8196 (mtpp) REVERT: A 1336 GLU cc_start: 0.8098 (tp30) cc_final: 0.7720 (tp30) REVERT: A 1366 VAL cc_start: 0.8641 (p) cc_final: 0.8404 (m) REVERT: A 1383 LYS cc_start: 0.8376 (mmtm) cc_final: 0.8109 (mmtm) REVERT: A 1400 LYS cc_start: 0.8798 (mmtm) cc_final: 0.8454 (mmtm) REVERT: A 1402 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8367 (mm-40) REVERT: B 10 ASP cc_start: 0.8030 (m-30) cc_final: 0.7635 (m-30) REVERT: B 82 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7559 (tmm) REVERT: B 90 ASP cc_start: 0.7898 (t0) cc_final: 0.7302 (t0) REVERT: B 91 ASN cc_start: 0.8106 (m110) cc_final: 0.6985 (m-40) REVERT: B 92 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8237 (tp) REVERT: B 110 ILE cc_start: 0.8602 (pt) cc_final: 0.7270 (mm) REVERT: B 132 ASN cc_start: 0.8198 (p0) cc_final: 0.7758 (p0) REVERT: B 136 GLN cc_start: 0.8214 (mt0) cc_final: 0.7964 (mt0) REVERT: B 154 PHE cc_start: 0.8136 (p90) cc_final: 0.7704 (p90) REVERT: B 155 GLU cc_start: 0.7514 (pt0) cc_final: 0.7197 (pm20) REVERT: B 162 ASP cc_start: 0.7780 (m-30) cc_final: 0.7486 (p0) REVERT: B 174 ARG cc_start: 0.8237 (ttt180) cc_final: 0.8017 (ttt180) REVERT: B 178 ASP cc_start: 0.7812 (t70) cc_final: 0.7575 (t0) REVERT: B 191 TYR cc_start: 0.8204 (t80) cc_final: 0.7930 (t80) REVERT: B 205 ARG cc_start: 0.7880 (tpp80) cc_final: 0.7573 (mmm-85) REVERT: B 228 LYS cc_start: 0.8344 (ttmm) cc_final: 0.8000 (ttmm) REVERT: B 333 ARG cc_start: 0.7648 (mtt90) cc_final: 0.6485 (mtt90) REVERT: B 346 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7256 (mm-30) REVERT: B 361 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7517 (mt-10) REVERT: B 368 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7365 (mt-10) REVERT: B 428 GLU cc_start: 0.7547 (tt0) cc_final: 0.6979 (tm-30) REVERT: B 499 LYS cc_start: 0.8230 (mtpp) cc_final: 0.7669 (mppt) REVERT: B 515 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7191 (tm-30) REVERT: B 547 GLN cc_start: 0.7285 (tp-100) cc_final: 0.6921 (tp-100) REVERT: B 580 MET cc_start: 0.7907 (tpp) cc_final: 0.7209 (tpp) REVERT: B 594 ASP cc_start: 0.7928 (m-30) cc_final: 0.7595 (m-30) REVERT: B 597 GLU cc_start: 0.7703 (tp30) cc_final: 0.7247 (tp30) REVERT: B 607 ASN cc_start: 0.7472 (t0) cc_final: 0.6811 (t0) REVERT: B 646 LEU cc_start: 0.8751 (mp) cc_final: 0.8534 (mp) REVERT: B 649 PHE cc_start: 0.7792 (p90) cc_final: 0.7512 (p90) REVERT: B 656 GLN cc_start: 0.7783 (mp10) cc_final: 0.6922 (mp10) REVERT: B 739 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.6581 (m-10) REVERT: B 807 ARG cc_start: 0.7903 (ttm170) cc_final: 0.7347 (ttp-170) REVERT: B 837 MET cc_start: 0.8153 (mmm) cc_final: 0.7785 (tpp) REVERT: B 1020 MET cc_start: 0.6853 (mmt) cc_final: 0.6528 (mmt) REVERT: B 1063 PHE cc_start: 0.8095 (t80) cc_final: 0.7764 (t80) REVERT: B 1066 GLU cc_start: 0.7963 (tt0) cc_final: 0.7410 (mm-30) REVERT: B 1080 PHE cc_start: 0.7337 (t80) cc_final: 0.6789 (t80) REVERT: B 1096 PHE cc_start: 0.6823 (OUTLIER) cc_final: 0.6490 (m-10) REVERT: B 1132 LYS cc_start: 0.8059 (mttt) cc_final: 0.7608 (mttm) REVERT: B 1154 GLN cc_start: 0.8440 (tt0) cc_final: 0.8109 (tt0) REVERT: B 1159 LEU cc_start: 0.8668 (mm) cc_final: 0.8454 (mm) REVERT: B 1191 MET cc_start: 0.7577 (tpp) cc_final: 0.7346 (tpp) REVERT: B 1200 GLU cc_start: 0.8181 (pt0) cc_final: 0.7949 (pt0) REVERT: B 1219 MET cc_start: 0.7482 (mmp) cc_final: 0.6832 (mmp) REVERT: B 1263 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7775 (mt-10) REVERT: B 1266 LEU cc_start: 0.7959 (mt) cc_final: 0.7676 (mt) REVERT: B 1383 LYS cc_start: 0.8874 (pttm) cc_final: 0.8456 (pttm) REVERT: B 1399 LYS cc_start: 0.8737 (pptt) cc_final: 0.8180 (pttm) outliers start: 76 outliers final: 58 residues processed: 708 average time/residue: 0.3769 time to fit residues: 406.5264 Evaluate side-chains 719 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 657 time to evaluate : 2.419 ------------------------------------------------------------------------------- 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 92 ILE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 844 CYS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 94 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 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 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 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 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 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 1250 HIS Chi-restraints excluded: chain B residue 1252 ILE Chi-restraints excluded: chain B residue 1290 ILE Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1367 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 228 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 110 optimal weight: 0.2980 chunk 155 optimal weight: 0.5980 chunk 231 optimal weight: 0.0770 chunk 245 optimal weight: 0.1980 chunk 121 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN A 337 ASN ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1285 ASN B 204 ASN B 709 ASN B1147 GLN ** B1178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1250 HIS ** B1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20796 Z= 0.195 Angle : 0.673 11.782 28095 Z= 0.345 Chirality : 0.041 0.186 3318 Planarity : 0.005 0.062 3545 Dihedral : 5.152 53.331 2693 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.73 % Favored : 91.11 % Rotamer: Outliers : 4.27 % Allowed : 18.90 % Favored : 76.83 % 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: 0.10 (0.17), residues: 2521 helix: 1.22 (0.12), residues: 1763 sheet: -2.90 (1.01), residues: 20 loop : -2.78 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 470 HIS 0.009 0.001 HIS A 617 PHE 0.031 0.002 PHE A1288 TYR 0.032 0.001 TYR B 138 ARG 0.005 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 790 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 689 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8424 (ttmt) cc_final: 0.8097 (ttmt) REVERT: A 78 GLN cc_start: 0.7890 (tp40) cc_final: 0.7596 (tp40) REVERT: A 82 MET cc_start: 0.8029 (ttm) cc_final: 0.7627 (tmm) REVERT: A 91 ASN cc_start: 0.7662 (t0) cc_final: 0.7270 (t0) REVERT: A 120 ASP cc_start: 0.7617 (t70) cc_final: 0.7141 (m-30) REVERT: A 155 GLU cc_start: 0.7578 (pt0) cc_final: 0.7138 (pt0) REVERT: A 184 LEU cc_start: 0.8209 (mt) cc_final: 0.7879 (mt) REVERT: A 199 SER cc_start: 0.8573 (t) cc_final: 0.8326 (t) REVERT: A 236 ASN cc_start: 0.7118 (m-40) cc_final: 0.6818 (m-40) REVERT: A 239 GLN cc_start: 0.7837 (mt0) cc_final: 0.7409 (mt0) REVERT: A 240 ILE cc_start: 0.8825 (mt) cc_final: 0.8512 (mm) REVERT: A 253 LYS cc_start: 0.8049 (pttt) cc_final: 0.7578 (pttt) REVERT: A 368 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7539 (mt-10) REVERT: A 523 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7463 (mm-30) REVERT: A 555 LYS cc_start: 0.8731 (mmmm) cc_final: 0.8458 (mmmm) REVERT: A 559 ARG cc_start: 0.7807 (tpp80) cc_final: 0.7164 (tpp80) REVERT: A 562 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7007 (mt-10) REVERT: A 565 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7848 (mm-30) REVERT: A 593 LYS cc_start: 0.7579 (tptm) cc_final: 0.7036 (tptm) REVERT: A 597 GLU cc_start: 0.7724 (tm-30) cc_final: 0.6840 (tm-30) REVERT: A 626 GLU cc_start: 0.7822 (tp30) cc_final: 0.7287 (tp30) REVERT: A 656 GLN cc_start: 0.7364 (tm-30) cc_final: 0.6688 (tm-30) REVERT: A 657 GLN cc_start: 0.7515 (mp10) cc_final: 0.7207 (mp10) REVERT: A 659 GLU cc_start: 0.7532 (mt-10) cc_final: 0.6442 (mp0) REVERT: A 663 GLU cc_start: 0.7623 (pt0) cc_final: 0.7160 (pt0) REVERT: A 745 ASP cc_start: 0.8075 (t70) cc_final: 0.7866 (t0) REVERT: A 811 LYS cc_start: 0.8571 (tptp) cc_final: 0.8356 (tptm) REVERT: A 852 ASP cc_start: 0.7415 (t0) cc_final: 0.7200 (t0) REVERT: A 911 ARG cc_start: 0.7533 (tpp-160) cc_final: 0.7182 (mmt-90) REVERT: A 917 LYS cc_start: 0.7511 (mmtt) cc_final: 0.7253 (mttt) REVERT: A 931 ARG cc_start: 0.7875 (ttp-110) cc_final: 0.7653 (ttp-110) REVERT: A 956 ASP cc_start: 0.6613 (p0) cc_final: 0.6207 (p0) REVERT: A 1017 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7798 (ttmm) REVERT: A 1020 MET cc_start: 0.7466 (tpp) cc_final: 0.7072 (tpp) REVERT: A 1021 GLU cc_start: 0.7844 (tp30) cc_final: 0.7165 (tp30) REVERT: A 1062 TYR cc_start: 0.7495 (p90) cc_final: 0.6908 (p90) REVERT: A 1072 GLU cc_start: 0.8275 (tt0) cc_final: 0.7775 (tt0) REVERT: A 1082 LYS cc_start: 0.7767 (mtpt) cc_final: 0.7337 (mtpt) REVERT: A 1089 LYS cc_start: 0.8493 (ttmm) cc_final: 0.8108 (ttmm) REVERT: A 1093 GLN cc_start: 0.8446 (tp40) cc_final: 0.8148 (tp40) REVERT: A 1112 MET cc_start: 0.7680 (mtp) cc_final: 0.7449 (mtm) REVERT: A 1113 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7838 (tp) REVERT: A 1116 LYS cc_start: 0.8666 (ttpt) cc_final: 0.8289 (ttmm) REVERT: A 1120 ILE cc_start: 0.9125 (mm) cc_final: 0.8710 (mm) REVERT: A 1126 GLN cc_start: 0.6893 (mm-40) cc_final: 0.6359 (mm-40) REVERT: A 1128 GLU cc_start: 0.7905 (tp30) cc_final: 0.7530 (tp30) REVERT: A 1132 LYS cc_start: 0.8344 (mmmm) cc_final: 0.7799 (mmmm) REVERT: A 1140 LYS cc_start: 0.7967 (mmmm) cc_final: 0.7522 (mmmm) REVERT: A 1152 THR cc_start: 0.8599 (t) cc_final: 0.8226 (p) REVERT: A 1153 ASN cc_start: 0.8445 (t0) cc_final: 0.7818 (t0) REVERT: A 1157 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7242 (mt-10) REVERT: A 1176 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.7102 (mp) REVERT: A 