Starting phenix.real_space_refine on Fri Feb 6 21:02:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h4q_51867/02_2026/9h4q_51867.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h4q_51867/02_2026/9h4q_51867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9h4q_51867/02_2026/9h4q_51867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h4q_51867/02_2026/9h4q_51867.map" model { file = "/net/cci-nas-00/data/ceres_data/9h4q_51867/02_2026/9h4q_51867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h4q_51867/02_2026/9h4q_51867.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 4 5.49 5 Mg 1 5.21 5 S 137 5.16 5 C 17646 2.51 5 N 4578 2.21 5 O 5115 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27485 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" Number of atoms: 4122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4122 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 31, 'TRANS': 477} Chain breaks: 3 Chain: "a" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2375 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 6, 'TRANS': 285} Chain breaks: 1 Chain: "c" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2230 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 7, 'TRANS': 272} Chain breaks: 2 Chain: "T" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3312 Classifications: {'peptide': 405} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 376} Chain breaks: 3 Chain: "h" Number of atoms: 4727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4727 Classifications: {'peptide': 573} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 545} Chain breaks: 6 Chain: "X" Number of atoms: 8187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 8187 Classifications: {'peptide': 990} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 948} Chain breaks: 7 Chain: "R" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 765 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain breaks: 2 Chain: "U" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 505 Classifications: {'peptide': 67} Link IDs: {'TRANS': 66} Chain: "Y" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1201 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain breaks: 1 Chain: "a" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'AF3': 1, 'GDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.87, per 1000 atoms: 0.21 Number of scatterers: 27485 At special positions: 0 Unit cell: (169.469, 168.449, 162.323, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 137 16.00 P 4 15.00 Al 1 13.00 Mg 1 11.99 F 3 9.00 O 5115 8.00 N 4578 7.00 C 17646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.2 seconds 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6462 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 45 sheets defined 37.2% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'C' and resid 341 through 348 Processing helix chain 'C' and resid 392 through 397 removed outlier: 4.056A pdb=" N LEU C 396 " --> pdb=" O THR C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 408 removed outlier: 3.636A pdb=" N THR C 405 " --> pdb=" O THR C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 441 Processing helix chain 'C' and resid 503 through 522 Processing helix chain 'C' and resid 529 through 538 Processing helix chain 'a' and resid 18 through 27 Processing helix chain 'a' and resid 32 through 36 removed outlier: 3.567A pdb=" N THR a 35 " --> pdb=" O ALA a 32 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG a 36 " --> pdb=" O PHE a 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 32 through 36' Processing helix chain 'a' and resid 65 through 73 removed outlier: 3.727A pdb=" N PHE a 73 " --> pdb=" O MET a 69 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 81 removed outlier: 3.979A pdb=" N PHE a 81 " --> pdb=" O LYS a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 97 through 116 Processing helix chain 'a' and resid 132 through 134 No H-bonds generated for 'chain 'a' and resid 132 through 134' Processing helix chain 'a' and resid 135 through 152 removed outlier: 4.019A pdb=" N ASN a 146 " --> pdb=" O ILE a 142 " (cutoff:3.500A) Processing helix chain 'a' and resid 169 through 181 removed outlier: 3.725A pdb=" N LYS a 173 " --> pdb=" O GLU a 169 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER a 181 " --> pdb=" O GLN a 177 " (cutoff:3.500A) Processing helix chain 'a' and resid 185 through 201 Processing helix chain 'a' and resid 241 through 258 Processing helix chain 'a' and resid 259 through 261 No H-bonds generated for 'chain 'a' and resid 259 through 261' Processing helix chain 'a' and resid 294 through 305 removed outlier: 3.714A pdb=" N VAL a 298 " --> pdb=" O PRO a 294 " (cutoff:3.500A) Processing helix chain 'c' and resid 21 through 32 Processing helix chain 'c' and resid 76 through 82 Processing helix chain 'c' and resid 96 through 114 removed outlier: 3.859A pdb=" N TYR c 109 " --> pdb=" O MET c 105 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS c 112 " --> pdb=" O GLU c 108 " (cutoff:3.500A) Processing helix chain 'c' and resid 130 through 152 Processing helix chain 'c' and resid 169 through 181 Processing helix chain 'c' and resid 185 through 199 Processing helix chain 'c' and resid 224 through 245 removed outlier: 3.633A pdb=" N TYR c 245 " --> pdb=" O LEU c 241 " (cutoff:3.500A) Processing helix chain 'c' and resid 302 through 324 removed outlier: 3.775A pdb=" N ASP c 323 " --> pdb=" O LYS c 319 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE c 324 " --> pdb=" O GLY c 320 " (cutoff:3.500A) Processing helix chain 'T' and resid 34 through 40 removed outlier: 3.605A pdb=" N ASN T 38 " --> pdb=" O ASN T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 46 through 51 Processing helix chain 'T' and resid 82 through 84 No H-bonds generated for 'chain 'T' and resid 82 through 84' Processing helix chain 'T' and resid 104 through 123 Processing helix chain 'T' and resid 126 through 130 removed outlier: 3.502A pdb=" N GLU T 129 " --> pdb=" O SER T 126 " (cutoff:3.500A) Processing helix chain 'T' and resid 131 through 135 removed outlier: 3.548A pdb=" N PHE T 134 " --> pdb=" O ASP T 131 " (cutoff:3.500A) Processing helix chain 'T' and resid 196 through 211 Processing helix chain 'T' and resid 260 through 267 removed outlier: 3.511A pdb=" N SER T 265 " --> pdb=" O PRO T 261 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL T 267 " --> pdb=" O MET T 263 " (cutoff:3.500A) Processing helix chain 'T' and resid 268 through 270 No H-bonds generated for 'chain 'T' and resid 268 through 270' Processing helix chain 'T' and resid 275 through 283 Processing helix chain 'T' and resid 286 through 300 Processing helix chain 'T' and resid 322 through 327 Processing helix chain 'T' and resid 330 through 338 removed outlier: 3.746A pdb=" N SER T 336 " --> pdb=" O SER T 332 " (cutoff:3.500A) Processing helix chain 'T' and resid 344 through 349 removed outlier: 3.683A pdb=" N LEU T 349 " --> pdb=" O ILE T 346 " (cutoff:3.500A) Processing helix chain 'T' and resid 434 through 443 Processing helix chain 'T' and resid 450 through 458 Processing helix chain 'T' and resid 460 through 465 Processing helix chain 'T' and resid 468 through 479 removed outlier: 3.502A pdb=" N GLY T 476 " --> pdb=" O PHE T 472 " (cutoff:3.500A) Processing helix chain 'T' and resid 569 through 582 Processing helix chain 'T' and resid 585 through 594 Processing helix chain 'T' and resid 596 through 608 Processing helix chain 'h' and resid 33 through 39 Processing helix chain 'h' and resid 367 through 377 Processing helix chain 'h' and resid 383 through 391 removed outlier: 3.557A pdb=" N GLU h 387 " --> pdb=" O ILE h 384 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLU h 388 " --> pdb=" O PHE h 385 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLU h 389 " --> pdb=" O PHE h 386 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE h 391 " --> pdb=" O GLU h 388 " (cutoff:3.500A) Processing helix chain 'h' and resid 402 through 409 Processing helix chain 'h' and resid 521 through 530 Processing helix chain 'h' and resid 545 through 557 removed outlier: 3.960A pdb=" N ASP h 551 " --> pdb=" O ASN h 547 " (cutoff:3.500A) Processing helix chain 'h' and resid 557 through 572 Processing helix chain 'h' and resid 574 through 591 Processing helix chain 'h' and resid 594 through 599 removed outlier: 3.556A pdb=" N ILE h 599 " --> pdb=" O THR h 595 " (cutoff:3.500A) Processing helix chain 'h' and resid 601 through 617 Processing helix chain 'h' and resid 618 through 632 removed outlier: 3.544A pdb=" N ARG h 632 " --> pdb=" O ASP h 628 " (cutoff:3.500A) Processing helix chain 'h' and resid 678 through 685 Processing helix chain 'h' and resid 743 through 747 Processing helix chain 'h' and resid 754 through 763 Processing helix chain 'h' and resid 771 through 782 removed outlier: 3.672A pdb=" N LYS h 777 " --> pdb=" O THR h 773 " (cutoff:3.500A) Processing helix chain 'h' and resid 788 through 791 Processing helix chain 'h' and resid 792 through 800 removed outlier: 4.184A pdb=" N ILE h 796 " --> pdb=" O TYR h 792 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU h 799 " --> pdb=" O LEU h 795 " (cutoff:3.500A) Processing helix chain 'h' and resid 815 through 831 Processing helix chain 'h' and resid 889 through 902 Processing helix chain 'h' and resid 907 through 917 removed outlier: 3.579A pdb=" N LEU h 915 " --> pdb=" O PHE h 911 " (cutoff:3.500A) Processing helix chain 'h' and resid 922 through 926 Processing helix chain 'h' and resid 932 through 947 Processing helix chain 'h' and resid 961 through 974 Processing helix chain 'h' and resid 1080 through 1090 Processing helix chain 'h' and resid 1095 through 1105 Processing helix chain 'h' and resid 1114 through 1123 Processing helix chain 'h' and resid 1125 through 1136 Processing helix chain 'X' and resid 160 through 166 Processing helix chain 'X' and resid 177 through 184 removed outlier: 3.739A pdb=" N THR X 181 " --> pdb=" O GLY X 177 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 228 Processing helix chain 'X' and resid 298 through 306 Processing helix chain 'X' and resid 307 through 318 Processing helix chain 'X' and resid 338 through 342 removed outlier: 3.585A pdb=" N LEU X 342 " --> pdb=" O PHE X 339 " (cutoff:3.500A) Processing helix chain 'X' and resid 366 through 380 Processing helix chain 'X' and resid 380 through 386 removed outlier: 3.763A pdb=" N ASP X 384 " --> pdb=" O GLU X 380 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU X 385 " --> pdb=" O ILE X 381 " (cutoff:3.500A) Processing helix chain 'X' and resid 408 through 417 Processing helix chain 'X' and resid 449 through 461 Processing helix chain 'X' and resid 522 through 527 Processing helix chain 'X' and resid 532 through 536 removed outlier: 3.960A pdb=" N ILE X 536 " --> pdb=" O ASN X 533 " (cutoff:3.500A) Processing helix chain 'X' and resid 552 through 563 Processing helix chain 'X' and resid 861 through 866 removed outlier: 3.505A pdb=" N ASN X 864 " --> pdb=" O GLU X 861 " (cutoff:3.500A) Processing helix chain 'X' and resid 871 through 875 removed outlier: 3.519A pdb=" N VAL X 874 " --> pdb=" O TRP X 871 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP X 875 " --> pdb=" O LYS X 872 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 871 through 875' Processing helix chain 'X' and resid 885 through 891 removed outlier: 3.930A pdb=" N PHE X 889 " --> pdb=" O LYS X 885 " (cutoff:3.500A) Processing helix chain 'X' and resid 904 through 909 removed outlier: 3.592A pdb=" N PHE X 908 " --> pdb=" O SER X 904 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP X 909 " --> pdb=" O LYS X 905 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 904 through 909' Processing helix chain 'X' and resid 924 through 928 Processing helix chain 'X' and resid 931 through 944 Processing helix chain 'X' and resid 953 through 962 removed outlier: 3.734A pdb=" N GLU X 957 " --> pdb=" O GLY X 953 " (cutoff:3.500A) Processing helix chain 'X' and resid 1053 through 1062 removed outlier: 3.512A pdb=" N ILE X1057 " --> pdb=" O ASN X1053 " (cutoff:3.500A) Processing helix chain 'X' and resid 1107 through 1123 Processing helix chain 'X' and resid 1127 through 1133 removed outlier: 3.509A pdb=" N GLY X1133 " --> pdb=" O LYS X1129 " (cutoff:3.500A) Processing helix chain 'X' and resid 1151 through 1157 removed outlier: 3.660A pdb=" N PHE X1155 " --> pdb=" O PRO X1151 " (cutoff:3.500A) Processing helix chain 'X' and resid 1389 through 1405 removed outlier: 3.884A pdb=" N TYR X1405 " --> pdb=" O LEU X1401 " (cutoff:3.500A) Processing helix chain 'X' and resid 1416 through 1420 Processing helix chain 'X' and resid 1446 through 1453 Processing helix chain 'X' and resid 1455 through 1465 Processing helix chain 'X' and resid 1522 through 1529 Processing helix chain 'X' and resid 1549 through 1561 removed outlier: 3.570A pdb=" N LEU X1553 " --> pdb=" O GLN X1549 " (cutoff:3.500A) Processing helix chain 'X' and resid 1561 through 1578 Processing helix chain 'R' and resid 46 through 69 Processing helix chain 'R' and resid 73 through 79 Processing helix chain 'R' and resid 87 through 100 Processing helix chain 'R' and resid 154 through 172 removed outlier: 3.619A pdb=" N GLN R 171 " --> pdb=" O GLU R 167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER R 172 " --> pdb=" O ILE R 168 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 33 removed outlier: 5.260A pdb=" N ILE U 32 " --> pdb=" O SER U 29 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLU U 33 " --> pdb=" O GLN U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 39 Processing helix chain 'Y' and resid 5 through 16 Processing helix chain 'Y' and resid 63 through 85 removed outlier: 4.070A pdb=" N GLU Y 82 " --> pdb=" O ASP Y 78 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP Y 83 " --> pdb=" O LYS Y 79 " (cutoff:3.500A) Processing helix chain 'Y' and resid 138 through 152 removed outlier: 3.616A pdb=" N GLU Y 152 " --> pdb=" O ARG Y 148 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 157 Processing sheet with id=AA1, first strand: chain 'C' and resid 304 through 310 removed outlier: 3.654A pdb=" N LEU C 19 " --> pdb=" O LEU C 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.760A pdb=" N ALA C 29 " --> pdb=" O ALA C 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 73 through 75 removed outlier: 3.722A pdb=" N ILE C 85 " --> pdb=" O TRP C 96 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE C 108 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ASN C 97 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE C 106 " --> pdb=" O ASN C 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 117 through 122 removed outlier: 6.617A pdb=" N CYS C 133 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE C 120 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA C 131 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE C 122 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL C 129 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR C 138 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR C 152 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 166 removed outlier: 6.658A pdb=" N SER C 177 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL C 164 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA C 175 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N TRP C 166 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL C 173 " --> pdb=" O TRP C 166 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 182 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS C 195 " --> pdb=" O VAL C 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 204 through 209 removed outlier: 4.330A pdb=" N SER C 206 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER C 221 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 248 through 253 removed outlier: 7.100A pdb=" N MET C 263 " --> pdb=" O TRP C 249 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLY C 251 " --> pdb=" O CYS C 261 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N CYS C 261 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N TYR C 253 " --> pdb=" O GLY C 259 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N GLY C 259 " --> pdb=" O TYR C 253 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR C 295 " --> pdb=" O LEU C 274 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 445 through 450 removed outlier: 6.492A pdb=" N CYS C 457 " --> pdb=" O GLU C 447 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE C 449 " --> pdb=" O GLU C 455 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLU C 455 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 460 " --> pdb=" O LEU C 475 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 445 through 450 removed outlier: 6.492A pdb=" N CYS C 457 " --> pdb=" O GLU C 447 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE C 449 " --> pdb=" O GLU C 455 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLU C 455 " --> pdb=" O ILE C 449 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a' and resid 45 through 51 removed outlier: 6.613A pdb=" N LYS a 7 " --> pdb=" O ASN a 58 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TRP a 60 " --> pdb=" O LYS a 7 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU a 9 " --> pdb=" O TRP a 60 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL a 86 " --> pdb=" O LYS a 8 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE a 160 " --> pdb=" O ILE a 121 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 215 through 218 removed outlier: 6.732A pdb=" N LEU a 207 " --> pdb=" O ILE a 216 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER a 218 " --> pdb=" O ILE a 205 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE a 205 " --> pdb=" O SER a 218 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 61 through 64 removed outlier: 3.718A pdb=" N MET c 61 " --> pdb=" O VAL c 12 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY c 16 " --> pdb=" O LEU c 63 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N MET c 11 " --> pdb=" O ALA c 85 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL c 87 " --> pdb=" O MET c 11 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU c 13 " --> pdb=" O VAL c 87 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL c 89 " --> pdb=" O LEU c 13 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N MET c 15 " --> pdb=" O VAL c 89 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ASP c 91 " --> pdb=" O MET c 15 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLY c 84 " --> pdb=" O ASN c 118 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N GLU c 120 " --> pdb=" O GLY c 84 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU c 86 " --> pdb=" O GLU c 120 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU c 122 " --> pdb=" O LEU c 86 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TYR c 88 " --> pdb=" O LEU c 122 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS c 124 " --> pdb=" O TYR c 88 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE c 90 " --> pdb=" O HIS c 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 24 through 31 removed outlier: 4.707A pdb=" N SER T 25 " --> pdb=" O HIS T 20 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N HIS T 20 " --> pdb=" O SER T 25 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE T 27 " --> pdb=" O VAL T 18 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL T 18 " --> pdb=" O ILE T 27 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N SER T 88 " --> pdb=" O PHE T 19 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 24 through 31 removed outlier: 4.707A pdb=" N SER T 25 " --> pdb=" O HIS T 20 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N HIS T 20 " --> pdb=" O SER T 25 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE T 27 " --> pdb=" O VAL T 18 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL T 18 " --> pdb=" O ILE T 27 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N SER T 88 " --> pdb=" O PHE T 19 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'T' and resid 213 through 217 Processing sheet with id=AB7, first strand: chain 'T' and resid 243 through 245 Processing sheet with id=AB8, first strand: chain 'T' and resid 316 through 317 Processing sheet with id=AB9, first strand: chain 'T' and resid 486 through 491 Processing sheet with id=AC1, first strand: chain 'h' and resid 22 through 28 removed outlier: 6.746A pdb=" N LEU h 15 " --> pdb=" O VAL h 26 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N HIS h 28 " --> pdb=" O VAL h 13 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL h 13 " --> pdb=" O HIS h 28 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL h 538 " --> pdb=" O LEU h 11 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL h 13 " --> pdb=" O CYS h 536 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N CYS h 536 " --> pdb=" O VAL h 13 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU h 15 " --> pdb=" O HIS h 534 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N HIS h 534 " --> pdb=" O LEU h 15 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE h 17 " --> pdb=" O MET h 532 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET h 532 " --> pdb=" O ILE h 17 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'h' and resid 22 through 28 removed outlier: 6.746A pdb=" N LEU h 15 " --> pdb=" O VAL h 26 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N HIS h 28 " --> pdb=" O VAL h 13 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL h 13 " --> pdb=" O HIS h 28 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL h 538 " --> pdb=" O LEU h 11 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL h 13 " --> pdb=" O CYS h 536 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N