Starting phenix.real_space_refine on Thu Apr 11 16:23:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezj_28743/04_2024/8ezj_28743_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezj_28743/04_2024/8ezj_28743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezj_28743/04_2024/8ezj_28743.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezj_28743/04_2024/8ezj_28743.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezj_28743/04_2024/8ezj_28743_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezj_28743/04_2024/8ezj_28743_updated.pdb" } resolution = 3.3 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 80 5.16 5 C 14868 2.51 5 N 3780 2.21 5 O 4481 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 23215 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 10319 Classifications: {'peptide': 1285} Link IDs: {'PTRANS': 39, 'TRANS': 1245} Chain breaks: 5 Chain: "B" Number of atoms: 10248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1276, 10248 Classifications: {'peptide': 1276} Link IDs: {'PTRANS': 39, 'TRANS': 1236} Chain breaks: 5 Chain: "C" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1292 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 3, 'TRANS': 161} Chain: "D" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1292 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 3, 'TRANS': 161} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.63, per 1000 atoms: 0.50 Number of scatterers: 23215 At special positions: 0 Unit cell: (123.372, 143.244, 305.532, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 6 15.00 O 4481 8.00 N 3780 7.00 C 14868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.47 Conformation dependent library (CDL) restraints added in 4.0 seconds 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5568 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 140 helices and 5 sheets defined 60.9% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.14 Creating SS restraints... Processing helix chain 'A' and resid 11 through 29 Processing helix chain 'A' and resid 71 through 84 Processing helix chain 'A' and resid 94 through 106 Proline residue: A 100 - end of helix Processing helix chain 'A' and resid 112 through 128 Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 159 through 178 Processing helix chain 'A' and resid 180 through 183 No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 187 through 201 Processing helix chain 'A' and resid 208 through 231 removed outlier: 3.860A pdb=" N THR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 343 Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 353 through 370 Processing helix chain 'A' and resid 378 through 385 Processing helix chain 'A' and resid 387 through 397 Processing helix chain 'A' and resid 402 through 418 Processing helix chain 'A' and resid 420 through 422 No H-bonds generated for 'chain 'A' and resid 420 through 422' Processing helix chain 'A' and resid 424 through 438 Processing helix chain 'A' and resid 456 through 471 removed outlier: 4.628A pdb=" N LEU A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TRP A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR A 471 " --> pdb=" O SER A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 No H-bonds generated for 'chain 'A' and resid 507 through 510' Processing helix chain 'A' and resid 517 through 536 removed outlier: 3.599A pdb=" N MET A 536 " --> pdb=" O MET A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 Processing helix chain 'A' and resid 552 through 572 removed outlier: 4.024A pdb=" N ARG A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N THR A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU A 562 " --> pdb=" O ASP A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 Proline residue: A 579 - end of helix Processing helix chain 'A' and resid 592 through 601 Processing helix chain 'A' and resid 608 through 614 Processing helix chain 'A' and resid 618 through 630 removed outlier: 4.588A pdb=" N SER A 622 " --> pdb=" O ASP A 619 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A 624 " --> pdb=" O VAL A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 648 removed outlier: 4.449A pdb=" N LYS A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 Processing helix chain 'A' and resid 696 through 712 removed outlier: 3.529A pdb=" N THR A 710 " --> pdb=" O ILE A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 730 No H-bonds generated for 'chain 'A' and resid 728 through 730' Processing helix chain 'A' and resid 734 through 736 No H-bonds generated for 'chain 'A' and resid 734 through 736' Processing helix chain 'A' and resid 741 through 752 Processing helix chain 'A' and resid 769 through 776 Processing helix chain 'A' and resid 794 through 796 No H-bonds generated for 'chain 'A' and resid 794 through 796' Processing helix chain 'A' and resid 799 through 827 Proline residue: A 815 - end of helix Processing helix chain 'A' and resid 831 through 851 Processing helix chain 'A' and resid 854 through 868 Processing helix chain 'A' and resid 907 through 913 Processing helix chain 'A' and resid 916 through 931 Processing helix chain 'A' and resid 940 through 955 Processing helix chain 'A' and resid 965 through 970 Processing helix chain 'A' and resid 1011 through 1025 Processing helix chain 'A' and resid 1028 through 1032 Processing helix chain 'A' and resid 1041 through 1049 Processing helix chain 'A' and resid 1060 through 1080 removed outlier: 4.015A pdb=" N PHE A1063 " --> pdb=" O SER A1060 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU A1064 " --> pdb=" O ARG A1061 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA A1065 " --> pdb=" O TYR A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1099 Processing helix chain 'A' and resid 1106 through 1122 Processing helix chain 'A' and resid 1127 through 1140 removed outlier: 3.533A pdb=" N LYS A1140 " --> pdb=" O ASP A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1150 No H-bonds generated for 'chain 'A' and resid 1148 through 1150' Processing helix chain 'A' and resid 1155 through 1165 Processing helix chain 'A' and resid 1173 through 1176 No H-bonds generated for 'chain 'A' and resid 1173 through 1176' Processing helix chain 'A' and resid 1180 through 1190 Processing helix chain 'A' and resid 1195 through 1208 Processing helix chain 'A' and resid 1218 through 1229 Processing helix chain 'A' and resid 1232 through 1246 removed outlier: 4.114A pdb=" N GLU A1241 " --> pdb=" O HIS A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1275 Processing helix chain 'A' and resid 1285 through 1298 Processing helix chain 'A' and resid 1303 through 1319 Processing helix chain 'A' and resid 1331 through 1345 removed outlier: 4.683A pdb=" N LEU A1340 " --> pdb=" O GLU A1336 " (cutoff:3.500A) Proline residue: A1341 - end of helix removed outlier: 3.733A pdb=" N SER A1345 " --> pdb=" O PRO A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1372 removed outlier: 4.003A pdb=" N ILE A1354 " --> pdb=" O ASP A1351 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR A1370 " --> pdb=" O TYR A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1390 Processing helix chain 'A' and resid 1396 through 1416 Processing helix chain 'B' and resid 12 through 29 Processing helix chain 'B' and resid 71 through 83 Processing helix chain 'B' and resid 94 through 106 Proline residue: B 100 - end of helix Processing helix chain 'B' and resid 112 through 127 Processing helix chain 'B' and resid 138 through 151 removed outlier: 3.625A pdb=" N HIS B 151 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 177 Processing helix chain 'B' and resid 180 through 183 No H-bonds generated for 'chain 'B' and resid 180 through 183' Processing helix chain 'B' and resid 187 through 201 Processing helix chain 'B' and resid 209 through 231 removed outlier: 4.057A pdb=" N THR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 342 Processing helix chain 'B' and resid 353 through 370 Processing helix chain 'B' and resid 378 through 385 Processing helix chain 'B' and resid 387 through 397 Processing helix chain 'B' and resid 402 through 418 Processing helix chain 'B' and resid 425 through 438 Processing helix chain 'B' and resid 457 through 470 removed outlier: 4.964A pdb=" N LEU B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TRP B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 484 removed outlier: 3.764A pdb=" N PHE B 477 " --> pdb=" O PRO B 474 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE B 484 " --> pdb=" O PHE B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 504 Processing helix chain 'B' and resid 507 through 510 No H-bonds generated for 'chain 'B' and resid 507 through 510' Processing helix chain 'B' and resid 517 through 535 Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 552 through 572 removed outlier: 3.926A pdb=" N ARG B 559 " --> pdb=" O LYS B 555 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N THR B 561 " --> pdb=" O ARG B 557 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLU B 562 " --> pdb=" O ASP B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 583 Proline residue: B 579 - end of helix Processing helix chain 'B' and resid 592 through 600 Processing helix chain 'B' and resid 608 through 615 Processing helix chain 'B' and resid 622 through 629 Processing helix chain 'B' and resid 638 through 648 removed outlier: 4.198A pdb=" N LYS B 648 " --> pdb=" O ILE B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 672 Processing helix chain 'B' and resid 697 through 712 Processing helix chain 'B' and resid 723 through 729 Processing helix chain 'B' and resid 741 through 753 Processing helix chain 'B' and resid 768 through 777 Processing helix chain 'B' and resid 793 through 796 removed outlier: 3.637A pdb=" N LYS B 796 " --> pdb=" O VAL B 793 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 793 through 796' Processing helix chain 'B' and resid 799 through 827 Proline residue: B 815 - end of helix Processing helix chain 'B' and resid 831 through 850 Processing helix chain 'B' and resid 854 through 868 Processing helix chain 'B' and resid 907 through 913 Processing helix chain 'B' and resid 916 through 931 Processing helix chain 'B' and resid 940 through 955 Processing helix chain 'B' and resid 965 through 971 Processing helix chain 'B' and resid 1011 through 1026 Processing helix chain 'B' and resid 1029 through 1032 No H-bonds generated for 'chain 'B' and resid 1029 through 1032' Processing helix chain 'B' and resid 1041 through 1049 Processing helix chain 'B' and resid 1063 through 1080 Processing helix chain 'B' and resid 1085 through 1099 Processing helix chain 'B' and resid 1106 through 1122 Processing helix chain 'B' and resid 1127 through 1136 Processing helix chain 'B' and resid 1147 through 1150 No H-bonds generated for 'chain 'B' and resid 1147 through 1150' Processing helix chain 'B' and resid 1153 through 1166 Processing helix chain 'B' and resid 1172 through 1177 removed outlier: 3.720A pdb=" N GLY B1177 " --> pdb=" O GLY B1173 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1189 Processing helix chain 'B' and resid 1195 through 1208 Processing helix chain 'B' and resid 1210 through 1212 No H-bonds generated for 'chain 'B' and resid 1210 through 1212' Processing helix chain 'B' and resid 1218 through 1231 Processing helix chain 'B' and resid 1234 through 1248 removed outlier: 4.729A pdb=" N SER B1248 " --> pdb=" O LYS B1244 " (cutoff:3.500A) Processing helix chain 'B' and resid 1259 through 1276 Processing helix chain 'B' and resid 1285 through 1298 Processing helix chain 'B' and resid 1304 through 1319 Processing helix chain 'B' and resid 1331 through 1343 Proline residue: B1341 - end of helix Processing helix chain 'B' and resid 1350 through 1373 removed outlier: 4.129A pdb=" N ILE B1354 " --> pdb=" O GLU B1350 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B1373 " --> pdb=" O HIS B1369 " (cutoff:3.500A) Processing helix chain 'B' and resid 1379 through 1390 Processing helix chain 'B' and resid 1395 through 1416 Processing helix chain 'C' and resid 31 through 39 Processing helix chain 'C' and resid 76 through 82 Processing helix chain 'C' and resid 98 through 113 removed outlier: 3.978A pdb=" N SER C 102 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 137 through 143 Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 167 through 181 Processing helix chain 'D' and resid 31 through 39 Processing helix chain 'D' and resid 76 through 82 Processing helix chain 'D' and resid 98 through 114 removed outlier: 4.286A pdb=" N SER D 102 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN D 113 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 137 through 143 Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 166 through 181 Processing sheet with id= A, first strand: chain 'A' and resid 892 through 894 Processing sheet with id= B, first strand: chain 'B' and resid 892 through 896 Processing sheet with id= C, first strand: chain 'C' and resid 88 through 92 removed outlier: 3.738A pdb=" N VAL C 92 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLY C 25 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 88 through 92 removed outlier: 5.321A pdb=" N GLY D 25 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 121 through 124 removed outlier: 6.190A pdb=" N SER D 153 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N VAL D 124 " --> pdb=" O SER D 153 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N SER D 155 " --> pdb=" O VAL D 124 " (cutoff:3.500A) No H-bonds generated for sheet with id= E 1191 hydrogen bonds defined for protein. 