1187 LYS cc_start: 0.8504 (mmmm) cc_final: 0.8208 (mmmm) REVERT: A 1200 GLU cc_start: 0.7845 (tp30) cc_final: 0.7502 (tp30) REVERT: A 1219 MET cc_start: 0.8189 (mmm) cc_final: 0.7941 (mmm) REVERT: A 1259 LYS cc_start: 0.8333 (mppt) cc_final: 0.7640 (mppt) REVERT: A 1263 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7481 (mt-10) REVERT: A 1267 LYS cc_start: 0.8508 (mttm) cc_final: 0.8161 (mtpp) REVERT: A 1317 LEU cc_start: 0.8440 (mm) cc_final: 0.8189 (mt) REVERT: A 1336 GLU cc_start: 0.8072 (tp30) cc_final: 0.7684 (tp30) REVERT: A 1366 VAL cc_start: 0.8595 (p) cc_final: 0.8348 (m) REVERT: A 1383 LYS cc_start: 0.8315 (mmtm) cc_final: 0.8058 (mmtm) REVERT: A 1400 LYS cc_start: 0.8786 (mmtm) cc_final: 0.8454 (mmtm) REVERT: A 1402 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8485 (mm110) REVERT: A 1409 LYS cc_start: 0.8053 (mmmt) cc_final: 0.7730 (pttm) REVERT: B 10 ASP cc_start: 0.8004 (m-30) cc_final: 0.7572 (m-30) REVERT: B 18 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7312 (mm-30) REVERT: B 82 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7496 (tmm) REVERT: B 90 ASP cc_start: 0.7900 (t0) cc_final: 0.7305 (t0) REVERT: B 91 ASN cc_start: 0.8099 (m110) cc_final: 0.6987 (m-40) REVERT: B 110 ILE cc_start: 0.8592 (pt) cc_final: 0.7236 (mm) REVERT: B 124 LYS cc_start: 0.8360 (ttmt) cc_final: 0.8024 (ttpt) REVERT: B 132 ASN cc_start: 0.8161 (p0) cc_final: 0.7728 (p0) REVERT: B 136 GLN cc_start: 0.8196 (mt0) cc_final: 0.7949 (mt0) REVERT: B 154 PHE cc_start: 0.8111 (p90) cc_final: 0.7743 (p90) REVERT: B 155 GLU cc_start: 0.7463 (pt0) cc_final: 0.7152 (pm20) REVERT: B 162 ASP cc_start: 0.7736 (m-30) cc_final: 0.7470 (p0) REVERT: B 174 ARG cc_start: 0.8191 (ttt180) cc_final: 0.7954 (ttt180) REVERT: B 205 ARG cc_start: 0.7885 (tpp80) cc_final: 0.7591 (mmm-85) REVERT: B 228 LYS cc_start: 0.8329 (ttmm) cc_final: 0.7982 (ttmm) REVERT: B 333 ARG cc_start: 0.7683 (mtt90) cc_final: 0.7274 (mtt90) REVERT: B 346 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7225 (mm-30) REVERT: B 361 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7528 (mt-10) REVERT: B 499 LYS cc_start: 0.8230 (mtpp) cc_final: 0.7933 (mmmm) REVERT: B 503 LYS cc_start: 0.8574 (tttt) cc_final: 0.7927 (ttmm) REVERT: B 515 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7170 (tm-30) REVERT: B 547 GLN cc_start: 0.7233 (tp-100) cc_final: 0.6770 (tp-100) REVERT: B 580 MET cc_start: 0.7888 (tpp) cc_final: 0.7171 (tpp) REVERT: B 594 ASP cc_start: 0.7916 (m-30) cc_final: 0.7582 (m-30) REVERT: B 597 GLU cc_start: 0.7695 (tp30) cc_final: 0.7220 (tp30) REVERT: B 607 ASN cc_start: 0.7465 (t0) cc_final: 0.6756 (t0) REVERT: B 640 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7629 (mm-30) REVERT: B 646 LEU cc_start: 0.8712 (mp) cc_final: 0.8489 (mp) REVERT: B 649 PHE cc_start: 0.7795 (p90) cc_final: 0.7511 (p90) REVERT: B 656 GLN cc_start: 0.7803 (mp10) cc_final: 0.7300 (mp10) REVERT: B 692 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7380 (mp-120) REVERT: B 739 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.6502 (m-10) REVERT: B 803 LEU cc_start: 0.8226 (mt) cc_final: 0.7929 (mt) REVERT: B 807 ARG cc_start: 0.7938 (ttm170) cc_final: 0.7519 (ttp-170) REVERT: B 821 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8105 (mt) REVERT: B 837 MET cc_start: 0.8166 (mmm) cc_final: 0.6838 (mmm) REVERT: B 1014 LYS cc_start: 0.8800 (pttp) cc_final: 0.8497 (pttp) REVERT: B 1020 MET cc_start: 0.6749 (mmt) cc_final: 0.6480 (mmt) REVERT: B 1063 PHE cc_start: 0.8041 (t80) cc_final: 0.7763 (t80) REVERT: B 1066 GLU cc_start: 0.7848 (tt0) cc_final: 0.7314 (mm-30) REVERT: B 1096 PHE cc_start: 0.6722 (OUTLIER) cc_final: 0.6435 (m-10) REVERT: B 1132 LYS cc_start: 0.8039 (mttt) cc_final: 0.7570 (mttm) REVERT: B 1154 GLN cc_start: 0.8438 (tt0) cc_final: 0.8142 (tt0) REVERT: B 1157 GLU cc_start: 0.7392 (tp30) cc_final: 0.6645 (tp30) REVERT: B 1200 GLU cc_start: 0.8109 (pt0) cc_final: 0.7807 (pt0) REVERT: B 1204 GLU cc_start: 0.7553 (pp20) cc_final: 0.7328 (pp20) REVERT: B 1219 MET cc_start: 0.7423 (mmp) cc_final: 0.6816 (mmp) REVERT: B 1263 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7744 (mt-10) REVERT: B 1266 LEU cc_start: 0.7895 (mt) cc_final: 0.7604 (mt) REVERT: B 1383 LYS cc_start: 0.8857 (pttm) cc_final: 0.8441 (pttm) REVERT: B 1399 LYS cc_start: 0.8702 (pptt) cc_final: 0.8140 (pttm) outliers start: 101 outliers final: 69 residues processed: 733 average time/residue: 0.3556 time to fit residues: 391.7742 Evaluate side-chains 732 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 657 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 844 CYS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 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 121 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 560 LYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 757 VAL 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 1039 ILE Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 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 1250 HIS 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: 0.0170 chunk 139 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 182 optimal weight: 0.0670 chunk 101 optimal weight: 0.4980 chunk 209 optimal weight: 0.6980 chunk 169 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 220 optimal weight: 0.6980 chunk 61 optimal weight: 0.0470 overall best weight: 0.1454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN B 919 GLN ** B1178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20796 Z= 0.179 Angle : 0.668 12.576 28095 Z= 0.340 Chirality : 0.040 0.213 3318 Planarity : 0.005 0.061 3545 Dihedral : 5.117 54.080 2693 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.69 % Favored : 91.19 % Rotamer: Outliers : 4.06 % Allowed : 20.04 % Favored : 75.90 % 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: 0.16 (0.17), residues: 2521 helix: 1.28 (0.12), residues: 1754 sheet: -2.75 (1.04), residues: 20 loop : -2.76 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 470 HIS 0.017 0.001 HIS B1250 PHE 0.033 0.002 PHE A1288 TYR 0.023 0.001 TYR B 138 ARG 0.005 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 765 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 669 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8400 (ttmt) cc_final: 0.8075 (ttmt) REVERT: A 27 ARG cc_start: 0.8054 (ttm170) cc_final: 0.7554 (mtm110) REVERT: A 78 GLN cc_start: 0.7816 (tp40) cc_final: 0.7556 (tp40) REVERT: A 91 ASN cc_start: 0.7634 (t0) cc_final: 0.7228 (t0) REVERT: A 120 ASP cc_start: 0.7581 (t70) cc_final: 0.7112 (m-30) REVERT: A 155 GLU cc_start: 0.7520 (pt0) cc_final: 0.7223 (pt0) REVERT: A 184 LEU cc_start: 0.8218 (mt) cc_final: 0.7882 (mt) REVERT: A 199 SER cc_start: 0.8611 (t) cc_final: 0.8383 (t) REVERT: A 236 ASN cc_start: 0.7170 (m-40) cc_final: 0.6925 (m-40) REVERT: A 239 GLN cc_start: 0.7834 (mt0) cc_final: 0.7416 (mt0) REVERT: A 240 ILE cc_start: 0.8806 (mt) cc_final: 0.8480 (mm) REVERT: A 253 LYS cc_start: 0.8053 (pttt) cc_final: 0.7561 (pttt) REVERT: A 368 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7499 (mt-10) REVERT: A 523 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7422 (mm-30) REVERT: A 555 LYS cc_start: 0.8708 (mmmm) cc_final: 0.8257 (mmmm) REVERT: A 559 ARG cc_start: 0.7756 (tpp80) cc_final: 0.7068 (tpp80) REVERT: A 562 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7024 (mt-10) REVERT: A 565 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7789 (mm-30) REVERT: A 593 LYS cc_start: 0.7567 (tptm) cc_final: 0.7189 (tptm) REVERT: A 597 GLU cc_start: 0.7707 (tm-30) cc_final: 0.6841 (tm-30) REVERT: A 600 PHE cc_start: 0.8554 (t80) cc_final: 0.8257 (t80) REVERT: A 615 LEU cc_start: 0.7494 (tp) cc_final: 0.7194 (tt) REVERT: A 626 GLU cc_start: 0.7822 (tp30) cc_final: 0.7525 (tp30) REVERT: A 656 GLN cc_start: 0.7343 (tm-30) cc_final: 0.6704 (tm-30) REVERT: A 657 GLN cc_start: 0.7586 (mp10) cc_final: 0.7228 (mp10) REVERT: A 659 GLU cc_start: 0.7490 (mt-10) cc_final: 0.6382 (mp0) REVERT: A 663 GLU cc_start: 0.7584 (pt0) cc_final: 0.7124 (pt0) REVERT: A 721 MET cc_start: 0.7616 (tpp) cc_final: 0.7196 (tpp) REVERT: A 745 ASP cc_start: 0.8071 (t70) cc_final: 0.7824 (t0) REVERT: A 811 LYS cc_start: 0.8488 (tptp) cc_final: 0.8271 (tptm) REVERT: A 852 ASP cc_start: 0.7434 (t0) cc_final: 0.7204 (t0) REVERT: A 911 ARG cc_start: 0.7493 (tpp-160) cc_final: 0.7212 (mmt-90) REVERT: A 931 ARG cc_start: 0.7860 (ttp-110) cc_final: 0.7636 (ttp-110) REVERT: A 956 ASP cc_start: 0.6619 (p0) cc_final: 0.6248 (p0) REVERT: A 1020 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7011 (tpp) REVERT: A 1021 GLU cc_start: 0.7853 (tp30) cc_final: 0.7190 (tp30) REVERT: A 1027 ASN cc_start: 0.6644 (p0) cc_final: 0.6335 (p0) REVERT: A 1062 TYR cc_start: 0.7484 (p90) cc_final: 0.6852 (p90) REVERT: A 1072 GLU cc_start: 0.8264 (tt0) cc_final: 0.7709 (tt0) REVERT: A 1082 LYS cc_start: 0.7701 (mtpt) cc_final: 0.7295 (mmtt) REVERT: A 1089 LYS cc_start: 0.8467 (ttmm) cc_final: 0.8065 (ttmm) REVERT: A 1093 GLN cc_start: 0.8414 (tp40) cc_final: 0.8123 (tp40) REVERT: A 1112 MET cc_start: 0.7574 (mtp) cc_final: 0.7332 (mtm) REVERT: A 1113 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7797 (tp) REVERT: A 1116 LYS cc_start: 0.8644 (ttpt) cc_final: 0.8333 (ttmm) REVERT: A 1117 ILE cc_start: 0.8881 (tt) cc_final: 0.8663 (tp) REVERT: A 1120 ILE cc_start: 0.9119 (mm) cc_final: 0.8722 (mm) REVERT: A 1126 GLN