CYS h 536 " --> pdb=" O VAL h 13 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU h 15 " --> pdb=" O HIS h 534 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N HIS h 534 " --> pdb=" O LEU h 15 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE h 17 " --> pdb=" O MET h 532 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET h 532 " --> pdb=" O ILE h 17 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'h' and resid 396 through 397 Processing sheet with id=AC4, first strand: chain 'h' and resid 636 through 640 Processing sheet with id=AC5, first strand: chain 'h' and resid 655 through 656 Processing sheet with id=AC6, first strand: chain 'h' and resid 748 through 751 Processing sheet with id=AC7, first strand: chain 'h' and resid 846 through 848 Processing sheet with id=AC8, first strand: chain 'h' and resid 1071 through 1073 removed outlier: 4.608A pdb=" N ILE h 958 " --> pdb=" O ILE h1073 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'X' and resid 118 through 120 removed outlier: 7.656A pdb=" N VAL X 172 " --> pdb=" O GLN X 103 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLU X 105 " --> pdb=" O VAL X 172 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE X 174 " --> pdb=" O GLU X 105 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY X 107 " --> pdb=" O ILE X 174 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE X 193 " --> pdb=" O TYR X 102 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'X' and resid 133 through 135 Processing sheet with id=AD2, first strand: chain 'X' and resid 257 through 259 removed outlier: 4.207A pdb=" N ILE X 252 " --> pdb=" O ILE X 259 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL X 206 " --> pdb=" O TYR X 253 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL X 207 " --> pdb=" O ARG X 269 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 231 through 234 removed outlier: 3.806A pdb=" N THR X 231 " --> pdb=" O ILE X 264 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE X 264 " --> pdb=" O THR X 231 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 240 through 241 Processing sheet with id=AD5, first strand: chain 'X' and resid 400 through 401 removed outlier: 4.152A pdb=" N ARG X 400 " --> pdb=" O ASP X 333 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ALA X 327 " --> pdb=" O LEU X 279 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N PHE X 281 " --> pdb=" O ALA X 327 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA X 329 " --> pdb=" O PHE X 281 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE X 283 " --> pdb=" O ALA X 329 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N SER X 331 " --> pdb=" O ILE X 283 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ILE X 285 " --> pdb=" O SER X 331 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP X 333 " --> pdb=" O ILE X 285 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG X 278 " --> pdb=" O HIS X 435 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N MET X 437 " --> pdb=" O ARG X 278 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE X 280 " --> pdb=" O MET X 437 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ILE X 439 " --> pdb=" O ILE X 280 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU X 282 " --> pdb=" O ILE X 439 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'X' and resid 400 through 401 removed outlier: 4.152A pdb=" N ARG X 400 " --> pdb=" O ASP X 333 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N LEU X1028 " --> pdb=" O SER X 351 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASP X 353 " --> pdb=" O LEU X1028 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LYS X1030 " --> pdb=" O ASP X 353 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE X 355 " --> pdb=" O LYS X1030 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'X' and resid 323 through 324 Processing sheet with id=AD8, first strand: chain 'X' and resid 387 through 389 Processing sheet with id=AD9, first strand: chain 'X' and resid 445 through 447 removed outlier: 6.679A pdb=" N PHE X 446 " --> pdb=" O ARG X 484 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N ARG X 486 " --> pdb=" O PHE X 446 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N HIS X 494 " --> pdb=" O ILE X 851 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'X' and resid 898 through 899 removed outlier: 4.485A pdb=" N TYR X 987 " --> pdb=" O CYS X 951 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL X1007 " --> pdb=" O HIS X 917 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'X' and resid 1344 through 1348 removed outlier: 3.701A pdb=" N ASP X1368 " --> pdb=" O HIS X1378 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N HIS X1378 " --> pdb=" O ASP X1368 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS X1079 " --> pdb=" O ILE X1412 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'X' and resid 1146 through 1147 removed outlier: 5.971A pdb=" N MET X1146 " --> pdb=" O HIS X1371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'X' and resid 1341 through 1342 removed outlier: 5.021A pdb=" N LEU X1341 " --> pdb=" O MET X1487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'X' and resid 1430 through 1432 removed outlier: 5.467A pdb=" N TYR X1507 " --> pdb=" O HIS X1502 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL X1498 " --> pdb=" O LEU X1511 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 83 through 84 removed outlier: 6.509A pdb=" N THR Y 39 " --> pdb=" O ILE Y 45 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE Y 45 " --> pdb=" O THR Y 39 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 142 through 143 removed outlier: 3.676A pdb=" N GLY U 11 " --> pdb=" O TYR U 71 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR U 12 " --> pdb=" O SER U 24 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER U 24 " --> pdb=" O THR U 12 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ALA U 14 " --> pdb=" O ILE U 22 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Y' and resid 21 through 22 removed outlier: 3.782A pdb=" N LEU Y 22 " --> pdb=" O PHE Y 27 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE Y 27 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'Y' and resid 99 through 100 1136 hydrogen bonds defined for protein. 3171 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: 6.67 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8633 1.34 - 1.46: 4490 1.46 - 1.57: 14743 1.57 - 1.69: 9 1.69 - 1.81: 218 Bond restraints: 28093 Sorted by residual: bond pdb=" N THR X1161 " pdb=" CA THR X1161 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.31e-02 5.83e+03 6.51e+00 bond pdb=" C TYR C 485 " pdb=" N PRO C 486 " ideal model delta sigma weight residual 1.332 1.354 -0.021 8.90e-03 1.26e+04 5.82e+00 bond pdb=" N GLN X1160 " pdb=" CA GLN X1160 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.27e-02 6.20e+03 5.69e+00 bond pdb=" N GLN X1159 " pdb=" CA GLN X1159 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.35e-02 5.49e+03 5.59e+00 bond pdb=" N GLU C 237 " pdb=" CA GLU C 237 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.55e+00 ... (remaining 28088 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 37116 1.72 - 3.43: 761 3.43 - 5.15: 74 5.15 - 6.86: 31 6.86 - 8.58: 13 Bond angle restraints: 37995 Sorted by residual: angle pdb=" N THR X 946 " pdb=" CA THR X 946 " pdb=" C THR X 946 " ideal model delta sigma weight residual 114.56 107.71 6.85 1.27e+00 6.20e-01 2.91e+01 angle pdb=" N GLU X1158 " pdb=" CA GLU X1158 " pdb=" C GLU X1158 " ideal model delta sigma weight residual 114.56 109.44 5.12 1.27e+00 6.20e-01 1.62e+01 angle pdb=" N LEU C 529 " pdb=" CA LEU C 529 " pdb=" C LEU C 529 " ideal model delta sigma weight residual 114.75 110.10 4.65 1.26e+00 6.30e-01 1.36e+01 angle pdb=" C ASP X1350 " pdb=" N VAL X1351 " pdb=" CA VAL X1351 " ideal model delta sigma weight residual 121.97 127.61 -5.64 1.80e+00 3.09e-01 9.81e+00 angle pdb=" CA THR X1161 " pdb=" C THR X1161 " pdb=" O THR X1161 " ideal model delta sigma weight residual 120.95 117.97 2.98 1.00e+00 1.00e+00 8.86e+00 ... (remaining 37990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 15202 17.65 - 35.31: 1510 35.31 - 52.96: 214 52.96 - 70.62: 45 70.62 - 88.27: 10 Dihedral angle restraints: 16981 sinusoidal: 7053 harmonic: 9928 Sorted by residual: dihedral pdb=" CA TRP C 229 " pdb=" C TRP C 229 " pdb=" N ASP C 230 " pdb=" CA ASP C 230 " ideal model delta harmonic sigma weight residual 180.00 161.17 18.83 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA GLN a 65 " pdb=" C GLN a 65 " pdb=" N ASP a 66 " pdb=" CA ASP a 66 " ideal model delta harmonic sigma weight residual -180.00 -161.36 -18.64 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PHE a 208 " pdb=" C PHE a 208 " pdb=" N GLU a 209 " pdb=" CA GLU a 209 " ideal model delta harmonic sigma weight residual 180.00 162.17 17.83 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 16978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2938 0.043 - 0.085: 924 0.085 - 0.128: 326 0.128 - 0.170: 37 0.170 - 0.213: 5 Chirality restraints: 4230 Sorted by residual: chirality pdb=" CB ILE X1168 " pdb=" CA ILE X1168 " pdb=" CG1 ILE X1168 " pdb=" CG2 ILE X1168 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB THR X 169 " pdb=" CA THR X 169 " pdb=" OG1 THR X 169 " pdb=" CG2 THR X 169 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB VAL c 17 " pdb=" CA VAL c 17 " pdb=" CG1 VAL c 17 " pdb=" CG2 VAL c 17 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.21e-01 ... (remaining 4227 not shown) Planarity restraints: 4808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE h 838 " -0.047 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO h 839 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO h 839 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO h 839 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU X 372 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C GLU X 372 " -0.039 2.00e-02 2.50e+03 pdb=" O GLU X 372 " 0.015 2.00e-02 2.50e+03 pdb=" N THR X 373 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR X 373 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.91e+00 pdb=" C THR X 373 " 0.038 2.00e-02 2.50e+03 pdb=" O THR X 373 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU X 374 " -0.013 2.00e-02 2.50e+03 ... (remaining 4805 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 206 2.60 - 3.18: 21570 3.18 - 3.75: 41590 3.75 - 4.33: 57766 4.33 - 4.90: 96539 Nonbonded interactions: 217671 Sorted by model distance: nonbonded pdb=" OG1 THR a 41 " pdb="MG MG a 401 " model vdw 2.028 2.170 nonbonded pdb=" F1 AF3 a 402 " pdb=" O3B GDP a 403 " model vdw 2.241 2.990 nonbonded pdb=" OG SER R 172 " pdb=" OH TYR Y 20 " model vdw 2.274 3.040 nonbonded pdb=" O VAL h 667 " pdb=" OH TYR h 862 " model vdw 2.280 3.040 nonbonded pdb=" OG SER C 203 " pdb=" OD1 ASN C 222 " model vdw 2.285 3.040 ... (remaining 217666 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.030 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.640 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28093 Z= 0.155 Angle : 0.604 8.579 37995 Z= 0.323 Chirality : 0.046 0.213 4230 Planarity : 0.005 0.071 4808 Dihedral : 13.767 88.272 10519 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.14), residues: 3294 helix: -0.16 (0.14), residues: 1147 sheet: -0.39 (0.20), residues: 722 loop : -1.11 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 471 TYR 0.017 0.001 TYR C 48 PHE 0.022 0.002 PHE h 408 TRP 0.021 0.001 TRP C 75 HIS 0.007 0.001 HIS c 124 Details of bonding type rmsd covalent geometry : bond 0.00322 (28093) covalent geometry : angle 0.60351 (37995) hydrogen bonds : bond 0.14931 ( 1115) hydrogen bonds : angle 6.41136 ( 3171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 3118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 937 time to evaluate : 1.031 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: C 14 THR cc_start: 0.7771 (p) cc_final: 0.6054 (m) REVERT: C 23 VAL cc_start: 0.8118 (t) cc_final: 0.7827 (t) REVERT: C 92 LYS cc_start: 0.8208 (ptpp) cc_final: 0.7851 (pttm) REVERT: C 95 ILE cc_start: 0.8308 (mp) cc_final: 0.8021 (mm) REVERT: C 138 TYR cc_start: 0.8118 (m-10) cc_final: 0.7618 (m-80) REVERT: C 189 LYS cc_start: 0.8084 (mttt) cc_final: 0.7878 (mttt) REVERT: C 191 SER cc_start: 0.7703 (m) cc_final: 0.6791 (t) REVERT: C 198 LYS cc_start: 0.8653 (mtpp) cc_final: 0.8110 (mtmm) REVERT: C 202 SER cc_start: 0.8458 (m) cc_final: 0.7977 (p) REVERT: C 217 ILE cc_start: 0.8027 (mt) cc_final: 0.7676 (tt) REVERT: C 221 SER cc_start: 0.8465 (t) cc_final: 0.7884 (t) REVERT: C 229 TRP cc_start: 0.8096 (m-90) cc_final: 0.6879 (m-90) REVERT: C 237 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7269 (mm-30) REVERT: C 239 LYS cc_start: 0.8096 (tmmt) cc_final: 0.7888 (tmmt) REVERT: C 298 LYS cc_start: 0.8078 (mmtp) cc_final: 0.7818 (mptt) REVERT: C 331 LYS cc_start: 0.8375 (tppp) cc_final: 0.8084 (tppp) REVERT: C 345 TYR cc_start: 0.8412 (m-80) cc_final: 0.8105 (m-80) REVERT: C 348 VAL cc_start: 0.7770 (t) cc_final: 0.7516 (p) REVERT: C 349 ASN cc_start: 0.7774 (t0) cc_final: 0.7153 (t0) REVERT: C 363 TYR cc_start: 0.9030 (m-80) cc_final: 0.8275 (m-80) REVERT: C 368 TYR cc_start: 0.8161 (m-80) cc_final: 0.7960 (m-80) REVERT: C 391 VAL cc_start: 0.8429 (p) cc_final: 0.8225 (t) REVERT: C 411 ARG cc_start: 0.7619 (mtm-85) cc_final: 0.7181 (mtm-85) REVERT: C 445 VAL cc_start: 0.8019 (t) cc_final: 0.7640 (p) REVERT: C 474 PHE cc_start: 0.7645 (t80) cc_final: 0.7323 (t80) REVERT: C 480 ASN cc_start: 0.7184 (m-40) cc_final: 0.6906 (t0) REVERT: C 484 ASN cc_start: 0.7735 (m-40) cc_final: 0.7515 (m-40) REVERT: C 527 TYR cc_start: 0.7927 (m-80) cc_final: 0.7611 (m-10) REVERT: a 44 VAL cc_start: 0.8410 (t) cc_final: 0.8183 (p) REVERT: a 61 ASP cc_start: 0.7654 (t70) cc_final: 0.7282 (t0) REVERT: a 71 ASN cc_start: 0.8369 (t0) cc_final: 0.7894 (t0) REVERT: a 97 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6588 (mt-10) REVERT: a 146 ASN cc_start: 0.7527 (m110) cc_final: 0.7153 (m-40) REVERT: a 154 PHE cc_start: 0.7657 (m-80) cc_final: 0.7402 (m-10) REVERT: a 192 ASN cc_start: 0.8160 (m-40) cc_final: 0.7870 (m-40) REVERT: a 194 LYS cc_start: 0.7822 (mttt) cc_final: 0.7420 (mtpp) REVERT: a 265 LYS cc_start: 0.8354 (tttt) cc_final: 0.8010 (ttmm) REVERT: a 268 ILE cc_start: 0.8392 (mt) cc_final: 0.8141 (mt) REVERT: a 304 LYS cc_start: 0.7785 (mmpt) cc_final: 0.7447 (mmtt) REVERT: c 15 MET cc_start: 0.6627 (mtp) cc_final: 0.6390 (mtt) REVERT: c 88 TYR cc_start: 0.7859 (t80) cc_final: 0.7619 (t80) REVERT: c 91 ASP cc_start: 0.7900 (t0) cc_final: 0.7636 (t0) REVERT: c 101 THR cc_start: 0.8120 (m) cc_final: 0.7715 (p) REVERT: c 102 ASN cc_start: 0.7405 (t0) cc_final: 0.7088 (m-40) REVERT: c 106 ILE cc_start: 0.8232 (mt) cc_final: 0.7840 (mm) REVERT: c 119 ILE cc_start: 0.8424 (mt) cc_final: 0.8055 (mm) REVERT: c 144 ARG cc_start: 0.8348 (mtt180) cc_final: 0.8101 (mtt90) REVERT: c 148 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7217 (mt-10) REVERT: c 173 GLU cc_start: 0.7872 (tt0) cc_final: 0.7481 (tt0) REVERT: c 193 LEU cc_start: 0.8611 (mt) cc_final: 0.8351 (tp) REVERT: c 233 GLU cc_start: 0.7112 (tt0) cc_final: 0.6832 (tt0) REVERT: c 242 PHE cc_start: 0.8028 (t80) cc_final: 0.7776 (t80) REVERT: c 243 ASP cc_start: 0.7577 (m-30) cc_final: 0.7194 (m-30) REVERT: c 273 SER cc_start: 0.7757 (t) cc_final: 0.7306 (p) REVERT: c 274 GLN cc_start: 0.8155 (tt0) cc_final: 0.7779 (tt0) REVERT: c 275 LEU cc_start: 0.8726 (mt) cc_final: 0.8504 (mm) REVERT: c 284 ARG cc_start: 0.7364 (ttm170) cc_final: 0.7148 (mtp-110) REVERT: c 303 MET cc_start: 0.5830 (ttt) cc_final: 0.5503 (ttt) REVERT: c 317 PHE cc_start: 0.7985 (t80) cc_final: 0.7677 (t80) REVERT: c 321 LEU cc_start: 0.7920 (tp) cc_final: 0.7019 (tt) REVERT: T 22 THR cc_start: 0.8212 (m) cc_final: 0.7970 (t) REVERT: T 28 LYS cc_start: 0.7818 (tptt) cc_final: 0.7365 (tppt) REVERT: T 37 LYS cc_start: 0.8161 (mmtp) cc_final: 0.7869 (mmtp) REVERT: T 81 ILE cc_start: 0.8560 (mt) cc_final: 0.8258 (mm) REVERT: T 90 ASN cc_start: 0.8044 (t0) cc_final: 0.7825 (t0) REVERT: T 98 ASP cc_start: 0.7712 (t0) cc_final: 0.7243 (t0) REVERT: T 136 ASP cc_start: 0.8143 (t0) cc_final: 0.7860 (t0) REVERT: T 196 SER cc_start: 0.8211 (t) cc_final: 0.7977 (p) REVERT: T 207 ASP cc_start: 0.7621 (m-30) cc_final: 0.7387 (m-30) REVERT: T 220 GLU cc_start: 0.7304 (mp0) cc_final: 0.6994 (mp0) REVERT: T 229 PHE cc_start: 0.8383 (m-80) cc_final: 0.7902 (m-80) REVERT: T 242 GLU cc_start: 0.7672 (pm20) cc_final: 0.7263 (pm20) REVERT: T 243 ASP cc_start: 0.6995 (m-30) cc_final: 0.6711 (m-30) REVERT: T 246 LEU cc_start: 0.8291 (mt) cc_final: 0.8053 (mt) REVERT: T 291 ILE cc_start: 0.7350 (mm) cc_final: 0.7146 (mt) REVERT: T 299 TYR cc_start: 0.8023 (t80) cc_final: 0.7665 (t80) REVERT: T 301 LYS cc_start: 0.8148 (mmmm) cc_final: 0.7785 (mmmm) REVERT: T 335 GLN cc_start: 0.7641 (mt0) cc_final: 0.7310 (mt0) REVERT: T 452 LYS cc_start: 0.8414 (tttt) cc_final: 0.7840 (tttp) REVERT: T 468 ASP cc_start: 0.7551 (t0) cc_final: 0.7309 (t70) REVERT: T 487 SER cc_start: 0.8083 (m) cc_final: 0.7694 (p) REVERT: T 606 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6593 (mm-30) REVERT: h 6 PRO cc_start: 0.8081 (Cg_endo) cc_final: 0.7808 (Cg_exo) REVERT: h 7 ASN cc_start: 0.8044 (t0) cc_final: 0.7787 (t0) REVERT: h 20 HIS cc_start: 0.7395 (m-70) cc_final: 0.7156 (m90) REVERT: h 368 MET cc_start: 0.7046 (tpt) cc_final: 0.6719 (tpt) REVERT: h 383 GLU cc_start: 0.7471 (mm-30) cc_final: 0.6907 (mm-30) REVERT: h 387 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7488 (mt-10) REVERT: h 401 ASP cc_start: 0.7808 (m-30) cc_final: 0.7415 (m-30) REVERT: h 528 LYS cc_start: 0.8356 (mtpt) cc_final: 0.8071 (mtpt) REVERT: h 569 GLN cc_start: 0.8278 (tp40) cc_final: 0.7990 (tp40) REVERT: h 577 SER cc_start: 0.7942 (m) cc_final: 0.7637 (t) REVERT: h 585 GLU cc_start: 0.7779 (tp30) cc_final: 0.7484 (tp30) REVERT: h 588 ARG cc_start: 0.7403 (ttt-90) cc_final: 0.6914 (ttt-90) REVERT: h 597 GLN cc_start: 0.8282 (mp10) cc_final: 0.7908 (mp10) REVERT: h 607 LYS cc_start: 0.8326 (ttmt) cc_final: 0.8047 (ttpt) REVERT: h 635 ILE cc_start: 0.8522 (mp) cc_final: 0.8274 (mt) REVERT: h 643 ASP cc_start: 0.7193 (t0) cc_final: 0.6918 (t0) REVERT: h 652 ILE cc_start: 0.7592 (mt) cc_final: 0.7334 (tt) REVERT: h 745 LEU cc_start: 0.7782 (mm) cc_final: 0.7343 (mt) REVERT: h 759 ILE cc_start: 0.8411 (mm) cc_final: 0.8101 (mm) REVERT: h 763 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6830 (mm-30) REVERT: h 771 ILE cc_start: 0.8526 (tp) cc_final: 0.8231 (tp) REVERT: h 777 LYS cc_start: 0.8032 (tttt) cc_final: 0.7071 (tttt) REVERT: h 787 ILE cc_start: 0.8985 (tp) cc_final: 0.8770 (tt) REVERT: h 795 LEU cc_start: 0.8149 (mt) cc_final: 0.7913 (mp) REVERT: h 857 TYR cc_start: 0.8095 (m-80) cc_final: 0.7778 (m-10) REVERT: h 895 SER cc_start: 0.8219 (t) cc_final: 0.7927 (p) REVERT: h 921 GLN cc_start: 0.8049 (pt0) cc_final: 0.7692 (pt0) REVERT: h 962 LYS cc_start: 0.8642 (ptmt) cc_final: 0.8286 (ptmt) REVERT: h 965 LYS cc_start: 0.8058 (mttt) cc_final: 0.7746 (mttt) REVERT: h 1066 MET cc_start: 0.6390 (mmm) cc_final: 0.6154 (mmm) REVERT: h 1139 TYR cc_start: 0.7733 (m-80) cc_final: 0.7507 (m-80) REVERT: X 105 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6833 (tt0) REVERT: X 136 LEU cc_start: 0.8056 (tp) cc_final: 0.7391 (tt) REVERT: X 151 LYS cc_start: 0.7468 (ptpt) cc_final: 0.7089 (ttmt) REVERT: X 203 GLN cc_start: 0.7145 (mt0) cc_final: 0.6403 (mt0) REVERT: X 244 SER cc_start: 0.8564 (t) cc_final: 0.8183 (p) REVERT: X 250 LYS cc_start: 0.8315 (mttm) cc_final: 0.8084 (mttm) REVERT: X 259 ILE cc_start: 0.8234 (pt) cc_final: 0.7831 (mm) REVERT: X 285 ILE cc_start: 0.7963 (mt) cc_final: 0.7762 (mp) REVERT: X 286 THR cc_start: 0.8358 (p) cc_final: 0.8075 (p) REVERT: X 294 GLU cc_start: 0.7175 (mp0) cc_final: 0.6803 (mp0) REVERT: X 314 LYS cc_start: 0.8409 (tptt) cc_final: 0.8202 (tptp) REVERT: X 332 MET cc_start: 0.7961 (mmm) cc_final: 0.7173 (mmm) REVERT: X 346 GLU cc_start: 0.7236 (tt0) cc_final: 0.6926 (tt0) REVERT: X 364 ILE cc_start: 0.8799 (pt) cc_final: 0.8487 (mt) REVERT: X 380 GLU cc_start: 0.7538 (tt0) cc_final: 0.7276 (mt-10) REVERT: X 454 ARG cc_start: 0.7754 (mtp180) cc_final: 0.7423 (mtp85) REVERT: X 470 ILE cc_start: 0.8279 (tt) cc_final: 0.7993 (pt) REVERT: X 566 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7493 (mp0) REVERT: X 887 ARG cc_start: 0.7502 (ttm170) cc_final: 0.7166 (ttp-170) REVERT: X 915 ARG cc_start: 0.7106 (mmt-90) cc_final: 0.6769 (mmt-90) REVERT: X 927 GLN cc_start: 0.7827 (mt0) cc_final: 0.7296 (mt0) REVERT: X 932 TYR cc_start: 0.8237 (p90) cc_final: 0.8027 (p90) REVERT: X 933 LYS cc_start: 0.8193 (mttt) cc_final: 0.7694 (mttt) REVERT: X 941 TYR cc_start: 0.7482 (t80) cc_final: 0.7257 (t80) REVERT: X 942 MET cc_start: 0.5860 (tpt) cc_final: 0.5274 (tmm) REVERT: X 946 THR cc_start: 0.8030 (m) cc_final: 0.7167 (p) REVERT: X 984 PHE cc_start: 0.8113 (m-80) cc_final: 0.7898 (m-80) REVERT: X 985 LYS cc_start: 0.8464 (ttpt) cc_final: 0.8211 (ttpp) REVERT: X 986 LEU cc_start: 0.8950 (pp) cc_final: 0.8699 (pt) REVERT: X 1046 HIS cc_start: 0.8418 (m-70) cc_final: 0.8164 (m90) REVERT: X 1152 LEU cc_start: 0.8372 (tp) cc_final: 0.8137 (tp) REVERT: X 1168 ILE cc_start: 0.9308 (mm) cc_final: 0.9018 (mt) REVERT: X 1416 GLU cc_start: 0.7529 (tt0) cc_final: 0.7188 (tp30) REVERT: X 1436 ILE cc_start: 0.8092 (mm) cc_final: 0.7792 (mt) REVERT: X 1444 PHE cc_start: 0.7214 (m-80) cc_final: 0.6184 (m-80) REVERT: X 1445 LYS cc_start: 0.7869 (ttmt) cc_final: 0.7472 (mtpt) REVERT: X 1454 LYS cc_start: 0.7235 (tttt) cc_final: 0.6934 (ptmm) REVERT: X 1463 LYS cc_start: 0.8169 (tppp) cc_final: 0.7772 (tppp) REVERT: X 1468 LEU cc_start: 0.8452 (mm) cc_final: 0.8064 (mt) REVERT: X 1495 PHE cc_start: 0.8176 (m-80) cc_final: 0.7645 (m-80) REVERT: X 1497 TYR cc_start: 0.7858 (m-80) cc_final: 0.7607 (m-80) REVERT: X 1510 GLU cc_start: 0.7544 (tt0) cc_final: 0.7044 (tt0) REVERT: X 1569 PHE cc_start: 0.7206 (m-10) cc_final: 0.6650 (m-80) REVERT: X 1574 GLU cc_start: 0.7547 (tt0) cc_final: 0.7288 (tt0) REVERT: X 1575 MET cc_start: 0.7313 (mtt) cc_final: 0.6855 (mtt) outliers start: 0 outliers final: 0 residues processed: 937 average time/residue: 0.1990 time to fit residues: 285.9528 Evaluate side-chains 797 residues out of total 3118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 797 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.0870 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN C 111 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 301 ASN ** c 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 14 HIS h 542 HIS h 665 GLN h 784 GLN h1144 HIS X 981 ASN X1157 ASN ** X1478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1499 GLN Y 8 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.145854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.123361 restraints weight = 43439.484| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.42 r_work: 0.3522 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 28093 Z= 0.238 Angle : 0.592 8.333 37995 Z= 0.307 Chirality : 0.046 0.168 4230 Planarity : 0.005 0.092 4808 Dihedral : 4.504 44.168 3642 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.86 % Allowed : 10.33 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 3294 helix: 0.48 (0.15), residues: 1168 sheet: -0.38 (0.20), residues: 715 loop : -1.03 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG X 254 TYR 0.028 0.002 TYR X1507 PHE 0.024 0.002 PHE h 408 TRP 0.016 0.002 TRP C 75 HIS 0.011 0.001 HIS c 124 Details of bonding type rmsd covalent geometry : bond 0.00544 (28093) covalent geometry : angle 0.59202 (37995) hydrogen bonds : bond 0.04484 ( 1115) hydrogen bonds : angle 4.91080 ( 3171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 3118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 816 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 THR cc_start: 0.7980 (p) cc_final: 0.6498 (m) REVERT: C 23 VAL cc_start: 0.8041 (t) cc_final: 0.7783 (t) REVERT: C 54 ASP cc_start: 0.7976 (t0) cc_final: 0.7543 (t0) REVERT: C 95 ILE cc_start: 0.8120 (mp) cc_final: 0.7895 (mm) REVERT: C 189 LYS cc_start: 0.8013 (mttt) cc_final: 0.7768 (mtmt) REVERT: C 191 SER cc_start: 0.7718 (m) cc_final: 0.7045 (t) REVERT: C 217 ILE cc_start: 0.8109 (mt) cc_final: 0.7776 (tt) REVERT: C 229 TRP cc_start: 0.8156 (m-90) cc_final: 0.7241 (m-90) REVERT: C 237 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7511 (mm-30) REVERT: C 239 LYS cc_start: 0.8230 (tmmt) cc_final: 0.8023 (tmmt) REVERT: C 298 LYS cc_start: 0.8218 (mmtp) cc_final: 0.7982 (mptt) REVERT: C 345 TYR cc_start: 0.8278 (m-80) cc_final: 0.7980 (m-80) REVERT: C 347 LYS cc_start: 0.8591 (mttt) cc_final: 0.8342 (mttp) REVERT: C 348 VAL cc_start: 0.7738 (t) cc_final: 0.7450 (p) REVERT: C 349 ASN cc_start: 0.7782 (t0) cc_final: 0.7199 (t0) REVERT: C 363 TYR cc_start: 0.9031 (m-80) cc_final: 0.8430 (m-80) REVERT: C 411 ARG cc_start: 0.7308 (mtm-85) cc_final: 0.7001 (mtm-85) REVERT: C 445 VAL cc_start: 0.8116 (t) cc_final: 0.7658 (p) REVERT: C 447 GLU cc_start: 0.6306 (mm-30) cc_final: 0.6074 (mt-10) REVERT: C 448 LYS cc_start: 0.8111 (tttt) cc_final: 0.7806 (tttp) REVERT: C 474 PHE cc_start: 0.7441 (t80) cc_final: 0.7146 (t80) REVERT: C 480 ASN cc_start: 0.7222 (m-40) cc_final: 0.6939 (t0) REVERT: a 61 ASP cc_start: 0.7455 (t70) cc_final: 0.7128 (t0) REVERT: a 97 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6945 (mt-10) REVERT: a 146 ASN cc_start: 0.7662 (m110) cc_final: 0.7253 (m-40) REVERT: a 154 PHE cc_start: 0.7853 (m-80) cc_final: 0.7547 (m-10) REVERT: a 170 SER cc_start: 0.7905 (p) cc_final: 0.7662 (t) REVERT: a 188 ASN cc_start: 0.7767 (m110) cc_final: 0.7447 (m-40) REVERT: a 192 ASN cc_start: 0.8242 (m-40) cc_final: 0.7976 (m-40) REVERT: a 194 LYS cc_start: 0.8015 (mttt) cc_final: 0.7582 (mtpp) REVERT: a 265 LYS cc_start: 0.8627 (tttt) cc_final: 0.8150 (ttmm) REVERT: c 15 MET cc_start: 0.6674 (mtp) cc_final: 0.6376 (mtt) REVERT: c 18 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7720 (mtt-85) REVERT: c 91 ASP cc_start: 0.7759 (t0) cc_final: 0.7417 (t70) REVERT: c 102 ASN cc_start: 0.7861 (t0) cc_final: 0.7399 (m-40) REVERT: c 103 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8121 (tp) REVERT: c 105 MET cc_start: 0.6844 (mtt) cc_final: 0.6543 (mtm) REVERT: c 106 ILE cc_start: 0.7978 (mt) cc_final: 0.7616 (mm) REVERT: c 119 ILE cc_start: 0.8034 (mt) cc_final: 0.7712 (mm) REVERT: c 124 HIS cc_start: 0.7936 (t70) cc_final: 0.7689 (t70) REVERT: c 148 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7353 (mt-10) REVERT: c 173 GLU cc_start: 0.8017 (tt0) cc_final: 0.7766 (tp30) REVERT: c 195 ASN cc_start: 0.7357 (m-40) cc_final: 0.7078 (m-40) REVERT: c 220 SER cc_start: 0.8522 (m) cc_final: 0.8171 (p) REVERT: c 242 PHE cc_start: 0.8244 (t80) cc_final: 0.8010 (t80) REVERT: c 243 ASP cc_start: 0.7777 (m-30) cc_final: 0.7344 (m-30) REVERT: c 274 GLN cc_start: 0.8326 (tt0) cc_final: 0.8046 (tt0) REVERT: c 284 ARG cc_start: 0.7694 (ttm170) cc_final: 0.7412 (mtp180) REVERT: c 303 MET cc_start: 0.5972 (ttt) cc_final: 0.5751 (ttt) REVERT: c 317 PHE cc_start: 0.8066 (t80) cc_final: 0.7855 (t80) REVERT: c 321 LEU cc_start: 0.8112 (tp) cc_final: 0.7745 (tt) REVERT: T 28 LYS cc_start: 0.7856 (tptt) cc_final: 0.7413 (tppt) REVERT: T 37 LYS cc_start: 0.8275 (mmtp) cc_final: 0.8017 (mmtp) REVERT: T 62 THR cc_start: 0.8281 (m) cc_final: 0.7873 (p) REVERT: T 90 ASN cc_start: 0.7836 (t0) cc_final: 0.7548 (t0) REVERT: T 98 ASP cc_start: 0.7971 (t0) cc_final: 0.7512 (t0) REVERT: T 120 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7466 (mt-10) REVERT: T 207 ASP cc_start: 0.7356 (m-30) cc_final: 0.7133 (m-30) REVERT: T 220 GLU cc_start: 0.7536 (mp0) cc_final: 0.7222 (mp0) REVERT: T 229 PHE cc_start: 0.8271 (m-80) cc_final: 0.7780 (m-80) REVERT: T 243 ASP cc_start: 0.7156 (m-30) cc_final: 0.6902 (m-30) REVERT: T 246 LEU cc_start: 0.8208 (mt) cc_final: 0.7928 (mt) REVERT: T 291 ILE cc_start: 0.7266 (mm) cc_final: 0.7062 (mt) REVERT: T 322 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7352 (ttt180) REVERT: T 335 GLN cc_start: 0.7603 (mt0) cc_final: 0.7238 (mt0) REVERT: T 352 ASN cc_start: 0.7681 (m-40) cc_final: 0.7371 (m-40) REVERT: T 452 LYS cc_start: 0.8482 (tttt) cc_final: 0.8072 (tttp) REVERT: T 487 SER cc_start: 0.7955 (m) cc_final: 0.7620 (p) REVERT: T 578 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7062 (mm-30) REVERT: T 606 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6735 (mm-30) REVERT: h 20 HIS cc_start: 0.7605 (m-70) cc_final: 0.7329 (m90) REVERT: h 368 MET cc_start: 0.7205 (tpt) cc_final: 0.6786 (tpt) REVERT: h 383 GLU cc_start: 0.7572 (mm-30) cc_final: 0.6928 (mm-30) REVERT: h 387 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7482 (mt-10) REVERT: h 528 LYS cc_start: 0.8536 (mtpt) cc_final: 0.8280 (mtpt) REVERT: h 577 SER cc_start: 0.7871 (m) cc_final: 0.7644 (t) REVERT: h 585 GLU cc_start: 0.7911 (tp30) cc_final: 0.7643 (tp30) REVERT: h 597 GLN cc_start: 0.8203 (mp10) cc_final: 0.7694 (mp10) REVERT: h 607 LYS cc_start: 0.8422 (ttmt) cc_final: 0.8153 (ttpt) REVERT: h 610 TYR cc_start: 0.8165 (m-80) cc_final: 0.7751 (m-80) REVERT: h 628 ASP cc_start: 0.7511 (m-30) cc_final: 0.6963 (m-30) REVERT: h 632 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7821 (ttm170) REVERT: h 635 ILE cc_start: 0.8467 (mp) cc_final: 0.8244 (mt) REVERT: h 643 ASP cc_start: 0.7382 (t0) cc_final: 0.7069 (t0) REVERT: h 652 ILE cc_start: 0.7640 (mt) cc_final: 0.7363 (tt) REVERT: h 745 LEU cc_start: 0.7884 (mm) cc_final: 0.7630 (mt) REVERT: h 759 ILE cc_start: 0.8430 (mm) cc_final: 0.8219 (mm) REVERT: h 763 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6898 (mm-30) REVERT: h 801 ASP cc_start: 0.6685 (OUTLIER) cc_final: 0.5952 (m-30) REVERT: h 857 TYR cc_start: 0.8318 (m-80) cc_final: 0.7988 (m-10) REVERT: h 860 ASP cc_start: 0.7799 (p0) cc_final: 0.7597 (p0) REVERT: h 895 SER cc_start: 0.8152 (t) cc_final: 0.7826 (p) REVERT: h 921 GLN cc_start: 0.8356 (pt0) cc_final: 0.7992 (pt0) REVERT: h 932 HIS cc_start: 0.6877 (m90) cc_final: 0.6444 (m90) REVERT: h 962 LYS cc_start: 0.8665 (ptmt) cc_final: 0.8293 (ptmt) REVERT: h 965 LYS cc_start: 0.7844 (mttt) cc_final: 0.7554 (mtpt) REVERT: h 1066 MET cc_start: 0.6443 (mmm) cc_final: 0.6177 (mmm) REVERT: h 1084 LYS cc_start: 0.8343 (mttt) cc_final: 0.8075 (mtpp) REVERT: h 1104 LYS cc_start: 0.8563 (ttpt) cc_final: 0.8353 (ttpp) REVERT: h 1112 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7723 (mtpt) REVERT: h 1116 GLU cc_start: 0.8104 (mp0) cc_final: 0.7754 (mp0) REVERT: h 1139 TYR cc_start: 0.7890 (m-80) cc_final: 0.7649 (m-80) REVERT: X 103 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7702 (tm-30) REVERT: X 105 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7101 (tt0) REVERT: X 136 LEU cc_start: 0.8074 (tp) cc_final: 0.7497 (tt) REVERT: X 203 GLN cc_start: 0.7029 (mt0) cc_final: 0.6785 (mt0) REVERT: X 244 SER cc_start: 0.8436 (t) cc_final: 0.8115 (p) REVERT: X 250 LYS cc_start: 0.8135 (mttm) cc_final: 0.7927 (mttp) REVERT: X 259 ILE cc_start: 0.8208 (pt) cc_final: 0.7882 (mm) REVERT: X 286 THR cc_start: 0.8229 (p) cc_final: 0.7980 (p) REVERT: X 294 GLU cc_start: 0.7003 (mp0) cc_final: 0.6421 (mp0) REVERT: X 310 LYS cc_start: 0.7779 (mttp) cc_final: 0.7576 (mttp) REVERT: X 314 LYS cc_start: 0.8407 (tptt) cc_final: 0.8187 (tptp) REVERT: X 332 MET cc_start: 0.7812 (mmm) cc_final: 0.7046 (mmm) REVERT: X 380 GLU cc_start: 0.7751 (tt0) cc_final: 0.7428 (mt-10) REVERT: X 454 ARG cc_start: 0.8019 (mtp180) cc_final: 0.7716 (mtp85) REVERT: X 470 ILE cc_start: 0.8268 (tt) cc_final: 0.7976 (pt) REVERT: X 503 PHE cc_start: 0.8173 (m-10) cc_final: 0.7961 (m-10) REVERT: X 566 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7446 (mp0) REVERT: X 887 ARG cc_start: 0.7495 (ttm170) cc_final: 0.7223 (ttp-170) REVERT: X 905 LYS cc_start: 0.8117 (tptp) cc_final: 0.7658 (tptp) REVERT: X 933 LYS cc_start: 0.8309 (mttt) cc_final: 0.7854 (mttt) REVERT: X 944 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8258 (mp) REVERT: X 946 THR cc_start: 0.8012 (m) cc_final: 0.6235 (t) REVERT: X 984 PHE cc_start: 0.8353 (m-80) cc_final: 0.8040 (m-80) REVERT: X 985 LYS cc_start: 0.8710 (ttpt) cc_final: 0.8432 (ttpp) REVERT: X 1152 LEU cc_start: 0.8381 (tp) cc_final: 0.8135 (tp) REVERT: X 1153 TYR cc_start: 0.7495 (m-80) cc_final: 0.7255 (m-80) REVERT: X 1436 ILE cc_start: 0.8219 (mm) cc_final: 0.7914 (mt) REVERT: X 1443 GLU cc_start: 0.7785 (tt0) cc_final: 0.7502 (tt0) REVERT: X 1444 PHE cc_start: 0.7035 (m-80) cc_final: 0.6497 (m-80) REVERT: X 1445 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7623 (mtpt) REVERT: X 1454 LYS cc_start: 0.7337 (tttt) cc_final: 0.6966 (tttt) REVERT: X 1463 LYS cc_start: 0.8167 (tppp) cc_final: 0.7770 (tppp) REVERT: X 1495 PHE cc_start: 0.8151 (m-80) cc_final: 0.7771 (m-80) REVERT: X 1499 GLN cc_start: 0.7367 (tt0) cc_final: 0.7134 (tt0) REVERT: X 1510 GLU cc_start: 0.7540 (tt0) cc_final: 0.7262 (tt0) REVERT: X 1569 PHE cc_start: 0.7183 (m-10) cc_final: 0.6543 (m-80) REVERT: X 1574 GLU cc_start: 0.7632 (tt0) cc_final: 0.7403 (tt0) REVERT: X 1575 MET cc_start: 0.7677 (mtt) cc_final: 0.7208 (mtt) REVERT: Y 36 MET cc_start: 0.5948 (ptp) cc_final: 0.5693 (ptp) REVERT: Y 131 PHE cc_start: 0.8034 (m-10) cc_final: 0.7784 (m-10) REVERT: Y 150 MET cc_start: 0.8149 (tpt) cc_final: 0.7401 (tmm) outliers start: 58 outliers final: 27 residues processed: 837 average time/residue: 0.2094 time to fit residues: 269.3581 Evaluate side-chains 810 residues out of total 3118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 778 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain a residue 15 SER Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 199 ILE Chi-restraints excluded: chain a residue 205 ILE Chi-restraints excluded: chain c residue 18 ARG Chi-restraints excluded: chain c residue 103 LEU Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain c residue 197 ILE Chi-restraints excluded: chain c residue 244 LEU Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 225 ASP Chi-restraints excluded: chain T residue 236 THR Chi-restraints excluded: chain T residue 322 ARG Chi-restraints excluded: chain h residue 410 SER Chi-restraints excluded: chain h residue 532 MET Chi-restraints excluded: chain h residue 545 GLU Chi-restraints excluded: chain h residue 633 ASN Chi-restraints excluded: chain h residue 801 ASP Chi-restraints excluded: chain h residue 1124 ILE Chi-restraints excluded: chain X residue 541 VAL Chi-restraints excluded: chain X residue 869 ILE Chi-restraints excluded: chain X residue 872 LYS Chi-restraints excluded: chain X residue 920 THR Chi-restraints excluded: chain X residue 944 LEU Chi-restraints excluded: chain X residue 951 CYS Chi-restraints excluded: chain X residue 1011 LEU Chi-restraints excluded: chain X residue 1374 ASP Chi-restraints excluded: chain X residue 1514 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 272 optimal weight: 0.5980 chunk 188 optimal weight: 0.9990 chunk 301 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 117 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 267 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 71 ASN c 191 ASN h 14 HIS ** h 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 542 HIS h 782 ASN X 981 ASN X1371 HIS ** X1478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.146049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.123484 restraints weight = 43490.651| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.43 r_work: 0.3522 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28093 Z= 0.191 Angle : 0.558 7.062 37995 Z= 0.287 Chirality : 0.046 0.205 4230 Planarity : 0.004 0.062 4808 Dihedral : 4.443 43.456 3642 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.18 % Allowed : 13.25 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.15), residues: 3294 helix: 0.77 (0.15), residues: 1163 sheet: -0.45 (0.20), residues: 724 loop : -0.98 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 254 TYR 0.041 0.002 TYR X1507 PHE 0.023 0.002 PHE T 472 TRP 0.015 0.002 TRP C 142 HIS 0.012 0.001 HIS h 534 Details of bonding type rmsd covalent geometry : bond 0.00436 (28093) covalent geometry : angle 0.55849 (37995) hydrogen bonds : bond 0.03843 ( 1115) hydrogen bonds : angle 4.70970 ( 3171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 3118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 796 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 THR cc_start: 0.8038 (p) cc_final: 0.6584 (m) REVERT: C 23 VAL cc_start: 0.8062 (t) cc_final: 0.7804 (t) REVERT: C 54 ASP cc_start: 0.7983 (t0) cc_final: 0.7612 (t0) REVERT: C 61 TRP cc_start: 0.8076 (t60) cc_final: 0.7754 (t60) REVERT: C 95 ILE cc_start: 0.8017 (mp) cc_final: 0.7798 (mm) REVERT: C 128 ASP cc_start: 0.7706 (m-30) cc_final: 0.7482 (m-30) REVERT: C 144 MET cc_start: 0.8165 (mmm) cc_final: 0.7636 (mtt) REVERT: C 189 LYS cc_start: 0.8001 (mttt) cc_final: 0.7768 (mtmt) REVERT: C 191 SER cc_start: 0.7816 (m) cc_final: 0.7141 (t) REVERT: C 217 ILE cc_start: 0.8069 (mt) cc_final: 0.7797 (tt) REVERT: C 229 TRP cc_start: 0.8170 (m-90) cc_final: 0.7235 (m-90) REVERT: C 237 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7555 (mm-30) REVERT: C 239 LYS cc_start: 0.8225 (tmmt) cc_final: 0.7988 (tmmt) REVERT: C 240 ARG cc_start: 0.7628 (ttm170) cc_final: 0.7413 (ttm-80) REVERT: C 298 LYS cc_start: 0.8242 (mmtp) cc_final: 0.7985 (mptt) REVERT: C 347 LYS cc_start: 0.8579 (mttt) cc_final: 0.8317 (mttp) REVERT: C 348 VAL cc_start: 0.7647 (t) cc_final: 0.7329 (p) REVERT: C 349 ASN cc_start: 0.7781 (t0) cc_final: 0.7165 (t0) REVERT: C 363 TYR cc_start: 0.9041 (m-80) cc_final: 0.8471 (m-80) REVERT: C 412 MET cc_start: 0.8107 (tpp) cc_final: 0.7823 (mmm) REVERT: C 445 VAL cc_start: 0.8106 (t) cc_final: 0.7627 (p) REVERT: C 448 LYS cc_start: 0.8045 (tttt) cc_final: 0.7725 (tttp) REVERT: C 480 ASN cc_start: 0.7255 (m-40) cc_final: 0.6957 (t0) REVERT: C 484 ASN cc_start: 0.7688 (m-40) cc_final: 0.7450 (m-40) REVERT: a 17 SER cc_start: 0.8499 (m) cc_final: 0.8262 (p) REVERT: a 61 ASP cc_start: 0.7460 (t70) cc_final: 0.7153 (t0) REVERT: a 97 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6925 (mt-10) REVERT: a 127 LYS cc_start: 0.8885 (mttt) cc_final: 0.8633 (mtpt) REVERT: a 146 ASN cc_start: 0.7675 (m110) cc_final: 0.7273 (m-40) REVERT: a 148 SER cc_start: 0.8540 (t) cc_final: 0.8253 (t) REVERT: a 154 PHE cc_start: 0.7877 (m-80) cc_final: 0.7566 (m-10) REVERT: a 170 SER cc_start: 0.7938 (p) cc_final: 0.7651 (t) REVERT: a 173 LYS cc_start: 0.7517 (tttt) cc_final: 0.7197 (ttpt) REVERT: a 188 ASN cc_start: 0.7808 (m110) cc_final: 0.7484 (m-40) REVERT: a 192 ASN cc_start: 0.8224 (m-40) cc_final: 0.7926 (m-40) REVERT: a 194 LYS cc_start: 0.8003 (mttt) cc_final: 0.7547 (mtpp) REVERT: a 213 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.7085 (t80) REVERT: a 245 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7867 (mtmt) REVERT: a 265 LYS cc_start: 0.8597 (tttt) cc_final: 0.8133 (ttmm) REVERT: c 15 MET cc_start: 0.6644 (mtp) cc_final: 0.6326 (mtt) REVERT: c 18 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7710 (mtt-85) REVERT: c 88 TYR cc_start: 0.7804 (t80) cc_final: 0.7540 (t80) REVERT: c 91 ASP cc_start: 0.7693 (t0) cc_final: 0.7350 (t70) REVERT: c 102 ASN cc_start: 0.7953 (t0) cc_final: 0.7269 (m-40) REVERT: c 103 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8128 (tp) REVERT: c 105 MET cc_start: 0.6884 (mtt) cc_final: 0.6555 (mtm) REVERT: c 106 ILE cc_start: 0.7963 (mt) cc_final: 0.7577 (mm) REVERT: c 119 ILE cc_start: 0.7990 (mt) cc_final: 0.7720 (mm) REVERT: c 120 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6455 (mm-30) REVERT: c 124 HIS cc_start: 0.7978 (t70) cc_final: 0.7446 (t-90) REVERT: c 148 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7392 (mt-10) REVERT: c 181 LYS cc_start: 0.8064 (mttt) cc_final: 0.7751 (mtpt) REVERT: c 191 ASN cc_start: 0.7767 (t0) cc_final: 0.7144 (t0) REVERT: c 195 ASN cc_start: 0.7344 (m-40) cc_final: 0.7048 (m-40) REVERT: c 220 SER cc_start: 0.8466 (m) cc_final: 0.7972 (p) REVERT: c 242 PHE cc_start: 0.8259 (t80) cc_final: 0.8034 (t80) REVERT: c 243 ASP cc_start: 0.7794 (m-30) cc_final: 0.7339 (m-30) REVERT: c 274 GLN cc_start: 0.8308 (tt0) cc_final: 0.7944 (tt0) REVERT: c 275 LEU cc_start: 0.8788 (mt) cc_final: 0.8503 (mt) REVERT: c 284 ARG cc_start: 0.7682 (ttm170) cc_final: 0.7351 (mtp180) REVERT: c 286 MET cc_start: 0.7543 (mmm) cc_final: 0.7278 (mtp) REVERT: c 317 PHE cc_start: 0.8107 (t80) cc_final: 0.7890 (t80) REVERT: T 28 LYS cc_start: 0.7843 (tptt) cc_final: 0.7421 (tppt) REVERT: T 37 LYS cc_start: 0.8282 (mmtp) cc_final: 0.8030 (mmtp) REVERT: T 62 THR cc_start: 0.8314 (m) cc_final: 0.7900 (p) REVERT: T 81 ILE cc_start: 0.8519 (mt) cc_final: 0.8286 (mm) REVERT: T 90 ASN cc_start: 0.7796 (t0) cc_final: 0.7551 (t0) REVERT: T 117 VAL cc_start: 0.7660 (t) cc_final: 0.7458 (p) REVERT: T 120 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7448 (mt-10) REVERT: T 207 ASP cc_start: 0.7291 (m-30) cc_final: 0.7048 (m-30) REVERT: T 220 GLU cc_start: 0.7530 (mp0) cc_final: 0.7213 (mp0) REVERT: T 229 PHE cc_start: 0.8253 (m-80) cc_final: 0.7794 (m-80) REVERT: T 243 ASP cc_start: 0.7192 (m-30) cc_final: 0.6943 (m-30) REVERT: T 246 LEU cc_start: 0.8164 (mt) cc_final: 0.7902 (mt) REVERT: T 260 ASP cc_start: 0.7438 (t0) cc_final: 0.7151 (m-30) REVERT: T 291 ILE cc_start: 0.7236 (mm) cc_final: 0.7031 (mt) REVERT: T 322 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7330 (ttt180) REVERT: T 333 ASP cc_start: 0.7849 (t70) cc_final: 0.7634 (t0) REVERT: T 335 GLN cc_start: 0.7588 (mt0) cc_final: 0.7217 (mt0) REVERT: T 352 ASN cc_start: 0.7687 (m-40) cc_final: 0.7384 (m-40) REVERT: T 452 LYS cc_start: 0.8501 (tttt) cc_final: 0.8184 (tttp) REVERT: T 487 SER cc_start: 0.7978 (m) cc_final: 0.7647 (p) REVERT: T 578 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6964 (mm-30) REVERT: T 588 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7398 (ttmt) REVERT: h 368 MET cc_start: 0.7151 (tpt) cc_final: 0.6800 (tpt) REVERT: h 383 GLU cc_start: 0.7519 (mm-30) cc_final: 0.6871 (mm-30) REVERT: h 387 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7454 (mt-10) REVERT: h 528 LYS cc_start: 0.8505 (mtpt) cc_final: 0.8273 (mtpt) REVERT: h 577 SER cc_start: 0.7908 (m) cc_final: 0.7688 (t) REVERT: h 580 HIS cc_start: 0.8257 (t-170) cc_final: 0.8000 (t-170) REVERT: h 597 GLN cc_start: 0.8217 (mp10) cc_final: 0.7776 (mp10) REVERT: h 607 LYS cc_start: 0.8419 (ttmt) cc_final: 0.7962 (ttmt) REVERT: h 610 TYR cc_start: 0.8139 (m-80) cc_final: 0.7687 (m-80) REVERT: h 628 ASP cc_start: 0.7411 (m-30) cc_final: 0.6855 (m-30) REVERT: h 632 ARG cc_start: 0.8153 (ttm170) cc_final: 0.7851 (ttm170) REVERT: h 635 ILE cc_start: 0.8495 (mp) cc_final: 0.8269 (mt) REVERT: h 643 ASP cc_start: 0.7310 (t0) cc_final: 0.7001 (t0) REVERT: h 652 ILE cc_start: 0.7688 (mt) cc_final: 0.7432 (tt) REVERT: h 658 LYS cc_start: 0.8259 (ptmt) cc_final: 0.8059 (ptmt) REVERT: h 745 LEU cc_start: 0.7824 (mm) cc_final: 0.7519 (mt) REVERT: h 759 ILE cc_start: 0.8433 (mm) cc_final: 0.8211 (mm) REVERT: h 776 LEU cc_start: 0.7867 (tp) cc_final: 0.7458 (mt) REVERT: h 782 ASN cc_start: 0.7342 (m-40) cc_final: 0.7072 (m-40) REVERT: h 801 ASP cc_start: 0.6824 (OUTLIER) cc_final: 0.6065 (m-30) REVERT: h 857 TYR cc_start: 0.8330 (m-80) cc_final: 0.8019 (m-10) REVERT: h 860 ASP cc_start: 0.7778 (p0) cc_final: 0.7511 (p0) REVERT: h 895 SER cc_start: 0.8117 (t) cc_final: 0.7836 (p) REVERT: h 921 GLN cc_start: 0.8275 (pt0) cc_final: 0.7883 (pt0) REVERT: h 932 HIS cc_start: 0.6772 (m90) cc_final: 0.6292 (m90) REVERT: h 962 LYS cc_start: 0.8571 (ptmt) cc_final: 0.8183 (ptmt) REVERT: h 965 LYS cc_start: 0.7834 (mttt) cc_final: 0.7457 (mtpp) REVERT: h 1066 MET cc_start: 0.6422 (mmm) cc_final: 0.6169 (mmm) REVERT: h 1084 LYS cc_start: 0.8338 (mttt) cc_final: 0.8066 (mtpp) REVERT: h 1112 LYS cc_start: 0.8265 (mtpt) cc_final: 0.7801 (mtpt) REVERT: h 1116 GLU cc_start: 0.8090 (mp0) cc_final: 0.7683 (mm-30) REVERT: h 1139 TYR cc_start: 0.7884 (m-80) cc_final: 0.7647 (m-80) REVERT: X 103 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7732 (tm-30) REVERT: X 105 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7040 (tt0) REVERT: X 136 LEU cc_start: 0.8070 (tp) cc_final: 0.7508 (tt) REVERT: X 150 LYS cc_start: 0.8184 (ptpt) cc_final: 0.7880 (pttt) REVERT: X 203 GLN cc_start: 0.7019 (mt0) cc_final: 0.6791 (mt0) REVERT: X 244 SER cc_start: 0.8463 (t) cc_final: 0.8099 (p) REVERT: X 250 LYS cc_start: 0.8150 (mttm) cc_final: 0.7944 (mttp) REVERT: X 259 ILE cc_start: 0.8208 (pt) cc_final: 0.7890 (mm) REVERT: X 269 ARG cc_start: 0.8393 (mtm-85) cc_final: 0.8126 (mtp180) REVERT: X 286 THR cc_start: 0.8192 (p) cc_final: 0.7952 (p) REVERT: X 310 LYS cc_start: 0.7762 (mttp) cc_final: 0.7559 (mttp) REVERT: X 314 LYS cc_start: 0.8399 (tptt) cc_final: 0.8194 (tptp) REVERT: X 332 MET cc_start: 0.7728 (mmm) cc_final: 0.6984 (mmm) REVERT: X 380 GLU cc_start: 0.7674 (tt0) cc_final: 0.7290 (mt-10) REVERT: X 454 ARG cc_start: 0.8036 (mtp180) cc_final: 0.7751 (mtp85) REVERT: X 566 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7481 (mp0) REVERT: X 887 ARG cc_start: 0.7513 (ttm170) cc_final: 0.7236 (ttp-170) REVERT: X 905 LYS cc_start: 0.8220 (tptp) cc_final: 0.7750 (tptp) REVERT: X 913 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8336 (mm) REVERT: X 933 LYS cc_start: 0.8336 (mttt) cc_final: 0.7902 (mttt) REVERT: X 946 THR cc_start: 0.7937 (m) cc_final: 0.6273 (t) REVERT: X 985 LYS cc_start: 0.8751 (ttpt) cc_final: 0.8462 (ttpp) REVERT: X 1152 LEU cc_start: 0.8451 (tp) cc_final: 0.8247 (tt) REVERT: X 1153 TYR cc_start: 0.7780 (m-80) cc_final: 0.7394 (m-80) REVERT: X 1436 ILE cc_start: 0.8176 (mm) cc_final: 0.7946 (mm) REVERT: X 1443 GLU cc_start: 0.7832 (tt0) cc_final: 0.7553 (tt0) REVERT: X 1444 PHE cc_start: 0.7054 (m-80) cc_final: 0.6379 (m-80) REVERT: X 1454 LYS cc_start: 0.7260 (tttt) cc_final: 0.6906 (tttt) REVERT: X 1463 LYS cc_start: 0.8166 (tppp) cc_final: 0.7749 (tppp) REVERT: X 1495 PHE cc_start: 0.7972 (m-80) cc_final: 0.7684 (m-80) REVERT: X 1510 GLU cc_start: 0.7580 (tt0) cc_final: 0.7112 (tt0) REVERT: X 1569 PHE cc_start: 0.7192 (m-10) cc_final: 0.6532 (m-80) REVERT: X 1574 GLU cc_start: 0.7631 (tt0) cc_final: 0.7400 (tt0) REVERT: X 1575 MET cc_start: 0.7629 (mtt) cc_final: 0.7168 (mtt) REVERT: Y 130 LEU cc_start: 0.8243 (tt) cc_final: 0.8030 (tt) REVERT: Y 131 PHE cc_start: 0.7947 (m-10) cc_final: 0.7709 (m-10) outliers start: 68 outliers final: 35 residues processed: 821 average time/residue: 0.2135 time to fit residues: 269.3966 Evaluate side-chains 819 residues out of total 3118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 776 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain a residue 98 VAL Chi-restraints excluded: chain a residue 99 LEU Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 199 ILE Chi-restraints excluded: chain a residue 205 ILE Chi-restraints excluded: chain a residue 213 PHE Chi-restraints excluded: chain a residue 245 LYS Chi-restraints excluded: chain a residue 275 VAL Chi-restraints excluded: chain c residue 18 ARG Chi-restraints excluded: chain c residue 103 LEU Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain c residue 197 ILE Chi-restraints excluded: chain c residue 244 LEU Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 322 ARG Chi-restraints excluded: chain T residue 462 LEU Chi-restraints excluded: chain T residue 588 LYS Chi-restraints excluded: chain h residue 410 SER Chi-restraints excluded: chain h residue 532 MET Chi-restraints excluded: chain h residue 545 GLU Chi-restraints excluded: chain h residue 633 ASN Chi-restraints excluded: chain h residue 801 ASP Chi-restraints excluded: chain h residue 954 THR Chi-restraints excluded: chain X residue 368 VAL Chi-restraints excluded: chain X residue 433 THR Chi-restraints excluded: chain X residue 528 MET Chi-restraints excluded: chain X residue 541 VAL Chi-restraints excluded: chain X residue 561 ASP Chi-restraints excluded: chain X residue 869 ILE Chi-restraints excluded: chain X residue 913 ILE Chi-restraints excluded: chain X residue 920 THR Chi-restraints excluded: chain X residue 951 CYS Chi-restraints excluded: chain X residue 1145 VAL Chi-restraints excluded: chain X residue 1146 MET Chi-restraints excluded: chain X residue 1374 ASP Chi-restraints excluded: chain X residue 1390 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 93 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 170 optimal weight: 0.9990 chunk 203 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 329 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 326 optimal weight: 0.8980 chunk 209 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 ASN C 90 ASN C 111 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 ASN a 71 ASN h 14 HIS h 20 HIS h 534 HIS h 542 HIS h 653 GLN X 981 ASN ** X1478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1499 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.145142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.122585 restraints weight = 43226.676| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.41 r_work: 0.3511 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28093 Z= 0.228 Angle : 0.574 8.192 37995 Z= 0.296 Chirality : 0.046 0.174 4230 Planarity : 0.004 0.056 4808 Dihedral : 4.498 43.009 3642 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.57 % Allowed : 14.34 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.15), residues: 3294 helix: 0.83 (0.15), residues: 1160 sheet: -0.48 (0.20), residues: 719 loop : -1.00 (0.16), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 254 TYR 0.044 0.002 TYR X1507 PHE 0.024 0.002 PHE T 472 TRP 0.013 0.002 TRP X 222 HIS 0.010 0.001 HIS X1371 Details of bonding type rmsd covalent geometry : bond 0.00521 (28093) covalent geometry : angle 0.57417 (37995) hydrogen bonds : bond 0.03919 ( 1115) hydrogen bonds : angle 4.69654 ( 3171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 3118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 788 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 THR cc_start: 0.8233 (p) cc_final: 0.6829 (m) REVERT: C 23 VAL cc_start: 0.8277 (t) cc_final: 0.8013 (t) REVERT: C 54 ASP cc_start: 0.8169 (t0) cc_final: 0.7809 (t0) REVERT: C 61 TRP cc_start: 0.8266 (t60) cc_final: 0.7962 (t60) REVERT: C 95 ILE cc_start: 0.8134 (mp) cc_final: 0.7911 (mm) REVERT: C 128 ASP cc_start: 0.8032 (m-30) cc_final: 0.7791 (m-30) REVERT: C 144 MET cc_start: 0.8288 (mmm) cc_final: 0.7786 (mtt) REVERT: C 189 LYS cc_start: 0.8136 (mttt) cc_final: 0.7850 (mtmt) REVERT: C 191 SER cc_start: 0.8013 (m) cc_final: 0.7328 (t) REVERT: C 217 ILE cc_start: 0.8213 (mt) cc_final: 0.7945 (tt) REVERT: C 229 TRP cc_start: 0.8299 (m-90) cc_final: 0.7389 (m-90) REVERT: C 237 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7861 (mm-30) REVERT: C 239 LYS cc_start: 0.8398 (tmmt) cc_final: 0.8152 (tmmt) REVERT: C 298 LYS cc_start: 0.8394 (mmtp) cc_final: 0.8069 (mptt) REVERT: C 343 SER cc_start: 0.8390 (m) cc_final: 0.8123 (m) REVERT: C 347 LYS cc_start: 0.8667 (mttt) cc_final: 0.8345 (mttp) REVERT: C 348 VAL cc_start: 0.7682 (t) cc_final: 0.7334 (p) REVERT: C 349 ASN cc_start: 0.7915 (t0) cc_final: 0.7271 (t0) REVERT: C 363 TYR cc_start: 0.9101 (m-80) cc_final: 0.8514 (m-80) REVERT: C 445 VAL cc_start: 0.8231 (t) cc_final: 0.7769 (p) REVERT: C 448 LYS cc_start: 0.8120 (tttt) cc_final: 0.7803 (tttp) REVERT: C 480 ASN cc_start: 0.7377 (m-40) cc_final: 0.7069 (t0) REVERT: C 484 ASN cc_start: 0.7849 (m-40) cc_final: 0.7623 (m-40) REVERT: a 15 SER cc_start: 0.8519 (p) cc_final: 0.8263 (t) REVERT: a 17 SER cc_start: 0.8603 (m) cc_final: 0.8349 (p) REVERT: a 61 ASP cc_start: 0.7740 (t70) cc_final: 0.7423 (t0) REVERT: a 97 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7203 (mt-10) REVERT: a 146 ASN cc_start: 0.7806 (m110) cc_final: 0.7398 (m-40) REVERT: a 147 LEU cc_start: 0.7784 (mt) cc_final: 0.7581 (mt) REVERT: a 148 SER cc_start: 0.8554 (t) cc_final: 0.8266 (t) REVERT: a 154 PHE cc_start: 0.8068 (m-80) cc_final: 0.7711 (m-10) REVERT: a 170 SER cc_start: 0.8106 (p) cc_final: 0.7779 (t) REVERT: a 188 ASN cc_start: 0.7931 (m110) cc_final: 0.7390 (m-40) REVERT: a 192 ASN cc_start: 0.8320 (m-40) cc_final: 0.7958 (m-40) REVERT: a 194 LYS cc_start: 0.8080 (mttt) cc_final: 0.7639 (mtpp) REVERT: a 213 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.7255 (t80) REVERT: a 248 ASN cc_start: 0.8059 (t0) cc_final: 0.7812 (t0) REVERT: a 265 LYS cc_start: 0.8672 (tttt) cc_final: 0.8173 (ttmm) REVERT: c 15 MET cc_start: 0.7025 (mtp) cc_final: 0.6697 (mtt) REVERT: c 18 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7880 (mtt-85) REVERT: c 102 ASN cc_start: 0.8060 (t0) cc_final: 0.7333 (m-40) REVERT: c 103 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8200 (tp) REVERT: c 105 MET cc_start: 0.7199 (mtt) cc_final: 0.6953 (mtm) REVERT: c 106 ILE cc_start: 0.8157 (mt) cc_final: 0.7841 (mt) REVERT: c 119 ILE cc_start: 0.8168 (mt) cc_final: 0.7805 (mm) REVERT: c 120 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6842 (mm-30) REVERT: c 124 HIS cc_start: 0.8177 (t70) cc_final: 0.7648 (t-90) REVERT: c 148 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7714 (mt-10) REVERT: c 181 LYS cc_start: 0.8270 (mttt) cc_final: 0.7945 (mtpt) REVERT: c 219 ASP cc_start: 0.8353 (p0) cc_final: 0.8082 (p0) REVERT: c 220 SER cc_start: 0.8479 (m) cc_final: 0.8058 (p) REVERT: c 242 PHE cc_start: 0.8385 (t80) cc_final: 0.8173 (t80) REVERT: c 243 ASP cc_start: 0.8043 (m-30) cc_final: 0.7599 (m-30) REVERT: c 246 LYS cc_start: 0.7694 (mtpt) cc_final: 0.7384 (mtpt) REVERT: c 274 GLN cc_start: 0.8421 (tt0) cc_final: 0.8194 (tt0) REVERT: c 275 LEU cc_start: 0.8874 (mt) cc_final: 0.8609 (mt) REVERT: c 284 ARG cc_start: 0.7862 (ttm170) cc_final: 0.7532 (mtp180) REVERT: c 286 MET cc_start: 0.7792 (mmm) cc_final: 0.6944 (mmm) REVERT: c 313 ASN cc_start: 0.6783 (m110) cc_final: 0.6487 (m110) REVERT: c 317 PHE cc_start: 0.8241 (t80) cc_final: 0.8032 (t80) REVERT: c 318 LYS cc_start: 0.7251 (tttt) cc_final: 0.6949 (tttt) REVERT: T 37 LYS cc_start: 0.8382 (mmtp) cc_final: 0.8130 (mmtp) REVERT: T 62 THR cc_start: 0.8442 (m) cc_final: 0.8056 (p) REVERT: T 81 ILE cc_start: 0.8681 (mt) cc_final: 0.8352 (mm) REVERT: T 90 ASN cc_start: 0.8003 (t0) cc_final: 0.7778 (t0) REVERT: T 120 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7654 (mt-10) REVERT: T 207 ASP cc_start: 0.7595 (m-30) cc_final: 0.7366 (m-30) REVERT: T 213 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7897 (mt-10) REVERT: T 220 GLU cc_start: 0.7847 (mp0) cc_final: 0.7549 (mp0) REVERT: T 229 PHE cc_start: 0.8406 (m-80) cc_final: 0.7935 (m-80) REVERT: T 243 ASP cc_start: 0.7433 (m-30) cc_final: 0.7177 (m-30) REVERT: T 246 LEU cc_start: 0.8388 (mt) cc_final: 0.8147 (mt) REVERT: T 260 ASP cc_start: 0.7753 (t0) cc_final: 0.7483 (m-30) REVERT: T 291 ILE cc_start: 0.7471 (mm) cc_final: 0.7229 (mt) REVERT: T 333 ASP cc_start: 0.8155 (t70) cc_final: 0.7949 (t0) REVERT: T 335 GLN cc_start: 0.7857 (mt0) cc_final: 0.7494 (mt0) REVERT: T 352 ASN cc_start: 0.7809 (m-40) cc_final: 0.7518 (m-40) REVERT: T 452 LYS cc_start: 0.8648 (tttt) cc_final: 0.8326 (tttp) REVERT: T 487 SER cc_start: 0.8144 (m) cc_final: 0.7808 (p) REVERT: T 588 LYS cc_start: 0.7847 (tttm) cc_final: 0.7638 (ttmt) REVERT: h 368 MET cc_start: 0.7336 (tpt) cc_final: 0.6899 (tpt) REVERT: h 383 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7138 (mm-30) REVERT: h 387 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7659 (mt-10) REVERT: h 528 LYS cc_start: 0.8610 (mtpt) cc_final: 0.8398 (mtpt) REVERT: h 577 SER cc_start: 0.8067 (m) cc_final: 0.7819 (t) REVERT: h 580 HIS cc_start: 0.8345 (t-170) cc_final: 0.8065 (t-170) REVERT: h 597 GLN cc_start: 0.8428 (mp10) cc_final: 0.7972 (mp10) REVERT: h 607 LYS cc_start: 0.8422 (ttmt) cc_final: 0.8111 (ttmt) REVERT: h 610 TYR cc_start: 0.8232 (m-80) cc_final: 0.7841 (m-80) REVERT: h 628 ASP cc_start: 0.7597 (m-30) cc_final: 0.7211 (m-30) REVERT: h 632 ARG cc_start: 0.8400 (ttm170) cc_final: 0.8118 (ttm170) REVERT: h 635 ILE cc_start: 0.8631 (mp) cc_final: 0.8405 (mt) REVERT: h 643 ASP cc_start: 0.7480 (t0) cc_final: 0.7167 (t0) REVERT: h 652 ILE cc_start: 0.7805 (mt) cc_final: 0.7516 (tt) REVERT: h 655 GLU cc_start: 0.8194 (pt0) cc_final: 0.7680 (mt-10) REVERT: h 679 MET cc_start: 0.7724 (ptm) cc_final: 0.7359 (ptm) REVERT: h 745 LEU cc_start: 0.7968 (mm) cc_final: 0.7675 (mt) REVERT: h 776 LEU cc_start: 0.8056 (tp) cc_final: 0.7722 (mt) REVERT: h 782 ASN cc_start: 0.7526 (m-40) cc_final: 0.7219 (m-40) REVERT: h 801 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6418 (m-30) REVERT: h 857 TYR cc_start: 0.8469 (m-80) cc_final: 0.8169 (m-10) REVERT: h 860 ASP cc_start: 0.7907 (p0) cc_final: 0.7644 (p0) REVERT: h 895 SER cc_start: 0.8218 (t) cc_final: 0.7927 (p) REVERT: h 921 GLN cc_start: 0.8456 (pt0) cc_final: 0.8080 (pt0) REVERT: h 932 HIS cc_start: 0.7056 (m90) cc_final: 0.6512 (m90) REVERT: h 962 LYS cc_start: 0.8708 (ptmt) cc_final: 0.8365 (ptmt) REVERT: h 965 LYS cc_start: 0.7956 (mttt) cc_final: 0.7665 (mtpt) REVERT: h 1066 MET cc_start: 0.6668 (mmm) cc_final: 0.6433 (mmm) REVERT: h 1084 LYS cc_start: 0.8529 (mttt) cc_final: 0.8273 (mtpp) REVERT: h 1112 LYS cc_start: 0.8485 (mtpt) cc_final: 0.8215 (mtpt) REVERT: h 1116 GLU cc_start: 0.8367 (mp0) cc_final: 0.8013 (mp0) REVERT: h 1139 TYR cc_start: 0.8060 (m-80) cc_final: 0.7791 (m-80) REVERT: X 103 GLN cc_start: 0.8299 (tm-30) cc_final: 0.7979 (tm-30) REVERT: X 105 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7309 (tt0) REVERT: X 129 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.7290 (ttmt) REVERT: X 136 LEU cc_start: 0.8220 (tp) cc_final: 0.7687 (tt) REVERT: X 150 LYS cc_start: 0.8310 (ptpt) cc_final: 0.7978 (ptpp) REVERT: X 160 ASP cc_start: 0.6820 (t0) cc_final: 0.6543 (t0) REVERT: X 203 GLN cc_start: 0.7308 (mt0) cc_final: 0.7014 (mt0) REVERT: X 244 SER cc_start: 0.8570 (t) cc_final: 0.8283 (p) REVERT: X 250 LYS cc_start: 0.8385 (mttm) cc_final: 0.8178 (mttp) REVERT: X 259 ILE cc_start: 0.8274 (pt) cc_final: 0.7995 (mm) REVERT: X 286 THR cc_start: 0.8289 (p) cc_final: 0.8057 (p) REVERT: X 294 GLU cc_start: 0.7228 (mp0) cc_final: 0.6644 (mp0) REVERT: X 332 MET cc_start: 0.7751 (mmm) cc_final: 0.7124 (mmm) REVERT: X 380 GLU cc_start: 0.7952 (tt0) cc_final: 0.7555 (mt-10) REVERT: X 388 LYS cc_start: 0.8118 (pttt) cc_final: 0.7852 (pttt) REVERT: X 454 ARG cc_start: 0.8255 (mtp180) cc_final: 0.7983 (mtp85) REVERT: X 470 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8107 (pt) REVERT: X 566 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7565 (mp0) REVERT: X 887 ARG cc_start: 0.7784 (ttm170) cc_final: 0.7494 (ttp-170) REVERT: X 905 LYS cc_start: 0.8319 (tptp) cc_final: 0.7810 (tptp) REVERT: X 913 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8485 (mm) REVERT: X 915 ARG cc_start: 0.7878 (mmt-90) cc_final: 0.7519 (mmt-90) REVERT: X 933 LYS cc_start: 0.8459 (mttt) cc_final: 0.8045 (mttt) REVERT: X 946 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.6530 (t) REVERT: X 985 LYS cc_start: 0.8902 (ttpt) cc_final: 0.8584 (ttpp) REVERT: X 986 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8742 (pt) REVERT: X 989 MET cc_start: 0.8078 (tpp) cc_final: 0.7601 (tpt) REVERT: X 1064 TYR cc_start: 0.8308 (m-80) cc_final: 0.7957 (m-10) REVERT: X 1126 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.7038 (ptp90) REVERT: X 1152 LEU cc_start: 0.8655 (tp) cc_final: 0.8445 (tt) REVERT: X 1153 TYR cc_start: 0.8145 (m-80) cc_final: 0.7644 (m-80) REVERT: X 1436 ILE cc_start: 0.8284 (mm) cc_final: 0.8070 (mm) REVERT: X 1443 GLU cc_start: 0.8083 (tt0) cc_final: 0.7690 (tt0) REVERT: X 1454 LYS cc_start: 0.7346 (tttt) cc_final: 0.6985 (tttt) REVERT: X 1495 PHE cc_start: 0.8229 (m-80) cc_final: 0.7880 (m-80) REVERT: X 1510 GLU cc_start: 0.7763 (tt0) cc_final: 0.7483 (tt0) REVERT: X 1569 PHE cc_start: 0.7285 (m-10) cc_final: 0.6726 (m-80) REVERT: X 1574 GLU cc_start: 0.7828 (tt0) cc_final: 0.7609 (tt0) REVERT: X 1575 MET cc_start: 0.7896 (mtt) cc_final: 0.7451 (mtt) REVERT: Y 131 PHE cc_start: 0.8060 (m-10) cc_final: 0.7778 (m-10) outliers start: 80 outliers final: 56 residues processed: 814 average time/residue: 0.2144 time to fit residues: 267.7482 Evaluate side-chains 837 residues out of total 3118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 771 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain a residue 98 VAL Chi-restraints excluded: chain a residue 99 LEU Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 169 GLU Chi-restraints excluded: chain a residue 199 ILE Chi-restraints excluded: chain a residue 205 ILE Chi-restraints excluded: chain a residue 213 PHE Chi-restraints excluded: chain a residue 216 ILE Chi-restraints excluded: chain a residue 275 VAL Chi-restraints excluded: chain c residue 18 ARG Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain c residue 103 LEU Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain c residue 307 LEU Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 225 ASP Chi-restraints excluded: chain T residue 263 MET Chi-restraints excluded: chain T residue 336 SER Chi-restraints excluded: chain T residue 462 LEU Chi-restraints excluded: chain h residue 410 SER Chi-restraints excluded: chain h residue 532 MET Chi-restraints excluded: chain h residue 545 GLU Chi-restraints excluded: chain h residue 633 ASN Chi-restraints excluded: chain h residue 634 GLU Chi-restraints excluded: chain h residue 673 LEU Chi-restraints excluded: chain h residue 752 LEU Chi-restraints excluded: chain h residue 801 ASP Chi-restraints excluded: chain h residue 838 ILE Chi-restraints excluded: chain h residue 954 THR Chi-restraints excluded: chain X residue 129 LYS Chi-restraints excluded: chain X residue 174 ILE Chi-restraints excluded: chain X residue 235 MET Chi-restraints excluded: chain X residue 368 VAL Chi-restraints excluded: chain X residue 433 THR Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain X residue 465 MET Chi-restraints excluded: chain X residue 470 ILE Chi-restraints excluded: chain X residue 528 MET Chi-restraints excluded: chain X residue 541 VAL Chi-restraints excluded: chain X residue 561 ASP Chi-restraints excluded: chain X residue 869 ILE Chi-restraints excluded: chain X residue 913 ILE Chi-restraints excluded: chain X residue 920 THR Chi-restraints excluded: chain X residue 946 THR Chi-restraints excluded: chain X residue 951 CYS Chi-restraints excluded: chain X residue 958 LYS Chi-restraints excluded: chain X residue 986 LEU Chi-restraints excluded: chain X residue 1126 ARG Chi-restraints excluded: chain X residue 1145 VAL Chi-restraints excluded: chain X residue 1146 MET Chi-restraints excluded: chain X residue 1168 ILE Chi-restraints excluded: chain X residue 1374 ASP Chi-restraints excluded: chain X residue 1390 LEU Chi-restraints excluded: chain X residue 1459 VAL Chi-restraints excluded: chain X residue 1477 LEU Chi-restraints excluded: chain X residue 1514 ASN Chi-restraints excluded: chain Y residue 153 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 4 optimal weight: 0.8980 chunk 308 optimal weight: 10.0000 chunk 272 optimal weight: 0.7980 chunk 186 optimal weight: 0.0770 chunk 280 optimal weight: 2.9990 chunk 196 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 332 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 ASN C 90 ASN C 111 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 191 ASN ** c 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 14 HIS h 542 HIS h 653 GLN X 981 ASN ** X1478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.145206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.122686 restraints weight = 43247.278| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.41 r_work: 0.3510 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 28093 Z= 0.211 Angle : 0.563 8.799 37995 Z= 0.290 Chirality : 0.046 0.181 4230 Planarity : 0.004 0.054 4808 Dihedral : 4.494 42.311 3642 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.95 % Allowed : 15.20 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.15), residues: 3294 helix: 0.86 (0.15), residues: 1162 sheet: -0.50 (0.20), residues: 720 loop : -1.00 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG h 835 TYR 0.043 0.002 TYR X1507 PHE 0.024 0.002 PHE T 472 TRP 0.014 0.002 TRP C 229 HIS 0.011 0.001 HIS X1371 Details of bonding type rmsd covalent geometry : bond 0.00482 (28093) covalent geometry : angle 0.56276 (37995) hydrogen bonds : bond 0.03829 ( 1115) hydrogen bonds : angle 4.67520 ( 3171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 3118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 784 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 THR cc_start: 0.8315 (p) cc_final: 0.7770 (t) REVERT: C 23 VAL cc_start: 0.8274 (t) cc_final: 0.8008 (t) REVERT: C 54 ASP cc_start: 0.8166 (t0) cc_final: 0.7803 (t0) REVERT: C 61 TRP cc_start: 0.8261 (t60) cc_final: 0.7990 (t60) REVERT: C 128 ASP cc_start: 0.8002 (m-30) cc_final: 0.7750 (m-30) REVERT: C 144 MET cc_start: 0.8293 (mmm) cc_final: 0.7820 (mtt) REVERT: C 189 LYS cc_start: 0.8132 (mttt) cc_final: 0.7852 (mtmt) REVERT: C 191 SER cc_start: 0.8040 (m) cc_final: 0.7350 (t) REVERT: C 207 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7175 (pt) REVERT: C 217 ILE cc_start: 0.8224 (mt) cc_final: 0.7905 (tt) REVERT: C 229 TRP cc_start: 0.8283 (m-90) cc_final: 0.7353 (m-90) REVERT: C 237 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7835 (mm-30) REVERT: C 239 LYS cc_start: 0.8380 (tmmt) cc_final: 0.8127 (tmmt) REVERT: C 298 LYS cc_start: 0.8419 (mmtp) cc_final: 0.8073 (mptt) REVERT: C 347 LYS cc_start: 0.8634 (mttt) cc_final: 0.8373 (mttp) REVERT: C 348 VAL cc_start: 0.7703 (t) cc_final: 0.7359 (p) REVERT: C 349 ASN cc_start: 0.7908 (t0) cc_final: 0.7264 (t0) REVERT: C 363 TYR cc_start: 0.9075 (m-80) cc_final: 0.8403 (m-80) REVERT: C 445 VAL cc_start: 0.8208 (t) cc_final: 0.7724 (p) REVERT: C 480 ASN cc_start: 0.7379 (m-40) cc_final: 0.7068 (t0) REVERT: C 484 ASN cc_start: 0.7848 (m-40) cc_final: 0.7630 (m-40) REVERT: a 15 SER cc_start: 0.8551 (p) cc_final: 0.8324 (t) REVERT: a 17 SER cc_start: 0.8608 (m) cc_final: 0.8344 (p) REVERT: a 61 ASP cc_start: 0.7725 (t70) cc_final: 0.7431 (t0) REVERT: a 97 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7151 (mt-10) REVERT: a 146 ASN cc_start: 0.7760 (m110) cc_final: 0.7350 (m-40) REVERT: a 148 SER cc_start: 0.8545 (t) cc_final: 0.8250 (t) REVERT: a 154 PHE cc_start: 0.8057 (m-80) cc_final: 0.7706 (m-10) REVERT: a 170 SER cc_start: 0.8090 (p) cc_final: 0.7779 (t) REVERT: a 188 ASN cc_start: 0.7901 (m110) cc_final: 0.7555 (m-40) REVERT: a 192 ASN cc_start: 0.8280 (m-40) cc_final: 0.8051 (m-40) REVERT: a 194 LYS cc_start: 0.8100 (mttt) cc_final: 0.7652 (mtpp) REVERT: a 197 LYS cc_start: 0.8133 (tttm) cc_final: 0.7912 (tttt) REVERT: a 200 MET cc_start: 0.7588 (mmm) cc_final: 0.7332 (mmm) REVERT: a 213 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.7234 (t80) REVERT: a 248 ASN cc_start: 0.8058 (t0) cc_final: 0.7724 (t0) REVERT: a 265 LYS cc_start: 0.8650 (tttt) cc_final: 0.8178 (ttmm) REVERT: c 15 MET cc_start: 0.7004 (mtp) cc_final: 0.6674 (mtt) REVERT: c 18 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7842 (mtt-85) REVERT: c 88 TYR cc_start: 0.7926 (t80) cc_final: 0.7565 (t80) REVERT: c 102 ASN cc_start: 0.8098 (t0) cc_final: 0.7357 (m-40) REVERT: c 105 MET cc_start: 0.7149 (mtt) cc_final: 0.6913 (mtm) REVERT: c 106 ILE cc_start: 0.8151 (mt) cc_final: 0.7870 (mt) REVERT: c 119 ILE cc_start: 0.8148 (mt) cc_final: 0.7731 (mm) REVERT: c 120 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6847 (mm-30) REVERT: c 124 HIS cc_start: 0.8174 (t70) cc_final: 0.7594 (t-90) REVERT: c 148 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7614 (mt-10) REVERT: c 181 LYS cc_start: 0.8291 (mttt) cc_final: 0.7979 (mtpt) REVERT: c 204 LYS cc_start: 0.7872 (tptt) cc_final: 0.7670 (tppt) REVERT: c 219 ASP cc_start: 0.8277 (p0) cc_final: 0.7918 (p0) REVERT: c 220 SER cc_start: 0.8481 (m) cc_final: 0.8149 (p) REVERT: c 242 PHE cc_start: 0.8390 (t80) cc_final: 0.8184 (t80) REVERT: c 243 ASP cc_start: 0.8020 (m-30) cc_final: 0.7595 (m-30) REVERT: c 246 LYS cc_start: 0.7688 (mtpt) cc_final: 0.7385 (mtpt) REVERT: c 273 SER cc_start: 0.7943 (t) cc_final: 0.7243 (p) REVERT: c 274 GLN cc_start: 0.8403 (tt0) cc_final: 0.7514 (tt0) REVERT: c 275 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8551 (mt) REVERT: c 284 ARG cc_start: 0.7865 (ttm170) cc_final: 0.7557 (mtp180) REVERT: c 286 MET cc_start: 0.7773 (mmm) cc_final: 0.6961 (mmm) REVERT: c 303 MET cc_start: 0.6168 (ttt) cc_final: 0.5949 (ttt) REVERT: c 313 ASN cc_start: 0.6827 (m110) cc_final: 0.6489 (m110) REVERT: c 317 PHE cc_start: 0.8126 (t80) cc_final: 0.7914 (t80) REVERT: c 318 LYS cc_start: 0.7249 (tttt) cc_final: 0.6939 (tttt) REVERT: T 37 LYS cc_start: 0.8399 (mmtp) cc_final: 0.8138 (mmtp) REVERT: T 62 THR cc_start: 0.8379 (m) cc_final: 0.7985 (p) REVERT: T 81 ILE cc_start: 0.8603 (mt) cc_final: 0.8312 (mm) REVERT: T 90 ASN cc_start: 0.8009 (t0) cc_final: 0.7787 (t0) REVERT: T 120 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7659 (mt-10) REVERT: T 207 ASP cc_start: 0.7564 (m-30) cc_final: 0.7329 (m-30) REVERT: T 229 PHE cc_start: 0.8393 (m-80) cc_final: 0.7864 (m-80) REVERT: T 243 ASP cc_start: 0.7501 (m-30) cc_final: 0.7221 (m-30) REVERT: T 246 LEU cc_start: 0.8374 (mt) cc_final: 0.8143 (mt) REVERT: T 260 ASP cc_start: 0.7746 (t0) cc_final: 0.7466 (m-30) REVERT: T 291 ILE cc_start: 0.7485 (mm) cc_final: 0.7245 (mt) REVERT: T 335 GLN cc_start: 0.7848 (mt0) cc_final: 0.7489 (mt0) REVERT: T 343 VAL cc_start: 0.8286 (t) cc_final: 0.8028 (p) REVERT: T 352 ASN cc_start: 0.7810 (m-40) cc_final: 0.7516 (m-40) REVERT: T 452 LYS cc_start: 0.8618 (tttt) cc_final: 0.8327 (tttp) REVERT: T 487 SER cc_start: 0.8124 (m) cc_final: 0.7823 (p) REVERT: T 588 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7662 (ttmt) REVERT: h 368 MET cc_start: 0.7296 (tpt) cc_final: 0.6864 (tpt) REVERT: h 383 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7114 (mm-30) REVERT: h 387 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7566 (mt-10) REVERT: h 577 SER cc_start: 0.8095 (m) cc_final: 0.7840 (t) REVERT: h 580 HIS cc_start: 0.8325 (t-170) cc_final: 0.8048 (t-170) REVERT: h 596 TYR cc_start: 0.8636 (t80) cc_final: 0.8425 (t80) REVERT: h 597 GLN cc_start: 0.8436 (mp10) cc_final: 0.7946 (mp10) REVERT: h 607 LYS cc_start: 0.8431 (ttmt) cc_final: 0.8114 (ttmt) REVERT: h 610 TYR cc_start: 0.8220 (m-80) cc_final: 0.7812 (m-80) REVERT: h 628 ASP cc_start: 0.7593 (m-30) cc_final: 0.7091 (m-30) REVERT: h 632 ARG cc_start: 0.8404 (ttm170) cc_final: 0.8098 (ttm170) REVERT: h 635 ILE cc_start: 0.8627 (mp) cc_final: 0.8387 (mt) REVERT: h 643 ASP cc_start: 0.7470 (t0) cc_final: 0.7156 (t0) REVERT: h 652 ILE cc_start: 0.7787 (mt) cc_final: 0.7502 (tt) REVERT: h 655 GLU cc_start: 0.8265 (pt0) cc_final: 0.7540 (mt-10) REVERT: h 679 MET cc_start: 0.7701 (ptm) cc_final: 0.7397 (ptm) REVERT: h 745 LEU cc_start: 0.7959 (mm) cc_final: 0.7676 (mt) REVERT: h 753 ASP cc_start: 0.7720 (t0) cc_final: 0.7519 (t0) REVERT: h 782 ASN cc_start: 0.7524 (m-40) cc_final: 0.7230 (m-40) REVERT: h 801 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6480 (m-30) REVERT: h 857 TYR cc_start: 0.8495 (m-80) cc_final: 0.8201 (m-10) REVERT: h 860 ASP cc_start: 0.7893 (p0) cc_final: 0.7642 (p0) REVERT: h 895 SER cc_start: 0.8215 (t) cc_final: 0.7916 (p) REVERT: h 921 GLN cc_start: 0.8465 (pt0) cc_final: 0.8068 (pt0) REVERT: h 932 HIS cc_start: 0.7148 (m90) cc_final: 0.6563 (m90) REVERT: h 962 LYS cc_start: 0.8675 (ptmt) cc_final: 0.8344 (ptmt) REVERT: h 1066 MET cc_start: 0.6644 (mmm) cc_final: 0.6414 (mmm) REVERT: h 1084 LYS cc_start: 0.8519 (mttt) cc_final: 0.8266 (mtpp) REVERT: h 1112 LYS cc_start: 0.8496 (mtpt) cc_final: 0.8208 (mtpt) REVERT: h 1116 GLU cc_start: 0.8358 (mp0) cc_final: 0.7837 (mp0) REVERT: h 1134 ASN cc_start: 0.7407 (m-40) cc_final: 0.6948 (m-40) REVERT: h 1139 TYR cc_start: 0.8065 (m-80) cc_final: 0.7833 (m-80) REVERT: X 103 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7995 (tm-30) REVERT: X 105 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7359 (tt0) REVERT: X 129 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.7239 (ttmt) REVERT: X 136 LEU cc_start: 0.8183 (tp) cc_final: 0.7633 (tt) REVERT: X 150 LYS cc_start: 0.8295 (ptpt) cc_final: 0.8021 (pttm) REVERT: X 160 ASP cc_start: 0.6938 (t0) cc_final: 0.6618 (t0) REVERT: X 203 GLN cc_start: 0.7412 (mt0) cc_final: 0.7132 (mt0) REVERT: X 230 ASP cc_start: 0.7749 (t0) cc_final: 0.7524 (t0) REVERT: X 244 SER cc_start: 0.8586 (t) cc_final: 0.8301 (p) REVERT: X 250 LYS cc_start: 0.8385 (mttm) cc_final: 0.8181 (mttp) REVERT: X 259 ILE cc_start: 0.8271 (pt) cc_final: 0.7987 (mm) REVERT: X 286 THR cc_start: 0.8263 (p) cc_final: 0.8047 (p) REVERT: X 332 MET cc_start: 0.7751 (mmm) cc_final: 0.7175 (mmm) REVERT: X 380 GLU cc_start: 0.7937 (tt0) cc_final: 0.7566 (mt-10) REVERT: X 388 LYS cc_start: 0.8106 (pttt) cc_final: 0.7833 (pttt) REVERT: X 454 ARG cc_start: 0.8250 (mtp180) cc_final: 0.7993 (mtp85) REVERT: X 470 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8118 (pt) REVERT: X 566 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7586 (mp0) REVERT: X 887 ARG cc_start: 0.7808 (ttm170) cc_final: 0.7525 (ttp-170) REVERT: X 905 LYS cc_start: 0.8324 (tptp) cc_final: 0.7787 (tptp) REVERT: X 913 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8491 (mm) REVERT: X 915 ARG cc_start: 0.7938 (mmt-90) cc_final: 0.7539 (mmt-90) REVERT: X 916 ASN cc_start: 0.8457 (t0) cc_final: 0.8183 (t0) REVERT: X 927 GLN cc_start: 0.8188 (mt0) cc_final: 0.7937 (mt0) REVERT: X 933 LYS cc_start: 0.8445 (mttt) cc_final: 0.8046 (mttt) REVERT: X 946 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.6670 (t) REVERT: X 985 LYS cc_start: 0.8923 (ttpt) cc_final: 0.8639 (ttpp) REVERT: X 986 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8698 (pt) REVERT: X 1049 ARG cc_start: 0.8594 (tpp80) cc_final: 0.8353 (tpp-160) REVERT: X 1061 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8282 (mt) REVERT: X 1064 TYR cc_start: 0.8273 (m-80) cc_final: 0.7902 (m-10) REVERT: X 1126 ARG cc_start: 0.7283 (ptp90) cc_final: 0.7069 (ptp90) REVERT: X 1152 LEU cc_start: 0.8665 (tp) cc_final: 0.8457 (tt) REVERT: X 1443 GLU cc_start: 0.8051 (tt0) cc_final: 0.7614 (tt0) REVERT: X 1454 LYS cc_start: 0.7323 (tttt) cc_final: 0.6966 (tttt) REVERT: X 1475 LYS cc_start: 0.8138 (mttt) cc_final: 0.7843 (mtpp) REVERT: X 1495 PHE cc_start: 0.8193 (m-80) cc_final: 0.7809 (m-80) REVERT: X 1510 GLU cc_start: 0.7741 (tt0) cc_final: 0.7500 (tt0) REVERT: X 1569 PHE cc_start: 0.7317 (m-10) cc_final: 0.6738 (m-80) REVERT: X 1574 GLU cc_start: 0.7815 (tt0) cc_final: 0.7604 (tt0) REVERT: X 1575 MET cc_start: 0.7878 (mtt) cc_final: 0.7437 (mtt) REVERT: Y 131 PHE cc_start: 0.8032 (m-80) cc_final: 0.7715 (m-10) outliers start: 92 outliers final: 57 residues processed: 819 average time/residue: 0.2166 time to fit residues: 272.6081 Evaluate side-chains 833 residues out of total 3118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 764 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain a residue 19 LYS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 98 VAL Chi-restraints excluded: chain a residue 99 LEU Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 169 GLU Chi-restraints excluded: chain a residue 171 LEU Chi-restraints excluded: chain a residue 199 ILE Chi-restraints excluded: chain a residue 205 ILE Chi-restraints excluded: chain a residue 213 PHE Chi-restraints excluded: chain a residue 275 VAL Chi-restraints excluded: chain c residue 18 ARG Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain c residue 275 LEU Chi-restraints excluded: chain c residue 307 LEU Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 336 SER Chi-restraints excluded: chain T residue 349 LEU Chi-restraints excluded: chain T residue 462 LEU Chi-restraints excluded: chain T residue 588 LYS Chi-restraints excluded: chain h residue 381 MET Chi-restraints excluded: chain h residue 410 SER Chi-restraints excluded: chain h residue 532 MET Chi-restraints excluded: chain h residue 545 GLU Chi-restraints excluded: chain h residue 633 ASN Chi-restraints excluded: chain h residue 673 LEU Chi-restraints excluded: chain h residue 752 LEU Chi-restraints excluded: chain h residue 801 ASP Chi-restraints excluded: chain h residue 838 ILE Chi-restraints excluded: chain h residue 954 THR Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 129 LYS Chi-restraints excluded: chain X residue 174 ILE Chi-restraints excluded: chain X residue 368 VAL Chi-restraints excluded: chain X residue 433 THR Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain X residue 470 ILE Chi-restraints excluded: chain X residue 528 MET Chi-restraints excluded: chain X residue 541 VAL Chi-restraints excluded: chain X residue 561 ASP Chi-restraints excluded: chain X residue 851 ILE Chi-restraints excluded: chain X residue 869 ILE Chi-restraints excluded: chain X residue 913 ILE Chi-restraints excluded: chain X residue 919 VAL Chi-restraints excluded: chain X residue 920 THR Chi-restraints excluded: chain X residue 946 THR Chi-restraints excluded: chain X residue 951 CYS Chi-restraints excluded: chain X residue 958 LYS Chi-restraints excluded: chain X residue 986 LEU Chi-restraints excluded: chain X residue 1011 LEU Chi-restraints excluded: chain X residue 1061 LEU Chi-restraints excluded: chain X residue 1145 VAL Chi-restraints excluded: chain X residue 1146 MET Chi-restraints excluded: chain X residue 1168 ILE Chi-restraints excluded: chain X residue 1390 LEU Chi-restraints excluded: chain X residue 1459 VAL Chi-restraints excluded: chain X residue 1477 LEU Chi-restraints excluded: chain X residue 1514 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 291 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 230 optimal weight: 0.8980 chunk 302 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 315 optimal weight: 0.0670 chunk 41 optimal weight: 1.9990 chunk 283 optimal weight: 0.6980 chunk 321 optimal weight: 5.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN C 111 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS a 71 ASN c 191 ASN ** c 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 14 HIS h 20 HIS h 542 HIS h 653 GLN X 981 ASN ** X1478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.145345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.122847 restraints weight = 43348.446| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.42 r_work: 0.3513 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 28093 Z= 0.206 Angle : 0.566 8.244 37995 Z= 0.291 Chirality : 0.046 0.173 4230 Planarity : 0.004 0.053 4808 Dihedral : 4.488 42.107 3642 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.08 % Allowed : 16.20 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.15), residues: 3294 helix: 0.89 (0.15), residues: 1166 sheet: -0.51 (0.20), residues: 718 loop : -1.01 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 454 TYR 0.037 0.002 TYR C 260 PHE 0.024 0.002 PHE X 415 TRP 0.013 0.002 TRP C 229 HIS 0.013 0.001 HIS X1371 Details of bonding type rmsd covalent geometry : bond 0.00473 (28093) covalent geometry : angle 0.56610 (37995) hydrogen bonds : bond 0.03794 ( 1115) hydrogen bonds : angle 4.65232 ( 3171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 3118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 781 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 VAL cc_start: 0.8236 (t) cc_final: 0.7973 (t) REVERT: C 54 ASP cc_start: 0.8180 (t0) cc_final: 0.7815 (t0) REVERT: C 61 TRP cc_start: 0.8260 (t60) cc_final: 0.7989 (t60) REVERT: C 128 ASP cc_start: 0.8019 (m-30) cc_final: 0.7768 (m-30) REVERT: C 144 MET cc_start: 0.8314 (mmm) cc_final: 0.7829 (mtt) REVERT: C 189 LYS cc_start: 0.8115 (mttt) cc_final: 0.7825 (mtmt) REVERT: C 191 SER cc_start: 0.8059 (m) cc_final: 0.7327 (t) REVERT: C 207 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7243 (pt) REVERT: C 217 ILE cc_start: 0.8233 (mt) cc_final: 0.7879 (tt) REVERT: C 229 TRP cc_start: 0.8289 (m-90) cc_final: 0.7279 (m-90) REVERT: C 237 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7801 (mm-30) REVERT: C 239 LYS cc_start: 0.8365 (tmmt) cc_final: 0.8111 (tmmt) REVERT: C 298 LYS cc_start: 0.8411 (mmtp) cc_final: 0.8056 (mptt) REVERT: C 347 LYS cc_start: 0.8648 (mttt) cc_final: 0.8374 (mttp) REVERT: C 349 ASN cc_start: 0.7911 (t0) cc_final: 0.7303 (t0) REVERT: C 363 TYR cc_start: 0.9065 (m-80) cc_final: 0.8341 (m-80) REVERT: C 433 GLU cc_start: 0.7327 (tt0) cc_final: 0.7000 (tt0) REVERT: C 445 VAL cc_start: 0.8178 (t) cc_final: 0.7686 (p) REVERT: C 448 LYS cc_start: 0.8117 (tttt) cc_final: 0.7642 (tttp) REVERT: C 480 ASN cc_start: 0.7347 (m-40) cc_final: 0.7034 (t0) REVERT: C 484 ASN cc_start: 0.7815 (m-40) cc_final: 0.7530 (m-40) REVERT: a 15 SER cc_start: 0.8550 (p) cc_final: 0.8309 (t) REVERT: a 17 SER cc_start: 0.8603 (m) cc_final: 0.8318 (p) REVERT: a 61 ASP cc_start: 0.7703 (t70) cc_final: 0.7409 (t0) REVERT: a 97 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7161 (mt-10) REVERT: a 146 ASN cc_start: 0.7742 (m110) cc_final: 0.7332 (m-40) REVERT: a 148 SER cc_start: 0.8563 (t) cc_final: 0.8258 (t) REVERT: a 154 PHE cc_start: 0.8062 (m-80) cc_final: 0.7707 (m-10) REVERT: a 170 SER cc_start: 0.8072 (p) cc_final: 0.7862 (p) REVERT: a 188 ASN cc_start: 0.7863 (m110) cc_final: 0.7629 (m-40) REVERT: a 194 LYS cc_start: 0.8096 (mttt) cc_final: 0.7665 (mtpp) REVERT: a 197 LYS cc_start: 0.8132 (tttm) cc_final: 0.7903 (tttt) REVERT: a 201 ASN cc_start: 0.8164 (t0) cc_final: 0.7742 (t0) REVERT: a 213 PHE cc_start: 0.7606 (OUTLIER) cc_final: 0.7212 (t80) REVERT: a 248 ASN cc_start: 0.8046 (t0) cc_final: 0.7724 (t0) REVERT: a 265 LYS cc_start: 0.8647 (tttt) cc_final: 0.8161 (ttmm) REVERT: c 15 MET cc_start: 0.6986 (mtp) cc_final: 0.6660 (mtt) REVERT: c 18 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7831 (mtt-85) REVERT: c 91 ASP cc_start: 0.8036 (t70) cc_final: 0.7666 (t70) REVERT: c 102 ASN cc_start: 0.8121 (t0) cc_final: 0.7461 (m-40) REVERT: c 105 MET cc_start: 0.7180 (mtt) cc_final: 0.6963 (mtm) REVERT: c 106 ILE cc_start: 0.8138 (mt) cc_final: 0.7862 (mt) REVERT: c 119 ILE cc_start: 0.8157 (mt) cc_final: 0.7719 (mm) REVERT: c 120 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6883 (mm-30) REVERT: c 124 HIS cc_start: 0.8139 (t70) cc_final: 0.7764 (t70) REVERT: c 148 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7591 (mt-10) REVERT: c 181 LYS cc_start: 0.8277 (mttt) cc_final: 0.7979 (mtpt) REVERT: c 204 LYS cc_start: 0.7902 (tptt) cc_final: 0.7642 (tppt) REVERT: c 219 ASP cc_start: 0.8240 (p0) cc_final: 0.7913 (p0) REVERT: c 220 SER cc_start: 0.8552 (m) cc_final: 0.8178 (p) REVERT: c 243 ASP cc_start: 0.8047 (m-30) cc_final: 0.7558 (m-30) REVERT: c 246 LYS cc_start: 0.7685 (mtpt) cc_final: 0.7375 (mtpt) REVERT: c 273 SER cc_start: 0.7975 (t) cc_final: 0.7229 (p) REVERT: c 274 GLN cc_start: 0.8408 (tt0) cc_final: 0.7570 (tt0) REVERT: c 275 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8565 (mt) REVERT: c 284 ARG cc_start: 0.7830 (ttm170) cc_final: 0.7524 (mtp180) REVERT: c 286 MET cc_start: 0.7888 (mmm) cc_final: 0.7224 (ttm) REVERT: c 303 MET cc_start: 0.6176 (ttt) cc_final: 0.5920 (ttt) REVERT: c 313 ASN cc_start: 0.6842 (m110) cc_final: 0.6565 (m110) REVERT: c 318 LYS cc_start: 0.7244 (tttt) cc_final: 0.6979 (tttt) REVERT: T 37 LYS cc_start: 0.8397 (mmtp) cc_final: 0.8137 (mmtp) REVERT: T 81 ILE cc_start: 0.8583 (mt) cc_final: 0.8301 (mm) REVERT: T 90 ASN cc_start: 0.8035 (t0) cc_final: 0.7815 (t0) REVERT: T 120 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7687 (mt-10) REVERT: T 207 ASP cc_start: 0.7571 (m-30) cc_final: 0.7336 (m-30) REVERT: T 229 PHE cc_start: 0.8387 (m-80) cc_final: 0.7904 (m-80) REVERT: T 239 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.8043 (t) REVERT: T 243 ASP cc_start: 0.7489 (m-30) cc_final: 0.7202 (m-30) REVERT: T 246 LEU cc_start: 0.8369 (mt) cc_final: 0.8127 (mt) REVERT: T 291 ILE cc_start: 0.7476 (mm) cc_final: 0.7242 (mt) REVERT: T 335 GLN cc_start: 0.7839 (mt0) cc_final: 0.7455 (mt0) REVERT: T 343 VAL cc_start: 0.8296 (t) cc_final: 0.8037 (p) REVERT: T 352 ASN cc_start: 0.7825 (m-40) cc_final: 0.7530 (m-40) REVERT: T 452 LYS cc_start: 0.8600 (tttt) cc_final: 0.8309 (tttp) REVERT: T 487 SER cc_start: 0.8193 (m) cc_final: 0.7885 (p) REVERT: T 588 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7645 (ttmt) REVERT: h 368 MET cc_start: 0.7322 (tpt) cc_final: 0.6807 (tpt) REVERT: h 383 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7096 (mm-30) REVERT: h 387 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7684 (mt-10) REVERT: h 569 GLN cc_start: 0.8266 (tp40) cc_final: 0.7369 (tp40) REVERT: h 577 SER cc_start: 0.8109 (m) cc_final: 0.7850 (t) REVERT: h 580 HIS cc_start: 0.8303 (t-170) cc_final: 0.8054 (t-170) REVERT: h 597 GLN cc_start: 0.8428 (mp10) cc_final: 0.7975 (mp10) REVERT: h 607 LYS cc_start: 0.8411 (ttmt) cc_final: 0.8091 (ttmt) REVERT: h 610 TYR cc_start: 0.8201 (m-80) cc_final: 0.7811 (m-80) REVERT: h 628 ASP cc_start: 0.7578 (m-30) cc_final: 0.7183 (m-30) REVERT: h 632 ARG cc_start: 0.8414 (ttm170) cc_final: 0.8108 (ttm170) REVERT: h 635 ILE cc_start: 0.8630 (mp) cc_final: 0.8389 (mt) REVERT: h 643 ASP cc_start: 0.7469 (t0) cc_final: 0.7160 (t0) REVERT: h 652 ILE cc_start: 0.7775 (mt) cc_final: 0.7495 (tt) REVERT: h 655 GLU cc_start: 0.8284 (pt0) cc_final: 0.7491 (mt-10) REVERT: h 679 MET cc_start: 0.7725 (ptm) cc_final: 0.7411 (ptm) REVERT: h 745 LEU cc_start: 0.7946 (mm) cc_final: 0.7681 (mt) REVERT: h 753 ASP cc_start: 0.7734 (t0) cc_final: 0.7533 (t0) REVERT: h 776 LEU cc_start: 0.8094 (tp) cc_final: 0.7786 (mt) REVERT: h 782 ASN cc_start: 0.7541 (m-40) cc_final: 0.7223 (m-40) REVERT: h 801 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6470 (m-30) REVERT: h 857 TYR cc_start: 0.8504 (m-80) cc_final: 0.8204 (m-10) REVERT: h 860 ASP cc_start: 0.7898 (p0) cc_final: 0.7644 (p0) REVERT: h 895 SER cc_start: 0.8206 (t) cc_final: 0.7909 (p) REVERT: h 921 GLN cc_start: 0.8485 (pt0) cc_final: 0.8099 (pt0) REVERT: h 932 HIS cc_start: 0.7163 (m90) cc_final: 0.6555 (m90) REVERT: h 962 LYS cc_start: 0.8677 (ptmt) cc_final: 0.8348 (ptmt) REVERT: h 1066 MET cc_start: 0.6649 (mmm) cc_final: 0.6408 (mmm) REVERT: h 1084 LYS cc_start: 0.8501 (mttt) cc_final: 0.8241 (mtpp) REVERT: h 1112 LYS cc_start: 0.8506 (mtpt) cc_final: 0.8191 (mtpt) REVERT: h 1116 GLU cc_start: 0.8360 (mp0) cc_final: 0.8006 (mp0) REVERT: h 1134 ASN cc_start: 0.7407 (m-40) cc_final: 0.6955 (m-40) REVERT: h 1139 TYR cc_start: 0.8079 (m-80) cc_final: 0.7841 (m-80) REVERT: X 103 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7998 (tm-30) REVERT: X 105 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7334 (tt0) REVERT: X 129 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7202 (ttmt) REVERT: X 136 LEU cc_start: 0.8187 (tp) cc_final: 0.7641 (tt) REVERT: X 150 LYS cc_start: 0.8297 (ptpt) cc_final: 0.7964 (ptpp) REVERT: X 160 ASP cc_start: 0.6958 (t0) cc_final: 0.6581 (t0) REVERT: X 203 GLN cc_start: 0.7403 (mt0) cc_final: 0.7129 (mt0) REVERT: X 230 ASP cc_start: 0.7800 (t0) cc_final: 0.7562 (t0) REVERT: X 244 SER cc_start: 0.8583 (t) cc_final: 0.8354 (p) REVERT: X 250 LYS cc_start: 0.8401 (mttm) cc_final: 0.8190 (mttp) REVERT: X 259 ILE cc_start: 0.8282 (pt) cc_final: 0.8003 (mm) REVERT: X 286 THR cc_start: 0.8258 (p) cc_final: 0.8001 (m) REVERT: X 332 MET cc_start: 0.7766 (mmm) cc_final: 0.7221 (mmm) REVERT: X 350 ASN cc_start: 0.7670 (t0) cc_final: 0.7252 (p0) REVERT: X 377 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7819 (mm-30) REVERT: X 380 GLU cc_start: 0.7940 (tt0) cc_final: 0.7548 (mt-10) REVERT: X 388 LYS cc_start: 0.8138 (pttt) cc_final: 0.7855 (pttt) REVERT: X 454 ARG cc_start: 0.8243 (mtp180) cc_final: 0.7990 (mtp85) REVERT: X 470 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8116 (pt) REVERT: X 566 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7583 (mp0) REVERT: X 887 ARG cc_start: 0.7791 (ttm170) cc_final: 0.7494 (ttp-170) REVERT: X 905 LYS cc_start: 0.8362 (tptp) cc_final: 0.7787 (tptp) REVERT: X 913 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8477 (mm) REVERT: X 915 ARG cc_start: 0.7920 (mmt-90) cc_final: 0.7534 (mmt-90) REVERT: X 916 ASN cc_start: 0.8467 (t0) cc_final: 0.8114 (t0) REVERT: X 927 GLN cc_start: 0.8233 (mt0) cc_final: 0.7980 (mt0) REVERT: X 933 LYS cc_start: 0.8450 (mttt) cc_final: 0.8045 (mttt) REVERT: X 946 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.6734 (t) REVERT: X 985 LYS cc_start: 0.8920 (ttpt) cc_final: 0.8621 (ttpp) REVERT: X 986 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8658 (pt) REVERT: X 989 MET cc_start: 0.7915 (mmm) cc_final: 0.7584 (tmm) REVERT: X 1064 TYR cc_start: 0.8267 (m-80) cc_final: 0.7873 (m-10) REVERT: X 1126 ARG cc_start: 0.7321 (ptp90) cc_final: 0.7054 (ptp90) REVERT: X 1152 LEU cc_start: 0.8672 (tp) cc_final: 0.8453 (tt) REVERT: X 1153 TYR cc_start: 0.8260 (m-80) cc_final: 0.7799 (m-80) REVERT: X 1436 ILE cc_start: 0.8092 (mm) cc_final: 0.7881 (mt) REVERT: X 1443 GLU cc_start: 0.8060 (tt0) cc_final: 0.7609 (tt0) REVERT: X 1454 LYS cc_start: 0.7307 (tttt) cc_final: 0.6952 (tttt) REVERT: X 1475 LYS cc_start: 0.8138 (mttt) cc_final: 0.7851 (mtpp) REVERT: X 1495 PHE cc_start: 0.8191 (m-80) cc_final: 0.7801 (m-80) REVERT: X 1510 GLU cc_start: 0.7750 (tt0) cc_final: 0.7503 (tt0) REVERT: X 1569 PHE cc_start: 0.7314 (m-10) cc_final: 0.6708 (m-80) REVERT: X 1574 GLU cc_start: 0.7799 (tt0) cc_final: 0.7586 (tt0) REVERT: X 1575 MET cc_start: 0.7918 (mtt) cc_final: 0.7478 (mtt) REVERT: Y 131 PHE cc_start: 0.8068 (m-80) cc_final: 0.7703 (m-10) REVERT: Y 150 MET cc_start: 0.8241 (tpt) cc_final: 0.7955 (tpp) outliers start: 96 outliers final: 71 residues processed: 817 average time/residue: 0.2108 time to fit residues: 264.7601 Evaluate side-chains 848 residues out of total 3118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 765 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain a residue 19 LYS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 98 VAL Chi-restraints excluded: chain a residue 99 LEU Chi-restraints excluded: chain a residue 129 ASP Chi-restraints excluded: chain a residue 145 LYS Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 169 GLU Chi-restraints excluded: chain a residue 171 LEU Chi-restraints excluded: chain a residue 199 ILE Chi-restraints excluded: chain a residue 205 ILE Chi-restraints excluded: chain a residue 213 PHE Chi-restraints excluded: chain a residue 216 ILE Chi-restraints excluded: chain a residue 275 VAL Chi-restraints excluded: chain c residue 18 ARG Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain c residue 269 LEU Chi-restraints excluded: chain c residue 275 LEU Chi-restraints excluded: chain c residue 306 CYS Chi-restraints excluded: chain c residue 307 LEU Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 211 TYR Chi-restraints excluded: chain T residue 225 ASP Chi-restraints excluded: chain T residue 239 VAL Chi-restraints excluded: chain T residue 263 MET Chi-restraints excluded: chain T residue 322 ARG Chi-restraints excluded: chain T residue 336 SER Chi-restraints excluded: chain T residue 349 LEU Chi-restraints excluded: chain T residue 442 TYR Chi-restraints excluded: chain T residue 462 LEU Chi-restraints excluded: chain T residue 588 LYS Chi-restraints excluded: chain h residue 381 MET Chi-restraints excluded: chain h residue 410 SER Chi-restraints excluded: chain h residue 532 MET Chi-restraints excluded: chain h residue 545 GLU Chi-restraints excluded: chain h residue 592 HIS Chi-restraints excluded: chain h residue 633 ASN Chi-restraints excluded: chain h residue 673 LEU Chi-restraints excluded: chain h residue 752 LEU Chi-restraints excluded: chain h residue 801 ASP Chi-restraints excluded: chain h residue 838 ILE Chi-restraints excluded: chain h residue 954 THR Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 129 LYS Chi-restraints excluded: chain X residue 174 ILE Chi-restraints excluded: chain X residue 235 MET Chi-restraints excluded: chain X residue 368 VAL Chi-restraints excluded: chain X residue 433 THR Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain X residue 465 MET Chi-restraints excluded: chain X residue 470 ILE Chi-restraints excluded: chain X residue 528 MET Chi-restraints excluded: chain X residue 541 VAL Chi-restraints excluded: chain X residue 557 MET Chi-restraints excluded: chain X residue 561 ASP Chi-restraints excluded: chain X residue 851 ILE Chi-restraints excluded: chain X residue 869 ILE Chi-restraints excluded: chain X residue 913 ILE Chi-restraints excluded: chain X residue 920 THR Chi-restraints excluded: chain X residue 946 THR Chi-restraints excluded: chain X residue 951 CYS Chi-restraints excluded: chain X residue 958 LYS Chi-restraints excluded: chain X residue 986 LEU Chi-restraints excluded: chain X residue 1011 LEU Chi-restraints excluded: chain X residue 1146 MET Chi-restraints excluded: chain X residue 1168 ILE Chi-restraints excluded: chain X residue 1390 LEU Chi-restraints excluded: chain X residue 1459 VAL Chi-restraints excluded: chain X residue 1514 ASN Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain Y residue 129 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 248 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 292 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 124 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 247 optimal weight: 0.6980 chunk 303 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 266 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN C 111 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS C 484 ASN a 71 ASN c 191 ASN c 313 ASN h 14 HIS h 20 HIS ** h 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 542 HIS h 653 GLN X 981 ASN ** X1478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.145171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.122786 restraints weight = 43302.817| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.41 r_work: 0.3509 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 28093 Z= 0.212 Angle : 0.571 8.137 37995 Z= 0.295 Chirality : 0.046 0.190 4230 Planarity : 0.004 0.054 4808 Dihedral : 4.533 40.927 3642 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.27 % Allowed : 16.87 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.15), residues: 3294 helix: 0.92 (0.15), residues: 1162 sheet: -0.56 (0.20), residues: 720 loop : -0.98 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 454 TYR 0.039 0.002 TYR C 260 PHE 0.035 0.002 PHE a 308 TRP 0.013 0.002 TRP X 222 HIS 0.014 0.001 HIS X1371 Details of bonding type rmsd covalent geometry : bond 0.00488 (28093) covalent geometry : angle 0.57092 (37995) hydrogen bonds : bond 0.03783 ( 1115) hydrogen bonds : angle 4.65323 ( 3171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 3118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 769 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 VAL cc_start: 0.8210 (t) cc_final: 0.7941 (t) REVERT: C 54 ASP cc_start: 0.8168 (t0) cc_final: 0.7807 (t0) REVERT: C 61 TRP cc_start: 0.8260 (t60) cc_final: 0.8029 (t60) REVERT: C 128 ASP cc_start: 0.7983 (m-30) cc_final: 0.7725 (m-30) REVERT: C 144 MET cc_start: 0.8304 (mmm) cc_final: 0.7801 (mtt) REVERT: C 189 LYS cc_start: 0.8133 (mttt) cc_final: 0.7849 (mtmt) REVERT: C 191 SER cc_start: 0.8083 (m) cc_final: 0.7362 (t) REVERT: C 207 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7302 (pt) REVERT: C 213 LYS cc_start: 0.8517 (tptm) cc_final: 0.8172 (tppp) REVERT: C 217 ILE cc_start: 0.8231 (mt) cc_final: 0.7872 (tt) REVERT: C 229 TRP cc_start: 0.8297 (m-90) cc_final: 0.7365 (m-90) REVERT: C 237 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7763 (mm-30) REVERT: C 239 LYS cc_start: 0.8374 (tmmt) cc_final: 0.8105 (tmmt) REVERT: C 298 LYS cc_start: 0.8413 (mmtp) cc_final: 0.8080 (mptt) REVERT: C 347 LYS cc_start: 0.8637 (mttt) cc_final: 0.8367 (mttp) REVERT: C 349 ASN cc_start: 0.7878 (t0) cc_final: 0.7263 (t0) REVERT: C 363 TYR cc_start: 0.9063 (m-80) cc_final: 0.8307 (m-80) REVERT: C 433 GLU cc_start: 0.7258 (tt0) cc_final: 0.6964 (tt0) REVERT: C 445 VAL cc_start: 0.8147 (t) cc_final: 0.7643 (p) REVERT: C 448 LYS cc_start: 0.8111 (tttt) cc_final: 0.7809 (tttp) REVERT: C 480 ASN cc_start: 0.7385 (m-40) cc_final: 0.7083 (t0) REVERT: a 15 SER cc_start: 0.8556 (p) cc_final: 0.8313 (t) REVERT: a 17 SER cc_start: 0.8586 (m) cc_final: 0.8307 (p) REVERT: a 61 ASP cc_start: 0.7704 (t70) cc_final: 0.7419 (t0) REVERT: a 97 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7143 (mt-10) REVERT: a 146 ASN cc_start: 0.7770 (m110) cc_final: 0.7365 (m-40) REVERT: a 148 SER cc_start: 0.8566 (t) cc_final: 0.8224 (t) REVERT: a 154 PHE cc_start: 0.8059 (m-80) cc_final: 0.7703 (m-10) REVERT: a 188 ASN cc_start: 0.7882 (m110) cc_final: 0.7641 (m-40) REVERT: a 194 LYS cc_start: 0.8130 (mttt) cc_final: 0.7693 (mtpp) REVERT: a 197 LYS cc_start: 0.8172 (tttm) cc_final: 0.7967 (tttt) REVERT: a 213 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.7233 (t80) REVERT: a 248 ASN cc_start: 0.8014 (t0) cc_final: 0.7705 (t0) REVERT: a 265 LYS cc_start: 0.8661 (tttt) cc_final: 0.8152 (ttmm) REVERT: c 15 MET cc_start: 0.7005 (mtp) cc_final: 0.6581 (mtp) REVERT: c 18 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7810 (mtt-85) REVERT: c 102 ASN cc_start: 0.8135 (t0) cc_final: 0.7693 (m-40) REVERT: c 106 ILE cc_start: 0.8142 (mt) cc_final: 0.7893 (mt) REVERT: c 119 ILE cc_start: 0.8181 (mt) cc_final: 0.7712 (mm) REVERT: c 120 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6862 (mm-30) REVERT: c 124 HIS cc_start: 0.8132 (t70) cc_final: 0.7742 (t70) REVERT: c 148 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7622 (mt-10) REVERT: c 181 LYS cc_start: 0.8319 (mttt) cc_final: 0.8007 (mtpt) REVERT: c 204 LYS cc_start: 0.7884 (tptt) cc_final: 0.7644 (tppt) REVERT: c 219 ASP cc_start: 0.8246 (p0) cc_final: 0.7950 (p0) REVERT: c 220 SER cc_start: 0.8569 (m) cc_final: 0.8187 (p) REVERT: c 243 ASP cc_start: 0.8059 (m-30) cc_final: 0.7559 (m-30) REVERT: c 246 LYS cc_start: 0.7690 (mtpt) cc_final: 0.7370 (mtpt) REVERT: c 273 SER cc_start: 0.7992 (t) cc_final: 0.7247 (p) REVERT: c 274 GLN cc_start: 0.8415 (tt0) cc_final: 0.7533 (tt0) REVERT: c 275 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8559 (mt) REVERT: c 284 ARG cc_start: 0.7903 (ttm170) cc_final: 0.7579 (mtp180) REVERT: c 286 MET cc_start: 0.7875 (mmm) cc_final: 0.7540 (ttm) REVERT: c 303 MET cc_start: 0.6210 (ttt) cc_final: 0.5865 (ttt) REVERT: c 313 ASN cc_start: 0.6844 (m-40) cc_final: 0.6521 (m110) REVERT: c 318 LYS cc_start: 0.7265 (tttt) cc_final: 0.6771 (tptt) REVERT: T 37 LYS cc_start: 0.8337 (mmtp) cc_final: 0.8074 (mmtp) REVERT: T 81 ILE cc_start: 0.8582 (mt) cc_final: 0.8371 (mm) REVERT: T 90 ASN cc_start: 0.8021 (t0) cc_final: 0.7805 (t0) REVERT: T 207 ASP cc_start: 0.7568 (m-30) cc_final: 0.7324 (m-30) REVERT: T 229 PHE cc_start: 0.8365 (m-80) cc_final: 0.7897 (m-80) REVERT: T 239 VAL cc_start: 0.8315 (OUTLIER) cc_final: 0.8018 (t) REVERT: T 243 ASP cc_start: 0.7511 (m-30) cc_final: 0.7223 (m-30) REVERT: T 246 LEU cc_start: 0.8368 (mt) cc_final: 0.8128 (mt) REVERT: T 291 ILE cc_start: 0.7483 (mm) cc_final: 0.7255 (mt) REVERT: T 335 GLN cc_start: 0.7851 (mt0) cc_final: 0.7465 (mt0) REVERT: T 343 VAL cc_start: 0.8191 (t) cc_final: 0.7934 (p) REVERT: T 352 ASN cc_start: 0.7859 (m-40) cc_final: 0.7601 (m-40) REVERT: T 452 LYS cc_start: 0.8604 (tttt) cc_final: 0.8312 (tttp) REVERT: T 487 SER cc_start: 0.8216 (m) cc_final: 0.7886 (p) REVERT: T 588 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7674 (ttmt) REVERT: h 368 MET cc_start: 0.7327 (tpt) cc_final: 0.6866 (tpt) REVERT: h 383 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7082 (mm-30) REVERT: h 387 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7684 (mt-10) REVERT: h 539 MET cc_start: 0.8489 (mtt) cc_final: 0.8289 (mtt) REVERT: h 569 GLN cc_start: 0.8235 (tp40) cc_final: 0.7410 (tp40) REVERT: h 575 ILE cc_start: 0.7728 (mm) cc_final: 0.6695 (mm) REVERT: h 577 SER cc_start: 0.8177 (m) cc_final: 0.7925 (t) REVERT: h 580 HIS cc_start: 0.8322 (t-170) cc_final: 0.8080 (t-170) REVERT: h 597 GLN cc_start: 0.8436 (mp10) cc_final: 0.7974 (mp10) REVERT: h 607 LYS cc_start: 0.8425 (ttmt) cc_final: 0.8105 (ttmt) REVERT: h 610 TYR cc_start: 0.8186 (m-80) cc_final: 0.7764 (m-80) REVERT: h 628 ASP cc_start: 0.7559 (m-30) cc_final: 0.7067 (m-30) REVERT: h 632 ARG cc_start: 0.8422 (ttm170) cc_final: 0.8105 (ttm170) REVERT: h 635 ILE cc_start: 0.8619 (mp) cc_final: 0.8384 (mt) REVERT: h 643 ASP cc_start: 0.7464 (t0) cc_final: 0.7160 (t0) REVERT: h 652 ILE cc_start: 0.7767 (mt) cc_final: 0.7498 (tt) REVERT: h 655 GLU cc_start: 0.8350 (pt0) cc_final: 0.7450 (mt-10) REVERT: h 745 LEU cc_start: 0.7942 (mm) cc_final: 0.7735 (mt) REVERT: h 782 ASN cc_start: 0.7526 (m-40) cc_final: 0.7215 (m-40) REVERT: h 801 ASP cc_start: 0.7110 (OUTLIER) cc_final: 0.6324 (m-30) REVERT: h 857 TYR cc_start: 0.8501 (m-80) cc_final: 0.8248 (m-10) REVERT: h 860 ASP cc_start: 0.7900 (p0) cc_final: 0.7660 (p0) REVERT: h 895 SER cc_start: 0.8209 (t) cc_final: 0.7919 (p) REVERT: h 921 GLN cc_start: 0.8487 (pt0) cc_final: 0.8118 (pt0) REVERT: h 932 HIS cc_start: 0.7133 (m90) cc_final: 0.6526 (m90) REVERT: h 962 LYS cc_start: 0.8668 (ptmt) cc_final: 0.8299 (ptmt) REVERT: h 1066 MET cc_start: 0.6656 (mmm) cc_final: 0.6407 (mmm) REVERT: h 1084 LYS cc_start: 0.8517 (mttt) cc_final: 0.8251 (mtpp) REVERT: h 1112 LYS cc_start: 0.8498 (mtpt) cc_final: 0.8193 (mtpt) REVERT: h 1116 GLU cc_start: 0.8368 (mp0) cc_final: 0.8017 (mp0) REVERT: h 1134 ASN cc_start: 0.7476 (m-40) cc_final: 0.7019 (m-40) REVERT: h 1139 TYR cc_start: 0.8069 (m-80) cc_final: 0.7839 (m-80) REVERT: X 103 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7931 (tm-30) REVERT: X 105 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7373 (tt0) REVERT: X 129 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.7175 (ttmt) REVERT: X 136 LEU cc_start: 0.8187 (tp) cc_final: 0.7641 (tt) REVERT: X 150 LYS cc_start: 0.8281 (ptpt) cc_final: 0.7931 (pttt) REVERT: X 160 ASP cc_start: 0.6939 (t0) cc_final: 0.6572 (t0) REVERT: X 203 GLN cc_start: 0.7396 (mt0) cc_final: 0.7119 (mt0) REVERT: X 244 SER cc_start: 0.8598 (t) cc_final: 0.8368 (p) REVERT: X 250 LYS cc_start: 0.8406 (mttm) cc_final: 0.8190 (mttp) REVERT: X 259 ILE cc_start: 0.8282 (pt) cc_final: 0.8000 (mm) REVERT: X 286 THR cc_start: 0.8262 (p) cc_final: 0.8043 (m) REVERT: X 332 MET cc_start: 0.7744 (mmm) cc_final: 0.7210 (mmm) REVERT: X 350 ASN cc_start: 0.7671 (t0) cc_final: 0.7276 (p0) REVERT: X 380 GLU cc_start: 0.7975 (tt0) cc_final: 0.7576 (mt-10) REVERT: X 388 LYS cc_start: 0.8135 (pttt) cc_final: 0.7847 (pttt) REVERT: X 454 ARG cc_start: 0.8246 (mtp180) cc_final: 0.7994 (mtp85) REVERT: X 470 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8090 (pt) REVERT: X 566 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7627 (mp0) REVERT: X 887 ARG cc_start: 0.7817 (ttm170) cc_final: 0.7522 (ttp-170) REVERT: X 905 LYS cc_start: 0.8395 (tptp) cc_final: 0.8032 (tptp) REVERT: X 913 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8473 (mm) REVERT: X 915 ARG cc_start: 0.7925 (mmt-90) cc_final: 0.7540 (mmt-90) REVERT: X 916 ASN cc_start: 0.8468 (t0) cc_final: 0.8114 (t0) REVERT: X 927 GLN cc_start: 0.8240 (mt0) cc_final: 0.8030 (mt0) REVERT: X 933 LYS cc_start: 0.8447 (mttt) cc_final: 0.8041 (mttt) REVERT: X 946 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.6841 (t) REVERT: X 985 LYS cc_start: 0.8900 (ttpt) cc_final: 0.8614 (ttpp) REVERT: X 986 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8662 (pt) REVERT: X 989 MET cc_start: 0.8070 (mmm) cc_final: 0.7684 (tpp) REVERT: X 1064 TYR cc_start: 0.8267 (m-80) cc_final: 0.7942 (m-10) REVERT: X 1124 ARG cc_start: 0.8132 (ttm-80) cc_final: 0.7644 (ttm-80) REVERT: X 1126 ARG cc_start: 0.7334 (ptp90) cc_final: 0.6979 (ptp90) REVERT: X 1152 LEU cc_start: 0.8685 (tp) cc_final: 0.8467 (tt) REVERT: X 1153 TYR cc_start: 0.8318 (m-80) cc_final: 0.7873 (m-80) REVERT: X 1436 ILE cc_start: 0.8163 (mm) cc_final: 0.7944 (mt) REVERT: X 1443 GLU cc_start: 0.8067 (tt0) cc_final: 0.7703 (tt0) REVERT: X 1454 LYS cc_start: 0.7321 (tttt) cc_final: 0.6961 (tttt) REVERT: X 1475 LYS cc_start: 0.8136 (mttt) cc_final: 0.7837 (mtpp) REVERT: X 1495 PHE cc_start: 0.8159 (m-80) cc_final: 0.7781 (m-80) REVERT: X 1510 GLU cc_start: 0.7769 (tt0) cc_final: 0.7462 (tt0) REVERT: X 1569 PHE cc_start: 0.7356 (m-10) cc_final: 0.6756 (m-80) REVERT: X 1574 GLU cc_start: 0.7811 (tt0) cc_final: 0.7599 (tt0) REVERT: X 1575 MET cc_start: 0.7906 (mtt) cc_final: 0.7454 (mtt) REVERT: Y 131 PHE cc_start: 0.8060 (m-80) cc_final: 0.7673 (m-80) REVERT: Y 150 MET cc_start: 0.8249 (tpt) cc_final: 0.7945 (tpp) outliers start: 102 outliers final: 73 residues processed: 810 average time/residue: 0.1929 time to fit residues: 239.9868 Evaluate side-chains 842 residues out of total 3118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 757 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain a residue 19 LYS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 98 VAL Chi-restraints excluded: chain a residue 99 LEU Chi-restraints excluded: chain a residue 145 LYS Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 169 GLU Chi-restraints excluded: chain a residue 171 LEU Chi-restraints excluded: chain a residue 199 ILE Chi-restraints excluded: chain a residue 205 ILE Chi-restraints excluded: chain a residue 213 PHE Chi-restraints excluded: chain a residue 216 ILE Chi-restraints excluded: chain a residue 275 VAL Chi-restraints excluded: chain a residue 276 SER Chi-restraints excluded: chain c residue 18 ARG Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain c residue 269 LEU Chi-restraints excluded: chain c residue 275 LEU Chi-restraints excluded: chain c residue 306 CYS Chi-restraints excluded: chain c residue 307 LEU Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 211 TYR Chi-restraints excluded: chain T residue 225 ASP Chi-restraints excluded: chain T residue 239 VAL Chi-restraints excluded: chain T residue 263 MET Chi-restraints excluded: chain T residue 336 SER Chi-restraints excluded: chain T residue 349 LEU Chi-restraints excluded: chain T residue 442 TYR Chi-restraints excluded: chain T residue 462 LEU Chi-restraints excluded: chain T residue 588 LYS Chi-restraints excluded: chain h residue 381 MET Chi-restraints excluded: chain h residue 410 SER Chi-restraints excluded: chain h residue 532 MET Chi-restraints excluded: chain h residue 545 GLU Chi-restraints excluded: chain h residue 605 LYS Chi-restraints excluded: chain h residue 633 ASN Chi-restraints excluded: chain h residue 673 LEU Chi-restraints excluded: chain h residue 752 LEU Chi-restraints excluded: chain h residue 801 ASP Chi-restraints excluded: chain h residue 838 ILE Chi-restraints excluded: chain h residue 954 THR Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 129 LYS Chi-restraints excluded: chain X residue 174 ILE Chi-restraints excluded: chain X residue 368 VAL Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain X residue 465 MET Chi-restraints excluded: chain X residue 470 ILE Chi-restraints excluded: chain X residue 528 MET Chi-restraints excluded: chain X residue 541 VAL Chi-restraints excluded: chain X residue 557 MET Chi-restraints excluded: chain X residue 561 ASP Chi-restraints excluded: chain X residue 851 ILE Chi-restraints excluded: chain X residue 869 ILE Chi-restraints excluded: chain X residue 913 ILE Chi-restraints excluded: chain X residue 920 THR Chi-restraints excluded: chain X residue 946 THR Chi-restraints excluded: chain X residue 951 CYS Chi-restraints excluded: chain X residue 958 LYS Chi-restraints excluded: chain X residue 986 LEU Chi-restraints excluded: chain X residue 1011 LEU Chi-restraints excluded: chain X residue 1022 VAL Chi-restraints excluded: chain X residue 1081 VAL Chi-restraints excluded: chain X residue 1146 MET Chi-restraints excluded: chain X residue 1168 ILE Chi-restraints excluded: chain X residue 1390 LEU Chi-restraints excluded: chain X residue 1459 VAL Chi-restraints excluded: chain X residue 1514 ASN Chi-restraints excluded: chain Y residue 129 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 186 optimal weight: 0.9990 chunk 168 optimal weight: 0.3980 chunk 298 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 233 optimal weight: 2.9990 chunk 324 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 chunk 34 optimal weight: 0.0970 chunk 255 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 260 optimal weight: 0.2980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN C 111 HIS C 121 ASN C 140 HIS a 71 ASN c 191 ASN c 271 ASN h 20 HIS ** h 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 542 HIS h 653 GLN h 784 GLN X 981 ASN ** X1478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.146111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.123624 restraints weight = 43326.221| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.43 r_work: 0.3525 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28093 Z= 0.147 Angle : 0.550 8.683 37995 Z= 0.282 Chirality : 0.044 0.186 4230 Planarity : 0.004 0.053 4808 Dihedral : 4.405 40.173 3642 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.60 % Allowed : 18.38 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.15), residues: 3294 helix: 1.06 (0.15), residues: 1163 sheet: -0.55 (0.20), residues: 717 loop : -0.94 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG h 588 TYR 0.041 0.001 TYR C 260 PHE 0.024 0.002 PHE X1555 TRP 0.013 0.001 TRP C 229 HIS 0.012 0.001 HIS X1371 Details of bonding type rmsd covalent geometry : bond 0.00339 (28093) covalent geometry : angle 0.55002 (37995) hydrogen bonds : bond 0.03496 ( 1115) hydrogen bonds : angle 4.55966 ( 3171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 3118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 767 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 VAL cc_start: 0.8055 (t) cc_final: 0.7790 (t) REVERT: C 54 ASP cc_start: 0.7995 (t0) cc_final: 0.7622 (t0) REVERT: C 61 TRP cc_start: 0.8077 (t60) cc_final: 0.7831 (t60) REVERT: C 101 SER cc_start: 0.8366 (t) cc_final: 0.8158 (p) REVERT: C 128 ASP cc_start: 0.7685 (m-30) cc_final: 0.7455 (m-30) REVERT: C 144 MET cc_start: 0.8111 (mmm) cc_final: 0.7583 (mtt) REVERT: C 189 LYS cc_start: 0.7981 (mttt) cc_final: 0.7739 (mtmt) REVERT: C 191 SER cc_start: 0.7998 (m) cc_final: 0.7276 (t) REVERT: C 207 ILE cc_start: 0.7349 (OUTLIER) cc_final: 0.7100 (pt) REVERT: C 213 LYS cc_start: 0.8380 (tptm) cc_final: 0.8046 (tppp) REVERT: C 217 ILE cc_start: 0.8149 (mt) cc_final: 0.7830 (tt) REVERT: C 229 TRP cc_start: 0.8165 (m-90) cc_final: 0.7794 (m-10) REVERT: C 237 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7428 (mm-30) REVERT: C 239 LYS cc_start: 0.8222 (tmmt) cc_final: 0.7899 (tmmt) REVERT: C 298 LYS cc_start: 0.8272 (mmtp) cc_final: 0.8001 (mmtt) REVERT: C 347 LYS cc_start: 0.8542 (mttt) cc_final: 0.8305 (mttp) REVERT: C 349 ASN cc_start: 0.7783 (t0) cc_final: 0.7170 (t0) REVERT: C 363 TYR cc_start: 0.8965 (m-80) cc_final: 0.8237 (m-80) REVERT: C 433 GLU cc_start: 0.6948 (tt0) cc_final: 0.6657 (tt0) REVERT: C 445 VAL cc_start: 0.7999 (t) cc_final: 0.7468 (p) REVERT: C 448 LYS cc_start: 0.8000 (tttt) cc_final: 0.7705 (tttp) REVERT: C 454 ARG cc_start: 0.6800 (mtp180) cc_final: 0.6597 (mtm180) REVERT: C 480 ASN cc_start: 0.7218 (m-40) cc_final: 0.6928 (t0) REVERT: a 17 SER cc_start: 0.8505 (m) cc_final: 0.8218 (p) REVERT: a 61 ASP cc_start: 0.7347 (t70) cc_final: 0.7081 (t0) REVERT: a 97 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6843 (mt-10) REVERT: a 114 LYS cc_start: 0.8439 (tttt) cc_final: 0.8226 (tttm) REVERT: a 128 MET cc_start: 0.8406 (mtp) cc_final: 0.8065 (ttm) REVERT: a 146 ASN cc_start: 0.7649 (m110) cc_final: 0.7278 (m-40) REVERT: a 148 SER cc_start: 0.8521 (t) cc_final: 0.8202 (t) REVERT: a 154 PHE cc_start: 0.7878 (m-80) cc_final: 0.7540 (m-10) REVERT: a 194 LYS cc_start: 0.8035 (mttt) cc_final: 0.7600 (mtpp) REVERT: a 197 LYS cc_start: 0.8034 (tttm) cc_final: 0.7830 (tttt) REVERT: a 211 THR cc_start: 0.8614 (m) cc_final: 0.8388 (p) REVERT: a 213 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.6984 (t80) REVERT: a 265 LYS cc_start: 0.8564 (tttt) cc_final: 0.8062 (ttmm) REVERT: c 15 MET cc_start: 0.6581 (mtp) cc_final: 0.6131 (mtp) REVERT: c 18 ARG cc_start: 0.7922 (ttt-90) cc_final: 0.7651 (mtt-85) REVERT: c 102 ASN cc_start: 0.8020 (t0) cc_final: 0.7798 (m-40) REVERT: c 106 ILE cc_start: 0.7985 (mt) cc_final: 0.7715 (mt) REVERT: c 119 ILE cc_start: 0.8033 (mt) cc_final: 0.7525 (mm) REVERT: c 120 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6483 (mm-30) REVERT: c 124 HIS cc_start: 0.7837 (t70) cc_final: 0.7453 (t70) REVERT: c 148 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7309 (mt-10) REVERT: c 181 LYS cc_start: 0.8126 (mttt) cc_final: 0.7826 (mtpt) REVERT: c 204 LYS cc_start: 0.7656 (tptt) cc_final: 0.7419 (tppt) REVERT: c 219 ASP cc_start: 0.8141 (p0) cc_final: 0.7888 (p0) REVERT: c 220 SER cc_start: 0.8482 (m) cc_final: 0.8092 (p) REVERT: c 227 MET cc_start: 0.6433 (ptp) cc_final: 0.6151 (ttp) REVERT: c 232 SER cc_start: 0.7781 (m) cc_final: 0.7306 (p) REVERT: c 243 ASP cc_start: 0.7843 (m-30) cc_final: 0.7312 (m-30) REVERT: c 246 LYS cc_start: 0.7412 (mtpt) cc_final: 0.7103 (mtpt) REVERT: c 273 SER cc_start: 0.7869 (t) cc_final: 0.7046 (p) REVERT: c 274 GLN cc_start: 0.8257 (tt0) cc_final: 0.7217 (tt0) REVERT: c 275 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8474 (mt) REVERT: c 284 ARG cc_start: 0.7711 (ttm170) cc_final: 0.7390 (mtp180) REVERT: c 286 MET cc_start: 0.7666 (mmm) cc_final: 0.7392 (mtp) REVERT: c 303 MET cc_start: 0.5865 (ttt) cc_final: 0.5513 (ttt) REVERT: c 313 ASN cc_start: 0.6743 (m-40) cc_final: 0.6514 (m110) REVERT: T 37 LYS cc_start: 0.8216 (mmtp) cc_final: 0.7951 (mmtp) REVERT: T 62 THR cc_start: 0.8237 (m) cc_final: 0.7803 (p) REVERT: T 81 ILE cc_start: 0.8609 (mt) cc_final: 0.8298 (mm) REVERT: T 90 ASN cc_start: 0.7788 (t0) cc_final: 0.7584 (t0) REVERT: T 117 VAL cc_start: 0.7670 (t) cc_final: 0.7460 (p) REVERT: T 207 ASP cc_start: 0.7362 (m-30) cc_final: 0.7100 (m-30) REVERT: T 229 PHE cc_start: 0.8243 (m-80) cc_final: 0.7764 (m-80) REVERT: T 239 VAL cc_start: 0.8215 (OUTLIER) cc_final: 0.7983 (t) REVERT: T 243 ASP cc_start: 0.7247 (m-30) cc_final: 0.6939 (m-30) REVERT: T 246 LEU cc_start: 0.8129 (mt) cc_final: 0.7876 (mt) REVERT: T 335 GLN cc_start: 0.7587 (mt0) cc_final: 0.7230 (mt0) REVERT: T 343 VAL cc_start: 0.8106 (t) cc_final: 0.7846 (p) REVERT: T 352 ASN cc_start: 0.7766 (m-40) cc_final: 0.7503 (m-40) REVERT: T 452 LYS cc_start: 0.8477 (tttt) cc_final: 0.8162 (tttp) REVERT: T 487 SER cc_start: 0.8043 (m) cc_final: 0.7752 (p) REVERT: T 573 GLU cc_start: 0.7523 (pt0) cc_final: 0.7060 (pt0) REVERT: h 368 MET cc_start: 0.7155 (tpt) cc_final: 0.6633 (tpt) REVERT: h 383 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6798 (mm-30) REVERT: h 387 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7438 (mt-10) REVERT: h 569 GLN cc_start: 0.8033 (tp40) cc_final: 0.7216 (tp40) REVERT: h 575 ILE cc_start: 0.7668 (mm) cc_final: 0.6557 (mm) REVERT: h 577 SER cc_start: 0.8033 (m) cc_final: 0.7797 (t) REVERT: h 580 HIS cc_start: 0.8164 (t-170) cc_final: 0.7912 (t-170) REVERT: h 596 TYR cc_start: 0.8565 (t80) cc_final: 0.8325 (t80) REVERT: h 597 GLN cc_start: 0.8276 (mp10) cc_final: 0.7762 (mp10) REVERT: h 607 LYS cc_start: 0.8367 (ttmt) cc_final: 0.7987 (ttmt) REVERT: h 610 TYR cc_start: 0.8084 (m-80) cc_final: 0.7698 (m-80) REVERT: h 628 ASP cc_start: 0.7364 (m-30) cc_final: 0.6937 (m-30) REVERT: h 632 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7890 (ttm170) REVERT: h 635 ILE cc_start: 0.8473 (mp) cc_final: 0.8226 (mt) REVERT: h 643 ASP cc_start: 0.7314 (t0) cc_final: 0.7020 (t0) REVERT: h 652 ILE cc_start: 0.7665 (mt) cc_final: 0.7437 (tt) REVERT: h 655 GLU cc_start: 0.8125 (pt0) cc_final: 0.7185 (mt-10) REVERT: h 776 LEU cc_start: 0.7950 (tp) cc_final: 0.7679 (mt) REVERT: h 782 ASN cc_start: 0.7280 (m-40) cc_final: 0.6986 (m-40) REVERT: h 857 TYR cc_start: 0.8343 (m-80) cc_final: 0.8085 (m-10) REVERT: h 860 ASP cc_start: 0.7767 (p0) cc_final: 0.7499 (p0) REVERT: h 895 SER cc_start: 0.8117 (t) cc_final: 0.7842 (p) REVERT: h 921 GLN cc_start: 0.8377 (pt0) cc_final: 0.7991 (pt0) REVERT: h 932 HIS cc_start: 0.6878 (m90) cc_final: 0.6309 (m90) REVERT: h 962 LYS cc_start: 0.8516 (ptmt) cc_final: 0.8176 (ptmt) REVERT: h 965 LYS cc_start: 0.7784 (mttm) cc_final: 0.7577 (mttt) REVERT: h 1066 MET cc_start: 0.6554 (mmm) cc_final: 0.6294 (mmm) REVERT: h 1084 LYS cc_start: 0.8288 (mttt) cc_final: 0.8027 (mtpp) REVERT: h 1112 LYS cc_start: 0.8314 (mtpt) cc_final: 0.8005 (mtpt) REVERT: h 1116 GLU cc_start: 0.8105 (mp0) cc_final: 0.7710 (mp0) REVERT: h 1134 ASN cc_start: 0.7313 (m-40) cc_final: 0.6851 (m-40) REVERT: h 1139 TYR cc_start: 0.7899 (m-80) cc_final: 0.7644 (m-80) REVERT: X 103 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7751 (tm-30) REVERT: X 105 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7144 (tt0) REVERT: X 129 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.7064 (ttmt) REVERT: X 136 LEU cc_start: 0.8059 (tp) cc_final: 0.7361 (tt) REVERT: X 150 LYS cc_start: 0.8138 (ptpt) cc_final: 0.7749 (pttt) REVERT: X 203 GLN cc_start: 0.7121 (mt0) cc_final: 0.6917 (mt0) REVERT: X 244 SER cc_start: 0.8510 (t) cc_final: 0.8276 (p) REVERT: X 250 LYS cc_start: 0.8180 (mttm) cc_final: 0.7949 (mttp) REVERT: X 259 ILE cc_start: 0.8187 (pt) cc_final: 0.7882 (mm) REVERT: X 332 MET cc_start: 0.7494 (mmm) cc_final: 0.6961 (mmm) REVERT: X 350 ASN cc_start: 0.7455 (t0) cc_final: 0.7167 (p0) REVERT: X 380 GLU cc_start: 0.7654 (tt0) cc_final: 0.7409 (mt-10) REVERT: X 388 LYS cc_start: 0.8048 (pttt) cc_final: 0.7779 (pttt) REVERT: X 454 ARG cc_start: 0.7998 (mtp180) cc_final: 0.7742 (mtp85) REVERT: X 470 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8002 (pt) REVERT: X 566 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7531 (mp0) REVERT: X 887 ARG cc_start: 0.7551 (ttm170) cc_final: 0.7269 (ttp-170) REVERT: X 905 LYS cc_start: 0.8344 (tptp) cc_final: 0.7991 (tptp) REVERT: X 913 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8327 (mm) REVERT: X 915 ARG cc_start: 0.7566 (mmt-90) cc_final: 0.7211 (mmt-90) REVERT: X 916 ASN cc_start: 0.8304 (t0) cc_final: 0.7950 (t0) REVERT: X 933 LYS cc_start: 0.8293 (mttt) cc_final: 0.7880 (mttt) REVERT: X 946 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.6758 (t) REVERT: X 985 LYS cc_start: 0.8735 (ttpt) cc_final: 0.8379 (ttpp) REVERT: X 986 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8592 (pt) REVERT: X 989 MET cc_start: 0.7667 (mmm) cc_final: 0.7407 (tpp) REVERT: X 1064 TYR cc_start: 0.8198 (m-80) cc_final: 0.7886 (m-10) REVERT: X 1126 ARG cc_start: 0.7063 (ptp90) cc_final: 0.6705 (ptp90) REVERT: X 1152 LEU cc_start: 0.8622 (tp) cc_final: 0.8416 (tt) REVERT: X 1153 TYR cc_start: 0.8142 (m-80) cc_final: 0.7568 (m-80) REVERT: X 1436 ILE cc_start: 0.8068 (mm) cc_final: 0.7852 (mt) REVERT: X 1443 GLU cc_start: 0.7870 (tt0) cc_final: 0.7545 (tt0) REVERT: X 1454 LYS cc_start: 0.7211 (tttt) cc_final: 0.6861 (tttt) REVERT: X 1475 LYS cc_start: 0.8025 (mttt) cc_final: 0.7715 (mtpp) REVERT: X 1495 PHE cc_start: 0.7929 (m-80) cc_final: 0.7578 (m-80) REVERT: X 1510 GLU cc_start: 0.7368 (tt0) cc_final: 0.7143 (tt0) REVERT: X 1564 LYS cc_start: 0.7828 (mmtp) cc_final: 0.7535 (mmtp) REVERT: X 1569 PHE cc_start: 0.7280 (m-10) cc_final: 0.6700 (m-80) REVERT: X 1574 GLU cc_start: 0.7613 (tt0) cc_final: 0.7393 (tt0) REVERT: X 1575 MET cc_start: 0.7651 (mtt) cc_final: 0.7177 (mtt) REVERT: Y 131 PHE cc_start: 0.7872 (m-80) cc_final: 0.7435 (m-80) REVERT: Y 150 MET cc_start: 0.8167 (tpt) cc_final: 0.7856 (tpp) outliers start: 81 outliers final: 59 residues processed: 801 average time/residue: 0.1980 time to fit residues: 243.1508 Evaluate side-chains 832 residues out of total 3118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 764 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 98 VAL Chi-restraints excluded: chain a residue 99 LEU Chi-restraints excluded: chain a residue 145 LYS Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 169 GLU Chi-restraints excluded: chain a residue 171 LEU Chi-restraints excluded: chain a residue 199 ILE Chi-restraints excluded: chain a residue 205 ILE Chi-restraints excluded: chain a residue 213 PHE Chi-restraints excluded: chain a residue 276 SER Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain c residue 275 LEU Chi-restraints excluded: chain c residue 306 CYS Chi-restraints excluded: chain c residue 307 LEU Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 211 TYR Chi-restraints excluded: chain T residue 239 VAL Chi-restraints excluded: chain T residue 263 MET Chi-restraints excluded: chain T residue 336 SER Chi-restraints excluded: chain T residue 349 LEU Chi-restraints excluded: chain T residue 442 TYR Chi-restraints excluded: chain T residue 462 LEU Chi-restraints excluded: chain h residue 381 MET Chi-restraints excluded: chain h residue 410 SER Chi-restraints excluded: chain h residue 545 GLU Chi-restraints excluded: chain h residue 605 LYS Chi-restraints excluded: chain h residue 673 LEU Chi-restraints excluded: chain h residue 752 LEU Chi-restraints excluded: chain h residue 801 ASP Chi-restraints excluded: chain h residue 838 ILE Chi-restraints excluded: chain h residue 954 THR Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 129 LYS Chi-restraints excluded: chain X residue 174 ILE Chi-restraints excluded: chain X residue 235 MET Chi-restraints excluded: chain X residue 368 VAL Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain X residue 470 ILE Chi-restraints excluded: chain X residue 517 THR Chi-restraints excluded: chain X residue 528 MET Chi-restraints excluded: chain X residue 561 ASP Chi-restraints excluded: chain X residue 851 ILE Chi-restraints excluded: chain X residue 869 ILE Chi-restraints excluded: chain X residue 913 ILE Chi-restraints excluded: chain X residue 920 THR Chi-restraints excluded: chain X residue 946 THR Chi-restraints excluded: chain X residue 951 CYS Chi-restraints excluded: chain X residue 986 LEU Chi-restraints excluded: chain X residue 1011 LEU Chi-restraints excluded: chain X residue 1146 MET Chi-restraints excluded: chain X residue 1168 ILE Chi-restraints excluded: chain X residue 1390 LEU Chi-restraints excluded: chain X residue 1459 VAL Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain Y residue 129 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 233 optimal weight: 0.8980 chunk 288 optimal weight: 0.5980 chunk 200 optimal weight: 0.7980 chunk 195 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 290 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 HIS C 140 HIS a 71 ASN h 20 HIS ** h 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 542 HIS h 653 GLN X 981 ASN ** X1478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.144413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.122080 restraints weight = 43434.816| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.40 r_work: 0.3505 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 28093 Z= 0.244 Angle : 0.601 10.233 37995 Z= 0.310 Chirality : 0.047 0.175 4230 Planarity : 0.004 0.053 4808 Dihedral : 4.569 40.122 3642 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.79 % Allowed : 18.70 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.15), residues: 3294 helix: 0.93 (0.15), residues: 1162 sheet: -0.62 (0.20), residues: 713 loop : -1.02 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG h 781 TYR 0.044 0.002 TYR C 260 PHE 0.026 0.002 PHE T 472 TRP 0.014 0.002 TRP X1414 HIS 0.012 0.001 HIS X1371 Details of bonding type rmsd covalent geometry : bond 0.00563 (28093) covalent geometry : angle 0.60075 (37995) hydrogen bonds : bond 0.03962 ( 1115) hydrogen bonds : angle 4.67078 ( 3171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 3118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 770 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 VAL cc_start: 0.8228 (t) cc_final: 0.7952 (t) REVERT: C 54 ASP cc_start: 0.8174 (t0) cc_final: 0.7828 (t0) REVERT: C 61 TRP cc_start: 0.8272 (t60) cc_final: 0.8053 (t60) REVERT: C 101 SER cc_start: 0.8471 (t) cc_final: 0.8239 (p) REVERT: C 128 ASP cc_start: 0.7977 (m-30) cc_final: 0.7766 (m-30) REVERT: C 189 LYS cc_start: 0.8151 (mttt) cc_final: 0.7863 (mtmt) REVERT: C 191 SER cc_start: 0.8129 (m) cc_final: 0.7405 (t) REVERT: C 207 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7382 (pt) REVERT: C 213 LYS cc_start: 0.8509 (tptm) cc_final: 0.8159 (tppp) REVERT: C 217 ILE cc_start: 0.8241 (mt) cc_final: 0.7880 (tt) REVERT: C 229 TRP cc_start: 0.8295 (m-90) cc_final: 0.7370 (m-90) REVERT: C 237 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7703 (mm-30) REVERT: C 239 LYS cc_start: 0.8388 (tmmt) cc_final: 0.8061 (tmmt) REVERT: C 298 LYS cc_start: 0.8431 (mmtp) cc_final: 0.8080 (mptt) REVERT: C 347 LYS cc_start: 0.8660 (mttt) cc_final: 0.8424 (mttp) REVERT: C 349 ASN cc_start: 0.7895 (t0) cc_final: 0.7272 (t0) REVERT: C 363 TYR cc_start: 0.9015 (m-80) cc_final: 0.8292 (m-80) REVERT: C 408 SER cc_start: 0.8663 (t) cc_final: 0.8271 (p) REVERT: C 433 GLU cc_start: 0.7219 (tt0) cc_final: 0.6943 (tt0) REVERT: C 448 LYS cc_start: 0.8100 (tttt) cc_final: 0.7839 (tttp) REVERT: C 454 ARG cc_start: 0.7086 (mtp180) cc_final: 0.6863 (mtm180) REVERT: C 480 ASN cc_start: 0.7433 (m-40) cc_final: 0.7124 (t0) REVERT: a 15 SER cc_start: 0.8561 (p) cc_final: 0.8335 (t) REVERT: a 17 SER cc_start: 0.8601 (m) cc_final: 0.8330 (p) REVERT: a 61 ASP cc_start: 0.7711 (t70) cc_final: 0.7288 (t0) REVERT: a 97 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7144 (mt-10) REVERT: a 146 ASN cc_start: 0.7795 (m110) cc_final: 0.7405 (m-40) REVERT: a 148 SER cc_start: 0.8548 (t) cc_final: 0.8224 (t) REVERT: a 154 PHE cc_start: 0.8041 (m-80) cc_final: 0.7687 (m-10) REVERT: a 194 LYS cc_start: 0.8156 (mttt) cc_final: 0.7725 (mtpp) REVERT: a 197 LYS cc_start: 0.8210 (tttm) cc_final: 0.8001 (tttt) REVERT: a 201 ASN cc_start: 0.8139 (t0) cc_final: 0.7609 (t0) REVERT: a 213 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.7167 (t80) REVERT: a 248 ASN cc_start: 0.8056 (t0) cc_final: 0.7735 (t0) REVERT: a 250 MET cc_start: 0.8215 (mmm) cc_final: 0.7827 (mmm) REVERT: a 265 LYS cc_start: 0.8632 (tttt) cc_final: 0.8121 (ttmm) REVERT: a 289 LYS cc_start: 0.7786 (mtmt) cc_final: 0.7482 (mttp) REVERT: c 15 MET cc_start: 0.6975 (mtp) cc_final: 0.6538 (mtp) REVERT: c 18 ARG cc_start: 0.8166 (ttt-90) cc_final: 0.7848 (mtt-85) REVERT: c 106 ILE cc_start: 0.8161 (mt) cc_final: 0.7923 (mt) REVERT: c 119 ILE cc_start: 0.8194 (mt) cc_final: 0.7688 (mm) REVERT: c 120 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6871 (mm-30) REVERT: c 124 HIS cc_start: 0.8074 (t70) cc_final: 0.7687 (t70) REVERT: c 148 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7637 (mt-10) REVERT: c 181 LYS cc_start: 0.8314 (mttt) cc_final: 0.8001 (mtpt) REVERT: c 204 LYS cc_start: 0.7874 (tptt) cc_final: 0.7623 (tppt) REVERT: c 219 ASP cc_start: 0.8229 (p0) cc_final: 0.7940 (p0) REVERT: c 220 SER cc_start: 0.8594 (m) cc_final: 0.8184 (p) REVERT: c 227 MET cc_start: 0.6824 (ptp) cc_final: 0.6531 (ttp) REVERT: c 243 ASP cc_start: 0.8090 (m-30) cc_final: 0.7600 (m-30) REVERT: c 246 LYS cc_start: 0.7687 (mtpt) cc_final: 0.7367 (mtpt) REVERT: c 273 SER cc_start: 0.8023 (t) cc_final: 0.7296 (p) REVERT: c 274 GLN cc_start: 0.8463 (tt0) cc_final: 0.7564 (tt0) REVERT: c 275 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8564 (mt) REVERT: c 284 ARG cc_start: 0.7944 (ttm170) cc_final: 0.7569 (mtp180) REVERT: c 286 MET cc_start: 0.7914 (mmm) cc_final: 0.7625 (mtp) REVERT: c 303 MET cc_start: 0.6243 (ttt) cc_final: 0.5883 (ttt) REVERT: c 313 ASN cc_start: 0.6940 (m-40) cc_final: 0.6658 (m110) REVERT: T 37 LYS cc_start: 0.8331 (mmtp) cc_final: 0.8071 (mmtp) REVERT: T 81 ILE cc_start: 0.8653 (mt) cc_final: 0.8400 (mm) REVERT: T 90 ASN cc_start: 0.8031 (t0) cc_final: 0.7817 (t0) REVERT: T 207 ASP cc_start: 0.7595 (m-30) cc_final: 0.7351 (m-30) REVERT: T 229 PHE cc_start: 0.8371 (m-80) cc_final: 0.7863 (m-80) REVERT: T 243 ASP cc_start: 0.7502 (m-30) cc_final: 0.7253 (m-30) REVERT: T 246 LEU cc_start: 0.8373 (mt) cc_final: 0.8143 (mt) REVERT: T 335 GLN cc_start: 0.7859 (mt0) cc_final: 0.7469 (mt0) REVERT: T 343 VAL cc_start: 0.8229 (t) cc_final: 0.7969 (p) REVERT: T 352 ASN cc_start: 0.7875 (m-40) cc_final: 0.7632 (m-40) REVERT: T 452 LYS cc_start: 0.8614 (tttt) cc_final: 0.8364 (tttp) REVERT: T 487 SER cc_start: 0.8233 (m) cc_final: 0.7925 (p) REVERT: h 368 MET cc_start: 0.7278 (tpt) cc_final: 0.6698 (tpt) REVERT: h 383 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7002 (mm-30) REVERT: h 387 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7707 (mt-10) REVERT: h 569 GLN cc_start: 0.8239 (tp40) cc_final: 0.7381 (tp40) REVERT: h 575 ILE cc_start: 0.7751 (mm) cc_final: 0.6646 (mm) REVERT: h 577 SER cc_start: 0.8188 (m) cc_final: 0.7963 (t) REVERT: h 580 HIS cc_start: 0.8352 (t-170) cc_final: 0.8116 (t-170) REVERT: h 597 GLN cc_start: 0.8466 (mp10) cc_final: 0.7998 (mp10) REVERT: h 607 LYS cc_start: 0.8429 (ttmt) cc_final: 0.8113 (ttmt) REVERT: h 610 TYR cc_start: 0.8205 (m-80) cc_final: 0.7839 (m-80) REVERT: h 628 ASP cc_start: 0.7604 (m-30) cc_final: 0.7209 (m-30) REVERT: h 632 ARG cc_start: 0.8439 (ttm170) cc_final: 0.8166 (ttm-80) REVERT: h 635 ILE cc_start: 0.8612 (mp) cc_final: 0.8378 (mt) REVERT: h 643 ASP cc_start: 0.7466 (t0) cc_final: 0.7174 (t0) REVERT: h 652 ILE cc_start: 0.7770 (mt) cc_final: 0.7514 (tt) REVERT: h 655 GLU cc_start: 0.8357 (pt0) cc_final: 0.7432 (mt-10) REVERT: h 782 ASN cc_start: 0.7507 (m-40) cc_final: 0.7192 (m-40) REVERT: h 857 TYR cc_start: 0.8496 (m-80) cc_final: 0.8231 (m-10) REVERT: h 860 ASP cc_start: 0.7925 (p0) cc_final: 0.7688 (p0) REVERT: h 895 SER cc_start: 0.8219 (t) cc_final: 0.7939 (p) REVERT: h 921 GLN cc_start: 0.8522 (pt0) cc_final: 0.8129 (pt0) REVERT: h 932 HIS cc_start: 0.7167 (m90) cc_final: 0.6545 (m90) REVERT: h 962 LYS cc_start: 0.8640 (ptmt) cc_final: 0.8287 (ptmt) REVERT: h 965 LYS cc_start: 0.7891 (mttm) cc_final: 0.7501 (mtpt) REVERT: h 1066 MET cc_start: 0.6790 (mmm) cc_final: 0.6545 (mmm) REVERT: h 1084 LYS cc_start: 0.8521 (mttt) cc_final: 0.8245 (mtpp) REVERT: h 1112 LYS cc_start: 0.8522 (mtpt) cc_final: 0.8192 (mtpt) REVERT: h 1116 GLU cc_start: 0.8372 (mp0) cc_final: 0.7969 (mm-30) REVERT: h 1134 ASN cc_start: 0.7505 (m-40) cc_final: 0.7043 (m-40) REVERT: h 1139 TYR cc_start: 0.8086 (m-80) cc_final: 0.7843 (m-80) REVERT: X 103 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7947 (tm-30) REVERT: X 105 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7394 (tt0) REVERT: X 129 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.7197 (ttmt) REVERT: X 136 LEU cc_start: 0.8110 (tp) cc_final: 0.7597 (tt) REVERT: X 150 LYS cc_start: 0.8316 (ptpt) cc_final: 0.7866 (pttt) REVERT: X 244 SER cc_start: 0.8618 (t) cc_final: 0.8380 (p) REVERT: X 250 LYS cc_start: 0.8396 (mttm) cc_final: 0.8172 (mttp) REVERT: X 259 ILE cc_start: 0.8283 (pt) cc_final: 0.7997 (mm) REVERT: X 306 SER cc_start: 0.8264 (m) cc_final: 0.7992 (p) REVERT: X 332 MET cc_start: 0.7773 (mmm) cc_final: 0.7257 (mmm) REVERT: X 350 ASN cc_start: 0.7702 (t0) cc_final: 0.7330 (p0) REVERT: X 380 GLU cc_start: 0.7983 (tt0) cc_final: 0.7595 (mt-10) REVERT: X 388 LYS cc_start: 0.8130 (pttt) cc_final: 0.7838 (pttt) REVERT: X 454 ARG cc_start: 0.8301 (mtp180) cc_final: 0.8045 (mtp85) REVERT: X 465 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7736 (ttm) REVERT: X 566 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7631 (mp0) REVERT: X 887 ARG cc_start: 0.7813 (ttm170) cc_final: 0.7518 (ttp-170) REVERT: X 891 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8372 (m) REVERT: X 905 LYS cc_start: 0.8445 (tptp) cc_final: 0.7999 (tptp) REVERT: X 913 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8468 (mm) REVERT: X 916 ASN cc_start: 0.8467 (t0) cc_final: 0.8127 (t0) REVERT: X 932 TYR cc_start: 0.8664 (p90) cc_final: 0.8326 (p90) REVERT: X 933 LYS cc_start: 0.8463 (mttt) cc_final: 0.8054 (mttt) REVERT: X 946 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.6916 (t) REVERT: X 985 LYS cc_start: 0.8901 (ttpt) cc_final: 0.8689 (ttpt) REVERT: X 986 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8531 (pt) REVERT: X 989 MET cc_start: 0.8075 (mmm) cc_final: 0.7532 (tpp) REVERT: X 1064 TYR cc_start: 0.8270 (m-80) cc_final: 0.7943 (m-10) REVERT: X 1124 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7603 (ttm-80) REVERT: X 1126 ARG cc_start: 0.7324 (ptp90) cc_final: 0.6949 (ptp90) REVERT: X 1152 LEU cc_start: 0.8737 (tp) cc_final: 0.8524 (tt) REVERT: X 1436 ILE cc_start: 0.8257 (mm) cc_final: 0.7969 (mt) REVERT: X 1454 LYS cc_start: 0.7398 (tttt) cc_final: 0.7020 (tttt) REVERT: X 1475 LYS cc_start: 0.8126 (mttt) cc_final: 0.7825 (mtpp) REVERT: X 1495 PHE cc_start: 0.8083 (m-80) cc_final: 0.7702 (m-80) REVERT: X 1510 GLU cc_start: 0.7764 (tt0) cc_final: 0.7378 (tt0) REVERT: X 1564 LYS cc_start: 0.7899 (mmtp) cc_final: 0.7620 (mmtp) REVERT: X 1569 PHE cc_start: 0.7385 (m-10) cc_final: 0.6769 (m-80) REVERT: X 1574 GLU cc_start: 0.7786 (tt0) cc_final: 0.7583 (tt0) REVERT: X 1575 MET cc_start: 0.7914 (mtt) cc_final: 0.7456 (mtt) REVERT: Y 131 PHE cc_start: 0.8078 (m-80) cc_final: 0.7644 (m-80) REVERT: Y 150 MET cc_start: 0.8243 (tpt) cc_final: 0.7947 (tpp) outliers start: 87 outliers final: 66 residues processed: 802 average time/residue: 0.1962 time to fit residues: 242.8983 Evaluate side-chains 837 residues out of total 3118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 762 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 98 VAL Chi-restraints excluded: chain a residue 99 LEU Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 169 GLU Chi-restraints excluded: chain a residue 199 ILE Chi-restraints excluded: chain a residue 205 ILE Chi-restraints excluded: chain a residue 213 PHE Chi-restraints excluded: chain a residue 275 VAL Chi-restraints excluded: chain a residue 276 SER Chi-restraints excluded: chain c residue 27 LYS Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain c residue 269 LEU Chi-restraints excluded: chain c residue 275 LEU Chi-restraints excluded: chain c residue 306 CYS Chi-restraints excluded: chain c residue 307 LEU Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 30 GLU Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 211 TYR Chi-restraints excluded: chain T residue 336 SER Chi-restraints excluded: chain T residue 349 LEU Chi-restraints excluded: chain T residue 442 TYR Chi-restraints excluded: chain T residue 462 LEU Chi-restraints excluded: chain h residue 381 MET Chi-restraints excluded: chain h residue 410 SER Chi-restraints excluded: chain h residue 532 MET Chi-restraints excluded: chain h residue 545 GLU Chi-restraints excluded: chain h residue 572 THR Chi-restraints excluded: chain h residue 605 LYS Chi-restraints excluded: chain h residue 633 ASN Chi-restraints excluded: chain h residue 673 LEU Chi-restraints excluded: chain h residue 752 LEU Chi-restraints excluded: chain h residue 801 ASP Chi-restraints excluded: chain h residue 838 ILE Chi-restraints excluded: chain h residue 954 THR Chi-restraints excluded: chain h residue 1068 HIS Chi-restraints excluded: chain X residue 129 LYS Chi-restraints excluded: chain X residue 174 ILE Chi-restraints excluded: chain X residue 368 VAL Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain X residue 465 MET Chi-restraints excluded: chain X residue 470 ILE Chi-restraints excluded: chain X residue 517 THR Chi-restraints excluded: chain X residue 528 MET Chi-restraints excluded: chain X residue 541 VAL Chi-restraints excluded: chain X residue 561 ASP Chi-restraints excluded: chain X residue 851 ILE Chi-restraints excluded: chain X residue 869 ILE Chi-restraints excluded: chain X residue 891 THR Chi-restraints excluded: chain X residue 913 ILE Chi-restraints excluded: chain X residue 920 THR Chi-restraints excluded: chain X residue 946 THR Chi-restraints excluded: chain X residue 951 CYS Chi-restraints excluded: chain X residue 986 LEU Chi-restraints excluded: chain X residue 1011 LEU Chi-restraints excluded: chain X residue 1048 LYS Chi-restraints excluded: chain X residue 1081 VAL Chi-restraints excluded: chain X residue 1146 MET Chi-restraints excluded: chain X residue 1168 ILE Chi-restraints excluded: chain X residue 1390 LEU Chi-restraints excluded: chain X residue 1459 VAL Chi-restraints excluded: chain X residue 1514 ASN Chi-restraints excluded: chain Y residue 129 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 249 optimal weight: 0.9980 chunk 241 optimal weight: 0.7980 chunk 236 optimal weight: 0.9990 chunk 312 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 233 optimal weight: 3.9990 chunk 323 optimal weight: 3.9990 chunk 307 optimal weight: 0.9980 chunk 246 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 160 optimal weight: 0.0980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 HIS C 140 HIS a 71 ASN a 188 ASN ** T 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 20 HIS ** h 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 542 HIS h 653 GLN X 981 ASN ** X1478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.144695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.122534 restraints weight = 43338.782| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.40 r_work: 0.3510 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 28093 Z= 0.224 Angle : 0.599 8.951 37995 Z= 0.308 Chirality : 0.047 0.257 4230 Planarity : 0.004 0.054 4808 Dihedral : 4.598 37.532 3642 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.69 % Allowed : 18.92 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.15), residues: 3294 helix: 0.89 (0.15), residues: 1163 sheet: -0.64 (0.20), residues: 715 loop : -1.03 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG T 69 TYR 0.044 0.002 TYR C 260 PHE 0.024 0.002 PHE T 472 TRP 0.017 0.002 TRP X1414 HIS 0.011 0.001 HIS X1371 Details of bonding type rmsd covalent geometry : bond 0.00517 (28093) covalent geometry : angle 0.59856 (37995) hydrogen bonds : bond 0.03885 ( 1115) hydrogen bonds : angle 4.68315 ( 3171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 3118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 772 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 VAL cc_start: 0.8220 (t) cc_final: 0.7946 (t) REVERT: C 54 ASP cc_start: 0.8180 (t0) cc_final: 0.7816 (t0) REVERT: C 61 TRP cc_start: 0.8251 (t60) cc_final: 0.8042 (t60) REVERT: C 101 SER cc_start: 0.8469 (t) cc_final: 0.8245 (p) REVERT: C 128 ASP cc_start: 0.8022 (m-30) cc_final: 0.7799 (m-30) REVERT: C 189 LYS cc_start: 0.8150 (mttt) cc_final: 0.7835 (mtmt) REVERT: C 191 SER cc_start: 0.8123 (m) cc_final: 0.7395 (t) REVERT: C 213 LYS cc_start: 0.8514 (tptm) cc_final: 0.8163 (tppp) REVERT: C 217 ILE cc_start: 0.8230 (mt) cc_final: 0.7852 (tt) REVERT: C 229 TRP cc_start: 0.8292 (m-90) cc_final: 0.7366 (m-90) REVERT: C 237 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7815 (mm-30) REVERT: C 239 LYS cc_start: 0.8377 (tmmt) cc_final: 0.8054 (tmmt) REVERT: C 298 LYS cc_start: 0.8430 (mmtp) cc_final: 0.8080 (mptt) REVERT: C 347 LYS cc_start: 0.8655 (mttt) cc_final: 0.8416 (mttp) REVERT: C 349 ASN cc_start: 0.7886 (t0) cc_final: 0.7266 (t0) REVERT: C 363 TYR cc_start: 0.9014 (m-80) cc_final: 0.8281 (m-80) REVERT: C 408 SER cc_start: 0.8643 (t) cc_final: 0.8256 (p) REVERT: C 480 ASN cc_start: 0.7437 (m-40) cc_final: 0.7167 (t0) REVERT: a 17 SER cc_start: 0.8580 (m) cc_final: 0.8306 (p) REVERT: a 61 ASP cc_start: 0.7706 (t70) cc_final: 0.7297 (t0) REVERT: a 97 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7143 (mt-10) REVERT: a 128 MET cc_start: 0.8681 (ttm) cc_final: 0.8424 (ttm) REVERT: a 143 MET cc_start: 0.8288 (tpp) cc_final: 0.8065 (tpt) REVERT: a 146 ASN cc_start: 0.7813 (m110) cc_final: 0.7413 (m-40) REVERT: a 148 SER cc_start: 0.8570 (t) cc_final: 0.8246 (t) REVERT: a 154 PHE cc_start: 0.8038 (m-80) cc_final: 0.7688 (m-10) REVERT: a 194 LYS cc_start: 0.8143 (mttt) cc_final: 0.7720 (mtpp) REVERT: a 197 LYS cc_start: 0.8209 (tttm) cc_final: 0.7992 (tttt) REVERT: a 201 ASN cc_start: 0.8116 (t0) cc_final: 0.7622 (t0) REVERT: a 213 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.7145 (t80) REVERT: a 248 ASN cc_start: 0.8038 (t0) cc_final: 0.7704 (t0) REVERT: a 250 MET cc_start: 0.8235 (mmm) cc_final: 0.7837 (mmm) REVERT: a 265 LYS cc_start: 0.8640 (tttt) cc_final: 0.8130 (ttmm) REVERT: a 289 LYS cc_start: 0.7786 (mtmt) cc_final: 0.7490 (mttp) REVERT: c 15 MET cc_start: 0.6998 (mtp) cc_final: 0.6567 (mtp) REVERT: c 18 ARG cc_start: 0.8124 (ttt-90) cc_final: 0.7822 (mtt-85) REVERT: c 23 SER cc_start: 0.7901 (m) cc_final: 0.7641 (p) REVERT: c 61 MET cc_start: 0.6606 (ttt) cc_final: 0.6402 (ttt) REVERT: c 106 ILE cc_start: 0.8114 (mt) cc_final: 0.7839 (mm) REVERT: c 119 ILE cc_start: 0.8195 (mt) cc_final: 0.7678 (mm) REVERT: c 120 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6852 (mm-30) REVERT: c 124 HIS cc_start: 0.8082 (t70) cc_final: 0.7694 (t70) REVERT: c 148 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7612 (mt-10) REVERT: c 181 LYS cc_start: 0.8322 (mttt) cc_final: 0.8005 (mtpt) REVERT: c 204 LYS cc_start: 0.7881 (tptt) cc_final: 0.7610 (tppt) REVERT: c 219 ASP cc_start: 0.8237 (p0) cc_final: 0.7976 (p0) REVERT: c 220 SER cc_start: 0.8565 (m) cc_final: 0.8152 (p) REVERT: c 227 MET cc_start: 0.6941 (ptp) cc_final: 0.6654 (ttp) REVERT: c 243 ASP cc_start: 0.8112 (m-30) cc_final: 0.7612 (m-30) REVERT: c 246 LYS cc_start: 0.7678 (mtpt) cc_final: 0.7373 (mtpt) REVERT: c 273 SER cc_start: 0.8033 (t) cc_final: 0.7251 (p) REVERT: c 274 GLN cc_start: 0.8456 (tt0) cc_final: 0.7569 (tt0) REVERT: c 275 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8552 (mt) REVERT: c 284 ARG cc_start: 0.7935 (ttm170) cc_final: 0.7569 (mtp180) REVERT: c 286 MET cc_start: 0.7896 (mmm) cc_final: 0.7533 (ttm) REVERT: c 303 MET cc_start: 0.6258 (ttt) cc_final: 0.5909 (ttt) REVERT: c 313 ASN cc_start: 0.6954 (m-40) cc_final: 0.6606 (m110) REVERT: T 23 GLU cc_start: 0.8246 (pm20) cc_final: 0.7869 (pm20) REVERT: T 37 LYS cc_start: 0.8329 (mmtp) cc_final: 0.8073 (mmtp) REVERT: T 81 ILE cc_start: 0.8626 (mt) cc_final: 0.8365 (mm) REVERT: T 90 ASN cc_start: 0.8030 (t0) cc_final: 0.7755 (t0) REVERT: T 207 ASP cc_start: 0.7613 (m-30) cc_final: 0.7371 (m-30) REVERT: T 229 PHE cc_start: 0.8382 (m-80) cc_final: 0.7893 (m-80) REVERT: T 240 SER cc_start: 0.7977 (p) cc_final: 0.7624 (p) REVERT: T 246 LEU cc_start: 0.8360 (mt) cc_final: 0.8135 (mt) REVERT: T 335 GLN cc_start: 0.7851 (mt0) cc_final: 0.7476 (mt0) REVERT: T 343 VAL cc_start: 0.8220 (t) cc_final: 0.7959 (p) REVERT: T 352 ASN cc_start: 0.7878 (m-40) cc_final: 0.7614 (m-40) REVERT: T 452 LYS cc_start: 0.8625 (tttt) cc_final: 0.8371 (tttp) REVERT: T 487 SER cc_start: 0.8225 (m) cc_final: 0.7928 (p) REVERT: h 368 MET cc_start: 0.7293 (tpt) cc_final: 0.6737 (tpt) REVERT: h 383 GLU cc_start: 0.7583 (mm-30) cc_final: 0.6963 (mm-30) REVERT: h 387 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7710 (mt-10) REVERT: h 412 GLU cc_start: 0.7856 (mp0) cc_final: 0.7304 (mp0) REVERT: h 569 GLN cc_start: 0.8214 (tp40) cc_final: 0.7350 (tp40) REVERT: h 575 ILE cc_start: 0.7730 (mm) cc_final: 0.6591 (mm) REVERT: h 577 SER cc_start: 0.8183 (m) cc_final: 0.7957 (t) REVERT: h 580 HIS cc_start: 0.8335 (t-170) cc_final: 0.8112 (t-170) REVERT: h 597 GLN cc_start: 0.8471 (mp10) cc_final: 0.7999 (mp10) REVERT: h 607 LYS cc_start: 0.8438 (ttmt) cc_final: 0.8115 (ttmt) REVERT: h 610 TYR cc_start: 0.8181 (m-80) cc_final: 0.7784 (m-80) REVERT: h 628 ASP cc_start: 0.7601 (m-30) cc_final: 0.7219 (m-30) REVERT: h 632 ARG cc_start: 0.8445 (ttm170) cc_final: 0.8129 (ttm170) REVERT: h 635 ILE cc_start: 0.8610 (mp) cc_final: 0.8375 (mt) REVERT: h 643 ASP cc_start: 0.7457 (t0) cc_final: 0.7165 (t0) REVERT: h 652 ILE cc_start: 0.7766 (mt) cc_final: 0.7520 (tt) REVERT: h 655 GLU cc_start: 0.8344 (pt0) cc_final: 0.7336 (mt-10) REVERT: h 782 ASN cc_start: 0.7511 (m-40) cc_final: 0.7196 (m-40) REVERT: h 857 TYR cc_start: 0.8520 (m-80) cc_final: 0.8263 (m-10) REVERT: h 860 ASP cc_start: 0.7925 (p0) cc_final: 0.7687 (p0) REVERT: h 895 SER cc_start: 0.8236 (t) cc_final: 0.7934 (p) REVERT: h 921 GLN cc_start: 0.8509 (pt0) cc_final: 0.8114 (pt0) REVERT: h 932 HIS cc_start: 0.7126 (m90) cc_final: 0.6502 (m90) REVERT: h 962 LYS cc_start: 0.8634 (ptmt) cc_final: 0.8341 (ptmt) REVERT: h 965 LYS cc_start: 0.7888 (mttm) cc_final: 0.7507 (mtpt) REVERT: h 1066 MET cc_start: 0.6768 (mmm) cc_final: 0.6522 (mmm) REVERT: h 1084 LYS cc_start: 0.8506 (mttt) cc_final: 0.8255 (mtpp) REVERT: h 1112 LYS cc_start: 0.8591 (mtpt) cc_final: 0.8260 (mtpt) REVERT: h 1116 GLU cc_start: 0.8368 (mp0) cc_final: 0.7962 (mm-30) REVERT: h 1134 ASN cc_start: 0.7516 (m-40) cc_final: 0.7060 (m-40) REVERT: X 105 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7404 (tt0) REVERT: X 129 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.7212 (ttmt) REVERT: X 136 LEU cc_start: 0.8111 (tp) cc_final: 0.7598 (tt) REVERT: X 150 LYS cc_start: 0.8329 (ptpt) cc_final: 0.7865 (pttt) REVERT: X 162 GLU cc_start: 0.8307 (mp0) cc_final: 0.7984 (mp0) REVERT: X 244 SER cc_start: 0.8612 (t) cc_final: 0.8366 (p) REVERT: X 250 LYS cc_start: 0.8395 (mttm) cc_final: 0.8171 (mttp) REVERT: X 259 ILE cc_start: 0.8282 (pt) cc_final: 0.7989 (mm) REVERT: X 306 SER cc_start: 0.8250 (m) cc_final: 0.7979 (p) REVERT: X 332 MET cc_start: 0.7749 (mmm) cc_final: 0.7235 (mmm) REVERT: X 350 ASN cc_start: 0.7657 (t0) cc_final: 0.7340 (p0) REVERT: X 380 GLU cc_start: 0.7982 (tt0) cc_final: 0.7705 (mt-10) REVERT: X 388 LYS cc_start: 0.8141 (pttt) cc_final: 0.7849 (pttt) REVERT: X 454 ARG cc_start: 0.8243 (mtp180) cc_final: 0.7975 (mtp85) REVERT: X 465 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7753 (ttm) REVERT: X 470 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8133 (pt) REVERT: X 566 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7614 (mp0) REVERT: X 887 ARG cc_start: 0.7805 (ttm170) cc_final: 0.7519 (ttp-170) REVERT: X 891 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8355 (m) REVERT: X 905 LYS cc_start: 0.8435 (tptp) cc_final: 0.7978 (tptp) REVERT: X 913 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8482 (mm) REVERT: X 915 ARG cc_start: 0.7884 (mmt-90) cc_final: 0.7502 (mmt-90) REVERT: X 916 ASN cc_start: 0.8460 (t0) cc_final: 0.8116 (t0) REVERT: X 932 TYR cc_start: 0.8686 (p90) cc_final: 0.8323 (p90) REVERT: X 933 LYS cc_start: 0.8464 (mttt) cc_final: 0.8028 (mttt) REVERT: X 946 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.6979 (t) REVERT: X 981 ASN cc_start: 0.8284 (m-40) cc_final: 0.8061 (m110) REVERT: X 985 LYS cc_start: 0.8910 (ttpt) cc_final: 0.8592 (ttpp) REVERT: X 986 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8526 (pt) REVERT: X 989 MET cc_start: 0.8068 (mmm) cc_final: 0.7531 (tpp) REVERT: X 1107 GLU cc_start: 0.7638 (mp0) cc_final: 0.7136 (mp0) REVERT: X 1124 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7559 (ttm-80) REVERT: X 1126 ARG cc_start: 0.7346 (ptp90) cc_final: 0.7021 (ptp90) REVERT: X 1152 LEU cc_start: 0.8703 (tp) cc_final: 0.8485 (tt) REVERT: X 1436 ILE cc_start: 0.8275 (mm) cc_final: 0.7989 (mt) REVERT: X 1454 LYS cc_start: 0.7373 (tttt) cc_final: 0.7111 (ptmm) REVERT: X 1475 LYS cc_start: 0.8109 (mttt) cc_final: 0.7795 (mtpp) REVERT: X 1495 PHE cc_start: 0.8061 (m-80) cc_final: 0.7670 (m-80) REVERT: X 1510 GLU cc_start: 0.7770 (tt0) cc_final: 0.7417 (tt0) REVERT: X 1574 GLU cc_start: 0.7775 (tt0) cc_final: 0.7571 (tt0) REVERT: X 1575 MET cc_start: 0.7912 (mtt) cc_final: 0.7453 (mtt) REVERT: Y 131 PHE cc_start: 0.8077 (m-80) cc_final: 0.7614 (m-80) outliers start: 84 outliers final: 64 residues processed: 805 average time/residue: 0.1921 time to fit residues: 238.9932 Evaluate side-chains 834 residues out of total 3118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 761 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain a residue 19 LYS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 98 VAL Chi-restraints excluded: chain a residue 99 LEU Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 169 GLU Chi-restraints excluded: chain a residue 188 ASN Chi-restraints excluded: chain a residue 199 ILE Chi-restraints excluded: chain a residue 205 ILE Chi-restraints excluded: chain a residue 213 PHE Chi-restraints excluded: chain a residue 275 VAL Chi-restraints excluded: chain a residue 276 SER Chi-restraints excluded: chain c residue 27 LYS Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain c residue 275 LEU Chi-restraints excluded: chain c residue 306 CYS Chi-restraints excluded: chain c residue 307 LEU Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 30 GLU Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 211 TYR Chi-restraints excluded: chain T residue 336 SER Chi-restraints excluded: chain T residue 349 LEU Chi-restraints excluded: chain T residue 442 TYR Chi-restraints excluded: chain T residue 462 LEU Chi-restraints excluded: chain h residue 381 MET Chi-restraints excluded: chain h residue 410 SER Chi-restraints excluded: chain h residue 532 MET Chi-restraints excluded: chain h residue 545 GLU Chi-restraints excluded: chain h residue 572 THR Chi-restraints excluded: chain h residue 605 LYS Chi-restraints excluded: chain h residue 673 LEU Chi-restraints excluded: chain h residue 752 LEU Chi-restraints excluded: chain h residue 801 ASP Chi-restraints excluded: chain h residue 838 ILE Chi-restraints excluded: chain h residue 954 THR Chi-restraints excluded: chain h residue 1068 HIS Chi-restraints excluded: chain X residue 129 LYS Chi-restraints excluded: chain X residue 174 ILE Chi-restraints excluded: chain X residue 368 VAL Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain X residue 465 MET Chi-restraints excluded: chain X residue 470 ILE Chi-restraints excluded: chain X residue 541 VAL Chi-restraints excluded: chain X residue 561 ASP Chi-restraints excluded: chain X residue 851 ILE Chi-restraints excluded: chain X residue 869 ILE Chi-restraints excluded: chain X residue 891 THR Chi-restraints excluded: chain X residue 913 ILE Chi-restraints excluded: chain X residue 920 THR Chi-restraints excluded: chain X residue 946 THR Chi-restraints excluded: chain X residue 951 CYS Chi-restraints excluded: chain X residue 986 LEU Chi-restraints excluded: chain X residue 1011 LEU Chi-restraints excluded: chain X residue 1081 VAL Chi-restraints excluded: chain X residue 1146 MET Chi-restraints excluded: chain X residue 1168 ILE Chi-restraints excluded: chain X residue 1390 LEU Chi-restraints excluded: chain X residue 1459 VAL Chi-restraints excluded: chain X residue 1514 ASN Chi-restraints excluded: chain Y residue 129 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 318 optimal weight: 0.5980 chunk 163 optimal weight: 0.4980 chunk 126 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 329 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 218 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 289 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 HIS C 140 HIS a 71 ASN h 20 HIS ** h 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 542 HIS h 778 HIS X 927 GLN ** X1478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.144708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.122537 restraints weight = 43289.582| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.40 r_work: 0.3511 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.181 28093 Z= 0.245 Angle : 0.713 59.197 37995 Z= 0.399 Chirality : 0.046 0.225 4230 Planarity : 0.004 0.053 4808 Dihedral : 4.607 37.498 3642 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.63 % Allowed : 19.11 % Favored : 78.26 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.15), residues: 3294 helix: 0.88 (0.15), residues: 1163 sheet: -0.67 (0.20), residues: 721 loop : -1.02 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG h 781 TYR 0.039 0.002 TYR C 260 PHE 0.024 0.002 PHE T 472 TRP 0.016 0.002 TRP X1414 HIS 0.015 0.001 HIS h 534 Details of bonding type rmsd covalent geometry : bond 0.00528 (28093) covalent geometry : angle 0.71347 (37995) hydrogen bonds : bond 0.03875 ( 1115) hydrogen bonds : angle 4.68381 ( 3171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9299.34 seconds wall clock time: 159 minutes 30.44 seconds (9570.44 seconds total)