3300 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: 8.03 Time building geometry restraints manager: 10.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7450 1.34 - 1.46: 4454 1.46 - 1.58: 11564 1.58 - 1.69: 10 1.69 - 1.81: 124 Bond restraints: 23602 Sorted by residual: bond pdb=" C TRP A1220 " pdb=" N VAL A1221 " ideal model delta sigma weight residual 1.334 1.380 -0.046 1.26e-02 6.30e+03 1.34e+01 bond pdb=" N SER A 974 " pdb=" CA SER A 974 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.07e+00 bond pdb=" N TYR D 78 " pdb=" CA TYR D 78 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.77e+00 bond pdb=" N ASN A 326 " pdb=" CA ASN A 326 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.32e-02 5.74e+03 4.65e+00 bond pdb=" N ALA A 695 " pdb=" CA ALA A 695 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.09e+00 ... (remaining 23597 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.39: 440 106.39 - 113.28: 13430 113.28 - 120.18: 8521 120.18 - 127.08: 9355 127.08 - 133.98: 167 Bond angle restraints: 31913 Sorted by residual: angle pdb=" C ILE A 644 " pdb=" CA ILE A 644 " pdb=" CB ILE A 644 " ideal model delta sigma weight residual 111.77 103.27 8.50 2.27e+00 1.94e-01 1.40e+01 angle pdb=" C ASN A 326 " pdb=" N TYR A 327 " pdb=" CA TYR A 327 " ideal model delta sigma weight residual 122.09 117.15 4.94 1.48e+00 4.57e-01 1.11e+01 angle pdb=" C ILE B 232 " pdb=" CA ILE B 232 " pdb=" CB ILE B 232 " ideal model delta sigma weight residual 110.91 114.76 -3.85 1.24e+00 6.50e-01 9.63e+00 angle pdb=" CA TRP D 79 " pdb=" CB TRP D 79 " pdb=" CG TRP D 79 " ideal model delta sigma weight residual 113.60 119.42 -5.82 1.90e+00 2.77e-01 9.38e+00 angle pdb=" C ILE B 219 " pdb=" CA ILE B 219 " pdb=" CB ILE B 219 " ideal model delta sigma weight residual 112.14 108.02 4.12 1.35e+00 5.49e-01 9.32e+00 ... (remaining 31908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.77: 14268 33.77 - 67.54: 164 67.54 - 101.32: 3 101.32 - 135.09: 0 135.09 - 168.86: 2 Dihedral angle restraints: 14437 sinusoidal: 5917 harmonic: 8520 Sorted by residual: dihedral pdb=" O3B GTP D 301 " pdb=" O3A GTP D 301 " pdb=" PB GTP D 301 " pdb=" PA GTP D 301 " ideal model delta sinusoidal sigma weight residual -68.92 99.94 -168.86 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O3B GTP C 301 " pdb=" O3A GTP C 301 " pdb=" PB GTP C 301 " pdb=" PA GTP C 301 " ideal model delta sinusoidal sigma weight residual 291.08 141.31 149.77 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" C8 GTP D 301 " pdb=" C1' GTP D 301 " pdb=" N9 GTP D 301 " pdb=" O4' GTP D 301 " ideal model delta sinusoidal sigma weight residual 104.59 18.73 85.86 1 2.00e+01 2.50e-03 2.23e+01 ... (remaining 14434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2339 0.032 - 0.064: 1033 0.064 - 0.097: 290 0.097 - 0.129: 96 0.129 - 0.161: 8 Chirality restraints: 3766 Sorted by residual: chirality pdb=" CA ILE A 644 " pdb=" N ILE A 644 " pdb=" C ILE A 644 " pdb=" CB ILE A 644 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA THR A 869 " pdb=" N THR A 869 " pdb=" C THR A 869 " pdb=" CB THR A 869 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA GLN A 99 " pdb=" N GLN A 99 " pdb=" C GLN A 99 " pdb=" CB GLN A 99 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 3763 not shown) Planarity restraints: 4009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A1179 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C GLU A1179 " -0.044 2.00e-02 2.50e+03 pdb=" O GLU A1179 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN A1180 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B1284 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.94e+00 pdb=" C LYS B1284 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS B1284 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN B1285 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1010 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C GLU A1010 " 0.040 2.00e-02 2.50e+03 pdb=" O GLU A1010 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A1011 " -0.013 2.00e-02 2.50e+03 ... (remaining 4006 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2276 2.74 - 3.28: 25491 3.28 - 3.82: 38534 3.82 - 4.36: 44867 4.36 - 4.90: 75598 Nonbonded interactions: 186766 Sorted by model distance: nonbonded pdb=" O ASN B1056 " pdb=" OG SER B1060 " model vdw 2.195 2.440 nonbonded pdb=" O GLU B1204 " pdb=" OG1 THR B1208 " model vdw 2.216 2.440 nonbonded pdb=" O SER B 509 " pdb=" OG1 THR B 513 " model vdw 2.216 2.440 nonbonded pdb=" O LEU B1339 " pdb=" N LEU B1343 " model vdw 2.217 2.520 nonbonded pdb=" OG1 THR B1009 " pdb=" OE2 GLU B1011 " model vdw 2.217 2.440 ... (remaining 186761 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 871 or resid 888 through 1417)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.660 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: 0.020 Extract box with map and model: 28.240 Check model and map are aligned: 0.360 Set scattering table: 0.200 Process input model: 61.110 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.130 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23602 Z= 0.283 Angle : 0.554 8.499 31913 Z= 0.300 Chirality : 0.040 0.161 3766 Planarity : 0.004 0.051 4009 Dihedral : 11.204 168.859 8869 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.23 % Allowed : 7.90 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.16), residues: 2863 helix: 1.59 (0.12), residues: 1879 sheet: -0.97 (0.58), residues: 94 loop : -2.23 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 470 HIS 0.003 0.001 HIS A 762 PHE 0.011 0.001 PHE B 926 TYR 0.027 0.001 TYR D 78 ARG 0.003 0.000 ARG A 605 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 643 time to evaluate : 2.671 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 12 VAL cc_start: 0.8674 (t) cc_final: 0.8392 (m) REVERT: A 86 LEU cc_start: 0.6760 (mt) cc_final: 0.6553 (mm) REVERT: A 92 ILE cc_start: 0.8308 (tp) cc_final: 0.8082 (tp) REVERT: A 134 SER cc_start: 0.8244 (p) cc_final: 0.8040 (p) REVERT: A 171 PHE cc_start: 0.8079 (m-80) cc_final: 0.7844 (m-80) REVERT: A 184 LEU cc_start: 0.8425 (mt) cc_final: 0.8185 (mp) REVERT: A 216 SER cc_start: 0.8433 (t) cc_final: 0.8159 (t) REVERT: A 253 LYS cc_start: 0.7461 (mptt) cc_final: 0.7216 (mptt) REVERT: A 343 ILE cc_start: 0.8606 (pt) cc_final: 0.8178 (pt) REVERT: A 347 ASN cc_start: 0.8122 (p0) cc_final: 0.7503 (p0) REVERT: A 368 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7274 (mt-10) REVERT: A 415 LEU cc_start: 0.8065 (mt) cc_final: 0.7688 (mp) REVERT: A 487 ASN cc_start: 0.8393 (t0) cc_final: 0.8164 (t0) REVERT: A 515 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6931 (tm-30) REVERT: A 523 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6643 (mm-30) REVERT: A 559 ARG cc_start: 0.7679 (mtp85) cc_final: 0.7362 (mtm110) REVERT: A 563 PHE cc_start: 0.7720 (t80) cc_final: 0.7461 (t80) REVERT: A 566 CYS cc_start: 0.8100 (m) cc_final: 0.7780 (m) REVERT: A 575 LYS cc_start: 0.8434 (mptt) cc_final: 0.8186 (mmtt) REVERT: A 576 LYS cc_start: 0.7552 (tppt) cc_final: 0.6774 (tppt) REVERT: A 584 LYS cc_start: 0.8403 (mtpt) cc_final: 0.8188 (mtpp) REVERT: A 671 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7138 (tm-30) REVERT: A 673 GLN cc_start: 0.6905 (tp40) cc_final: 0.6461 (tp40) REVERT: A 738 ASP cc_start: 0.7112 (p0) cc_final: 0.6888 (p0) REVERT: A 830 ASP cc_start: 0.7718 (t0) cc_final: 0.7421 (t70) REVERT: A 862 ASN cc_start: 0.7911 (m-40) cc_final: 0.7685 (m110) REVERT: A 866 LYS cc_start: 0.8228 (ttmm) cc_final: 0.7939 (ttmm) REVERT: A 889 MET cc_start: 0.7458 (tmm) cc_final: 0.7060 (tmm) REVERT: A 1036 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7118 (mm-30) REVERT: A 1074 THR cc_start: 0.8499 (t) cc_final: 0.8211 (p) REVERT: A 1089 LYS cc_start: 0.8340 (mtpp) cc_final: 0.7951 (mtmm) REVERT: A 1093 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8021 (tm-30) REVERT: A 1128 GLU cc_start: 0.7499 (tp30) cc_final: 0.6905 (tp30) REVERT: A 1179 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7366 (tm-30) REVERT: A 1187 LYS cc_start: 0.8541 (tptp) cc_final: 0.8337 (tptp) REVERT: A 1191 MET cc_start: 0.5573 (mmm) cc_final: 0.5009 (mmm) REVERT: A 1196 GLU cc_start: 0.8205 (tt0) cc_final: 0.7677 (tm-30) REVERT: A 1199 PHE cc_start: 0.8573 (t80) cc_final: 0.8278 (t80) REVERT: A 1204 GLU cc_start: 0.7928 (tp30) cc_final: 0.7601 (mm-30) REVERT: A 1328 MET cc_start: 0.5291 (tpt) cc_final: 0.5017 (tpt) REVERT: A 1400 LYS cc_start: 0.8515 (mmtm) cc_final: 0.8188 (mmtm) REVERT: B 93 ASP cc_start: 0.7809 (t70) cc_final: 0.7511 (t70) REVERT: B 103 LEU cc_start: 0.8532 (tp) cc_final: 0.8332 (tp) REVERT: B 120 ASP cc_start: 0.7443 (m-30) cc_final: 0.7065 (m-30) REVERT: B 199 SER cc_start: 0.8839 (m) cc_final: 0.8624 (m) REVERT: B 245 GLU cc_start: 0.6629 (mp0) cc_final: 0.6407 (mp0) REVERT: B 375 GLN cc_start: 0.8197 (pt0) cc_final: 0.7989 (pt0) REVERT: B 503 LYS cc_start: 0.8333 (ttmm) cc_final: 0.8065 (ttmm) REVERT: B 533 PHE cc_start: 0.8192 (t80) cc_final: 0.7944 (t80) REVERT: B 568 ASN cc_start: 0.7638 (t0) cc_final: 0.7340 (t0) REVERT: B 625 ASN cc_start: 0.8414 (m-40) cc_final: 0.8111 (m110) REVERT: B 626 GLU cc_start: 0.7932 (tt0) cc_final: 0.7649 (tt0) REVERT: B 628 ILE cc_start: 0.8258 (tp) cc_final: 0.7997 (tt) REVERT: B 660 ARG cc_start: 0.8447 (mtt90) cc_final: 0.8176 (mtt90) REVERT: B 663 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7452 (tm-30) REVERT: B 703 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.8164 (m-80) REVERT: B 737 LYS cc_start: 0.8057 (tppt) cc_final: 0.7743 (mppt) REVERT: B 753 ASP cc_start: 0.7735 (m-30) cc_final: 0.7201 (m-30) REVERT: B 754 LYS cc_start: 0.8353 (tptp) cc_final: 0.8094 (tptp) REVERT: B 770 GLU cc_start: 0.7511 (tp30) cc_final: 0.7259 (tp30) REVERT: B 825 TYR cc_start: 0.7908 (t80) cc_final: 0.7685 (t80) REVERT: B 837 MET cc_start: 0.7720 (mmp) cc_final: 0.7412 (mmm) REVERT: B 929 ILE cc_start: 0.8693 (mm) cc_final: 0.8343 (mt) REVERT: B 1089 LYS cc_start: 0.7976 (ptpt) cc_final: 0.7626 (ptpp) REVERT: B 1128 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7854 (tm-30) REVERT: B 1132 LYS cc_start: 0.8043 (tppt) cc_final: 0.7610 (tppt) REVERT: B 1147 GLN cc_start: 0.8087 (tt0) cc_final: 0.7811 (tt0) REVERT: B 1156 LYS cc_start: 0.8103 (ttmt) cc_final: 0.7872 (ttmm) REVERT: B 1157 GLU cc_start: 0.7856 (tp30) cc_final: 0.7449 (tp30) REVERT: B 1165 LEU cc_start: 0.8282 (tp) cc_final: 0.8047 (tt) REVERT: B 1180 ASN cc_start: 0.8159 (m-40) cc_final: 0.7893 (m-40) REVERT: B 1183 LYS cc_start: 0.8189 (tptp) cc_final: 0.7901 (tptm) REVERT: B 1191 MET cc_start: 0.7123 (mtm) cc_final: 0.6580 (mtm) REVERT: B 1199 PHE cc_start: 0.8573 (t80) cc_final: 0.8152 (t80) REVERT: B 1200 GLU cc_start: 0.7733 (tp30) cc_final: 0.7370 (tp30) REVERT: B 1204 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7219 (mt-10) REVERT: B 1214 THR cc_start: 0.7690 (p) cc_final: 0.7306 (t) REVERT: B 1218 PHE cc_start: 0.7388 (m-80) cc_final: 0.7057 (t80) REVERT: B 1265 SER cc_start: 0.8032 (t) cc_final: 0.7806 (t) REVERT: B 1266 LEU cc_start: 0.8310 (mt) cc_final: 0.8093 (mt) REVERT: B 1274 HIS cc_start: 0.7516 (t-90) cc_final: 0.7301 (t-90) REVERT: B 1288 PHE cc_start: 0.8549 (m-80) cc_final: 0.8083 (m-80) REVERT: B 1332 GLU cc_start: 0.7925 (mp0) cc_final: 0.6741 (mp0) REVERT: B 1383 LYS cc_start: 0.8414 (mttt) cc_final: 0.8130 (mtmt) REVERT: C 22 LEU cc_start: 0.7541 (tp) cc_final: 0.7341 (tp) REVERT: C 24 LEU cc_start: 0.7548 (mp) cc_final: 0.7251 (mp) REVERT: C 101 MET cc_start: 0.7222 (tmm) cc_final: 0.6927 (mmm) REVERT: C 111 MET cc_start: 0.7262 (ttm) cc_final: 0.7023 (ttm) REVERT: D 101 MET cc_start: 0.8144 (mmt) cc_final: 0.7922 (mmt) REVERT: D 111 MET cc_start: 0.7249 (tmm) cc_final: 0.6961 (tmm) REVERT: D 173 TRP cc_start: 0.7743 (t60) cc_final: 0.7463 (t60) outliers start: 6 outliers final: 3 residues processed: 647 average time/residue: 0.4073 time to fit residues: 410.2293 Evaluate side-chains 572 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 568 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 703 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 0.1980 chunk 217 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 146 optimal weight: 0.0060 chunk 116 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 87 optimal weight: 0.0470 chunk 136 optimal weight: 0.9980 chunk 167 optimal weight: 0.4980 chunk 260 optimal weight: 4.9990 overall best weight: 0.3494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 GLN ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 GLN ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 571 ASN ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 GLN B1180 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23602 Z= 0.181 Angle : 0.540 11.012 31913 Z= 0.281 Chirality : 0.039 0.193 3766 Planarity : 0.004 0.046 4009 Dihedral : 6.982 167.028 3086 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.09 % Favored : 92.87 % Rotamer: Outliers : 1.81 % Allowed : 13.09 % Favored : 85.11 % 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: 0.61 (0.16), residues: 2863 helix: 1.62 (0.12), residues: 1873 sheet: -0.97 (0.58), residues: 94 loop : -2.16 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 470 HIS 0.010 0.001 HIS B1369 PHE 0.030 0.001 PHE A1069 TYR 0.019 0.001 TYR D 78 ARG 0.006 0.000 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 581 time to evaluate : 2.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.6858 (mt) cc_final: 0.6634 (mm) REVERT: A 171 PHE cc_start: 0.8106 (m-80) cc_final: 0.7846 (m-80) REVERT: A 184 LEU cc_start: 0.8452 (mt) cc_final: 0.8188 (mp) REVERT: A 192 ASP cc_start: 0.7659 (m-30) cc_final: 0.7375 (m-30) REVERT: A 253 LYS cc_start: 0.7456 (mptt) cc_final: 0.7196 (mptt) REVERT: A 343 ILE cc_start: 0.8502 (pt) cc_final: 0.8228 (pt) REVERT: A 347 ASN cc_start: 0.8043 (p0) cc_final: 0.7400 (p0) REVERT: A 368 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7246 (mt-10) REVERT: A 415 LEU cc_start: 0.8025 (mt) cc_final: 0.7634 (mp) REVERT: A 487 ASN cc_start: 0.8372 (t0) cc_final: 0.8156 (t0) REVERT: A 515 GLU cc_start: 0.7205 (tm-30) cc_final: 0.6876 (tm-30) REVERT: A 523 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6479 (mm-30) REVERT: A 559 ARG cc_start: 0.7485 (mtp85) cc_final: 0.7085 (mtm110) REVERT: A 563 PHE cc_start: 0.7706 (t80) cc_final: 0.7470 (t80) REVERT: A 566 CYS cc_start: 0.8037 (m) cc_final: 0.7671 (m) REVERT: A 575 LYS cc_start: 0.8439 (mptt) cc_final: 0.8193 (mmtt) REVERT: A 576 LYS cc_start: 0.7589 (tppt) cc_final: 0.6647 (tppt) REVERT: A 580 MET cc_start: 0.8271 (mtp) cc_final: 0.7664 (mtp) REVERT: A 636 LEU cc_start: 0.8056 (mt) cc_final: 0.7813 (mp) REVERT: A 671 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7078 (tm-30) REVERT: A 673 GLN cc_start: 0.6828 (tp40) cc_final: 0.6379 (tp40) REVERT: A 738 ASP cc_start: 0.7113 (p0) cc_final: 0.6813 (p0) REVERT: A 806 ASP cc_start: 0.7465 (m-30) cc_final: 0.7258 (m-30) REVERT: A 830 ASP cc_start: 0.7704 (t0) cc_final: 0.7418 (t70) REVERT: A 862 ASN cc_start: 0.7812 (m-40) cc_final: 0.7550 (m-40) REVERT: A 866 LYS cc_start: 0.8241 (ttmm) cc_final: 0.7946 (ttmm) REVERT: A 889 MET cc_start: 0.7444 (tmm) cc_final: 0.6722 (tmm) REVERT: A 902 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6933 (mm-30) REVERT: A 1074 THR cc_start: 0.8353 (t) cc_final: 0.8106 (p) REVERT: A 1080 PHE cc_start: 0.7444 (m-80) cc_final: 0.7212 (m-80) REVERT: A 1089 LYS cc_start: 0.8295 (mtpp) cc_final: 0.7911 (mtmm) REVERT: A 1093 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7950 (tm-30) REVERT: A 1128 GLU cc_start: 0.7458 (tp30) cc_final: 0.6855 (tp30) REVERT: A 1179 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7100 (tm-30) REVERT: A 1187 LYS cc_start: 0.8503 (tptp) cc_final: 0.8291 (tptp) REVERT: A 1196 GLU cc_start: 0.8154 (tt0) cc_final: 0.7657 (tm-30) REVERT: A 1199 PHE cc_start: 0.8569 (t80) cc_final: 0.8265 (t80) REVERT: A 1204 GLU cc_start: 0.7886 (tp30) cc_final: 0.7551 (mm-30) REVERT: A 1290 ILE cc_start: 0.8684 (mm) cc_final: 0.8478 (mm) REVERT: A 1328 MET cc_start: 0.5098 (tpt) cc_final: 0.4823 (tpt) REVERT: B 10 ASP cc_start: 0.6742 (OUTLIER) cc_final: 0.6523 (p0) REVERT: B 103 LEU cc_start: 0.8532 (tp) cc_final: 0.8294 (tp) REVERT: B 120 ASP cc_start: 0.7416 (m-30) cc_final: 0.7047 (m-30) REVERT: B 199 SER cc_start: 0.8821 (m) cc_final: 0.8243 (p) REVERT: B 205 ARG cc_start: 0.8035 (mmm-85) cc_final: 0.7628 (mmm-85) REVERT: B 228 LYS cc_start: 0.8361 (ttmm) cc_final: 0.8073 (ttmm) REVERT: B 245 GLU cc_start: 0.6583 (mp0) cc_final: 0.6334 (mp0) REVERT: B 253 LYS cc_start: 0.7491 (mttm) cc_final: 0.6959 (mttm) REVERT: B 368 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: B 375 GLN cc_start: 0.8103 (pt0) cc_final: 0.7833 (pt0) REVERT: B 503 LYS cc_start: 0.8365 (ttmm) cc_final: 0.8134 (ttmm) REVERT: B 508 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7807 (tm-30) REVERT: B 533 PHE cc_start: 0.8183 (t80) cc_final: 0.7965 (t80) REVERT: B 625 ASN cc_start: 0.8469 (m-40) cc_final: 0.8133 (m110) REVERT: B 626 GLU cc_start: 0.7954 (tt0) cc_final: 0.7750 (tt0) REVERT: B 631 PHE cc_start: 0.8003 (m-80) cc_final: 0.7631 (m-80) REVERT: B 660 ARG cc_start: 0.8487 (mtt90) cc_final: 0.8241 (mtt90) REVERT: B 663 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7419 (tm-30) REVERT: B 737 LYS cc_start: 0.8058 (tppt) cc_final: 0.7789 (mppt) REVERT: B 753 ASP cc_start: 0.7736 (m-30) cc_final: 0.7186 (m-30) REVERT: B 754 LYS cc_start: 0.8333 (tptp) cc_final: 0.8095 (tptp) REVERT: B 770 GLU cc_start: 0.7514 (tp30) cc_final: 0.7256 (tp30) REVERT: B 837 MET cc_start: 0.7650 (mmp) cc_final: 0.7339 (mmp) REVERT: B 958 ILE cc_start: 0.8919 (mm) cc_final: 0.8717 (tp) REVERT: B 1089 LYS cc_start: 0.8241 (ptpt) cc_final: 0.7876 (ptpp) REVERT: B 1128 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7817 (tm-30) REVERT: B 1132 LYS cc_start: 0.7942 (tppt) cc_final: 0.7543 (tppt) REVERT: B 1147 GLN cc_start: 0.8227 (tt0) cc_final: 0.7829 (tt0) REVERT: B 1156 LYS cc_start: 0.7999 (ttmt) cc_final: 0.7769 (ttmm) REVERT: B 1157 GLU cc_start: 0.7809 (tp30) cc_final: 0.7447 (tp30) REVERT: B 1165 LEU cc_start: 0.8239 (tp) cc_final: 0.8033 (tt) REVERT: B 1180 ASN cc_start: 0.8060 (m110) cc_final: 0.7815 (m-40) REVERT: B 1183 LYS cc_start: 0.8116 (tptp) cc_final: 0.7914 (tptm) REVERT: B 1191 MET cc_start: 0.7133 (mtm) cc_final: 0.6572 (mtm) REVERT: B 1193 GLU cc_start: 0.7585 (tp30) cc_final: 0.7254 (tp30) REVERT: B 1199 PHE cc_start: 0.8466 (t80) cc_final: 0.8142 (t80) REVERT: B 1200 GLU cc_start: 0.7679 (tp30) cc_final: 0.7291 (tp30) REVERT: B 1204 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7167 (mt-10) REVERT: B 1214 THR cc_start: 0.7685 (p) cc_final: 0.7238 (t) REVERT: B 1218 PHE cc_start: 0.7332 (m-80) cc_final: 0.6984 (t80) REVERT: B 1265 SER cc_start: 0.8044 (t) cc_final: 0.7831 (t) REVERT: B 1266 LEU cc_start: 0.8260 (mt) cc_final: 0.8037 (mt) REVERT: B 1288 PHE cc_start: 0.8512 (m-80) cc_final: 0.8111 (m-80) REVERT: B 1332 GLU cc_start: 0.7835 (mp0) cc_final: 0.6912 (mp0) REVERT: B 1350 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.6193 (pm20) REVERT: B 1383 LYS cc_start: 0.8342 (mttt) cc_final: 0.8021 (mtmt) REVERT: C 101 MET cc_start: 0.7499 (tmm) cc_final: 0.7148 (mmm) REVERT: D 22 LEU cc_start: 0.7602 (mp) cc_final: 0.7210 (mp) REVERT: D 111 MET cc_start: 0.7182 (tmm) cc_final: 0.6659 (tmm) REVERT: D 173 TRP cc_start: 0.7731 (t60) cc_final: 0.7510 (t60) outliers start: 48 outliers final: 30 residues processed: 607 average time/residue: 0.3725 time to fit residues: 349.9597 Evaluate side-chains 594 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 561 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1194 GLN Chi-restraints excluded: chain B residue 1198 ILE Chi-restraints excluded: chain B residue 1300 ASN Chi-restraints excluded: chain B residue 1307 GLU Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1350 GLU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 144 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 216 optimal weight: 0.9990 chunk 177 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 282 optimal weight: 0.0770 chunk 232 optimal weight: 0.5980 chunk 258 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 GLN ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23602 Z= 0.218 Angle : 0.542 11.505 31913 Z= 0.280 Chirality : 0.040 0.206 3766 Planarity : 0.004 0.046 4009 Dihedral : 6.896 168.158 3084 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.82 % Favored : 92.14 % Rotamer: Outliers : 2.41 % Allowed : 14.59 % Favored : 83.00 % 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: 0.49 (0.16), residues: 2863 helix: 1.52 (0.12), residues: 1867 sheet: -1.06 (0.57), residues: 94 loop : -2.16 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 173 HIS 0.007 0.001 HIS B1369 PHE 0.027 0.001 PHE A1069 TYR 0.016 0.001 TYR A 327 ARG 0.009 0.000 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 579 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8584 (t) cc_final: 0.8346 (m) REVERT: A 78 GLN cc_start: 0.7625 (tt0) cc_final: 0.7247 (tt0) REVERT: A 86 LEU cc_start: 0.7035 (mt) cc_final: 0.6744 (mm) REVERT: A 192 ASP cc_start: 0.7670 (m-30) cc_final: 0.7382 (m-30) REVERT: A 253 LYS cc_start: 0.7445 (mptt) cc_final: 0.7200 (mptt) REVERT: A 343 ILE cc_start: 0.8512 (pt) cc_final: 0.8204 (pt) REVERT: A 347 ASN cc_start: 0.8181 (p0) cc_final: 0.7858 (p0) REVERT: A 368 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7254 (mt-10) REVERT: A 487 ASN cc_start: 0.8376 (t0) cc_final: 0.8137 (t0) REVERT: A 515 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6867 (tm-30) REVERT: A 523 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6514 (mm-30) REVERT: A 559 ARG cc_start: 0.7499 (mtp85) cc_final: 0.7095 (mtm110) REVERT: A 563 PHE cc_start: 0.7709 (t80) cc_final: 0.7466 (t80) REVERT: A 566 CYS cc_start: 0.7999 (m) cc_final: 0.7699 (m) REVERT: A 575 LYS cc_start: 0.8456 (mptt) cc_final: 0.8200 (mmtt) REVERT: A 576 LYS cc_start: 0.7673 (tppt) cc_final: 0.6912 (tppt) REVERT: A 578 ILE cc_start: 0.7926 (mm) cc_final: 0.7656 (mm) REVERT: A 606 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7604 (mtp) REVERT: A 636 LEU cc_start: 0.8055 (mt) cc_final: 0.7827 (mp) REVERT: A 671 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7106 (tm-30) REVERT: A 673 GLN cc_start: 0.6829 (tp40) cc_final: 0.6368 (tp40) REVERT: A 738 ASP cc_start: 0.7106 (p0) cc_final: 0.6803 (p0) REVERT: A 806 ASP cc_start: 0.7468 (m-30) cc_final: 0.7240 (m-30) REVERT: A 830 ASP cc_start: 0.7716 (t0) cc_final: 0.7395 (t70) REVERT: A 837 MET cc_start: 0.7421 (mmp) cc_final: 0.7100 (mmm) REVERT: A 862 ASN cc_start: 0.7843 (m-40) cc_final: 0.7556 (m-40) REVERT: A 866 LYS cc_start: 0.8234 (ttmm) cc_final: 0.7935 (ttmm) REVERT: A 889 MET cc_start: 0.7468 (tmm) cc_final: 0.6771 (tmm) REVERT: A 1074 THR cc_start: 0.8345 (t) cc_final: 0.8103 (p) REVERT: A 1080 PHE cc_start: 0.7425 (m-80) cc_final: 0.7126 (m-80) REVERT: A 1089 LYS cc_start: 0.8298 (mtpp) cc_final: 0.7966 (mtmm) REVERT: A 1093 GLN cc_start: 0.8368 (tm-30) cc_final: 0.7963 (tm-30) REVERT: A 1128 GLU cc_start: 0.7496 (tp30) cc_final: 0.6890 (tp30) REVERT: A 1179 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7123 (tp30) REVERT: A 1196 GLU cc_start: 0.8154 (tt0) cc_final: 0.7662 (tm-30) REVERT: A 1199 PHE cc_start: 0.8562 (t80) cc_final: 0.8241 (t80) REVERT: A 1204 GLU cc_start: 0.7878 (tp30) cc_final: 0.7506 (mm-30) REVERT: A 1290 ILE cc_start: 0.8679 (mm) cc_final: 0.8470 (mm) REVERT: A 1299 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8236 (mm) REVERT: A 1328 MET cc_start: 0.5211 (tpt) cc_final: 0.4958 (tpt) REVERT: B 10 ASP cc_start: 0.6700 (OUTLIER) cc_final: 0.6482 (p0) REVERT: B 103 LEU cc_start: 