cc_start: 0.6883 (mm-40) cc_final: 0.6326 (mm-40) REVERT: A 1128 GLU cc_start: 0.7886 (tp30) cc_final: 0.7495 (tp30) REVERT: A 1132 LYS cc_start: 0.8312 (mmmm) cc_final: 0.7759 (mmmm) REVERT: A 1152 THR cc_start: 0.8598 (t) cc_final: 0.8186 (p) REVERT: A 1153 ASN cc_start: 0.8379 (t0) cc_final: 0.7744 (m-40) REVERT: A 1157 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7166 (mt-10) REVERT: A 1176 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.7062 (mp) REVERT: A 1184 PHE cc_start: 0.8705 (t80) cc_final: 0.8396 (t80) REVERT: A 1187 LYS cc_start: 0.8496 (mmmm) cc_final: 0.8213 (mmmm) REVERT: A 1200 GLU cc_start: 0.7817 (tp30) cc_final: 0.7471 (tp30) REVERT: A 1219 MET cc_start: 0.8175 (mmm) cc_final: 0.7923 (mmm) REVERT: A 1231 MET cc_start: 0.7956 (mmt) cc_final: 0.7657 (mpp) REVERT: A 1259 LYS cc_start: 0.8298 (mppt) cc_final: 0.7469 (mppt) REVERT: A 1263 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7399 (mt-10) REVERT: A 1267 LYS cc_start: 0.8489 (mttm) cc_final: 0.8153 (mtpp) REVERT: A 1336 GLU cc_start: 0.8044 (tp30) cc_final: 0.7649 (tp30) REVERT: A 1365 ASN cc_start: 0.8337 (m-40) cc_final: 0.7910 (m-40) REVERT: A 1366 VAL cc_start: 0.8560 (p) cc_final: 0.8324 (m) REVERT: A 1383 LYS cc_start: 0.8330 (mmtm) cc_final: 0.8091 (mmtm) REVERT: A 1400 LYS cc_start: 0.8789 (mmtm) cc_final: 0.8440 (mmtm) REVERT: A 1409 LYS cc_start: 0.8069 (mmmt) cc_final: 0.7842 (pttm) REVERT: B 18 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7250 (mm-30) REVERT: B 82 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7468 (tmm) REVERT: B 90 ASP cc_start: 0.7885 (t0) cc_final: 0.7367 (t0) REVERT: B 91 ASN cc_start: 0.8099 (m110) cc_final: 0.7039 (m-40) REVERT: B 110 ILE cc_start: 0.8574 (pt) cc_final: 0.8126 (mm) REVERT: B 124 LYS cc_start: 0.8366 (ttmt) cc_final: 0.8020 (ttpt) REVERT: B 132 ASN cc_start: 0.8190 (p0) cc_final: 0.7723 (p0) REVERT: B 136 GLN cc_start: 0.8187 (mt0) cc_final: 0.7969 (mt0) REVERT: B 162 ASP cc_start: 0.7713 (m-30) cc_final: 0.7468 (p0) REVERT: B 174 ARG cc_start: 0.8168 (ttt180) cc_final: 0.7953 (ttt180) REVERT: B 205 ARG cc_start: 0.7881 (tpp80) cc_final: 0.7593 (mmm-85) REVERT: B 228 LYS cc_start: 0.8283 (ttmm) cc_final: 0.7712 (ttmm) REVERT: B 333 ARG cc_start: 0.7670 (mtt90) cc_final: 0.7264 (mtt90) REVERT: B 346 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7211 (mm-30) REVERT: B 361 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7524 (mt-10) REVERT: B 485 ASP cc_start: 0.6588 (m-30) cc_final: 0.6138 (m-30) REVERT: B 503 LYS cc_start: 0.8534 (tttt) cc_final: 0.7896 (ttmm) REVERT: B 515 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7144 (tm-30) REVERT: B 547 GLN cc_start: 0.7153 (tp-100) cc_final: 0.6742 (tp40) REVERT: B 580 MET cc_start: 0.7874 (tpp) cc_final: 0.7153 (tpp) REVERT: B 594 ASP cc_start: 0.7912 (m-30) cc_final: 0.7574 (m-30) REVERT: B 597 GLU cc_start: 0.7653 (tp30) cc_final: 0.7172 (tp30) REVERT: B 607 ASN cc_start: 0.7453 (t0) cc_final: 0.6809 (t0) REVERT: B 627 TYR cc_start: 0.8659 (t80) cc_final: 0.8253 (t80) REVERT: B 640 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7604 (mm-30) REVERT: B 646 LEU cc_start: 0.8668 (mp) cc_final: 0.8445 (mp) REVERT: B 650 ARG cc_start: 0.7497 (tpt-90) cc_final: 0.7026 (tpp80) REVERT: B 656 GLN cc_start: 0.7809 (mp10) cc_final: 0.7316 (mp10) REVERT: B 692 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7444 (mp-120) REVERT: B 707 MET cc_start: 0.7967 (tpp) cc_final: 0.7179 (tpp) REVERT: B 739 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.6468 (m-10) REVERT: B 803 LEU cc_start: 0.8181 (mt) cc_final: 0.7903 (mt) REVERT: B 807 ARG cc_start: 0.7988 (ttm170) cc_final: 0.7640 (ttp-170) REVERT: B 861 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7952 (mm) REVERT: B 919 GLN cc_start: 0.7418 (mt0) cc_final: 0.7141 (mt0) REVERT: B 1020 MET cc_start: 0.6701 (mmt) cc_final: 0.6456 (mmt) REVERT: B 1063 PHE cc_start: 0.8065 (t80) cc_final: 0.7832 (t80) REVERT: B 1066 GLU cc_start: 0.7867 (tt0) cc_final: 0.7460 (mm-30) REVERT: B 1096 PHE cc_start: 0.6620 (OUTLIER) cc_final: 0.6310 (m-10) REVERT: B 1132 LYS cc_start: 0.8000 (mttt) cc_final: 0.7601 (mttt) REVERT: B 1154 GLN cc_start: 0.8398 (tt0) cc_final: 0.8158 (tt0) REVERT: B 1156 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6779 (mmtp) REVERT: B 1157 GLU cc_start: 0.7357 (tp30) cc_final: 0.6595 (tp30) REVERT: B 1200 GLU cc_start: 0.8048 (pt0) cc_final: 0.7806 (pt0) REVERT: B 1201 TYR cc_start: 0.8294 (t80) cc_final: 0.8049 (t80) REVERT: B 1219 MET cc_start: 0.7395 (mmp) cc_final: 0.6948 (mmp) REVERT: B 1231 MET cc_start: 0.6790 (mpp) cc_final: 0.6546 (mpp) REVERT: B 1263 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7942 (mt-10) REVERT: B 1266 LEU cc_start: 0.7843 (mt) cc_final: 0.7550 (mt) REVERT: B 1383 LYS cc_start: 0.8815 (pttm) cc_final: 0.8388 (pttm) REVERT: B 1399 LYS cc_start: 0.8678 (pptt) cc_final: 0.8355 (pptt) outliers start: 96 outliers final: 65 residues processed: 711 average time/residue: 0.3728 time to fit residues: 399.7027 Evaluate side-chains 720 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 647 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 844 CYS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 520 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 757 VAL Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 1028 ILE Chi-restraints excluded: chain B residue 1039 ILE Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 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 1156 LYS Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1218 PHE Chi-restraints excluded: chain B residue 1290 ILE Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 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: 0.8980 chunk 221 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 144 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 245 optimal weight: 0.8980 chunk 204 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 HIS A 465 GLN ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1217 ASN B 334 GLN B 709 ASN B 713 HIS ** B1178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1250 HIS ** B1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20796 Z= 0.285 Angle : 0.713 11.634 28095 Z= 0.373 Chirality : 0.043 0.202 3318 Planarity : 0.005 0.062 3545 Dihedral : 5.260 55.836 2693 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.40 % Favored : 90.48 % Rotamer: Outliers : 3.85 % Allowed : 21.56 % Favored : 74.59 % 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: -0.01 (0.17), residues: 2521 helix: 1.10 (0.12), residues: 1760 sheet: -2.91 (1.00), residues: 20 loop : -2.73 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 773 HIS 0.009 0.001 HIS A 617 PHE 0.034 0.002 PHE A1288 TYR 0.031 0.002 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 768 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 677 time to evaluate : 2.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8426 (ttmt) cc_final: 0.8101 (ttmt) REVERT: A 78 GLN cc_start: 0.7908 (tp40) cc_final: 0.7647 (tp40) REVERT: A 91 ASN cc_start: 0.7704 (t0) cc_final: 0.7309 (t0) REVERT: A 154 PHE cc_start: 0.8388 (p90) cc_final: 0.8163 (p90) REVERT: A 155 GLU cc_start: 0.7494 (pt0) cc_final: 0.7214 (pt0) REVERT: A 184 LEU cc_start: 0.8247 (mt) cc_final: 0.7882 (mt) REVERT: A 199 SER cc_start: 0.8520 (t) cc_final: 0.8256 (t) REVERT: A 236 ASN cc_start: 0.7130 (m-40) cc_final: 0.6895 (m-40) REVERT: A 239 GLN cc_start: 0.7857 (mt0) cc_final: 0.7448 (mt0) REVERT: A 240 ILE cc_start: 0.8781 (mt) cc_final: 0.8473 (mm) REVERT: A 253 LYS cc_start: 0.8046 (pttt) cc_final: 0.7568 (pttt) REVERT: A 368 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7570 (mt-10) REVERT: A 523 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7500 (mm-30) REVERT: A 559 ARG cc_start: 0.7784 (tpp80) cc_final: 0.7043 (tpp80) REVERT: A 562 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7069 (mt-10) REVERT: A 565 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7822 (mm-30) REVERT: A 593 LYS cc_start: 0.7618 (tptm) cc_final: 0.7237 (tptm) REVERT: A 597 GLU cc_start: 0.7781 (tm-30) cc_final: 0.6906 (tm-30) REVERT: A 600 PHE cc_start: 0.8588 (t80) cc_final: 0.8334 (t80) REVERT: A 615 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7792 (tt) REVERT: A 626 GLU cc_start: 0.7901 (tp30) cc_final: 0.7590 (tp30) REVERT: A 656 GLN cc_start: 0.7511 (tm-30) cc_final: 0.6960 (tm-30) REVERT: A 657 GLN cc_start: 0.7647 (mp10) cc_final: 0.7313 (mp10) REVERT: A 659 GLU cc_start: 0.7584 (mt-10) cc_final: 0.6489 (mp0) REVERT: A 663 GLU cc_start: 0.7644 (pt0) cc_final: 0.7194 (pt0) REVERT: A 745 ASP cc_start: 0.8107 (t70) cc_final: 0.7901 (t0) REVERT: A 811 LYS cc_start: 0.8550 (tptp) cc_final: 0.8322 (tptm) REVERT: A 911 ARG cc_start: 0.7566 (tpp-160) cc_final: 0.7232 (mmt-90) REVERT: A 917 LYS cc_start: 0.7541 (mmtt) cc_final: 0.7002 (mttp) REVERT: A 931 ARG cc_start: 0.7980 (ttp-110) cc_final: 0.7734 (ttp-110) REVERT: A 956 ASP cc_start: 0.6336 (p0) cc_final: 0.6074 (p0) REVERT: A 975 ASN cc_start: 0.8260 (m-40) cc_final: 0.8047 (t0) REVERT: A 1020 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7115 (tpp) REVERT: A 1021 GLU cc_start: 0.7873 (tp30) cc_final: 0.7202 (tp30) REVERT: A 1027 ASN cc_start: 0.6665 (p0) cc_final: 0.6367 (p0) REVERT: A 1062 TYR cc_start: 0.7570 (p90) cc_final: 0.6878 (p90) REVERT: A 1072 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7646 (tt0) REVERT: A 1082 LYS cc_start: 0.7723 (mtpt) cc_final: 0.7362 (mmtt) REVERT: A 1089 LYS cc_start: 0.8503 (ttmm) cc_final: 0.8114 (ttmm) REVERT: A 1093 GLN cc_start: 0.8459 (tp40) cc_final: 0.8146 (tp40) REVERT: A 1112 MET cc_start: 0.7768 (mtp) cc_final: 0.7560 (mtp) REVERT: A 1113 LEU cc_start: 0.8254 (tp) cc_final: 0.7956 (tp) REVERT: A 1116 LYS cc_start: 0.8685 (ttpt) cc_final: 0.8364 (ttmm) REVERT: A 1120 ILE cc_start: 0.9134 (mm) cc_final: 0.8724 (mm) REVERT: A 1122 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8635 (mm) REVERT: A 1126 GLN cc_start: 0.6939 (mm-40) cc_final: 0.6391 (mm-40) REVERT: A 1128 GLU cc_start: 0.7974 (tp30) cc_final: 0.7608 (tp30) REVERT: A 1132 LYS cc_start: 0.8347 (mmmm) cc_final: 0.7797 (mmmm) REVERT: A 1152 THR cc_start: 0.8629 (t) cc_final: 0.8184 (p) REVERT: A 1157 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7314 (mt-10) REVERT: A 1175 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8058 (mm) REVERT: A 1186 ARG cc_start: 0.8071 (ttt90) cc_final: 0.7227 (ttm-80) REVERT: A 1187 LYS cc_start: 0.8533 (mmmm) cc_final: 0.8243 (mmmm) REVERT: A 1200 GLU cc_start: 0.7887 (tp30) cc_final: 0.7543 (tp30) REVERT: A 1219 MET cc_start: 0.8183 (mmm) cc_final: 0.7879 (mmm) REVERT: A 1227 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7242 (mm-30) REVERT: A 1243 LYS cc_start: 0.7886 (mmmt) cc_final: 0.7535 (mmmt) REVERT: A 1259 LYS cc_start: 0.8360 (mppt) cc_final: 0.7752 (mppt) REVERT: A 1263 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7551 (mt-10) REVERT: A 1267 LYS cc_start: 0.8554 (mttm) cc_final: 0.8216 (mtpp) REVERT: A 1336 GLU cc_start: 0.8079 (tp30) cc_final: 0.7723 (tp30) REVERT: A 1365 ASN cc_start: 0.8449 (m-40) cc_final: 0.8232 (m-40) REVERT: A 1366 VAL cc_start: 0.8685 (p) cc_final: 0.8455 (m) REVERT: A 1383 LYS cc_start: 0.8390 (mmtm) cc_final: 0.8132 (mmtm) REVERT: A 1400 LYS cc_start: 0.8787 (mmtm) cc_final: 0.8518 (mptt) REVERT: B 18 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7229 (mm-30) REVERT: B 81 LEU cc_start: 0.7981 (mt) cc_final: 0.7743 (mt) REVERT: B 82 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7346 (tmm) REVERT: B 91 ASN cc_start: 0.8134 (m110) cc_final: 0.7873 (m-40) REVERT: B 110 ILE cc_start: 0.8608 (pt) cc_final: 0.7342 (mm) REVERT: B 124 LYS cc_start: 0.8418 (ttmt) cc_final: 0.8056 (ttpt) REVERT: B 132 ASN cc_start: 0.8178 (p0) cc_final: 0.7760 (p0) REVERT: B 154 PHE cc_start: 0.8236 (p90) cc_final: 0.7852 (p90) REVERT: B 155 GLU cc_start: 0.7447 (pt0) cc_final: 0.6980 (pm20) REVERT: B 205 ARG cc_start: 0.7924 (tpp80) cc_final: 0.7618 (mmm-85) REVERT: B 228 LYS cc_start: 0.8344 (ttmm) cc_final: 0.7964 (ttmm) REVERT: B 333 ARG cc_start: 0.7712 (mtt90) cc_final: 0.7290 (mtt90) REVERT: B 346 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7256 (mm-30) REVERT: B 361 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7557 (mt-10) REVERT: B 428 GLU cc_start: 0.7549 (tt0) cc_final: 0.6973 (tp30) REVERT: B 433 ARG cc_start: 0.8376 (tpp80) cc_final: 0.8049 (mmm160) REVERT: B 485 ASP cc_start: 0.6735 (m-30) cc_final: 0.6225 (m-30) REVERT: B 515 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7266 (tm-30) REVERT: B 547 GLN cc_start: 0.7240 (tp-100) cc_final: 0.6858 (tp40) REVERT: B 580 MET cc_start: 0.7922 (tpp) cc_final: 0.7206 (tpp) REVERT: B 594 ASP cc_start: 0.7972 (m-30) cc_final: 0.7640 (m-30) REVERT: B 597 GLU cc_start: 0.7740 (tp30) cc_final: 0.7242 (tp30) REVERT: B 607 ASN cc_start: 0.7540 (t0) cc_final: 0.6939 (t0) REVERT: B 649 PHE cc_start: 0.7754 (p90) cc_final: 0.7439 (p90) REVERT: B 650 ARG cc_start: 0.7545 (tpt-90) cc_final: 0.7201 (ttm-80) REVERT: B 656 GLN cc_start: 0.7822 (mp10) cc_final: 0.7600 (mp10) REVERT: B 692 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7523 (mp-120) REVERT: B 707 MET cc_start: 0.7931 (tpp) cc_final: 0.7217 (tpp) REVERT: B 739 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.6531 (m-10) REVERT: B 803 LEU cc_start: 0.8226 (mt) cc_final: 0.7924 (mt) REVERT: B 807 ARG cc_start: 0.7948 (ttm170) cc_final: 0.7504 (ttp-170) REVERT: B 857 PHE cc_start: 0.7388 (t80) cc_final: 0.7160 (t80) REVERT: B 861 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8010 (mm) REVERT: B 973 LEU cc_start: 0.8446 (mm) cc_final: 0.8203 (mp) REVERT: B 1014 LYS cc_start: 0.8778 (pttp) cc_final: 0.8478 (pttp) REVERT: B 1063 PHE cc_start: 0.8083 (t80) cc_final: 0.7767 (t80) REVERT: B 1066 GLU cc_start: 0.7944 (tt0) cc_final: 0.7529 (mm-30) REVERT: B 1096 PHE cc_start: 0.6737 (OUTLIER) cc_final: 0.6473 (m-10) REVERT: B 1132 LYS cc_start: 0.8076 (mttt) cc_final: 0.7634 (mttm) REVERT: B 1157 GLU cc_start: 0.7455 (tp30) cc_final: 0.6651 (tp30) REVERT: B 1200 GLU cc_start: 0.8137 (pt0) cc_final: 0.7702 (pt0) REVERT: B 1201 TYR cc_start: 0.8340 (t80) cc_final: 0.7366 (t80) REVERT: B 1204 GLU cc_start: 0.7648 (pp20) cc_final: 0.7318 (pp20) REVERT: B 1219 MET cc_start: 0.7553 (mmp) cc_final: 0.7166 (mmp) REVERT: B 1263 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7975 (mt-10) REVERT: B 1266 LEU cc_start: 0.7942 (mt) cc_final: 0.7649 (mt) REVERT: B 1383 LYS cc_start: 0.8847 (pttm) cc_final: 0.8432 (pttm) REVERT: B 1399 LYS cc_start: 0.8701 (pptt) cc_final: 0.8371 (pptt) REVERT: B 1412 GLU cc_start: 0.5843 (OUTLIER) cc_final: 0.4181 (mm-30) outliers start: 91 outliers final: 68 residues processed: 719 average time/residue: 0.3591 time to fit residues: 392.2297 Evaluate side-chains 733 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 655 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 844 CYS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 1028 ILE Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 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 1290 ILE Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1325 THR Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1367 TYR Chi-restraints excluded: chain B residue 1412 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 236 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 140 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 206 optimal weight: 0.9980 chunk 137 optimal weight: 0.4980 chunk 244 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 149 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1217 ASN ** B 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20796 Z= 0.241 Angle : 0.715 12.720 28095 Z= 0.367 Chirality : 0.043 0.300 3318 Planarity : 0.005 0.062 3545 Dihedral : 5.277 57.737 2693 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.24 % Favored : 90.64 % Rotamer: Outliers : 4.06 % Allowed : 22.20 % 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: -0.04 (0.17), residues: 2521 helix: 1.11 (0.12), residues: 1757 sheet: -3.21 (0.95), residues: 22 loop : -2.79 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 773 HIS 0.009 0.001 HIS A 617 PHE 0.038 0.002 PHE A1288 TYR 0.031 0.002 TYR B 138 ARG 0.007 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 766 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 670 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8419 (ttmt) cc_final: 0.8111 (ttmt) REVERT: A 78 GLN cc_start: 0.7893 (tp40) cc_final: 0.7638 (tp40) REVERT: A 91 ASN cc_start: 0.7693 (t0) cc_final: 0.7268 (t0) REVERT: A 154 PHE cc_start: 0.8385 (p90) cc_final: 0.8173 (p90) REVERT: A 155 GLU cc_start: 0.7496 (pt0) cc_final: 0.7201 (pt0) REVERT: A 184 LEU cc_start: 0.8233 (mt) cc_final: 0.7879 (mt) REVERT: A 199 SER cc_start: 0.8544 (t) cc_final: 0.8275 (t) REVERT: A 236 ASN cc_start: 0.7136 (m-40) cc_final: 0.6914 (m-40) REVERT: A 239 GLN cc_start: 0.7843 (mt0) cc_final: 0.7449 (mt0) REVERT: A 240 ILE cc_start: 0.8771 (mt) cc_final: 0.8485 (mm) REVERT: A 253 LYS cc_start: 0.8025 (pttt) cc_final: 0.7552 (pttt) REVERT: A 368 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7575 (mt-10) REVERT: A 460 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7324 (tm-30) REVERT: A 523 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7475 (mm-30) REVERT: A 555 LYS cc_start: 0.8612 (mmmm) cc_final: 0.8156 (mmmm) REVERT: A 559 ARG cc_start: 0.7785 (tpp80) cc_final: 0.7086 (tpp80) REVERT: A 562 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7036 (mt-10) REVERT: A 565 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7815 (mm-30) REVERT: A 593 LYS cc_start: 0.7612 (tptm) cc_final: 0.7227 (tptm) REVERT: A 597 GLU cc_start: 0.7777 (tm-30) cc_final: 0.6917 (tm-30) REVERT: A 600 PHE cc_start: 0.8598 (t80) cc_final: 0.8275 (t80) REVERT: A 615 LEU cc_start: 0.8177 (tp) cc_final: 0.7709 (tt) REVERT: A 626 GLU cc_start: 0.7890 (tp30) cc_final: 0.7571 (tp30) REVERT: A 656 GLN cc_start: 0.7494 (tm-30) cc_final: 0.6908 (tm-30) REVERT: A 657 GLN cc_start: 0.7648 (mp10) cc_final: 0.7265 (mp10) REVERT: A 659 GLU cc_start: 0.7555 (mt-10) cc_final: 0.6479 (mp0) REVERT: A 663 GLU cc_start: 0.7649 (pt0) cc_final: 0.7198 (pt0) REVERT: A 745 ASP cc_start: 0.8126 (t70) cc_final: 0.7920 (t0) REVERT: A 819 SER cc_start: 0.8288 (m) cc_final: 0.7954 (p) REVERT: A 911 ARG cc_start: 0.7551 (tpp-160) cc_final: 0.7217 (mmt-90) REVERT: A 917 LYS cc_start: 0.7530 (mmtt) cc_final: 0.7022 (mttp) REVERT: A 931 ARG cc_start: 0.7993 (ttp-110) cc_final: 0.7762 (ttp-110) REVERT: A 956 ASP cc_start: 0.6418 (p0) cc_final: 0.6106 (p0) REVERT: A 1020 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7073 (tpp) REVERT: A 1021 GLU cc_start: 0.7893 (tp30) cc_final: 0.7248 (tp30) REVERT: A 1027 ASN cc_start: 0.6638 (p0) cc_final: 0.6328 (p0) REVERT: A 1072 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7757 (tt0) REVERT: A 1082 LYS cc_start: 0.7700 (mtpt) cc_final: 0.7275 (mtpt) REVERT: A 1086 GLU cc_start: 0.5851 (tm-30) cc_final: 0.5639 (tm-30) REVERT: A 1089 LYS cc_start: 0.8488 (ttmm) cc_final: 0.8091 (ttmm) REVERT: A 1093 GLN cc_start: 0.8445 (tp40) cc_final: 0.8129 (tp40) REVERT: A 1112 MET cc_start: 0.7779 (mtp) cc_final: 0.7502 (mtp) REVERT: A 1113 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7910 (tp) REVERT: A 1116 LYS cc_start: 0.8651 (ttpt) cc_final: 0.8296 (ttmm) REVERT: A 1120 ILE cc_start: 0.9132 (mm) cc_final: 0.8711 (mm) REVERT: A 1122 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8644 (mm) REVERT: A 1126 GLN cc_start: 0.6920 (mm-40) cc_final: 0.6364 (mm-40) REVERT: A 1128 GLU cc_start: 0.7969 (tp30) cc_final: 0.7621 (tp30) REVERT: A 1132 LYS cc_start: 0.8337 (mmmm) cc_final: 0.7781 (mmmm) REVERT: A 1152 THR cc_start: 0.8618 (t) cc_final: 0.8159 (p) REVERT: A 1157 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7255 (mt-10) REVERT: A 1187 LYS cc_start: 0.8537 (mmmm) cc_final: 0.8253 (mmmm) REVERT: A 1200 GLU cc_start: 0.7871 (tp30) cc_final: 0.7531 (tp30) REVERT: A 1219 MET cc_start: 0.8169 (mmm) cc_final: 0.7880 (mmm) REVERT: A 1227 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7217 (mt-10) REVERT: A 1256 ASN cc_start: 0.6947 (p0) cc_final: 0.6451 (p0) REVERT: A 1259 LYS cc_start: 0.8368 (mppt) cc_final: 0.7439 (mppt) REVERT: A 1263 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7470 (mt-10) REVERT: A 1267 LYS cc_start: 0.8543 (mttm) cc_final: 0.8205 (mtpp) REVERT: A 1336 GLU cc_start: 0.8068 (tp30) cc_final: 0.7727 (tp30) REVERT: A 1365 ASN cc_start: 0.8422 (m-40) cc_final: 0.8202 (m-40) REVERT: A 1366 VAL cc_start: 0.8677 (p) cc_final: 0.8442 (m) REVERT: A 1383 LYS cc_start: 0.8354 (mmtm) cc_final: 0.8112 (mmtm) REVERT: A 1385 LEU cc_start: 0.8309 (mm) cc_final: 0.7986 (mt) REVERT: A 1399 LYS cc_start: 0.8636 (ptpp) cc_final: 0.8332 (pttm) REVERT: A 1400 LYS cc_start: 0.8777 (mmtm) cc_final: 0.8518 (mmtm) REVERT: A 1409 LYS cc_start: 0.8206 (mmmt) cc_final: 0.7651 (pttm) REVERT: B 18 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7228 (mm-30) REVERT: B 81 LEU cc_start: 0.8005 (mt) cc_final: 0.7790 (mt) REVERT: B 82 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7331 (tmm) REVERT: B 90 ASP cc_start: 0.7908 (t0) cc_final: 0.7359 (t0) REVERT: B 91 ASN cc_start: 0.8135 (m110) cc_final: 0.6892 (m-40) REVERT: B 110 ILE cc_start: 0.8629 (pt) cc_final: 0.7276 (mm) REVERT: B 124 LYS cc_start: 0.8418 (ttmt) cc_final: 0.8064 (ttpt) REVERT: B 132 ASN cc_start: 0.8183 (p0) cc_final: 0.7733 (p0) REVERT: B 154 PHE cc_start: 0.8111 (p90) cc_final: 0.7669 (p90) REVERT: B 155 GLU cc_start: 0.7500 (pt0) cc_final: 0.7008 (pm20) REVERT: B 205 ARG cc_start: 0.7933 (tpp80) cc_final: 0.7665 (mmm-85) REVERT: B 228 LYS cc_start: 0.8333 (ttmm) cc_final: 0.7752 (ttmm) REVERT: B 333 ARG cc_start: 0.7722 (mtt90) cc_final: 0.7306 (mtt90) REVERT: B 346 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7254 (mm-30) REVERT: B 361 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7550 (mt-10) REVERT: B 485 ASP cc_start: 0.6767 (m-30) cc_final: 0.6287 (m-30) REVERT: B 515 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7212 (tm-30) REVERT: B 547 GLN cc_start: 0.7233 (tp-100) cc_final: 0.6817 (tp-100) REVERT: B 580 MET cc_start: 0.7890 (tpp) cc_final: 0.7170 (tpp) REVERT: B 594 ASP cc_start: 0.7951 (m-30) cc_final: 0.7620 (m-30) REVERT: B 597 GLU cc_start: 0.7677 (tp30) cc_final: 0.7200 (tp30) REVERT: B 607 ASN cc_start: 0.7574 (t0) cc_final: 0.7003 (t0) REVERT: B 640 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7690 (mm-30) REVERT: B 649 PHE cc_start: 0.7738 (p90) cc_final: 0.7433 (p90) REVERT: B 650 ARG cc_start: 0.7538 (tpt-90) cc_final: 0.7182 (ttm-80) REVERT: B 656 GLN cc_start: 0.8040 (mp10) cc_final: 0.7634 (mp10) REVERT: B 692 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7522 (mp10) REVERT: B 707 MET cc_start: 0.7987 (tpp) cc_final: 0.7253 (tpp) REVERT: B 739 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.6505 (m-10) REVERT: B 803 LEU cc_start: 0.8222 (mt) cc_final: 0.7918 (mt) REVERT: B 807 ARG cc_start: 0.7923 (ttm170) cc_final: 0.7539 (ttp-170) REVERT: B 861 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7891 (mm) REVERT: B 1020 MET cc_start: 0.6696 (mmt) cc_final: 0.6421 (mmt) REVERT: B 1063 PHE cc_start: 0.8099 (t80) cc_final: 0.7846 (t80) REVERT: B 1066 GLU cc_start: 0.7943 (tt0) cc_final: 0.7552 (mm-30) REVERT: B 1096 PHE cc_start: 0.6710 (OUTLIER) cc_final: 0.6428 (m-10) REVERT: B 1132 LYS cc_start: 0.8076 (mttt) cc_final: 0.7592 (mttm) REVERT: B 1157 GLU cc_start: 0.7430 (tp30) cc_final: 0.6649 (tp30) REVERT: B 1200 GLU cc_start: 0.8109 (pt0) cc_final: 0.7677 (pt0) REVERT: B 1201 TYR cc_start: 0.8328 (t80) cc_final: 0.7312 (t80) REVERT: B 1204 GLU cc_start: 0.7634 (pp20) cc_final: 0.7274 (pp20) REVERT: B 1219 MET cc_start: 0.7523 (mmp) cc_final: 0.6990 (mmp) REVERT: B 1231 MET cc_start: 0.6928 (mpp) cc_final: 0.6724 (mpp) REVERT: B 1266 LEU cc_start: 0.7883 (mt) cc_final: 0.7588 (mt) REVERT: B 1383 LYS cc_start: 0.8826 (pttm) cc_final: 0.8398 (pttm) REVERT: B 1399 LYS cc_start: 0.8705 (pptt) cc_final: 0.8364 (pptt) REVERT: B 1412 GLU cc_start: 0.5871 (OUTLIER) cc_final: 0.4299 (mm-30) outliers start: 96 outliers final: 72 residues processed: 713 average time/residue: 0.3518 time to fit residues: 378.1232 Evaluate side-chains 736 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 655 time to evaluate : 2.521 ------------------------------------------------------------------------------- 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 331 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 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 845 SER Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1185 LEU 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 121 SER Chi-restraints excluded: chain B residue 149 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 229 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 520 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 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 783 ILE Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 1028 ILE Chi-restraints excluded: chain B residue 1039 ILE Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1213 LEU Chi-restraints excluded: chain B residue 1290 ILE Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1313 LEU Chi-restraints excluded: chain B residue 1320 LYS Chi-restraints excluded: chain B residue 1325 THR Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1367 TYR Chi-restraints excluded: chain B residue 1412 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 151 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 chunk 166 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 192 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 215 GLN B 334 GLN ** B 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2389 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= 0.237 Angle : 0.726 12.882 28095 Z= 0.373 Chirality : 0.043 0.328 3318 Planarity : 0.005 0.064 3545 Dihedral : 5.296 59.815 2693 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.36 % Favored : 90.52 % Rotamer: Outliers : 4.23 % Allowed : 22.28 % Favored : 73.49 % 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: 1.10 (0.12), residues: 1757 sheet: -3.21 (0.95), residues: 22 loop : -2.80 (0.22), residues: 742 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 0.040 0.002 PHE A1288 TYR 0.031 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 754 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 654 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8420 (ttmt) cc_final: 0.8118 (ttmt) REVERT: A 78 GLN cc_start: 0.7892 (tp40) cc_final: 0.7617 (tp40) REVERT: A 91 ASN cc_start: 0.7678 (t0) cc_final: 0.7248 (t0) REVERT: A 154 PHE cc_start: 0.8372 (p90) cc_final: 0.8080 (p90) REVERT: A 155 GLU cc_start: 0.7517 (pt0) cc_final: 0.7224 (pt0) REVERT: A 184 LEU cc_start: 0.8235 (mt) cc_final: 0.7872 (mt) REVERT: A 199 SER cc_start: 0.8545 (t) cc_final: 0.8282 (t) REVERT: A 240 ILE cc_start: 0.8770 (mt) cc_final: 0.8485 (mm) REVERT: A 253 LYS cc_start: 0.8011 (pttt) cc_final: 0.7540 (pttt) REVERT: A 368 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7592 (mt-10) REVERT: A 460 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7317 (tm-30) REVERT: A 523 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7459 (mm-30) REVERT: A 559 ARG cc_start: 0.7716 (tpp80) cc_final: 0.7010 (tpp80) REVERT: A 562 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7022 (mt-10) REVERT: A 565 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7780 (mm-30) REVERT: A 593 LYS cc_start: 0.7617 (tptm) cc_final: 0.7229 (tptm) REVERT: A 597 GLU cc_start: 0.7780 (tm-30) cc_final: 0.6933 (tm-30) REVERT: A 600 PHE cc_start: 0.8619 (t80) cc_final: 0.8289 (t80) REVERT: A 606 MET cc_start: 0.7301 (mmm) cc_final: 0.7020 (ttt) REVERT: A 615 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7794 (tt) REVERT: A 626 GLU cc_start: 0.7906 (tp30) cc_final: 0.7584 (tp30) REVERT: A 656 GLN cc_start: 0.7513 (tm-30) cc_final: 0.6857 (tm-30) REVERT: A 657 GLN cc_start: 0.7651 (mp10) cc_final: 0.7416 (mp10) REVERT: A 659 GLU cc_start: 0.7540 (mt-10) cc_final: 0.6468 (mp0) REVERT: A 663 GLU cc_start: 0.7653 (pt0) cc_final: 0.7201 (pt0) REVERT: A 745 ASP cc_start: 0.8121 (t70) cc_final: 0.7917 (t0) REVERT: A 819 SER cc_start: 0.8301 (m) cc_final: 0.7954 (p) REVERT: A 852 ASP cc_start: 0.7429 (t0) cc_final: 0.7195 (t0) REVERT: A 911 ARG cc_start: 0.7546 (tpp-160) cc_final: 0.7218 (mmt-90) REVERT: A 917 LYS cc_start: 0.7539 (mmtt) cc_final: 0.7069 (mttp) REVERT: A 931 ARG cc_start: 0.8023 (ttp-110) cc_final: 0.7734 (ttp-110) REVERT: A 956 ASP cc_start: 0.6421 (p0) cc_final: 0.6111 (p0) REVERT: A 978 LYS cc_start: 0.8308 (tptt) cc_final: 0.8100 (tptt) REVERT: A 1020 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7047 (tpp) REVERT: A 1021 GLU cc_start: 0.7899 (tp30) cc_final: 0.7252 (tp30) REVERT: A 1027 ASN cc_start: 0.6625 (p0) cc_final: 0.6322 (p0) REVERT: A 1072 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7550 (tt0) REVERT: A 1082 LYS cc_start: 0.7711 (mtpt) cc_final: 0.7304 (mtpt) REVERT: A 1086 GLU cc_start: 0.5876 (tm-30) cc_final: 0.5616 (tm-30) REVERT: A 1089 LYS cc_start: 0.8463 (ttmm) cc_final: 0.8064 (ttmm) REVERT: A 1093 GLN cc_start: 0.8436 (tp40) cc_final: 0.8115 (tp40) REVERT: A 1112 MET cc_start: 0.7762 (mtp) cc_final: 0.7454 (mtp) REVERT: A 1113 LEU cc_start: 0.8182 (tp) cc_final: 0.7873 (tp) REVERT: A 1116 LYS cc_start: 0.8639 (ttpt) cc_final: 0.8303 (ttmm) REVERT: A 1120 ILE cc_start: 0.9106 (mm) cc_final: 0.8695 (mm) REVERT: A 1122 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8643 (mm) REVERT: A 1126 GLN cc_start: 0.6929 (mm-40) cc_final: 0.6341 (mm-40) REVERT: A 1128 GLU cc_start: 0.7968 (tp30) cc_final: 0.7626 (tp30) REVERT: A 1132 LYS cc_start: 0.8324 (mmmm) cc_final: 0.7770 (mmmm) REVERT: A 1152 THR cc_start: 0.8610 (t) cc_final: 0.8144 (p) REVERT: A 1157 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7254 (mt-10) REVERT: A 1186 ARG cc_start: 0.8072 (ttt90) cc_final: 0.7412 (ttm-80) REVERT: A 1187 LYS cc_start: 0.8565 (mmmm) cc_final: 0.8276 (mmmm) REVERT: A 1200 GLU cc_start: 0.7873 (tp30) cc_final: 0.7531 (tp30) REVERT: A 1219 MET cc_start: 0.8203 (mmm) cc_final: 0.7839 (mmm) REVERT: A 1256 ASN cc_start: 0.7016 (p0) cc_final: 0.6487 (p0) REVERT: A 1259 LYS cc_start: 0.8361 (mppt) cc_final: 0.7453 (mppt) REVERT: A 1263 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7477 (mt-10) REVERT: A 1267 LYS cc_start: 0.8529 (mttm) cc_final: 0.8197 (mtpp) REVERT: A 1336 GLU cc_start: 0.8068 (tp30) cc_final: 0.7725 (tp30) REVERT: A 1365 ASN cc_start: 0.8420 (m-40) cc_final: 0.8197 (m-40) REVERT: A 1366 VAL cc_start: 0.8662 (p) cc_final: 0.8437 (m) REVERT: A 1383 LYS cc_start: 0.8335 (mmtm) cc_final: 0.8089 (mmtm) REVERT: A 1385 LEU cc_start: 0.8310 (mm) cc_final: 0.7964 (mm) REVERT: A 1399 LYS cc_start: 0.8627 (ptpp) cc_final: 0.8315 (pttm) REVERT: A 1400 LYS cc_start: 0.8775 (mmtm) cc_final: 0.8516 (mmtm) REVERT: A 1409 LYS cc_start: 0.8210 (mmmt) cc_final: 0.7696 (pttm) REVERT: B 18 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7232 (mm-30) REVERT: B 81 LEU cc_start: 0.8017 (mt) cc_final: 0.7802 (mt) REVERT: B 82 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7306 (tmm) REVERT: B 90 ASP cc_start: 0.7923 (t0) cc_final: 0.7359 (t0) REVERT: B 91 ASN cc_start: 0.8145 (m110) cc_final: 0.6889 (m-40) REVERT: B 110 ILE cc_start: 0.8611 (pt) cc_final: 0.7242 (mm) REVERT: B 124 LYS cc_start: 0.8418 (ttmt) cc_final: 0.8059 (ttpt) REVERT: B 132 ASN cc_start: 0.8201 (p0) cc_final: 0.7774 (p0) REVERT: B 154 PHE cc_start: 0.8128 (p90) cc_final: 0.7695 (p90) REVERT: B 155 GLU cc_start: 0.7469 (pt0) cc_final: 0.6913 (pm20) REVERT: B 205 ARG cc_start: 0.7946 (tpp80) cc_final: 0.7683 (mmm-85) REVERT: B 228 LYS cc_start: 0.8342 (tttm) cc_final: 0.7768 (ttmm) REVERT: B 333 ARG cc_start: 0.7728 (mtt90) cc_final: 0.7326 (mtt90) REVERT: B 346 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7256 (mm-30) REVERT: B 361 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7551 (mt-10) REVERT: B 485 ASP cc_start: 0.6752 (m-30) cc_final: 0.6263 (m-30) REVERT: B 503 LYS cc_start: 0.8565 (tttt) cc_final: 0.8319 (tttt) REVERT: B 515 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7222 (tm-30) REVERT: B 547 GLN cc_start: 0.7232 (tp-100) cc_final: 0.6866 (tp40) REVERT: B 580 MET cc_start: 0.7879 (tpp) cc_final: 0.7154 (tpp) REVERT: B 594 ASP cc_start: 0.7952 (m-30) cc_final: 0.7635 (m-30) REVERT: B 597 GLU cc_start: 0.7712 (tp30) cc_final: 0.7203 (tp30) REVERT: B 607 ASN cc_start: 0.7523 (t0) cc_final: 0.6902 (t0) REVERT: B 650 ARG cc_start: 0.7518 (tpt-90) cc_final: 0.7192 (ttm-80) REVERT: B 656 GLN cc_start: 0.8033 (mp10) cc_final: 0.7656 (mp10) REVERT: B 692 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7541 (mp10) REVERT: B 739 PHE cc_start: 0.7449 (OUTLIER) cc_final: 0.6540 (m-10) REVERT: B 803 LEU cc_start: 0.8219 (mt) cc_final: 0.7891 (mt) REVERT: B 807 ARG cc_start: 0.7932 (ttm170) cc_final: 0.7574 (ttp-170) REVERT: B 861 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7889 (mm) REVERT: B 1014 LYS cc_start: 0.8779 (pttp) cc_final: 0.8480 (pttp) REVERT: B 1020 MET cc_start: 0.6696 (mmt) cc_final: 0.6403 (mmt) REVERT: B 1066 GLU cc_start: 0.7934 (tt0) cc_final: 0.7470 (mm-30) REVERT: B 1080 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6949 (t80) REVERT: B 1096 PHE cc_start: 0.6670 (OUTLIER) cc_final: 0.6381 (m-10) REVERT: B 1126 GLN cc_start: 0.7208 (tp40) cc_final: 0.6693 (tp40) REVERT: B 1132 LYS cc_start: 0.8082 (mttt) cc_final: 0.7638 (mttm) REVERT: B 1200 GLU cc_start: 0.8118 (pt0) cc_final: 0.7692 (pt0) REVERT: B 1201 TYR cc_start: 0.8324 (t80) cc_final: 0.7552 (t80) REVERT: B 1204 GLU cc_start: 0.7621 (pp20) cc_final: 0.7297 (pp20) REVERT: B 1219 MET cc_start: 0.7530 (mmp) cc_final: 0.6993 (mmp) REVERT: B 1231 MET cc_start: 0.6879 (mpp) cc_final: 0.6662 (mpp) REVERT: B 1259 LYS cc_start: 0.8291 (mmmt) cc_final: 0.8065 (mmtm) REVERT: B 1263 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7872 (mt-10) REVERT: B 1266 LEU cc_start: 0.7881 (mt) cc_final: 0.7594 (mt) REVERT: B 1383 LYS cc_start: 0.8809 (pttm) cc_final: 0.8379 (pttm) REVERT: B 1399 LYS cc_start: 0.8703 (pptt) cc_final: 0.8367 (pptt) REVERT: B 1412 GLU cc_start: 0.5942 (OUTLIER) cc_final: 0.4415 (mm-30) outliers start: 100 outliers final: 78 residues processed: 699 average time/residue: 0.3586 time to fit residues: 380.5015 Evaluate side-chains 737 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 649 time to evaluate : 2.215 ------------------------------------------------------------------------------- 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 331 VAL Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 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 845 SER Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1081 CYS Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1202 LEU 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 121 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 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 755 GLU Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 1028 ILE Chi-restraints excluded: chain B residue 1039 ILE Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1213 LEU Chi-restraints excluded: chain B residue 1290 ILE Chi-restraints excluded: chain B residue 1313 LEU Chi-restraints excluded: chain B residue 1320 LYS Chi-restraints excluded: chain B residue 1325 THR Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1333 GLU Chi-restraints excluded: chain B residue 1367 TYR Chi-restraints excluded: chain B residue 1412 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 222 optimal weight: 0.0670 chunk 234 optimal weight: 0.5980 chunk 213 optimal weight: 0.4980 chunk 228 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 206 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 227 optimal weight: 0.9980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20796 Z= 0.225 Angle : 0.748 16.126 28095 Z= 0.378 Chirality : 0.043 0.220 3318 Planarity : 0.005 0.065 3545 Dihedral : 5.258 58.192 2693 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.20 % Favored : 90.68 % Rotamer: Outliers : 4.40 % Allowed : 22.49 % Favored : 73.11 % 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: -0.04 (0.17), residues: 2521 helix: 1.10 (0.12), residues: 1761 sheet: -3.22 (0.95), residues: 22 loop : -2.80 (0.22), residues: 738 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 0.041 0.002 PHE A1288 TYR 0.024 0.001 TYR A1258 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 760 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 656 time to evaluate : 2.