0.8512 (tp) cc_final: 0.8291 (tp) REVERT: B 120 ASP cc_start: 0.7409 (m-30) cc_final: 0.7033 (m-30) REVERT: B 199 SER cc_start: 0.8789 (m) cc_final: 0.8304 (p) REVERT: B 205 ARG cc_start: 0.8029 (mmm-85) cc_final: 0.7689 (mmm-85) REVERT: B 228 LYS cc_start: 0.8404 (ttmm) cc_final: 0.8112 (ttmm) REVERT: B 245 GLU cc_start: 0.6597 (mp0) cc_final: 0.6330 (mp0) REVERT: B 253 LYS cc_start: 0.7429 (mttm) cc_final: 0.6970 (mttm) REVERT: B 368 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: B 422 ASN cc_start: 0.7749 (m-40) cc_final: 0.7504 (m-40) REVERT: B 503 LYS cc_start: 0.8376 (ttmm) cc_final: 0.8141 (ttmm) REVERT: B 508 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7861 (tm-30) REVERT: B 568 ASN cc_start: 0.8006 (t0) cc_final: 0.7776 (t0) REVERT: B 575 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8473 (mmmt) REVERT: B 625 ASN cc_start: 0.8486 (m-40) cc_final: 0.8183 (m-40) REVERT: B 626 GLU cc_start: 0.7962 (tt0) cc_final: 0.7726 (tt0) REVERT: B 631 PHE cc_start: 0.8017 (m-80) cc_final: 0.7813 (m-10) REVERT: B 657 GLN cc_start: 0.7563 (mp10) cc_final: 0.7077 (mp-120) REVERT: B 663 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7436 (tm-30) REVERT: B 737 LYS cc_start: 0.8079 (tppt) cc_final: 0.7800 (mppt) REVERT: B 753 ASP cc_start: 0.7743 (m-30) cc_final: 0.7299 (m-30) REVERT: B 754 LYS cc_start: 0.8367 (tptp) cc_final: 0.8129 (tptp) REVERT: B 770 GLU cc_start: 0.7505 (tp30) cc_final: 0.7237 (tp30) REVERT: B 837 MET cc_start: 0.7605 (mmp) cc_final: 0.7210 (mmp) REVERT: B 958 ILE cc_start: 0.8941 (mm) cc_final: 0.8649 (tt) REVERT: B 1052 LYS cc_start: 0.7861 (ptpt) cc_final: 0.7558 (mttp) REVERT: B 1089 LYS cc_start: 0.8228 (ptpt) cc_final: 0.7824 (ptpp) REVERT: B 1128 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7819 (tm-30) REVERT: B 1132 LYS cc_start: 0.7903 (tppt) cc_final: 0.7535 (tppt) REVERT: B 1147 GLN cc_start: 0.8245 (tt0) cc_final: 0.7854 (tt0) REVERT: B 1156 LYS cc_start: 0.8045 (ttmt) cc_final: 0.7834 (ttmm) REVERT: B 1157 GLU cc_start: 0.7819 (tp30) cc_final: 0.7489 (tp30) REVERT: B 1165 LEU cc_start: 0.8239 (tp) cc_final: 0.8011 (tt) REVERT: B 1180 ASN cc_start: 0.8104 (m110) cc_final: 0.7850 (m-40) REVERT: B 1183 LYS cc_start: 0.8142 (tptp) cc_final: 0.7854 (tptm) REVERT: B 1186 ARG cc_start: 0.7979 (mmm160) cc_final: 0.7684 (mmm160) REVERT: B 1191 MET cc_start: 0.7224 (mtm) cc_final: 0.6665 (mtm) REVERT: B 1193 GLU cc_start: 0.7664 (tp30) cc_final: 0.7317 (tp30) REVERT: B 1199 PHE cc_start: 0.8484 (t80) cc_final: 0.8085 (t80) REVERT: B 1200 GLU cc_start: 0.7689 (tp30) cc_final: 0.7311 (tp30) REVERT: B 1204 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7142 (mt-10) REVERT: B 1214 THR cc_start: 0.7660 (p) cc_final: 0.7212 (t) REVERT: B 1218 PHE cc_start: 0.7397 (m-80) cc_final: 0.7039 (t80) REVERT: B 1265 SER cc_start: 0.8069 (t) cc_final: 0.7855 (t) REVERT: B 1266 LEU cc_start: 0.8270 (mt) cc_final: 0.8051 (mt) REVERT: B 1288 PHE cc_start: 0.8539 (m-80) cc_final: 0.8215 (m-80) REVERT: B 1332 GLU cc_start: 0.7942 (mp0) cc_final: 0.7161 (mp0) REVERT: B 1334 LEU cc_start: 0.8475 (mt) cc_final: 0.8222 (mt) REVERT: B 1350 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.6024 (pm20) REVERT: C 101 MET cc_start: 0.7541 (tmm) cc_final: 0.7167 (tmm) REVERT: D 22 LEU cc_start: 0.7639 (mp) cc_final: 0.7269 (mp) REVERT: D 111 MET cc_start: 0.7173 (tmm) cc_final: 0.6674 (tmm) REVERT: D 173 TRP cc_start: 0.7750 (t60) cc_final: 0.7495 (t60) outliers start: 64 outliers final: 41 residues processed: 614 average time/residue: 0.3756 time to fit residues: 359.6522 Evaluate side-chains 602 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 556 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1378 ASN Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 978 LYS Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1194 GLN Chi-restraints excluded: chain B residue 1307 GLU Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1340 LEU Chi-restraints excluded: chain B residue 1350 GLU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 257 optimal weight: 2.9990 chunk 196 optimal weight: 0.4980 chunk 135 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 262 optimal weight: 6.9990 chunk 277 optimal weight: 0.5980 chunk 136 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 GLN B1296 HIS B1297 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23602 Z= 0.286 Angle : 0.569 11.195 31913 Z= 0.295 Chirality : 0.041 0.214 3766 Planarity : 0.004 0.048 4009 Dihedral : 6.971 168.663 3084 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.10 % Favored : 91.86 % Rotamer: Outliers : 2.75 % Allowed : 15.64 % Favored : 81.61 % 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: 0.29 (0.16), residues: 2863 helix: 1.33 (0.12), residues: 1870 sheet: -1.19 (0.55), residues: 94 loop : -2.16 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 173 HIS 0.007 0.001 HIS B1369 PHE 0.020 0.002 PHE B1090 TYR 0.022 0.002 TYR A 327 ARG 0.008 0.000 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 574 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8631 (t) cc_final: 0.8362 (m) REVERT: A 78 GLN cc_start: 0.7705 (tt0) cc_final: 0.7376 (tt0) REVERT: A 86 LEU cc_start: 0.7217 (mt) cc_final: 0.6928 (mm) REVERT: A 153 ARG cc_start: 0.7545 (mtm-85) cc_final: 0.7317 (mtm-85) REVERT: A 184 LEU cc_start: 0.8430 (mt) cc_final: 0.8194 (mp) REVERT: A 253 LYS cc_start: 0.7454 (mptt) cc_final: 0.7196 (mptt) REVERT: A 343 ILE cc_start: 0.8530 (pt) cc_final: 0.8205 (pt) REVERT: A 347 ASN cc_start: 0.8282 (p0) cc_final: 0.7854 (p0) REVERT: A 368 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7292 (mt-10) REVERT: A 487 ASN cc_start: 0.8367 (t0) cc_final: 0.8128 (t0) REVERT: A 515 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6897 (tm-30) REVERT: A 523 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6619 (mm-30) REVERT: A 559 ARG cc_start: 0.7533 (mtp85) cc_final: 0.7114 (mtm110) REVERT: A 563 PHE cc_start: 0.7707 (t80) cc_final: 0.7478 (t80) REVERT: A 566 CYS cc_start: 0.8061 (m) cc_final: 0.7729 (m) REVERT: A 575 LYS cc_start: 0.8463 (mptt) cc_final: 0.8204 (mmtt) REVERT: A 576 LYS cc_start: 0.7690 (tppt) cc_final: 0.6956 (tppt) REVERT: A 622 SER cc_start: 0.8115 (p) cc_final: 0.7882 (t) REVERT: A 636 LEU cc_start: 0.8001 (mt) cc_final: 0.7755 (mp) REVERT: A 671 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7154 (tm-30) REVERT: A 673 GLN cc_start: 0.6856 (tp40) cc_final: 0.6388 (tp40) REVERT: A 738 ASP cc_start: 0.7078 (p0) cc_final: 0.6787 (p0) REVERT: A 806 ASP cc_start: 0.7488 (m-30) cc_final: 0.7245 (m-30) REVERT: A 830 ASP cc_start: 0.7714 (t0) cc_final: 0.7400 (t70) REVERT: A 862 ASN cc_start: 0.7880 (m-40) cc_final: 0.7657 (m110) REVERT: A 866 LYS cc_start: 0.8261 (ttmm) cc_final: 0.7950 (ttmm) REVERT: A 889 MET cc_start: 0.7476 (tmm) cc_final: 0.6788 (tmm) REVERT: A 1022 CYS cc_start: 0.7585 (t) cc_final: 0.6895 (t) REVERT: A 1074 THR cc_start: 0.8417 (t) cc_final: 0.8144 (p) REVERT: A 1080 PHE cc_start: 0.7469 (m-80) cc_final: 0.7065 (m-80) REVERT: A 1089 LYS cc_start: 0.8304 (mtpp) cc_final: 0.7923 (mtmm) REVERT: A 1093 GLN cc_start: 0.8400 (tm-30) cc_final: 0.7952 (tm-30) REVERT: A 1128 GLU cc_start: 0.7511 (tp30) cc_final: 0.6894 (tp30) REVERT: A 1179 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7122 (tp30) REVERT: A 1196 GLU cc_start: 0.8162 (tt0) cc_final: 0.7673 (tm-30) REVERT: A 1199 PHE cc_start: 0.8582 (t80) cc_final: 0.8262 (t80) REVERT: A 1204 GLU cc_start: 0.7898 (tp30) cc_final: 0.7504 (mm-30) REVERT: A 1222 LEU cc_start: 0.8428 (tp) cc_final: 0.8118 (tt) REVERT: A 1290 ILE cc_start: 0.8675 (mm) cc_final: 0.8471 (mm) REVERT: A 1299 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8287 (mm) REVERT: A 1328 MET cc_start: 0.5285 (tpt) cc_final: 0.5029 (tpt) REVERT: A 1336 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6638 (mp0) REVERT: A 1383 LYS cc_start: 0.8423 (mmtt) cc_final: 0.8051 (mmtm) REVERT: B 10 ASP cc_start: 0.6701 (OUTLIER) cc_final: 0.6492 (p0) REVERT: B 120 ASP cc_start: 0.7404 (m-30) cc_final: 0.7033 (m-30) REVERT: B 183 ASP cc_start: 0.7871 (t70) cc_final: 0.7530 (t0) REVERT: B 199 SER cc_start: 0.8831 (m) cc_final: 0.8355 (p) REVERT: B 205 ARG cc_start: 0.8045 (mmm-85) cc_final: 0.7678 (mmm-85) REVERT: B 228 LYS cc_start: 0.8422 (ttmm) cc_final: 0.8044 (ttmm) REVERT: B 231 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7594 (p) REVERT: B 245 GLU cc_start: 0.6609 (mp0) cc_final: 0.6313 (mp0) REVERT: B 253 LYS cc_start: 0.7447 (mttm) cc_final: 0.6989 (mttm) REVERT: B 368 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: B 422 ASN cc_start: 0.7755 (m-40) cc_final: 0.7479 (m-40) REVERT: B 433 ARG cc_start: 0.8307 (mpt180) cc_final: 0.8083 (mpt180) REVERT: B 488 LEU cc_start: 0.8226 (mp) cc_final: 0.7898 (mt) REVERT: B 503 LYS cc_start: 0.8336 (ttmm) cc_final: 0.8121 (ttmm) REVERT: B 508 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7971 (tm-30) REVERT: B 551 MET cc_start: 0.7265 (mtp) cc_final: 0.6809 (mtp) REVERT: B 575 LYS cc_start: 0.8773 (mmmt) cc_final: 0.8502 (mmmt) REVERT: B 626 GLU cc_start: 0.7956 (tt0) cc_final: 0.7703 (tt0) REVERT: B 663 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7446 (tm-30) REVERT: B 737 LYS cc_start: 0.8072 (tppt) cc_final: 0.7768 (mppt) REVERT: B 753 ASP cc_start: 0.7740 (m-30) cc_final: 0.7304 (m-30) REVERT: B 754 LYS cc_start: 0.8450 (tptp) cc_final: 0.8221 (tptp) REVERT: B 837 MET cc_start: 0.7576 (mmp) cc_final: 0.7190 (mmp) REVERT: B 1052 LYS cc_start: 0.7931 (ptpt) cc_final: 0.7622 (mttp) REVERT: B 1089 LYS cc_start: 0.8218 (ptpt) cc_final: 0.7812 (ptpp) REVERT: B 1128 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7825 (tm-30) REVERT: B 1132 LYS cc_start: 0.7946 (tppt) cc_final: 0.7574 (tppt) REVERT: B 1147 GLN cc_start: 0.8260 (tt0) cc_final: 0.7900 (tt0) REVERT: B 1156 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7870 (ttmm) REVERT: B 1157 GLU cc_start: 0.7819 (tp30) cc_final: 0.7428 (tp30) REVERT: B 1165 LEU cc_start: 0.8265 (tp) cc_final: 0.7990 (tt) REVERT: B 1180 ASN cc_start: 0.8150 (m110) cc_final: 0.7928 (m-40) REVERT: B 1183 LYS cc_start: 0.8177 (tptp) cc_final: 0.7885 (tptm) REVERT: B 1191 MET cc_start: 0.7228 (mtm) cc_final: 0.6704 (mtm) REVERT: B 1199 PHE cc_start: 0.8514 (t80) cc_final: 0.8097 (t80) REVERT: B 1200 GLU cc_start: 0.7705 (tp30) cc_final: 0.7330 (tp30) REVERT: B 1204 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7187 (mt-10) REVERT: B 1214 THR cc_start: 0.7785 (OUTLIER) cc_final: 0.7375 (t) REVERT: B 1218 PHE cc_start: 0.7509 (m-80) cc_final: 0.7098 (t80) REVERT: B 1266 LEU cc_start: 0.8284 (mt) cc_final: 0.8067 (mt) REVERT: B 1288 PHE cc_start: 0.8568 (m-80) cc_final: 0.8315 (m-80) REVERT: B 1350 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.6071 (pm20) REVERT: C 101 MET cc_start: 0.7559 (tmm) cc_final: 0.7248 (tmm) REVERT: D 22 LEU cc_start: 0.7654 (mp) cc_final: 0.7277 (mp) REVERT: D 111 MET cc_start: 0.7193 (tmm) cc_final: 0.6712 (tmm) REVERT: D 173 TRP cc_start: 0.7850 (t60) cc_final: 0.7516 (t60) outliers start: 73 outliers final: 49 residues processed: 614 average time/residue: 0.3703 time to fit residues: 350.7642 Evaluate side-chains 609 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 554 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 768 TRP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1253 ASP Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 978 LYS Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1194 GLN Chi-restraints excluded: chain B residue 1214 THR Chi-restraints excluded: chain B residue 1300 ASN Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1340 LEU Chi-restraints excluded: chain B residue 1350 GLU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 231 optimal weight: 0.6980 chunk 157 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 206 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 236 optimal weight: 0.5980 chunk 191 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 chunk 249 optimal weight: 0.5980 chunk 70 optimal weight: 0.3980 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 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 GLN ** B1369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23602 Z= 0.237 Angle : 0.559 12.110 31913 Z= 0.287 Chirality : 0.040 0.224 3766 Planarity : 0.004 0.047 4009 Dihedral : 6.949 167.976 3084 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.86 % Favored : 92.11 % Rotamer: Outliers : 3.16 % Allowed : 15.80 % Favored : 81.05 % 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: 0.33 (0.16), residues: 2863 helix: 1.37 (0.12), residues: 1868 sheet: -1.21 (0.55), residues: 94 loop : -2.15 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 173 HIS 0.007 0.001 HIS B1369 PHE 0.031 0.001 PHE A1069 TYR 0.024 0.001 TYR A1201 ARG 0.008 0.000 ARG A1061 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 569 time to evaluate : 3.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8616 (t) cc_final: 0.8356 (m) REVERT: A 78 GLN cc_start: 0.7661 (tt0) cc_final: 0.7319 (tt0) REVERT: A 86 LEU cc_start: 0.7343 (mt) cc_final: 0.7087 (mm) REVERT: A 153 ARG cc_start: 0.7585 (mtm-85) cc_final: 0.7368 (mtm-85) REVERT: A 184 LEU cc_start: 0.8437 (mt) cc_final: 0.8208 (mp) REVERT: A 253 LYS cc_start: 0.7438 (mptt) cc_final: 0.7195 (mptt) REVERT: A 343 ILE cc_start: 0.8493 (pt) cc_final: 0.8122 (pt) REVERT: A 347 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.7850 (p0) REVERT: A 368 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7247 (mt-10) REVERT: A 487 ASN cc_start: 0.8367 (t0) cc_final: 0.8122 (t0) REVERT: A 515 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6912 (tm-30) REVERT: A 523 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6574 (mm-30) REVERT: A 559 ARG cc_start: 0.7525 (mtp85) cc_final: 0.7105 (mtm110) REVERT: A 563 PHE cc_start: 0.7706 (t80) cc_final: 0.7460 (t80) REVERT: A 566 CYS cc_start: 0.8054 (m) cc_final: 0.7723 (m) REVERT: A 575 LYS cc_start: 0.8478 (mptt) cc_final: 0.8214 (mmtt) REVERT: A 576 LYS cc_start: 0.7722 (tppt) cc_final: 0.6984 (tppt) REVERT: A 578 ILE cc_start: 0.7960 (mm) cc_final: 0.7659 (mm) REVERT: A 622 SER cc_start: 0.8117 (p) cc_final: 0.7897 (t) REVERT: A 636 LEU cc_start: 0.7990 (mt) cc_final: 0.7737 (mp) REVERT: A 671 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7133 (tm-30) REVERT: A 673 GLN cc_start: 0.6835 (tp40) cc_final: 0.6356 (tp40) REVERT: A 738 ASP cc_start: 0.7067 (p0) cc_final: 0.6768 (p0) REVERT: A 806 ASP cc_start: 0.7480 (m-30) cc_final: 0.7226 (m-30) REVERT: A 830 ASP cc_start: 0.7659 (t0) cc_final: 0.7349 (t70) REVERT: A 862 ASN cc_start: 0.7876 (m-40) cc_final: 0.7632 (m-40) REVERT: A 866 LYS cc_start: 0.8254 (ttmm) cc_final: 0.7948 (ttmm) REVERT: A 889 MET cc_start: 0.7481 (tmm) cc_final: 0.6715 (tmm) REVERT: A 902 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6811 (mm-30) REVERT: A 1022 CYS cc_start: 0.7320 (t) cc_final: 0.6988 (t) REVERT: A 1074 THR cc_start: 0.8355 (t) cc_final: 0.8123 (p) REVERT: A 1080 PHE cc_start: 0.7461 (m-80) cc_final: 0.7050 (m-80) REVERT: A 1093 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7967 (tm-30) REVERT: A 1125 ASP cc_start: 0.7825 (t0) cc_final: 0.7585 (t0) REVERT: A 1128 GLU cc_start: 0.7502 (tp30) cc_final: 0.7004 (tp30) REVERT: A 1179 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7223 (tp30) REVERT: A 1196 GLU cc_start: 0.8139 (tt0) cc_final: 0.7654 (tm-30) REVERT: A 1199 PHE cc_start: 0.8568 (t80) cc_final: 0.8255 (t80) REVERT: A 1201 TYR cc_start: 0.8527 (t80) cc_final: 0.7981 (t80) REVERT: A 1204 GLU cc_start: 0.7863 (tp30) cc_final: 0.7453 (mm-30) REVERT: A 1290 ILE cc_start: 0.8654 (mm) cc_final: 0.8442 (mm) REVERT: A 1299 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8289 (mm) REVERT: A 1383 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8049 (mmtm) REVERT: B 120 ASP cc_start: 0.7388 (m-30) cc_final: 0.7030 (m-30) REVERT: B 183 ASP cc_start: 0.7882 (t70) cc_final: 0.7549 (t70) REVERT: B 199 SER cc_start: 0.8815 (m) cc_final: 0.8389 (p) REVERT: B 205 ARG cc_start: 0.8023 (mmm-85) cc_final: 0.7637 (mmm-85) REVERT: B 228 LYS cc_start: 0.8405 (ttmm) cc_final: 0.7997 (ttmm) REVERT: B 231 THR cc_start: 0.7999 (OUTLIER) cc_final: 0.7606 (p) REVERT: B 245 GLU cc_start: 0.6611 (mp0) cc_final: 0.6318 (mp0) REVERT: B 253 LYS cc_start: 0.7435 (mttm) cc_final: 0.6976 (mttm) REVERT: B 368 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: B 422 ASN cc_start: 0.7771 (m-40) cc_final: 0.7512 (m-40) REVERT: B 433 ARG cc_start: 0.8300 (mpt180) cc_final: 0.8079 (mpt180) REVERT: B 488 LEU cc_start: 0.8165 (mp) cc_final: 0.7826 (mt) REVERT: B 503 LYS cc_start: 0.8297 (ttmm) cc_final: 0.8074 (ttmm) REVERT: B 508 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7875 (tm-30) REVERT: B 551 MET cc_start: 0.7247 (mtp) cc_final: 0.6755 (mtp) REVERT: B 575 LYS cc_start: 0.8764 (mmmt) cc_final: 0.8504 (mmmt) REVERT: B 625 ASN cc_start: 0.8526 (m-40) cc_final: 0.8186 (m110) REVERT: B 626 GLU cc_start: 0.7983 (tt0) cc_final: 0.7696 (tt0) REVERT: B 663 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7447 (tm-30) REVERT: B 721 MET cc_start: 0.8287 (ttt) cc_final: 0.8051 (ttp) REVERT: B 737 LYS cc_start: 0.8067 (tppt) cc_final: 0.7761 (mppt) REVERT: B 753 ASP cc_start: 0.7741 (m-30) cc_final: 0.7296 (m-30) REVERT: B 754 LYS cc_start: 0.8416 (tptp) cc_final: 0.8162 (tptp) REVERT: B 779 SER cc_start: 0.8683 (m) cc_final: 0.8236 (p) REVERT: B 837 MET cc_start: 0.7545 (mmp) cc_final: 0.7158 (mmt) REVERT: B 1052 LYS cc_start: 0.7911 (ptpt) cc_final: 0.7648 (mttp) REVERT: B 1128 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7816 (tm-30) REVERT: B 1132 LYS cc_start: 0.7928 (tppt) cc_final: 0.7549 (tppt) REVERT: B 1133 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7695 (tp) REVERT: B 1147 GLN cc_start: 0.8233 (tt0) cc_final: 0.7885 (tt0) REVERT: B 1157 GLU cc_start: 0.7807 (tp30) cc_final: 0.7409 (tp30) REVERT: B 1165 LEU cc_start: 0.8256 (tp) cc_final: 0.8002 (tt) REVERT: B 1180 ASN cc_start: 0.8108 (m110) cc_final: 0.7881 (m-40) REVERT: B 1183 LYS cc_start: 0.8172 (tptp) cc_final: 0.7880 (tptm) REVERT: B 1186 ARG cc_start: 0.7981 (mmm160) cc_final: 0.7767 (mmm160) REVERT: B 1191 MET cc_start: 0.7128 (mtm) cc_final: 0.6580 (mtm) REVERT: B 1199 PHE cc_start: 0.8496 (t80) cc_final: 0.8094 (t80) REVERT: B 1200 GLU cc_start: 0.7681 (tp30) cc_final: 0.7295 (tp30) REVERT: B 1204 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7165 (mt-10) REVERT: B 1214 THR cc_start: 0.7734 (p) cc_final: 0.7333 (t) REVERT: B 1218 PHE cc_start: 0.7471 (m-80) cc_final: 0.7058 (t80) REVERT: B 1288 PHE cc_start: 0.8577 (m-80) cc_final: 0.8320 (m-80) REVERT: B 1350 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.6027 (pm20) REVERT: C 101 MET cc_start: 0.7539 (tmm) cc_final: 0.7257 (tmm) REVERT: D 22 LEU cc_start: 0.7643 (mp) cc_final: 0.7269 (mp) REVERT: D 111 MET cc_start: 0.7197 (tmm) cc_final: 0.6733 (tmm) REVERT: D 173 TRP cc_start: 0.7851 (t60) cc_final: 0.7504 (t60) outliers start: 84 outliers final: 62 residues processed: 617 average time/residue: 0.3634 time to fit residues: 346.9060 Evaluate side-chains 630 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 561 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 768 TRP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1378 ASN Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 978 LYS Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1133 LEU Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1194 GLN Chi-restraints excluded: chain B residue 1198 ILE Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain B residue 1300 ASN Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1340 LEU Chi-restraints excluded: chain B residue 1350 GLU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 93 optimal weight: 0.5980 chunk 249 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 162 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 277 optimal weight: 0.8980 chunk 230 optimal weight: 0.8980 chunk 128 optimal weight: 0.0770 chunk 23 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 GLN ** B1369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23602 Z= 0.218 Angle : 0.566 12.539 31913 Z= 0.288 Chirality : 0.040 0.225 3766 Planarity : 0.004 0.047 4009 Dihedral : 6.932 167.864 3084 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.03 % Favored : 91.93 % Rotamer: Outliers : 3.05 % Allowed : 16.81 % Favored : 80.14 % 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: 0.37 (0.16), residues: 2863 helix: 1.40 (0.12), residues: 1873 sheet: -1.22 (0.55), residues: 94 loop : -2.15 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 173 HIS 0.008 0.001 HIS B1369 PHE 0.025 0.002 PHE A1069 TYR 0.039 0.001 TYR A1201 ARG 0.010 0.000 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 563 time to evaluate : 2.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8608 (t) cc_final: 0.8347 (m) REVERT: A 78 GLN cc_start: 0.7652 (tt0) cc_final: 0.7274 (tt0) REVERT: A 86 LEU cc_start: 0.7309 (mt) cc_final: 0.7059 (mm) REVERT: A 153 ARG cc_start: 0.7582 (mtm-85) cc_final: 0.7368 (mtm-85) REVERT: A 184 LEU cc_start: 0.8437 (mt) cc_final: 0.8200 (mp) REVERT: A 253 LYS cc_start: 0.7428 (mptt) cc_final: 0.7185 (mptt) REVERT: A 343 ILE cc_start: 0.8472 (pt) cc_final: 0.8090 (pt) REVERT: A 347 ASN cc_start: 0.8243 (p0) cc_final: 0.7846 (p0) REVERT: A 368 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7244 (mt-10) REVERT: A 487 ASN cc_start: 0.8377 (t0) cc_final: 0.8148 (t0) REVERT: A 515 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6897 (tm-30) REVERT: A 523 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6525 (mm-30) REVERT: A 559 ARG cc_start: 0.7524 (mtp85) cc_final: 0.7104 (mtm110) REVERT: A 563 PHE cc_start: 0.7690 (t80) cc_final: 0.7452 (t80) REVERT: A 566 CYS cc_start: 0.8048 (m) cc_final: 0.7713 (m) REVERT: A 575 LYS cc_start: 0.8492 (mptt) cc_final: 0.8223 (mmtt) REVERT: A 576 LYS cc_start: 0.7764 (tppt) cc_final: 0.7020 (tppt) REVERT: A 578 ILE cc_start: 0.7949 (mm) cc_final: 0.7622 (mm) REVERT: A 622 SER cc_start: 0.8113 (p) cc_final: 0.7871 (t) REVERT: A 636 LEU cc_start: 0.7981 (mt) cc_final: 0.7734 (mp) REVERT: A 671 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7122 (tm-30) REVERT: A 673 GLN cc_start: 0.6826 (tp40) cc_final: 0.6350 (tp40) REVERT: A 738 ASP cc_start: 0.7048 (p0) cc_final: 0.6760 (p0) REVERT: A 806 ASP cc_start: 0.7462 (m-30) cc_final: 0.7229 (m-30) REVERT: A 830 ASP cc_start: 0.7653 (t0) cc_final: 0.7294 (t70) REVERT: A 835 THR cc_start: 0.8143 (t) cc_final: 0.7940 (t) REVERT: A 862 ASN cc_start: 0.7835 (m-40) cc_final: 0.7597 (m-40) REVERT: A 866 LYS cc_start: 0.8254 (ttmm) cc_final: 0.7948 (ttmm) REVERT: A 889 MET cc_start: 0.7486 (tmm) cc_final: 0.6715 (tmm) REVERT: A 902 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6779 (mm-30) REVERT: A 1022 CYS cc_start: 0.7103 (t) cc_final: 0.6797 (t) REVERT: A 1074 THR cc_start: 0.8330 (t) cc_final: 0.8096 (p) REVERT: A 1080 PHE cc_start: 0.7473 (m-80) cc_final: 0.7083 (m-80) REVERT: A 1093 GLN cc_start: 0.8416 (tm-30) cc_final: 0.7937 (tm-30) REVERT: A 1125 ASP cc_start: 0.7803 (t0) cc_final: 0.7573 (t0) REVERT: A 1128 GLU cc_start: 0.7503 (tp30) cc_final: 0.7002 (tp30) REVERT: A 1179 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7185 (tp30) REVERT: A 1196 GLU cc_start: 0.8124 (tt0) cc_final: 0.7640 (tm-30) REVERT: A 1199 PHE cc_start: 0.8536 (t80) cc_final: 0.8238 (t80) REVERT: A 1204 GLU cc_start: 0.7850 (tp30) cc_final: 0.7437 (mm-30) REVERT: A 1278 ASP cc_start: 0.3635 (OUTLIER) cc_final: 0.3394 (t70) REVERT: A 1290 ILE cc_start: 0.8674 (mm) cc_final: 0.8474 (mm) REVERT: A 1299 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8262 (mm) REVERT: A 1383 LYS cc_start: 0.8414 (mmtt) cc_final: 0.8031 (mmtm) REVERT: B 120 ASP cc_start: 0.7394 (m-30) cc_final: 0.7027 (m-30) REVERT: B 174 ARG cc_start: 0.7950 (ttt180) cc_final: 0.7706 (ttt180) REVERT: B 183 ASP cc_start: 0.7904 (t70) cc_final: 0.7656 (t70) REVERT: B 199 SER cc_start: 0.8812 (m) cc_final: 0.8395 (p) REVERT: B 205 ARG cc_start: 0.8054 (mmm-85) cc_final: 0.7658 (mmm-85) REVERT: B 228 LYS cc_start: 0.8346 (ttmm) cc_final: 0.7937 (ttmm) REVERT: B 231 THR cc_start: 0.7992 (OUTLIER) cc_final: 0.7593 (p) REVERT: B 245 GLU cc_start: 0.6611 (mp0) cc_final: 0.6271 (mp0) REVERT: B 253 LYS cc_start: 0.7439 (mttm) cc_final: 0.6978 (mttm) REVERT: B 368 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: B 422 ASN cc_start: 0.7766 (m-40) cc_final: 0.7505 (m-40) REVERT: B 488 LEU cc_start: 0.8145 (mp) cc_final: 0.7813 (mt) REVERT: B 503 LYS cc_start: 0.8288 (ttmm) cc_final: 0.8084 (ttmm) REVERT: B 508 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8096 (tm-30) REVERT: B 551 MET cc_start: 0.7224 (mtp) cc_final: 0.6735 (mtp) REVERT: B 575 LYS cc_start: 0.8764 (mmmt) cc_final: 0.8508 (mmmt) REVERT: B 626 GLU cc_start: 0.7993 (tt0) cc_final: 0.7670 (tt0) REVERT: B 663 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7433 (tm-30) REVERT: B 737 LYS cc_start: 0.8072 (tppt) cc_final: 0.7759 (mppt) REVERT: B 753 ASP cc_start: 0.7723 (m-30) cc_final: 0.7286 (m-30) REVERT: B 754 LYS cc_start: 0.8401 (tptp) cc_final: 0.8150 (tptp) REVERT: B 779 SER cc_start: 0.8686 (m) cc_final: 0.8257 (p) REVERT: B 837 MET cc_start: 0.7534 (mmp) cc_final: 0.7162 (mmt) REVERT: B 1052 LYS cc_start: 0.7892 (ptpt) cc_final: 0.7602 (mttp) REVERT: B 1054 GLU cc_start: 0.7019 (tm-30) cc_final: 0.6791 (tm-30) REVERT: B 1089 LYS cc_start: 0.8219 (ptpt) cc_final: 0.7764 (ptpp) REVERT: B 1128 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7805 (tm-30) REVERT: B 1132 LYS cc_start: 0.7920 (tppt) cc_final: 0.7540 (tppt) REVERT: B 1133 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7682 (tp) REVERT: B 1147 GLN cc_start: 0.8239 (tt0) cc_final: 0.7918 (tt0) REVERT: B 1156 LYS cc_start: 0.8057 (ttmt) cc_final: 0.7807 (ttmm) REVERT: B 1157 GLU cc_start: 0.7801 (tp30) cc_final: 0.7452 (tp30) REVERT: B 1165 LEU cc_start: 0.8249 (tp) cc_final: 0.7998 (tt) REVERT: B 1180 ASN cc_start: 0.8107 (m110) cc_final: 0.7885 (m-40) REVERT: B 1183 LYS cc_start: 0.8165 (tptp) cc_final: 0.7851 (tptm) REVERT: B 1191 MET cc_start: 0.7093 (mtm) cc_final: 0.6517 (mtm) REVERT: B 1199 PHE cc_start: 0.8466 (t80) cc_final: 0.8069 (t80) REVERT: B 1200 GLU cc_start: 0.7657 (tp30) cc_final: 0.7274 (tp30) REVERT: B 1204 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7161 (mt-10) REVERT: B 1214 THR cc_start: 0.7719 (p) cc_final: 0.7315 (t) REVERT: B 1218 PHE cc_start: 0.7464 (m-80) cc_final: 0.7051 (t80) REVERT: B 1288 PHE cc_start: 0.8565 (m-80) cc_final: 0.8313 (m-80) REVERT: B 1350 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.6047 (pm20) REVERT: C 101 MET cc_start: 0.7588 (tmm) cc_final: 0.7317 (tmm) REVERT: D 22 LEU cc_start: 0.7628 (mp) cc_final: 0.7255 (mp) REVERT: D 111 MET cc_start: 0.7189 (tmm) cc_final: 0.6725 (tmm) REVERT: D 173 TRP cc_start: 0.7844 (t60) cc_final: 0.7512 (t60) outliers start: 81 outliers final: 60 residues processed: 611 average time/residue: 0.3709 time to fit residues: 350.5052 Evaluate side-chains 621 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 554 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 768 TRP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1253 ASP Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1278 ASP Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 978 LYS Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1133 LEU Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1194 GLN Chi-restraints excluded: chain B residue 1198 ILE Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain B residue 1300 ASN Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1350 GLU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 267 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 158 optimal weight: 0.3980 chunk 202 optimal weight: 0.7980 chunk 157 optimal weight: 0.0870 chunk 233 optimal weight: 0.6980 chunk 155 optimal weight: 0.4980 chunk 276 optimal weight: 0.9990 chunk 173 optimal weight: 0.0770 chunk 168 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23602 Z= 0.181 Angle : 0.561 13.689 31913 Z= 0.284 Chirality : 0.039 0.260 3766 Planarity : 0.004 0.044 4009 Dihedral : 6.870 167.090 3084 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.68 % Favored : 92.28 % Rotamer: Outliers : 2.90 % Allowed : 17.37 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.16), residues: 2863 helix: 1.52 (0.12), residues: 1855 sheet: -1.18 (0.56), residues: 94 loop : -2.08 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 173 HIS 0.008 0.001 HIS B1369 PHE 0.027 0.001 PHE A1069 TYR 0.056 0.001 TYR A1201 ARG 0.009 0.000 ARG A1061 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 560 time to evaluate : 2.808 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 12 VAL cc_start: 0.8619 (t) cc_final: 0.8369 (m) REVERT: A 78 GLN cc_start: 0.7614 (tt0) cc_final: 0.7221 (tt0) REVERT: A 86 LEU cc_start: 0.7316 (mt) cc_final: 0.7072 (mm) REVERT: A 153 ARG cc_start: 0.7592 (mtm-85) cc_final: 0.7382 (mtm-85) REVERT: A 253 LYS cc_start: 0.7439 (mptt) cc_final: 0.7187 (mptt) REVERT: A 343 ILE cc_start: 0.8459 (pt) cc_final: 0.8145 (pt) REVERT: A 347 ASN cc_start: 0.8199 (OUTLIER) cc_final: 0.7803 (p0) REVERT: A 368 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7214 (mt-10) REVERT: A 487 ASN cc_start: 0.8371 (t0) cc_final: 0.8157 (t0) REVERT: A 515 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6868 (tm-30) REVERT: A 523 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6453 (mm-30) REVERT: A 559 ARG cc_start: 0.7501 (mtp85) cc_final: 0.7075 (mtm110) REVERT: A 563 PHE cc_start: 0.7671 (t80) cc_final: 0.7419 (t80) REVERT: A 566 CYS cc_start: 0.8042 (m) cc_final: 0.7708 (m) REVERT: A 575 LYS cc_start: 0.8485 (mptt) cc_final: 0.8218 (mmtt) REVERT: A 576 LYS cc_start: 0.7782 (tppt) cc_final: 0.6941 (tppt) REVERT: A 578 ILE cc_start: 0.7915 (mm) cc_final: 0.7377 (mt) REVERT: A 636 LEU cc_start: 0.7960 (mt) cc_final: 0.7730 (mp) REVERT: A 671 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7093 (tm-30) REVERT: A 673 GLN cc_start: 0.6783 (tp40) cc_final: 0.6314 (tp40) REVERT: A 738 ASP cc_start: 0.7071 (p0) cc_final: 0.6775 (p0) REVERT: A 806 ASP cc_start: 0.7437 (m-30) cc_final: 0.7196 (m-30) REVERT: A 830 ASP cc_start: 0.7629 (t0) cc_final: 0.7268 (t70) REVERT: A 835 THR cc_start: 0.8137 (t) cc_final: 0.7775 (p) REVERT: A 862 ASN cc_start: 0.7826 (m-40) cc_final: 0.7556 (m-40) REVERT: A 866 LYS cc_start: 0.8243 (ttmm) cc_final: 0.7936 (ttmm) REVERT: A 889 MET cc_start: 0.7444 (tmm) cc_final: 0.6628 (tmm) REVERT: A 902 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6741 (mm-30) REVERT: A 919 GLN cc_start: 0.6025 (mm-40) cc_final: 0.5705 (mm-40) REVERT: A 1080 PHE cc_start: 0.7454 (m-80) cc_final: 0.7044 (m-80) REVERT: A 1093 GLN cc_start: 0.8416 (tm-30) cc_final: 0.7906 (tm-30) REVERT: A 1128 GLU cc_start: 0.7491 (tp30) cc_final: 0.6973 (tp30) REVERT: A 1179 GLU cc_start: 0.7380 (tm-30) cc_final: 0.7155 (tp30) REVERT: A 1199 PHE cc_start: 0.8486 (t80) cc_final: 0.8189 (t80) REVERT: A 1204 GLU cc_start: 0.7835 (tp30) cc_final: 0.7367 (mm-30) REVERT: A 1263 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7890 (mm-30) REVERT: A 1278 ASP cc_start: 0.3614 (OUTLIER) cc_final: 0.3387 (t70) REVERT: A 1290 ILE cc_start: 0.8680 (mm) cc_final: 0.8442 (mm) REVERT: A 1299 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8278 (mm) REVERT: A 1383 LYS cc_start: 0.8382 (mmtt) cc_final: 0.7993 (mmtm) REVERT: B 120 ASP cc_start: 0.7383 (m-30) cc_final: 0.7008 (m-30) REVERT: B 183 ASP cc_start: 0.7891 (t70) cc_final: 0.7648 (t70) REVERT: B 199 SER cc_start: 0.8772 (m) cc_final: 0.8375 (p) REVERT: B 205 ARG cc_start: 0.8021 (mmm-85) cc_final: 0.7608 (mmm-85) REVERT: B 228 LYS cc_start: 0.8277 (ttmm) cc_final: 0.7876 (ttmm) REVERT: B 245 GLU cc_start: 0.6594 (mp0) cc_final: 0.6231 (mp0) REVERT: B 253 LYS cc_start: 0.7461 (mttm) cc_final: 0.6970 (mttm) REVERT: B 368 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: B 422 ASN cc_start: 0.7753 (m-40) cc_final: 0.7502 (m-40) REVERT: B 488 LEU cc_start: 0.8104 (mp) cc_final: 0.7760 (mt) REVERT: B 503 LYS cc_start: 0.8293 (ttmm) cc_final: 0.8093 (ttmm) REVERT: B 508 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7918 (tm-30) REVERT: B 538 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7434 (p0) REVERT: B 551 MET cc_start: 0.7179 (mtp) cc_final: 0.6720 (mtp) REVERT: B 575 LYS cc_start: 0.8752 (mmmt) cc_final: 0.8501 (mmmt) REVERT: B 626 GLU cc_start: 0.8006 (tt0) cc_final: 0.7658 (tt0) REVERT: B 663 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7434 (tm-30) REVERT: B 737 LYS cc_start: 0.8063 (tppt) cc_final: 0.7788 (mppt) REVERT: B 753 ASP cc_start: 0.7722 (m-30) cc_final: 0.7229 (m-30) REVERT: B 754 LYS cc_start: 0.8369 (tptp) cc_final: 0.8113 (tptp) REVERT: B 775 ASN cc_start: 0.8450 (m-40) cc_final: 0.8228 (m-40) REVERT: B 779 SER cc_start: 0.8633 (m) cc_final: 0.8242 (p) REVERT: B 837 MET cc_start: 0.7492 (mmp) cc_final: 0.7156 (mmt) REVERT: B 989 LYS cc_start: 0.5441 (OUTLIER) cc_final: 0.4653 (pttt) REVERT: B 1052 LYS cc_start: 0.7863 (ptpt) cc_final: 0.7565 (mttp) REVERT: B 1054 GLU cc_start: 0.6987 (tm-30) cc_final: 0.6718 (tm-30) REVERT: B 1089 LYS cc_start: 0.8181 (ptpt) cc_final: 0.7729 (ptpp) REVERT: B 1128 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7791 (tm-30) REVERT: B 1132 LYS cc_start: 0.7896 (tppt) cc_final: 0.7516 (tppt) REVERT: B 1133 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7644 (tp) REVERT: B 1147 GLN cc_start: 0.8247 (tt0) cc_final: 0.7999 (tt0) REVERT: B 1156 LYS cc_start: 0.7966 (ttmt) cc_final: 0.7710 (ttmm) REVERT: B 1157 GLU cc_start: 0.7781 (tp30) cc_final: 0.7456 (tp30) REVERT: B 1165 LEU cc_start: 0.8213 (tp) cc_final: 0.7994 (tt) REVERT: B 1180 ASN cc_start: 0.8064 (m110) cc_final: 0.7848 (m-40) REVERT: B 1183 LYS cc_start: 0.8128 (tptp) cc_final: 0.7836 (tptm) REVERT: B 1191 MET cc_start: 0.7012 (mtm) cc_final: 0.6424 (mtm) REVERT: B 1199 PHE cc_start: 0.8441 (t80) cc_final: 0.8123 (t80) REVERT: B 1200 GLU cc_start: 0.7635 (tp30) cc_final: 0.7238 (tp30) REVERT: B 1204 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7161 (mt-10) REVERT: B 1214 THR cc_start: 0.7689 (OUTLIER) cc_final: 0.7291 (t) REVERT: B 1218 PHE cc_start: 0.7439 (m-80) cc_final: 0.7030 (t80) REVERT: B 1288 PHE cc_start: 0.8543 (m-80) cc_final: 0.8285 (m-80) REVERT: B 1350 GLU cc_start: 0.6304 (OUTLIER) cc_final: 0.5984 (pm20) REVERT: D 22 LEU cc_start: 0.7616 (mp) cc_final: 0.7257 (mp) REVERT: D 111 MET cc_start: 0.7181 (tmm) cc_final: 0.6730 (tmm) REVERT: D 173 TRP cc_start: 0.7819 (t60) cc_final: 0.7538 (t60) outliers start: 77 outliers final: 60 residues processed: 603 average time/residue: 0.3709 time to fit residues: 345.4415 Evaluate side-chains 626 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 556 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 768 TRP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1253 ASP Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1278 ASP Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1378 ASN Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 978 LYS Chi-restraints excluded: chain B residue 989 LYS Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1133 LEU Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1194 GLN Chi-restraints excluded: chain B residue 1198 ILE Chi-restraints excluded: chain B residue 1214 THR Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain B residue 1300 ASN Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1350 GLU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 171 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 53 optimal weight: 0.3980 chunk 175 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 217 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 GLN ** B1369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23602 Z= 0.296 Angle : 0.603 14.413 31913 Z= 0.306 Chirality : 0.041 0.236 3766 Planarity : 0.004 0.058 4009 Dihedral : 6.971 168.756 3084 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.56 % Favored : 91.41 % Rotamer: Outliers : 3.23 % Allowed : 17.68 % Favored : 79.09 % 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: 0.22 (0.16), residues: 2863 helix: 1.28 (0.12), residues: 1868 sheet: -1.30 (0.55), residues: 94 loop : -2.17 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 173 HIS 0.008 0.001 HIS B1369 PHE 0.026 0.002 PHE A1158 TYR 0.050 0.002 TYR A1201 ARG 0.010 0.000 ARG A1061 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 566 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8638 (t) cc_final: 0.8372 (m) REVERT: A 78 GLN cc_start: 0.7675 (tt0) cc_final: 0.7308 (tt0) REVERT: A 86 LEU cc_start: 0.7411 (mt) cc_final: 0.7148 (mm) REVERT: A 253 LYS cc_start: 0.7445 (mptt) cc_final: 0.7193 (mptt) REVERT: A 347 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.7854 (p0) REVERT: A 368 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7219 (mt-10) REVERT: A 487 ASN cc_start: 0.8369 (t0) cc_final: 0.8141 (t0) REVERT: A 515 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6899 (tm-30) REVERT: A 523 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6629 (mm-30) REVERT: A 559 ARG cc_start: 0.7542 (mtp85) cc_final: 0.7183 (mtm110) REVERT: A 563 PHE cc_start: 0.7701 (t80) cc_final: 0.7434 (t80) REVERT: A 566 CYS cc_start: 0.8061 (m) cc_final: 0.7747 (m) REVERT: A 575 LYS cc_start: 0.8493 (mptt) cc_final: 0.8224 (mmtt) REVERT: A 576 LYS cc_start: 0.7808 (tppt) cc_final: 0.7089 (tppt) REVERT: A 578 ILE cc_start: 0.7955 (mm) cc_final: 0.7644 (mm) REVERT: A 622 SER cc_start: 0.8114 (p) cc_final: 0.7887 (t) REVERT: A 636 LEU cc_start: 0.7975 (mt) cc_final: 0.7712 (mp) REVERT: A 671 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7144 (tm-30) REVERT: A 673 GLN cc_start: 0.6854 (tp40) cc_final: 0.6369 (tp40) REVERT: A 738 ASP cc_start: 0.7050 (p0) cc_final: 0.6768 (p0) REVERT: A 806 ASP cc_start: 0.7490 (m-30) cc_final: 0.7249 (m-30) REVERT: A 830 ASP cc_start: 0.7656 (t0) cc_final: 0.7299 (t70) REVERT: A 835 THR cc_start: 0.8179 (t) cc_final: 0.7976 (t) REVERT: A 862 ASN cc_start: 0.7869 (m-40) cc_final: 0.7633 (m-40) REVERT: A 866 LYS cc_start: 0.8302 (ttmm) cc_final: 0.7990 (ttmm) REVERT: A 889 MET cc_start: 0.7491 (tmm) cc_final: 0.7242 (tmm) REVERT: A 902 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6744 (mm-30) REVERT: A 919 GLN cc_start: 0.6351 (mm-40) cc_final: 0.5548 (mm-40) REVERT: A 1022 CYS cc_start: 0.7236 (t) cc_final: 0.5062 (t) REVERT: A 1066 GLU cc_start: 0.8215 (tp30) cc_final: 0.7988 (tp30) REVERT: A 1080 PHE cc_start: 0.7485 (m-80) cc_final: 0.7164 (m-80) REVERT: A 1128 GLU cc_start: 0.7502 (tp30) cc_final: 0.7026 (tp30) REVERT: A 1179 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7154 (tp30) REVERT: A 1199 PHE cc_start: 0.8492 (t80) cc_final: 0.8198 (t80) REVERT: A 1204 GLU cc_start: 0.7836 (tp30) cc_final: 0.7389 (mm-30) REVERT: A 1263 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7943 (mm-30) REVERT: A 1278 ASP cc_start: 0.3562 (OUTLIER) cc_final: 0.3336 (t70) REVERT: A 1290 ILE cc_start: 0.8705 (mm) cc_final: 0.8495 (mm) REVERT: A 1299 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8328 (mm) REVERT: A 1336 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6595 (mp0) REVERT: A 1383 LYS cc_start: 0.8447 (mmtt) cc_final: 0.8051 (mmtm) REVERT: B 120 ASP cc_start: 0.7405 (m-30) cc_final: 0.7043 (m-30) REVERT: B 183 ASP cc_start: 0.7887 (t70) cc_final: 0.7547 (t70) REVERT: B 199 SER cc_start: 0.8806 (m) cc_final: 0.8406 (p) REVERT: B 205 ARG cc_start: 0.8064 (mmm-85) cc_final: 0.7633 (mmm-85) REVERT: B 228 LYS cc_start: 0.8397 (ttmm) cc_final: 0.7943 (ttmm) REVERT: B 231 THR cc_start: 0.7971 (OUTLIER) cc_final: 0.7609 (p) REVERT: B 245 GLU cc_start: 0.6633 (mp0) cc_final: 0.6312 (mp0) REVERT: B 368 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: B 375 GLN cc_start: 0.8066 (pt0) cc_final: 0.7447 (pt0) REVERT: B 422 ASN cc_start: 0.7775 (m-40) cc_final: 0.7342 (m-40) REVERT: B 433 ARG cc_start: 0.8296 (mpt180) cc_final: 0.8072 (mpt180) REVERT: B 488 LEU cc_start: 0.8113 (mp) cc_final: 0.7776 (mt) REVERT: B 508 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7967 (tm-30) REVERT: B 575 LYS cc_start: 0.8766 (mmmt) cc_final: 0.8510 (mmmt) REVERT: B 626 GLU cc_start: 0.8055 (tt0) cc_final: 0.7709 (tt0) REVERT: B 663 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7434 (tm-30) REVERT: B 737 LYS cc_start: 0.8081 (tppt) cc_final: 0.7844 (mppt) REVERT: B 753 ASP cc_start: 0.7734 (m-30) cc_final: 0.7311 (m-30) REVERT: B 754 LYS cc_start: 0.8420 (tptp) cc_final: 0.8166 (tptp) REVERT: B 779 SER cc_start: 0.8534 (m) cc_final: 0.8239 (p) REVERT: B 837 MET cc_start: 0.7519 (mmp) cc_final: 0.7253 (mmp) REVERT: B 1052 LYS cc_start: 0.7922 (ptpt) cc_final: 0.7652 (mttp) REVERT: B 1089 LYS cc_start: 0.8178 (ptpt) cc_final: 0.7732 (ptpp) REVERT: B 1128 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7821 (tm-30) REVERT: B 1132 LYS cc_start: 0.7945 (tppt) cc_final: 0.7567 (tppt) REVERT: B 1133 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7691 (tp) REVERT: B 1147 GLN cc_start: 0.8272 (tt0) cc_final: 0.7908 (tt0) REVERT: B 1156 LYS cc_start: 0.8103 (ttmt) cc_final: 0.7843 (ttmm) REVERT: B 1157 GLU cc_start: 0.7816 (tp30) cc_final: 0.7411 (tp30) REVERT: B 1165 LEU cc_start: 0.8253 (tp) cc_final: 0.8006 (tt) REVERT: B 1180 ASN cc_start: 0.8144 (m110) cc_final: 0.7939 (m-40) REVERT: B 1183 LYS cc_start: 0.8188 (tptp) cc_final: 0.7898 (tptm) REVERT: B 1191 MET cc_start: 0.7149 (mtm) cc_final: 0.6602 (mtm) REVERT: B 1199 PHE cc_start: 0.8496 (t80) cc_final: 0.8077 (t80) REVERT: B 1200 GLU cc_start: 0.7689 (tp30) cc_final: 0.7294 (tp30) REVERT: B 1204 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7181 (mt-10) REVERT: B 1214 THR cc_start: 0.7758 (OUTLIER) cc_final: 0.7365 (t) REVERT: B 1218 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.7100 (t80) REVERT: B 1276 LEU cc_start: 0.8613 (tp) cc_final: 0.8368 (tt) REVERT: B 1288 PHE cc_start: 0.8585 (m-80) cc_final: 0.8363 (m-80) REVERT: B 1350 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.6039 (pm20) REVERT: B 1383 LYS cc_start: 0.8428 (mttt) cc_final: 0.8195 (mtmt) REVERT: D 22 LEU cc_start: 0.7636 (mp) cc_final: 0.7256 (mp) REVERT: D 101 MET cc_start: 0.8180 (mmt) cc_final: 0.7978 (mmt) REVERT: D 111 MET cc_start: 0.7215 (tmm) cc_final: 0.6773 (tmm) REVERT: D 173 TRP cc_start: 0.7829 (t60) cc_final: 0.7594 (t60) outliers start: 86 outliers final: 58 residues processed: 617 average time/residue: 0.4078 time to fit residues: 392.7256 Evaluate side-chains 624 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 556 time to evaluate : 2.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 768 TRP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1253 ASP Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1278 ASP Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1378 ASN Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 978 LYS Chi-restraints excluded: chain B residue 1023 ILE Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1133 LEU Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1193 GLU Chi-restraints excluded: chain B residue 1194 GLN Chi-restraints excluded: chain B residue 1198 ILE Chi-restraints excluded: chain B residue 1214 THR Chi-restraints excluded: chain B residue 1218 PHE Chi-restraints excluded: chain B residue 1300 ASN Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1350 GLU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 251 optimal weight: 0.9980 chunk 265 optimal weight: 7.9990 chunk 241 optimal weight: 0.6980 chunk 257 optimal weight: 1.9990 chunk 264 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 202 optimal weight: 0.5980 chunk 79 optimal weight: 0.1980 chunk 232 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 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 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 347 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 GLN ** B1369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23602 Z= 0.246 Angle : 0.606 15.165 31913 Z= 0.304 Chirality : 0.041 0.249 3766 Planarity : 0.004 0.055 4009 Dihedral : 6.968 167.759 3084 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.10 % Favored : 91.86 % Rotamer: Outliers : 2.90 % Allowed : 18.58 % Favored : 78.53 % 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: 0.22 (0.16), residues: 2863 helix: 1.28 (0.12), residues: 1868 sheet: -1.28 (0.55), residues: 94 loop : -2.17 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 173 HIS 0.009 0.001 HIS B1369 PHE 0.033 0.002 PHE A1158 TYR 0.046 0.001 TYR A1201 ARG 0.011 0.000 ARG A1061 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 564 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8618 (t) cc_final: 0.8353 (m) REVERT: A 78 GLN cc_start: 0.7654 (tt0) cc_final: 0.7288 (tt0) REVERT: A 86 LEU cc_start: 0.7445 (mt) cc_final: 0.7205 (mm) REVERT: A 88 ASN cc_start: 0.7005 (p0) cc_final: 0.6513 (p0) REVERT: A 153 ARG cc_start: 0.7582 (mtm-85) cc_final: 0.7369 (mtm-85) REVERT: A 253 LYS cc_start: 0.7445 (mptt) cc_final: 0.7194 (mptt) REVERT: A 347 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7864 (p0) REVERT: A 368 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7243 (mt-10) REVERT: A 487 ASN cc_start: 0.8333 (t0) cc_final: 0.8104 (t0) REVERT: A 515 GLU cc_start: 0.7270 (tm-30) cc_final: 0.6878 (tm-30) REVERT: A 523 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6548 (mm-30) REVERT: A 559 ARG cc_start: 0.7533 (mtp85) cc_final: 0.7113 (mtm110) REVERT: A 563 PHE cc_start: 0.7692 (t80) cc_final: 0.7439 (t80) REVERT: A 566 CYS cc_start: 0.8057 (m) cc_final: 0.7731 (m) REVERT: A 575 LYS cc_start: 0.8492 (mptt) cc_final: 0.8206 (mmtt) REVERT: A 576 LYS cc_start: 0.7829 (tppt) cc_final: 0.7126 (tppt) REVERT: A 578 ILE cc_start: 0.7950 (mm) cc_final: 0.7424 (mt) REVERT: A 606 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7370 (mmm) REVERT: A 636 LEU cc_start: 0.7969 (mt) cc_final: 0.7754 (mp) REVERT: A 671 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7110 (tm-30) REVERT: A 673 GLN cc_start: 0.6836 (tp40) cc_final: 0.6360 (tp40) REVERT: A 738 ASP cc_start: 0.7046 (p0) cc_final: 0.6763 (p0) REVERT: A 806 ASP cc_start: 0.7483 (m-30) cc_final: 0.7257 (m-30) REVERT: A 830 ASP cc_start: 0.7647 (t0) cc_final: 0.7286 (t70) REVERT: A 862 ASN cc_start: 0.7866 (m-40) cc_final: 0.7631 (m-40) REVERT: A 866 LYS cc_start: 0.8272 (ttmm) cc_final: 0.7952 (ttmm) REVERT: A 889 MET cc_start: 0.7476 (tmm) cc_final: 0.7226 (tmm) REVERT: A 902 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6734 (mm-30) REVERT: A 919 GLN cc_start: 0.6299 (mm-40) cc_final: 0.5552 (mm-40) REVERT: A 1022 CYS cc_start: 0.7282 (t) cc_final: 0.5139 (t) REVERT: A 1045 LYS cc_start: 0.7715 (mmtp) cc_final: 0.7147 (mmtm) REVERT: A 1080 PHE cc_start: 0.7483 (m-80) cc_final: 0.7145 (m-80) REVERT: A 1106 LYS cc_start: 0.7728 (tttp) cc_final: 0.7445 (tttp) REVERT: A 1110 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.6415 (mmt90) REVERT: A 1112 MET cc_start: 0.7774 (mtp) cc_final: 0.7557 (mtt) REVERT: A 1128 GLU cc_start: 0.7497 (tp30) cc_final: 0.7026 (tp30) REVERT: A 1179 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7105 (tp30) REVERT: A 1199 PHE cc_start: 0.8471 (t80) cc_final: 0.8180 (t80) REVERT: A 1204 GLU cc_start: 0.7817 (tp30) cc_final: 0.7371 (mm-30) REVERT: A 1263 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7944 (mm-30) REVERT: A 1278 ASP cc_start: 0.3577 (OUTLIER) cc_final: 0.3344 (t70) REVERT: A 1290 ILE cc_start: 0.8701 (mm) cc_final: 0.8492 (mm) REVERT: A 1299 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8303 (mm) REVERT: A 1336 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6569 (mp0) REVERT: A 1383 LYS cc_start: 0.8420 (mmtt) cc_final: 0.8028 (mmtm) REVERT: B 120 ASP cc_start: 0.7382 (m-30) cc_final: 0.7036 (m-30) REVERT: B 183 ASP cc_start: 0.7870 (t70) cc_final: 0.7645 (t70) REVERT: B 199 SER cc_start: 0.8796 (m) cc_final: 0.8340 (p) REVERT: B 205 ARG cc_start: 0.8042 (mmm-85) cc_final: 0.7624 (mmm-85) REVERT: B 228 LYS cc_start: 0.8340 (ttmm) cc_final: 0.7936 (ttmm) REVERT: B 231 THR cc_start: 0.7950 (OUTLIER) cc_final: 0.7578 (p) REVERT: B 245 GLU cc_start: 0.6648 (mp0) cc_final: 0.6318 (mp0) REVERT: B 368 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: B 375 GLN cc_start: 0.8064 (pt0) cc_final: 0.7473 (pt0) REVERT: B 422 ASN cc_start: 0.7772 (m-40) cc_final: 0.7402 (m-40) REVERT: B 433 ARG cc_start: 0.8294 (mpt180) cc_final: 0.8071 (mpt180) REVERT: B 508 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8022 (tm-30) REVERT: B 575 LYS cc_start: 0.8757 (mmmt) cc_final: 0.8544 (mmtp) REVERT: B 625 ASN cc_start: 0.8552 (m-40) cc_final: 0.8187 (m110) REVERT: B 626 GLU cc_start: 0.8055 (tt0) cc_final: 0.7713 (tt0) REVERT: B 663 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7442 (tm-30) REVERT: B 737 LYS cc_start: 0.8036 (tppt) cc_final: 0.7819 (mppt) REVERT: B 753 ASP cc_start: 0.7717 (m-30) cc_final: 0.7309 (m-30) REVERT: B 754 LYS cc_start: 0.8410 (tptp) cc_final: 0.8168 (tptp) REVERT: B 779 SER cc_start: 0.8492 (m) cc_final: 0.8257 (p) REVERT: B 837 MET cc_start: 0.7482 (mmp) cc_final: 0.7250 (mmp) REVERT: B 989 LYS cc_start: 0.5521 (OUTLIER) cc_final: 0.4793 (pttt) REVERT: B 1020 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7519 (mtm) REVERT: B 1052 LYS cc_start: 0.7899 (ptpt) cc_final: 0.7659 (mttp) REVERT: B 1089 LYS cc_start: 0.8184 (ptpt) cc_final: 0.7740 (ptpp) REVERT: B 1128 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7815 (tm-30) REVERT: B 1132 LYS cc_start: 0.7928 (tppt) cc_final: 0.7550 (tppt) REVERT: B 1133 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7685 (tp) REVERT: B 1147 GLN cc_start: 0.8235 (tt0) cc_final: 0.7890 (tt0) REVERT: B 1156 LYS cc_start: 0.8065 (ttmt) cc_final: 0.7811 (ttmm) REVERT: B 1157 GLU cc_start: 0.7797 (tp30) cc_final: 0.7433 (tp30) REVERT: B 1165 LEU cc_start: 0.8249 (tp) cc_final: 0.7987 (tt) REVERT: B 1180 ASN cc_start: 0.8118 (m110) cc_final: 0.7908 (m-40) REVERT: B 1183 LYS cc_start: 0.8165 (tptp) cc_final: 0.7863 (tptm) REVERT: B 1191 MET cc_start: 0.7110 (mtm) cc_final: 0.6535 (mtm) REVERT: B 1199 PHE cc_start: 0.8476 (t80) cc_final: 0.8060 (t80) REVERT: B 1200 GLU cc_start: 0.7666 (tp30) cc_final: 0.7274 (tp30) REVERT: B 1204 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7177 (mt-10) REVERT: B 1214 THR cc_start: 0.7696 (OUTLIER) cc_final: 0.7282 (t) REVERT: B 1218 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.7072 (t80) REVERT: B 1276 LEU cc_start: 0.8575 (tp) cc_final: 0.8363 (tt) REVERT: B 1288 PHE cc_start: 0.8571 (m-80) cc_final: 0.8327 (m-80) REVERT: B 1343 LEU cc_start: 0.8266 (tp) cc_final: 0.7936 (tp) REVERT: B 1350 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.5996 (pm20) REVERT: B 1383 LYS cc_start: 0.8457 (mttt) cc_final: 0.8211 (mtmt) REVERT: D 22 LEU cc_start: 0.7634 (mp) cc_final: 0.7256 (mp) REVERT: D 111 MET cc_start: 0.7204 (tmm) cc_final: 0.6777 (tmm) REVERT: D 173 TRP cc_start: 0.7849 (t60) cc_final: 0.7540 (t60) outliers start: 77 outliers final: 55 residues processed: 606 average time/residue: 0.3749 time to fit residues: 351.3712 Evaluate side-chains 626 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 557 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 768 TRP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1110 ARG Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1253 ASP Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1278 ASP Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 978 LYS Chi-restraints excluded: chain B residue 989 LYS Chi-restraints excluded: chain B residue 1020 MET Chi-restraints excluded: chain B residue 1023 ILE Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1133 LEU Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1194 GLN Chi-restraints excluded: chain B residue 1198 ILE Chi-restraints excluded: chain B residue 1214 THR Chi-restraints excluded: chain B residue 1218 PHE Chi-restraints excluded: chain B residue 1300 ASN Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1350 GLU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 256 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 166 optimal weight: 0.5980 chunk 129 optimal weight: 0.7980 chunk 189 optimal weight: 5.9990 chunk 285 optimal weight: 4.9990 chunk 263 optimal weight: 0.5980 chunk 227 optimal weight: 0.2980 chunk 23 optimal weight: 0.5980 chunk 175 optimal weight: 0.8980 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 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 347 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 GLN ** B1369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23602 Z= 0.249 Angle : 0.613 15.709 31913 Z= 0.308 Chirality : 0.041 0.261 3766 Planarity : 0.004 0.045 4009 Dihedral : 6.975 168.069 3084 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.49 % Favored : 91.48 % Rotamer: Outliers : 2.67 % Allowed : 19.18 % Favored : 78.15 % 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: 0.24 (0.16), residues: 2863 helix: 1.28 (0.12), residues: 1862 sheet: -1.23 (0.56), residues: 94 loop : -2.13 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 173 HIS 0.010 0.001 HIS B1369 PHE 0.032 0.002 PHE A1158 TYR 0.019 0.001 TYR A 327 ARG 0.009 0.000 ARG B 807 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 556 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8615 (t) cc_final: 0.8354 (m) REVERT: A 78 GLN cc_start: 0.7652 (tt0) cc_final: 0.7289 (tt0) REVERT: A 86 LEU cc_start: 0.7461 (mt) cc_final: 0.7222 (mm) REVERT: A 88 ASN cc_start: 0.7068 (p0) cc_final: 0.6585 (p0) REVERT: A 153 ARG cc_start: 0.7575 (mtm-85) cc_final: 0.7363 (mtm-85) REVERT: A 253 LYS cc_start: 0.7446 (mptt) cc_final: 0.7193 (mptt) REVERT: A 347 ASN cc_start: 0.8272 (OUTLIER) cc_final: 0.7550 (p0) REVERT: A 368 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7245 (mt-10) REVERT: A 487 ASN cc_start: 0.8336 (t0) cc_final: 0.8113 (t0) REVERT: A 515 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6878 (tm-30) REVERT: A 523 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6595 (mm-30) REVERT: A 559 ARG cc_start: 0.7518 (mtp85) cc_final: 0.7097 (mtm110) REVERT: A 563 PHE cc_start: 0.7689 (t80) cc_final: 0.7431 (t80) REVERT: A 566 CYS cc_start: 0.8054 (m) cc_final: 0.7731 (m) REVERT: A 575 LYS cc_start: 0.8482 (mptt) cc_final: 0.8195 (mmtt) REVERT: A 576 LYS cc_start: 0.7842 (tppt) cc_final: 0.7194 (tppt) REVERT: A 578 ILE cc_start: 0.7946 (mm) cc_final: 0.7677 (mm) REVERT: A 606 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7367 (mmm) REVERT: A 619 ASP cc_start: 0.8017 (t0) cc_final: 0.7619 (t0) REVERT: A 671 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7103 (tm-30) REVERT: A 673 GLN cc_start: 0.6832 (tp40) cc_final: 0.6342 (tp40) REVERT: A 738 ASP cc_start: 0.7084 (p0) cc_final: 0.6796 (p0) REVERT: A 806 ASP cc_start: 0.7479 (m-30) cc_final: 0.7232 (m-30) REVERT: A 830 ASP cc_start: 0.7668 (t0) cc_final: 0.7307 (t70) REVERT: A 862 ASN cc_start: 0.7832 (m-40) cc_final: 0.7586 (m-40) REVERT: A 866 LYS cc_start: 0.8255 (ttmm) cc_final: 0.7948 (ttmm) REVERT: A 889 MET cc_start: 0.7483 (tmm) cc_final: 0.7230 (tmm) REVERT: A 902 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6713 (mm-30) REVERT: A 919 GLN cc_start: 0.6338 (mm-40) cc_final: 0.5543 (mm-40) REVERT: A 1022 CYS cc_start: 0.7296 (t) cc_final: 0.5214 (t) REVERT: A 1045 LYS cc_start: 0.7696 (mmtp) cc_final: 0.7185 (mmtm) REVERT: A 1080 PHE cc_start: 0.7494 (m-80) cc_final: 0.7154 (m-80) REVERT: A 1106 LYS cc_start: 0.7708 (tttp) cc_final: 0.7414 (tttp) REVERT: A 1110 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.6385 (mmt90) REVERT: A 1112 MET cc_start: 0.7757 (mtp) cc_final: 0.7544 (mtt) REVERT: A 1128 GLU cc_start: 0.7506 (tp30) cc_final: 0.7023 (tp30) REVERT: A 1179 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7086 (tp30) REVERT: A 1199 PHE cc_start: 0.8462 (t80) cc_final: 0.8185 (t80) REVERT: A 1204 GLU cc_start: 0.7825 (tp30) cc_final: 0.7383 (mm-30) REVERT: A 1263 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7940 (mm-30) REVERT: A 1278 ASP cc_start: 0.3489 (OUTLIER) cc_final: 0.3276 (t70) REVERT: A 1290 ILE cc_start: 0.8704 (mm) cc_final: 0.8488 (mm) REVERT: A 1299 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8308 (mm) REVERT: A 1317 LEU cc_start: 0.8176 (mt) cc_final: 0.7953 (mm) REVERT: A 1336 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6574 (mp0) REVERT: A 1383 LYS cc_start: 0.8417 (mmtt) cc_final: 0.8011 (mmtm) REVERT: B 120 ASP cc_start: 0.7408 (m-30) cc_final: 0.7040 (m-30) REVERT: B 183 ASP cc_start: 0.7868 (t70) cc_final: 0.7641 (t70) REVERT: B 199 SER cc_start: 0.8782 (m) cc_final: 0.8332 (p) REVERT: B 205 ARG cc_start: 0.8040 (mmm-85) cc_final: 0.7624 (mmm-85) REVERT: B 228 LYS cc_start: 0.8340 (ttmm) cc_final: 0.7931 (ttmm) REVERT: B 231 THR cc_start: 0.7952 (OUTLIER) cc_final: 0.7584 (p) REVERT: B 245 GLU cc_start: 0.6653 (mp0) cc_final: 0.6276 (mp0) REVERT: B 253 LYS cc_start: 0.7462 (mttm) cc_final: 0.6994 (mttm) REVERT: B 368 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: B 375 GLN cc_start: 0.8064 (pt0) cc_final: 0.7460 (pt0) REVERT: B 422 ASN cc_start: 0.7769 (m-40) cc_final: 0.7399 (m-40) REVERT: B 433 ARG cc_start: 0.8307 (mpt180) cc_final: 0.8080 (mpt180) REVERT: B 488 LEU cc_start: 0.8149 (mp) cc_final: 0.7847 (mt) REVERT: B 508 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8028 (tm-30) REVERT: B 575 LYS cc_start: 0.8758 (mmmt) cc_final: 0.8511 (mmmt) REVERT: B 625 ASN cc_start: 0.8535 (m-40) cc_final: 0.8173 (m110) REVERT: B 626 GLU cc_start: 0.8062 (tt0) cc_final: 0.7710 (tt0) REVERT: B 663 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7441 (tm-30) REVERT: B 737 LYS cc_start: 0.8047 (tppt) cc_final: 0.7816 (mppt) REVERT: B 753 ASP cc_start: 0.7714 (m-30) cc_final: 0.7309 (m-30) REVERT: B 754 LYS cc_start: 0.8411 (tptp) cc_final: 0.8173 (tptp) REVERT: B 837 MET cc_start: 0.7486 (mmp) cc_final: 0.7135 (mmp) REVERT: B 989 LYS cc_start: 0.5590 (OUTLIER) cc_final: 0.4940 (pttt) REVERT: B 1052 LYS cc_start: 0.7888 (ptpt) cc_final: 0.7600 (mttp) REVERT: B 1089 LYS cc_start: 0.8176 (ptpt) cc_final: 0.7732 (ptpp) REVERT: B 1128 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7819 (tm-30) REVERT: B 1132 LYS cc_start: 0.7930 (tppt) cc_final: 0.7554 (tppt) REVERT: B 1133 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7692 (tp) REVERT: B 1147 GLN cc_start: 0.8242 (tt0) cc_final: 0.7896 (tt0) REVERT: B 1156 LYS cc_start: 0.8061 (ttmt) cc_final: 0.7808 (ttmm) REVERT: B 1157 GLU cc_start: 0.7799 (tp30) cc_final: 0.7435 (tp30) REVERT: B 1165 LEU cc_start: 0.8251 (tp) cc_final: 0.7988 (tt) REVERT: B 1180 ASN cc_start: 0.8139 (m110) cc_final: 0.7934 (m-40) REVERT: B 1183 LYS cc_start: 0.8179 (tptp) cc_final: 0.7905 (tptm) REVERT: B 1191 MET cc_start: 0.7118 (mtm) cc_final: 0.6575 (mtm) REVERT: B 1199 PHE cc_start: 0.8464 (t80) cc_final: 0.8051 (t80) REVERT: B 1200 GLU cc_start: 0.7662 (tp30) cc_final: 0.7269 (tp30) REVERT: B 1204 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7175 (mt-10) REVERT: B 1214 THR cc_start: 0.7707 (OUTLIER) cc_final: 0.7278 (t) REVERT: B 1218 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.7095 (t80) REVERT: B 1276 LEU cc_start: 0.8573 (tp) cc_final: 0.8316 (tt) REVERT: B 1288 PHE cc_start: 0.8574 (m-80) cc_final: 0.8312 (m-80) REVERT: B 1343 LEU cc_start: 0.8271 (tp) cc_final: 0.7945 (tp) REVERT: B 1350 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.5996 (pm20) REVERT: B 1383 LYS cc_start: 0.8480 (mttt) cc_final: 0.8241 (mtmt) REVERT: D 22 LEU cc_start: 0.7643 (mp) cc_final: 0.7267 (mp) REVERT: D 111 MET cc_start: 0.7210 (tmm) cc_final: 0.6786 (tmm) REVERT: D 173 TRP cc_start: 0.7855 (t60) cc_final: 0.7541 (t60) outliers start: 71 outliers final: 57 residues processed: 597 average time/residue: 0.3770 time to fit residues: 345.0390 Evaluate side-chains 620 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 550 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 768 TRP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1110 ARG Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1253 ASP Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1278 ASP Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 978 LYS Chi-restraints excluded: chain B residue 989 LYS Chi-restraints excluded: chain B residue 1023 ILE Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1133 LEU Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1194 GLN Chi-restraints excluded: chain B residue 1198 ILE Chi-restraints excluded: chain B residue 1214 THR Chi-restraints excluded: chain B residue 1218 PHE Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain B residue 1300 ASN Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1350 GLU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 139 optimal weight: 0.2980 chunk 180 optimal weight: 0.1980 chunk 242 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 209 optimal weight: 0.0010 chunk 33 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 228 optimal weight: 0.8980 chunk 95 optimal weight: 0.3980 chunk 234 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 overall best weight: 0.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 347 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.155385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.132677 restraints weight = 41145.122| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.59 r_work: 0.3550 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23602 Z= 0.176 Angle : 0.595 15.805 31913 Z= 0.297 Chirality : 0.040 0.227 3766 Planarity : 0.004 0.044 4009 Dihedral : 6.903 166.762 3084 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.58 % Favored : 92.39 % Rotamer: Outliers : 2.52 % Allowed : 19.22 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.42 (0.16), residues: 2863 helix: 1.42 (0.12), residues: 1868 sheet: -1.20 (0.56), residues: 94 loop : -2.06 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 173 HIS 0.010 0.001 HIS B1369 PHE 0.033 0.001 PHE A1158 TYR 0.027 0.001 TYR A 954 ARG 0.010 0.000 ARG B 807 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7710.51 seconds wall clock time: 140 minutes 31.28 seconds (8431.28 seconds total)