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8425 (ttmt) cc_final: 0.8119 (ttmt) REVERT: A 78 GLN cc_start: 0.7883 (tp40) cc_final: 0.7617 (tp40) REVERT: A 91 ASN cc_start: 0.7677 (t0) cc_final: 0.7253 (t0) REVERT: A 120 ASP cc_start: 0.7641 (t70) cc_final: 0.7191 (m-30) REVERT: A 154 PHE cc_start: 0.8375 (p90) cc_final: 0.8165 (p90) REVERT: A 155 GLU cc_start: 0.7512 (pt0) cc_final: 0.7211 (pt0) REVERT: A 167 LEU cc_start: 0.8476 (tp) cc_final: 0.8228 (tp) REVERT: A 199 SER cc_start: 0.8557 (t) cc_final: 0.8308 (t) REVERT: A 240 ILE cc_start: 0.8791 (mt) cc_final: 0.8472 (mm) REVERT: A 253 LYS cc_start: 0.8017 (pttt) cc_final: 0.7547 (pttt) REVERT: A 368 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7576 (mt-10) REVERT: A 460 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7292 (tm-30) REVERT: A 523 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7447 (mm-30) REVERT: A 559 ARG cc_start: 0.7730 (tpp80) cc_final: 0.7031 (tpp80) REVERT: A 562 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7023 (mt-10) REVERT: A 565 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7729 (mm-30) REVERT: A 593 LYS cc_start: 0.7611 (tptm) cc_final: 0.7215 (tptm) REVERT: A 597 GLU cc_start: 0.7769 (tm-30) cc_final: 0.6917 (tm-30) REVERT: A 600 PHE cc_start: 0.8617 (t80) cc_final: 0.8333 (t80) REVERT: A 606 MET cc_start: 0.7317 (mmm) cc_final: 0.6921 (ttt) REVERT: A 615 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7739 (tt) REVERT: A 626 GLU cc_start: 0.7901 (tp30) cc_final: 0.7581 (tp30) REVERT: A 663 GLU cc_start: 0.7651 (pt0) cc_final: 0.7194 (pt0) REVERT: A 745 ASP cc_start: 0.8094 (t70) cc_final: 0.7881 (t0) REVERT: A 819 SER cc_start: 0.8281 (m) cc_final: 0.7961 (p) REVERT: A 852 ASP cc_start: 0.7433 (t0) cc_final: 0.7205 (t0) REVERT: A 908 ASP cc_start: 0.7475 (p0) cc_final: 0.7002 (p0) REVERT: A 911 ARG cc_start: 0.7536 (tpp-160) cc_final: 0.7209 (mmt-90) REVERT: A 917 LYS cc_start: 0.7484 (mmtt) cc_final: 0.7012 (mttp) REVERT: A 931 ARG cc_start: 0.7950 (ttp-110) cc_final: 0.7719 (ttp-110) REVERT: A 956 ASP cc_start: 0.6456 (p0) cc_final: 0.6054 (p0) REVERT: A 978 LYS cc_start: 0.8335 (tptt) cc_final: 0.8108 (tptt) REVERT: A 1020 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.7052 (tpp) REVERT: A 1021 GLU cc_start: 0.7898 (tp30) cc_final: 0.7245 (tp30) REVERT: A 1027 ASN cc_start: 0.6610 (p0) cc_final: 0.6300 (p0) REVERT: A 1072 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: A 1082 LYS cc_start: 0.7669 (mtpt) cc_final: 0.7268 (mtpt) REVERT: A 1086 GLU cc_start: 0.5901 (tm-30) cc_final: 0.5624 (tm-30) REVERT: A 1089 LYS cc_start: 0.8443 (ttmm) cc_final: 0.8044 (ttmm) REVERT: A 1093 GLN cc_start: 0.8420 (tp40) cc_final: 0.8094 (tp40) REVERT: A 1112 MET cc_start: 0.7754 (mtp) cc_final: 0.7443 (mtp) REVERT: A 1113 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7871 (tp) REVERT: A 1116 LYS cc_start: 0.8627 (ttpt) cc_final: 0.8303 (ttmm) REVERT: A 1120 ILE cc_start: 0.9108 (mm) cc_final: 0.8697 (mm) REVERT: A 1122 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8642 (mm) REVERT: A 1126 GLN cc_start: 0.6919 (mm-40) cc_final: 0.6405 (mm-40) REVERT: A 1128 GLU cc_start: 0.7967 (tp30) cc_final: 0.7610 (tp30) REVERT: A 1132 LYS cc_start: 0.8318 (mmmm) cc_final: 0.7758 (mmmm) REVERT: A 1152 THR cc_start: 0.8605 (t) cc_final: 0.8137 (p) REVERT: A 1157 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7215 (mt-10) REVERT: A 1187 LYS cc_start: 0.8517 (mmmm) cc_final: 0.8240 (mmmm) REVERT: A 1191 MET cc_start: 0.7288 (tpt) cc_final: 0.6799 (tpt) REVERT: A 1200 GLU cc_start: 0.7849 (tp30) cc_final: 0.7503 (tp30) REVERT: A 1219 MET cc_start: 0.8201 (mmm) cc_final: 0.7914 (mmm) REVERT: A 1256 ASN cc_start: 0.7010 (p0) cc_final: 0.6359 (p0) REVERT: A 1259 LYS cc_start: 0.8368 (mppt) cc_final: 0.7391 (mppt) REVERT: A 1263 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7467 (mt-10) REVERT: A 1267 LYS cc_start: 0.8527 (mttm) cc_final: 0.8200 (mtpp) REVERT: A 1336 GLU cc_start: 0.8065 (tp30) cc_final: 0.7724 (tp30) REVERT: A 1365 ASN cc_start: 0.8387 (m-40) cc_final: 0.8173 (m-40) REVERT: A 1366 VAL cc_start: 0.8682 (p) cc_final: 0.8453 (m) REVERT: A 1383 LYS cc_start: 0.8320 (mmtm) cc_final: 0.8076 (mmtm) REVERT: A 1385 LEU cc_start: 0.8310 (mm) cc_final: 0.7973 (mm) REVERT: A 1399 LYS cc_start: 0.8599 (ptpp) cc_final: 0.8277 (pttm) REVERT: A 1400 LYS cc_start: 0.8771 (mmtm) cc_final: 0.8508 (mmtm) REVERT: A 1409 LYS cc_start: 0.8201 (mmmt) cc_final: 0.7739 (pttm) REVERT: B 18 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7221 (mm-30) REVERT: B 81 LEU cc_start: 0.8014 (mt) cc_final: 0.7810 (mt) REVERT: B 82 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7296 (tmm) REVERT: B 90 ASP cc_start: 0.7916 (t0) cc_final: 0.7397 (t70) REVERT: B 91 ASN cc_start: 0.8133 (m110) cc_final: 0.6948 (m-40) REVERT: B 110 ILE cc_start: 0.8600 (pt) cc_final: 0.7229 (mm) REVERT: B 124 LYS cc_start: 0.8415 (ttmt) cc_final: 0.8053 (ttpt) REVERT: B 132 ASN cc_start: 0.8185 (p0) cc_final: 0.7723 (p0) REVERT: B 154 PHE cc_start: 0.8095 (p90) cc_final: 0.7679 (p90) REVERT: B 155 GLU cc_start: 0.7449 (pt0) cc_final: 0.6882 (pm20) REVERT: B 205 ARG cc_start: 0.7958 (tpp80) cc_final: 0.7686 (mmm-85) REVERT: B 333 ARG cc_start: 0.7723 (mtt90) cc_final: 0.7330 (mtt90) REVERT: B 346 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7263 (mm-30) REVERT: B 361 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7553 (mt-10) REVERT: B 485 ASP cc_start: 0.6752 (m-30) cc_final: 0.6253 (m-30) REVERT: B 499 LYS cc_start: 0.8125 (mmmm) cc_final: 0.7853 (mmmm) REVERT: B 515 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7206 (tm-30) REVERT: B 547 GLN cc_start: 0.7214 (tp-100) cc_final: 0.6846 (tp40) REVERT: B 580 MET cc_start: 0.7859 (tpp) cc_final: 0.7138 (tpp) REVERT: B 594 ASP cc_start: 0.7947 (m-30) cc_final: 0.7630 (m-30) REVERT: B 607 ASN cc_start: 0.7517 (t0) cc_final: 0.6883 (t0) REVERT: B 640 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7717 (mm-30) REVERT: B 650 ARG cc_start: 0.7507 (tpt-90) cc_final: 0.6996 (tpp80) REVERT: B 656 GLN cc_start: 0.8030 (mp10) cc_final: 0.7597 (mp10) REVERT: B 707 MET cc_start: 0.7932 (tpp) cc_final: 0.7224 (tpp) REVERT: B 739 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.6511 (m-10) REVERT: B 803 LEU cc_start: 0.8186 (mt) cc_final: 0.7882 (mt) REVERT: B 807 ARG cc_start: 0.7938 (ttm170) cc_final: 0.7591 (ttp-170) REVERT: B 857 PHE cc_start: 0.7435 (t80) cc_final: 0.7174 (t80) REVERT: B 861 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8028 (mm) REVERT: B 1020 MET cc_start: 0.6683 (mmt) cc_final: 0.6430 (mmt) REVERT: B 1066 GLU cc_start: 0.7843 (tt0) cc_final: 0.7453 (mm-30) REVERT: B 1080 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.7018 (t80) REVERT: B 1096 PHE cc_start: 0.6671 (OUTLIER) cc_final: 0.6368 (m-10) REVERT: B 1126 GLN cc_start: 0.7117 (tp40) cc_final: 0.6873 (tp40) REVERT: B 1132 LYS cc_start: 0.8068 (mttt) cc_final: 0.7615 (mttm) REVERT: B 1200 GLU cc_start: 0.8154 (pt0) cc_final: 0.7709 (pt0) REVERT: B 1201 TYR cc_start: 0.8358 (t80) cc_final: 0.7496 (t80) REVERT: B 1204 GLU cc_start: 0.7624 (pp20) cc_final: 0.7293 (pp20) REVERT: B 1219 MET cc_start: 0.7545 (mmp) cc_final: 0.7013 (mmp) REVERT: B 1231 MET cc_start: 0.6842 (mpp) cc_final: 0.6608 (mpp) REVERT: B 1263 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7797 (mt-10) REVERT: B 1266 LEU cc_start: 0.7864 (mt) cc_final: 0.7576 (mt) REVERT: B 1313 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8653 (mt) REVERT: B 1383 LYS cc_start: 0.8788 (pttm) cc_final: 0.8363 (pttm) REVERT: B 1399 LYS cc_start: 0.8680 (pptt) cc_final: 0.8363 (pptt) outliers start: 104 outliers final: 77 residues processed: 698 average time/residue: 0.3737 time to fit residues: 396.3875 Evaluate side-chains 737 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 649 time to evaluate : 1.935 ------------------------------------------------------------------------------- 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 331 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 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 845 SER Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1185 LEU 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 94 SER Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 525 LEU 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 942 LEU Chi-restraints excluded: chain B residue 1028 ILE Chi-restraints excluded: chain B residue 1039 ILE Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 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 1213 LEU Chi-restraints excluded: chain B residue 1313 LEU Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1333 GLU Chi-restraints excluded: chain B residue 1367 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 149 optimal weight: 0.7980 chunk 241 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 167 optimal weight: 0.6980 chunk 253 optimal weight: 0.7980 chunk 232 optimal weight: 0.9980 chunk 201 optimal weight: 0.0980 chunk 20 optimal weight: 0.0570 chunk 155 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2558 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= 0.227 Angle : 0.762 16.111 28095 Z= 0.385 Chirality : 0.043 0.252 3318 Planarity : 0.005 0.066 3545 Dihedral : 5.245 56.117 2693 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.12 % Favored : 90.76 % Rotamer: Outliers : 3.47 % Allowed : 23.59 % Favored : 72.94 % 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: 1.09 (0.12), residues: 1761 sheet: -3.27 (0.96), residues: 22 loop : -2.80 (0.22), residues: 738 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 0.035 0.002 PHE A1184 TYR 0.026 0.001 TYR A1258 ARG 0.007 0.000 ARG A 174 ********************** 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 746 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 664 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.7880 (tp40) cc_final: 0.7610 (tp40) REVERT: A 91 ASN cc_start: 0.7667 (t0) cc_final: 0.7234 (t0) REVERT: A 120 ASP cc_start: 0.7642 (t70) cc_final: 0.7189 (m-30) REVERT: A 154 PHE cc_start: 0.8370 (p90) cc_final: 0.8091 (p90) REVERT: A 155 GLU cc_start: 0.7496 (pt0) cc_final: 0.7200 (pt0) REVERT: A 167 LEU cc_start: 0.8479 (tp) cc_final: 0.8105 (tp) REVERT: A 199 SER cc_start: 0.8552 (t) cc_final: 0.8307 (t) REVERT: A 239 GLN cc_start: 0.7832 (mt0) cc_final: 0.7542 (tt0) REVERT: A 240 ILE cc_start: 0.8760 (mt) cc_final: 0.8360 (mm) REVERT: A 253 LYS cc_start: 0.7979 (pttt) cc_final: 0.7535 (pttt) REVERT: A 368 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7573 (mt-10) REVERT: A 460 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7315 (tm-30) REVERT: A 523 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7439 (mm-30) REVERT: A 559 ARG cc_start: 0.7726 (tpp80) cc_final: 0.7031 (tpp80) REVERT: A 562 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7012 (mt-10) REVERT: A 565 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7763 (mm-30) REVERT: A 593 LYS cc_start: 0.7600 (tptm) cc_final: 0.7202 (tptm) REVERT: A 597 GLU cc_start: 0.7758 (tm-30) cc_final: 0.6899 (tm-30) REVERT: A 600 PHE cc_start: 0.8628 (t80) cc_final: 0.8351 (t80) REVERT: A 606 MET cc_start: 0.7366 (mmm) cc_final: 0.7024 (tpp) REVERT: A 615 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7752 (tt) REVERT: A 626 GLU cc_start: 0.7896 (tp30) cc_final: 0.7572 (tp30) REVERT: A 656 GLN cc_start: 0.7128 (tm-30) cc_final: 0.6559 (tm-30) REVERT: A 659 GLU cc_start: 0.7543 (mt-10) cc_final: 0.6421 (mp0) REVERT: A 663 GLU cc_start: 0.7657 (pt0) cc_final: 0.7198 (pt0) REVERT: A 745 ASP cc_start: 0.8110 (t70) cc_final: 0.7898 (t0) REVERT: A 819 SER cc_start: 0.8315 (m) cc_final: 0.7969 (p) REVERT: A 852 ASP cc_start: 0.7435 (t0) cc_final: 0.7186 (t0) REVERT: A 858 ASN cc_start: 0.7431 (p0) cc_final: 0.7201 (p0) REVERT: A 908 ASP cc_start: 0.7456 (p0) cc_final: 0.6978 (p0) REVERT: A 911 ARG cc_start: 0.7524 (tpp-160) cc_final: 0.7205 (mmt-90) REVERT: A 917 LYS cc_start: 0.7477 (mmtt) cc_final: 0.7018 (mttp) REVERT: A 931 ARG cc_start: 0.7955 (ttp-110) cc_final: 0.7738 (ttp-110) REVERT: A 956 ASP cc_start: 0.6480 (p0) cc_final: 0.6071 (p0) REVERT: A 978 LYS cc_start: 0.8351 (tptt) cc_final: 0.8120 (tptt) REVERT: A 1020 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7046 (tpp) REVERT: A 1021 GLU cc_start: 0.7892 (tp30) cc_final: 0.7241 (tp30) REVERT: A 1027 ASN cc_start: 0.6615 (p0) cc_final: 0.6303 (p0) REVERT: A 1072 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: A 1082 LYS cc_start: 0.7665 (mtpt) cc_final: 0.7300 (mmtt) REVERT: A 1086 GLU cc_start: 0.5910 (tm-30) cc_final: 0.5636 (tm-30) REVERT: A 1089 LYS cc_start: 0.8422 (ttmm) cc_final: 0.8009 (ttmm) REVERT: A 1093 GLN cc_start: 0.8399 (tp40) cc_final: 0.8075 (tp40) REVERT: A 1112 MET cc_start: 0.7734 (mtp) cc_final: 0.7448 (mtp) REVERT: A 1113 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7959 (tp) REVERT: A 1116 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8293 (ttmm) REVERT: A 1120 ILE cc_start: 0.9097 (mm) cc_final: 0.8673 (mm) REVERT: A 1122 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8635 (mm) REVERT: A 1126 GLN cc_start: 0.6915 (mm-40) cc_final: 0.6415 (mm-40) REVERT: A 1128 GLU cc_start: 0.7960 (tp30) cc_final: 0.7611 (tp30) REVERT: A 1132 LYS cc_start: 0.8300 (mmmm) cc_final: 0.7737 (mmmm) REVERT: A 1152 THR cc_start: 0.8601 (t) cc_final: 0.8134 (p) REVERT: A 1157 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7271 (mt-10) REVERT: A 1186 ARG cc_start: 0.8168 (ttt90) cc_final: 0.7589 (ttm-80) REVERT: A 1187 LYS cc_start: 0.8538 (mmmm) cc_final: 0.8257 (mmmm) REVERT: A 1191 MET cc_start: 0.7209 (tpt) cc_final: 0.6821 (tpt) REVERT: A 1200 GLU cc_start: 0.7838 (tp30) cc_final: 0.7523 (tp30) REVERT: A 1219 MET cc_start: 0.8224 (mmm) cc_final: 0.7876 (mmm) REVERT: A 1256 ASN cc_start: 0.7004 (p0) cc_final: 0.6353 (p0) REVERT: A 1259 LYS cc_start: 0.8371 (mppt) cc_final: 0.7397 (mppt) REVERT: A 1263 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7476 (mt-10) REVERT: A 1267 LYS cc_start: 0.8540 (mttm) cc_final: 0.8210 (mtpp) REVERT: A 1270 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7222 (tm-30) REVERT: A 1336 GLU cc_start: 0.8065 (tp30) cc_final: 0.7847 (tp30) REVERT: A 1365 ASN cc_start: 0.8390 (m-40) cc_final: 0.8163 (m-40) REVERT: A 1366 VAL cc_start: 0.8645 (p) cc_final: 0.8432 (m) REVERT: A 1383 LYS cc_start: 0.8319 (mmtm) cc_final: 0.8090 (mmtm) REVERT: A 1385 LEU cc_start: 0.8312 (mm) cc_final: 0.7985 (mm) REVERT: A 1399 LYS cc_start: 0.8617 (ptpp) cc_final: 0.8324 (pttm) REVERT: A 1400 LYS cc_start: 0.8777 (mmtm) cc_final: 0.8502 (mmtm) REVERT: A 1409 LYS cc_start: 0.8192 (mmmt) cc_final: 0.7719 (pttm) REVERT: B 18 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7217 (mm-30) REVERT: B 81 LEU cc_start: 0.8012 (mt) cc_final: 0.7805 (mt) REVERT: B 82 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7287 (tmm) REVERT: B 90 ASP cc_start: 0.7903 (t0) cc_final: 0.7365 (t70) REVERT: B 91 ASN cc_start: 0.8085 (m110) cc_final: 0.6914 (m-40) REVERT: B 110 ILE cc_start: 0.8593 (pt) cc_final: 0.7221 (mm) REVERT: B 124 LYS cc_start: 0.8409 (ttmt) cc_final: 0.8048 (ttpt) REVERT: B 132 ASN cc_start: 0.8191 (p0) cc_final: 0.7738 (p0) REVERT: B 154 PHE cc_start: 0.8093 (p90) cc_final: 0.7667 (p90) REVERT: B 155 GLU cc_start: 0.7404 (pt0) cc_final: 0.6829 (pm20) REVERT: B 205 ARG cc_start: 0.7958 (tpp80) cc_final: 0.7687 (mmm-85) REVERT: B 228 LYS cc_start: 0.8293 (tttm) cc_final: 0.7935 (tttp) REVERT: B 333 ARG cc_start: 0.7717 (mtt90) cc_final: 0.7331 (mtt90) REVERT: B 346 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7272 (mm-30) REVERT: B 361 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7538 (mt-10) REVERT: B 433 ARG cc_start: 0.8357 (tpp80) cc_final: 0.8002 (mmm160) REVERT: B 485 ASP cc_start: 0.6753 (m-30) cc_final: 0.6235 (m-30) REVERT: B 499 LYS cc_start: 0.8127 (mmmm) cc_final: 0.7870 (mmmm) REVERT: B 503 LYS cc_start: 0.8498 (tttt) cc_final: 0.7933 (ttmm) REVERT: B 515 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7215 (tm-30) REVERT: B 547 GLN cc_start: 0.7208 (tp-100) cc_final: 0.6853 (tp40) REVERT: B 580 MET cc_start: 0.7853 (tpp) cc_final: 0.7087 (tpp) REVERT: B 591 SER cc_start: 0.8451 (OUTLIER) cc_final: 0.8161 (t) REVERT: B 607 ASN cc_start: 0.7516 (t0) cc_final: 0.6917 (t0) REVERT: B 640 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7708 (mm-30) REVERT: B 650 ARG cc_start: 0.7516 (tpt-90) cc_final: 0.7027 (tpp80) REVERT: B 656 GLN cc_start: 0.8032 (mp10) cc_final: 0.7658 (mp10) REVERT: B 707 MET cc_start: 0.7984 (tpp) cc_final: 0.7263 (tpp) REVERT: B 739 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.6484 (m-10) REVERT: B 803 LEU cc_start: 0.8185 (mt) cc_final: 0.7885 (mt) REVERT: B 807 ARG cc_start: 0.7938 (ttm170) cc_final: 0.7492 (ttp-170) REVERT: B 857 PHE cc_start: 0.7422 (t80) cc_final: 0.7161 (t80) REVERT: B 861 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8020 (mm) REVERT: B 989 LYS cc_start: 0.6299 (pttt) cc_final: 0.5250 (pttm) REVERT: B 1014 LYS cc_start: 0.8761 (pttp) cc_final: 0.7916 (pttp) REVERT: B 1017 LYS cc_start: 0.7646 (mtmt) cc_final: 0.7406 (mtmt) REVERT: B 1020 MET cc_start: 0.6683 (mmt) cc_final: 0.6421 (mmt) REVERT: B 1066 GLU cc_start: 0.7842 (tt0) cc_final: 0.7447 (mm-30) REVERT: B 1096 PHE cc_start: 0.6640 (OUTLIER) cc_final: 0.6315 (m-10) REVERT: B 1126 GLN cc_start: 0.7151 (tp40) cc_final: 0.6886 (tp40) REVERT: B 1132 LYS cc_start: 0.8066 (mttt) cc_final: 0.7619 (mttm) REVERT: B 1200 GLU cc_start: 0.8146 (pt0) cc_final: 0.7713 (pt0) REVERT: B 1201 TYR cc_start: 0.8344 (t80) cc_final: 0.7486 (t80) REVERT: B 1204 GLU cc_start: 0.7607 (pp20) cc_final: 0.7273 (pp20) REVERT: B 1219 MET cc_start: 0.7535 (mmp) cc_final: 0.6987 (mmp) REVERT: B 1231 MET cc_start: 0.6818 (mpp) cc_final: 0.6570 (mpp) REVERT: B 1263 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7813 (mt-10) REVERT: B 1266 LEU cc_start: 0.7897 (mt) cc_final: 0.7598 (mt) REVERT: B 1383 LYS cc_start: 0.8780 (pttm) cc_final: 0.8349 (pttm) REVERT: B 1399 LYS cc_start: 0.8667 (pptt) cc_final: 0.8348 (pptt) REVERT: B 1412 GLU cc_start: 0.6059 (OUTLIER) cc_final: 0.4353 (mm-30) outliers start: 82 outliers final: 66 residues processed: 699 average time/residue: 0.3496 time to fit residues: 368.0231 Evaluate side-chains 725 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 648 time to evaluate : 2.367 ------------------------------------------------------------------------------- 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 331 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 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 845 SER Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1202 LEU 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 121 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 560 LYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 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 1056 ASN 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 1096 PHE Chi-restraints excluded: chain B residue 1188 VAL 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: 0.9990 chunk 214 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 201 optimal weight: 0.0970 chunk 84 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 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 B1147 GLN ** B1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.118572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.102172 restraints weight = 48372.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.105436 restraints weight = 25130.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.107558 restraints weight = 15413.735| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2604 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: