Starting phenix.real_space_refine on Sat Aug 23 03:52:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8izp_35867/08_2025/8izp_35867.cif Found real_map, /net/cci-nas-00/data/ceres_data/8izp_35867/08_2025/8izp_35867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8izp_35867/08_2025/8izp_35867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8izp_35867/08_2025/8izp_35867.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8izp_35867/08_2025/8izp_35867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8izp_35867/08_2025/8izp_35867.map" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6084 2.51 5 N 1598 2.21 5 O 1695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9425 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1210, 9425 Classifications: {'peptide': 1210} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 51, 'TRANS': 1158} Chain breaks: 4 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 2.33, per 1000 atoms: 0.25 Number of scatterers: 9425 At special positions: 0 Unit cell: (83.46, 115.56, 141.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1695 8.00 N 1598 7.00 C 6084 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: 0.95 Conformation dependent library (CDL) restraints added in 374.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 6 sheets defined 65.7% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.562A pdb=" N TYR A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 273 removed outlier: 3.606A pdb=" N GLN A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 324 removed outlier: 4.864A pdb=" N SER A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N SER A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 336 removed outlier: 3.888A pdb=" N GLN A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 333 " --> pdb=" O PRO A 329 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 368 removed outlier: 4.253A pdb=" N GLY A 349 " --> pdb=" O PRO A 345 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER A 360 " --> pdb=" O MET A 356 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 397 through 404 removed outlier: 3.643A pdb=" N LYS A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 415 through 424 removed outlier: 3.795A pdb=" N PHE A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 432 through 449 removed outlier: 4.558A pdb=" N ILE A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN A 447 " --> pdb=" O PHE A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 461 removed outlier: 3.705A pdb=" N GLY A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET A 459 " --> pdb=" O GLY A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 496 removed outlier: 3.707A pdb=" N LEU A 483 " --> pdb=" O LYS A 479 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 485 " --> pdb=" O MET A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 506 through 527 removed outlier: 4.153A pdb=" N LYS A 512 " --> pdb=" O PRO A 508 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 514 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 517 " --> pdb=" O GLN A 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 520 " --> pdb=" O GLY A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 558 removed outlier: 3.925A pdb=" N THR A 534 " --> pdb=" O TYR A 530 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Proline residue: A 543 - end of helix removed outlier: 3.622A pdb=" N THR A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP A 558 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 572 through 584 removed outlier: 4.006A pdb=" N ILE A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 579 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 580 " --> pdb=" O ASN A 576 " (cutoff:3.500A) Proline residue: A 581 - end of helix Processing helix chain 'A' and resid 584 through 608 removed outlier: 3.959A pdb=" N SER A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 606 " --> pdb=" O ILE A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 675 removed outlier: 3.768A pdb=" N VAL A 671 " --> pdb=" O LYS A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 710 Processing helix chain 'A' and resid 716 through 727 Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'A' and resid 738 through 742 removed outlier: 3.899A pdb=" N GLN A 741 " --> pdb=" O GLY A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 768 removed outlier: 3.622A pdb=" N ASP A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 793 removed outlier: 3.842A pdb=" N HIS A 788 " --> pdb=" O HIS A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 818 Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 843 through 851 removed outlier: 3.846A pdb=" N ASN A 847 " --> pdb=" O GLY A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 952 Processing helix chain 'A' and resid 956 through 967 removed outlier: 3.524A pdb=" N TRP A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 996 removed outlier: 4.184A pdb=" N GLY A 980 " --> pdb=" O LEU A 976 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 983 " --> pdb=" O VAL A 979 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 984 " --> pdb=" O GLY A 980 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL A 990 " --> pdb=" O ILE A 986 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1002 Processing helix chain 'A' and resid 1008 through 1031 removed outlier: 3.670A pdb=" N TYR A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1055 Processing helix chain 'A' and resid 1056 through 1063 removed outlier: 4.153A pdb=" N PHE A1060 " --> pdb=" O PRO A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1072 removed outlier: 3.799A pdb=" N ILE A1068 " --> pdb=" O PRO A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1082 Processing helix chain 'A' and resid 1082 through 1108 removed outlier: 3.522A pdb=" N LEU A1088 " --> pdb=" O ALA A1084 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N MET A1089 " --> pdb=" O PRO A1085 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A1090 " --> pdb=" O VAL A1086 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A1091 " --> pdb=" O ILE A1087 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN A1092 " --> pdb=" O LEU A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1164 removed outlier: 3.747A pdb=" N ILE A1115 " --> pdb=" O PHE A1111 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A1116 " --> pdb=" O THR A1112 " (cutoff:3.500A) Proline residue: A1117 - end of helix removed outlier: 3.617A pdb=" N ALA A1131 " --> pdb=" O ARG A1127 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A1141 " --> pdb=" O LYS A1137 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) Proline residue: A1146 - end of helix removed outlier: 5.980A pdb=" N SER A1159 " --> pdb=" O VAL A1155 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A1160 " --> pdb=" O THR A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1176 removed outlier: 3.846A pdb=" N SER A1174 " --> pdb=" O PHE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1195 Proline residue: A1187 - end of helix removed outlier: 4.200A pdb=" N ARG A1193 " --> pdb=" O ILE A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1210 removed outlier: 4.764A pdb=" N VAL A1206 " --> pdb=" O VAL A1202 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A1207 " --> pdb=" O GLY A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1221 Processing helix chain 'A' and resid 1222 through 1234 removed outlier: 3.554A pdb=" N VAL A1226 " --> pdb=" O ASN A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1254 removed outlier: 3.679A pdb=" N ALA A1239 " --> pdb=" O GLN A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1265 removed outlier: 3.661A pdb=" N LYS A1265 " --> pdb=" O LYS A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1287 removed outlier: 4.048A pdb=" N ARG A1286 " --> pdb=" O TRP A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1329 through 1337 removed outlier: 4.297A pdb=" N THR A1333 " --> pdb=" O LYS A1329 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A1334 " --> pdb=" O SER A1330 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A1336 " --> pdb=" O MET A1332 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A1337 " --> pdb=" O THR A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1365 removed outlier: 3.560A pdb=" N GLN A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1385 Processing helix chain 'A' and resid 1393 through 1402 removed outlier: 3.963A pdb=" N TRP A1397 " --> pdb=" O GLU A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1411 Processing helix chain 'A' and resid 1420 through 1424 Processing helix chain 'A' and resid 1427 through 1443 Processing helix chain 'A' and resid 1457 through 1472 Processing helix chain 'A' and resid 1506 through 1513 Processing helix chain 'A' and resid 1515 through 1525 removed outlier: 3.502A pdb=" N GLY A1519 " --> pdb=" O GLY A1515 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 616 through 617 removed outlier: 5.581A pdb=" N GLU A 617 " --> pdb=" O MET A 687 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LYS A 680 " --> pdb=" O THR A 635 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N THR A 635 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LYS A 684 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N SER A 631 " --> pdb=" O LYS A 684 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N HIS A 686 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE A 629 " --> pdb=" O HIS A 686 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR A 628 " --> pdb=" O VAL A 651 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL A 651 " --> pdb=" O THR A 628 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS A 630 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE A 649 " --> pdb=" O HIS A 630 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY A 632 " --> pdb=" O LEU A 647 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE A 634 " --> pdb=" O HIS A 645 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N HIS A 645 " --> pdb=" O PHE A 634 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 691 through 694 removed outlier: 5.959A pdb=" N ALA A 692 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ASP A 775 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 694 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 824 " --> pdb=" O VAL A 660 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE A 821 " --> pdb=" O MET A 832 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N MET A 832 " --> pdb=" O ILE A 821 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 823 " --> pdb=" O SER A 830 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1306 through 1310 removed outlier: 6.230A pdb=" N ARG A1307 " --> pdb=" O VAL A1296 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL A1296 " --> pdb=" O ARG A1307 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR A1294 " --> pdb=" O LYS A1344 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LYS A1344 " --> pdb=" O TYR A1294 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1320 through 1323 removed outlier: 6.271A pdb=" N GLY A1320 " --> pdb=" O LEU A1494 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU A1496 " --> pdb=" O GLY A1320 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A1322 " --> pdb=" O LEU A1496 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL A1493 " --> pdb=" O PHE A1504 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE A1504 " --> pdb=" O VAL A1493 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL A1495 " --> pdb=" O ALA A1502 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1367 through 1368 removed outlier: 6.606A pdb=" N THR A1367 " --> pdb=" O VAL A1448 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU A1447 " --> pdb=" O LEU A1478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1378 through 1379 487 hydrogen bonds defined for protein. 1416 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: 1.64 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1509 1.28 - 1.42: 2439 1.42 - 1.55: 5598 1.55 - 1.69: 0 1.69 - 1.82: 80 Bond restraints: 9626 Sorted by residual: bond pdb=" C PRO A1187 " pdb=" O PRO A1187 " ideal model delta sigma weight residual 1.237 1.150 0.087 1.29e-02 6.01e+03 4.53e+01 bond pdb=" C PRO A1223 " pdb=" O PRO A1223 " ideal model delta sigma weight residual 1.237 1.153 0.085 1.26e-02 6.30e+03 4.52e+01 bond pdb=" C LEU A1012 " pdb=" O LEU A1012 " ideal model delta sigma weight residual 1.237 1.314 -0.078 1.19e-02 7.06e+03 4.25e+01 bond pdb=" C PRO A 329 " pdb=" O PRO A 329 " ideal model delta sigma weight residual 1.238 1.160 0.077 1.24e-02 6.50e+03 3.87e+01 bond pdb=" C ARG A 382 " pdb=" O ARG A 382 " ideal model delta sigma weight residual 1.237 1.170 0.066 1.17e-02 7.31e+03 3.20e+01 ... (remaining 9621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 11119 2.83 - 5.67: 1783 5.67 - 8.50: 147 8.50 - 11.34: 26 11.34 - 14.17: 2 Bond angle restraints: 13077 Sorted by residual: angle pdb=" N GLY A 664 " pdb=" CA GLY A 664 " pdb=" C GLY A 664 " ideal model delta sigma weight residual 115.27 101.10 14.17 1.41e+00 5.03e-01 1.01e+02 angle pdb=" N GLN A1039 " pdb=" CA GLN A1039 " pdb=" C GLN A1039 " ideal model delta sigma weight residual 113.88 102.56 11.32 1.23e+00 6.61e-01 8.47e+01 angle pdb=" N LEU A 412 " pdb=" CA LEU A 412 " pdb=" C LEU A 412 " ideal model delta sigma weight residual 112.92 102.09 10.83 1.23e+00 6.61e-01 7.76e+01 angle pdb=" N LEU A 218 " pdb=" CA LEU A 218 " pdb=" C LEU A 218 " ideal model delta sigma weight residual 113.88 103.16 10.72 1.23e+00 6.61e-01 7.59e+01 angle pdb=" N TYR A 370 " pdb=" CA TYR A 370 " pdb=" C TYR A 370 " ideal model delta sigma weight residual 112.45 100.53 11.92 1.39e+00 5.18e-01 7.36e+01 ... (remaining 13072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 4965 17.52 - 35.05: 518 35.05 - 52.57: 189 52.57 - 70.09: 61 70.09 - 87.62: 10 Dihedral angle restraints: 5743 sinusoidal: 2241 harmonic: 3502 Sorted by residual: dihedral pdb=" C THR A 535 " pdb=" N THR A 535 " pdb=" CA THR A 535 " pdb=" CB THR A 535 " ideal model delta harmonic sigma weight residual -122.00 -139.23 17.23 0 2.50e+00 1.60e-01 4.75e+01 dihedral pdb=" C ASP A 564 " pdb=" N ASP A 564 " pdb=" CA ASP A 564 " pdb=" CB ASP A 564 " ideal model delta harmonic sigma weight residual -122.60 -106.88 -15.72 0 2.50e+00 1.60e-01 3.95e+01 dihedral pdb=" C GLN A1465 " pdb=" N GLN A1465 " pdb=" CA GLN A1465 " pdb=" CB GLN A1465 " ideal model delta harmonic sigma weight residual -122.60 -137.18 14.58 0 2.50e+00 1.60e-01 3.40e+01 ... (remaining 5740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 989 0.124 - 0.248: 443 0.248 - 0.371: 86 0.371 - 0.495: 6 0.495 - 0.619: 2 Chirality restraints: 1526 Sorted by residual: chirality pdb=" CA THR A 535 " pdb=" N THR A 535 " pdb=" C THR A 535 " pdb=" CB THR A 535 " both_signs ideal model delta sigma weight residual False 2.53 1.91 0.62 2.00e-01 2.50e+01 9.58e+00 chirality pdb=" CA GLN A1465 " pdb=" N GLN A1465 " pdb=" C GLN A1465 " pdb=" CB GLN A1465 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.22e+00 chirality pdb=" CA PRO A1109 " pdb=" N PRO A1109 " pdb=" C PRO A1109 " pdb=" CB PRO A1109 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.68e+00 ... (remaining 1523 not shown) Planarity restraints: 1647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A1078 " 0.018 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C VAL A1078 " -0.065 2.00e-02 2.50e+03 pdb=" O VAL A1078 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL A1079 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 367 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C LEU A 367 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU A 367 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN A 368 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1263 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C TYR A1263 " 0.060 2.00e-02 2.50e+03 pdb=" O TYR A1263 " -0.022 2.00e-02 2.50e+03 pdb=" N SER A1264 " -0.021 2.00e-02 2.50e+03 ... (remaining 1644 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3224 2.83 - 3.35: 8859 3.35 - 3.87: 14823 3.87 - 4.38: 17836 4.38 - 4.90: 28897 Nonbonded interactions: 73639 Sorted by model distance: nonbonded pdb=" N PRO A 234 " pdb=" O PRO A 234 " model vdw 2.316 2.496 nonbonded pdb=" O SER A 993 " pdb=" OG SER A 993 " model vdw 2.335 3.040 nonbonded pdb=" N GLY A 664 " pdb=" N CYS A 665 " model vdw 2.338 2.560 nonbonded pdb=" OH TYR A 390 " pdb=" O PHE A1170 " model vdw 2.388 3.040 nonbonded pdb=" NZ LYS A1052 " pdb=" O TYR A1263 " model vdw 2.401 3.120 ... (remaining 73634 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.490 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 : 0.015 0.087 9626 Z= 1.110 Angle : 2.038 14.174 13077 Z= 1.540 Chirality : 0.132 0.619 1526 Planarity : 0.010 0.119 1647 Dihedral : 17.710 87.617 3479 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.67 % Favored : 96.17 % Rotamer: Outliers : 15.23 % Allowed : 14.65 % Favored : 70.12 % Cbeta Deviations : 1.68 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.22), residues: 1200 helix: -0.87 (0.17), residues: 761 sheet: -0.58 (0.69), residues: 54 loop : -1.22 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 601 TYR 0.036 0.004 TYR A 554 PHE 0.030 0.003 PHE A 357 TRP 0.040 0.003 TRP A 347 HIS 0.017 0.002 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.01497 ( 9626) covalent geometry : angle 2.03809 (13077) hydrogen bonds : bond 0.29057 ( 487) hydrogen bonds : angle 9.50363 ( 1416) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 180 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: A 261 ARG cc_start: 0.7945 (mmt90) cc_final: 0.7720 (mtm-85) REVERT: A 355 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8488 (mp) REVERT: A 386 MET cc_start: 0.9101 (mtt) cc_final: 0.8480 (mtt) REVERT: A 461 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8446 (mp) REVERT: A 524 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8277 (tt) REVERT: A 562 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8935 (m) REVERT: A 617 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7220 (tm-30) REVERT: A 620 THR cc_start: 0.8459 (p) cc_final: 0.8072 (t) REVERT: A 667 LYS cc_start: 0.6389 (mmtt) cc_final: 0.5768 (mtmm) REVERT: A 688 LYS cc_start: 0.8525 (tttt) cc_final: 0.8318 (tppt) REVERT: A 758 ARG cc_start: 0.8515 (ptp-110) cc_final: 0.8274 (ptp90) REVERT: A 772 PHE cc_start: 0.8616 (m-80) cc_final: 0.8403 (m-80) REVERT: A 776 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7959 (t70) REVERT: A 824 LEU cc_start: 0.8444 (pt) cc_final: 0.8199 (pp) REVERT: A 1222 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.8278 (p0) REVERT: A 1261 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7756 (mmtt) REVERT: A 1288 GLU cc_start: 0.5724 (mt-10) cc_final: 0.5514 (mp0) REVERT: A 1290 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6535 (tt0) REVERT: A 1297 ARG cc_start: 0.7899 (ptp-170) cc_final: 0.7357 (ptp-170) REVERT: A 1348 ARG cc_start: 0.7368 (mtt180) cc_final: 0.7092 (mtt-85) REVERT: A 1360 HIS cc_start: 0.8155 (OUTLIER) cc_final: 0.7931 (t-90) REVERT: A 1382 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7302 (ttm) REVERT: A 1432 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: A 1482 HIS cc_start: 0.6558 (t-90) cc_final: 0.6337 (t-170) REVERT: A 1491 THR cc_start: 0.7126 (OUTLIER) cc_final: 0.6847 (p) REVERT: A 1492 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6450 (mtp85) outliers start: 156 outliers final: 62 residues processed: 307 average time/residue: 0.1060 time to fit residues: 44.9486 Evaluate side-chains 214 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 137 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 464 PRO Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 788 HIS Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1174 SER Chi-restraints excluded: chain A residue 1184 SER Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1197 ILE Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1219 SER Chi-restraints excluded: chain A residue 1222 ASN Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1236 VAL Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1261 LYS Chi-restraints excluded: chain A residue 1283 TRP Chi-restraints excluded: chain A residue 1290 GLU Chi-restraints excluded: chain A residue 1308 ASP Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1360 HIS Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1417 PHE Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1432 GLN Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1459 GLU Chi-restraints excluded: chain A residue 1476 THR Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1492 ARG Chi-restraints excluded: chain A residue 1493 VAL Chi-restraints excluded: chain A residue 1504 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.0170 chunk 117 optimal weight: 5.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN A 561 ASN A 638 GLN A 645 HIS A 706 GLN A 981 GLN A 989 ASN ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 GLN A1165 ASN A1235 GLN A1253 ASN ** A1360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.177159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114854 restraints weight = 11335.648| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.32 r_work: 0.3255 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9626 Z= 0.166 Angle : 0.696 9.223 13077 Z= 0.371 Chirality : 0.043 0.181 1526 Planarity : 0.005 0.044 1647 Dihedral : 11.210 84.320 1437 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 6.93 % Allowed : 17.09 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.24), residues: 1200 helix: -0.05 (0.18), residues: 792 sheet: -1.29 (0.67), residues: 50 loop : -0.78 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1299 TYR 0.015 0.002 TYR A1490 PHE 0.018 0.002 PHE A1387 TRP 0.018 0.002 TRP A 347 HIS 0.013 0.001 HIS A1403 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9626) covalent geometry : angle 0.69566 (13077) hydrogen bonds : bond 0.06884 ( 487) hydrogen bonds : angle 5.20030 ( 1416) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 146 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7953 (tp-100) REVERT: A 261 ARG cc_start: 0.7639 (mmt90) cc_final: 0.6980 (mtm-85) REVERT: A 311 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7137 (t80) REVERT: A 386 MET cc_start: 0.8955 (mtt) cc_final: 0.8599 (mtm) REVERT: A 562 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8448 (m) REVERT: A 592 LEU cc_start: 0.8412 (tt) cc_final: 0.8200 (tp) REVERT: A 617 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6851 (tm-30) REVERT: A 620 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7789 (t) REVERT: A 669 SER cc_start: 0.6489 (OUTLIER) cc_final: 0.6199 (t) REVERT: A 688 LYS cc_start: 0.8400 (tttt) cc_final: 0.7863 (tppt) REVERT: A 713 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8322 (mmmm) REVERT: A 720 TYR cc_start: 0.7686 (t80) cc_final: 0.7388 (t80) REVERT: A 832 MET cc_start: 0.6877 (ttt) cc_final: 0.6545 (ttt) REVERT: A 998 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8079 (m-30) REVERT: A 1007 ASN cc_start: 0.7347 (p0) cc_final: 0.6907 (p0) REVERT: A 1290 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.6096 (pm20) REVERT: A 1297 ARG cc_start: 0.7049 (ptp-170) cc_final: 0.6386 (ptp-170) REVERT: A 1348 ARG cc_start: 0.6502 (mtt180) cc_final: 0.6197 (mtt180) REVERT: A 1360 HIS cc_start: 0.7106 (OUTLIER) cc_final: 0.6881 (t-90) REVERT: A 1451 GLU cc_start: 0.6175 (OUTLIER) cc_final: 0.5374 (tm-30) outliers start: 71 outliers final: 44 residues processed: 212 average time/residue: 0.0979 time to fit residues: 29.2580 Evaluate side-chains 174 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 120 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 788 HIS Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1184 SER Chi-restraints excluded: chain A residue 1197 ILE Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1236 VAL Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1283 TRP Chi-restraints excluded: chain A residue 1290 GLU Chi-restraints excluded: chain A residue 1333 THR Chi-restraints excluded: chain A residue 1360 HIS Chi-restraints excluded: chain A residue 1362 VAL Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1432 GLN Chi-restraints excluded: chain A residue 1451 GLU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1459 GLU Chi-restraints excluded: chain A residue 1460 THR Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1493 VAL Chi-restraints excluded: chain A residue 1504 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 GLN A1057 GLN A1360 HIS A1403 HIS A1509 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.175011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.110721 restraints weight = 11535.951| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.39 r_work: 0.3214 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9626 Z= 0.151 Angle : 0.613 7.907 13077 Z= 0.319 Chirality : 0.041 0.194 1526 Planarity : 0.004 0.044 1647 Dihedral : 9.306 77.731 1370 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 5.76 % Allowed : 19.04 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.24), residues: 1200 helix: 0.21 (0.19), residues: 792 sheet: -1.10 (0.60), residues: 60 loop : -0.88 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 474 TYR 0.025 0.002 TYR A 625 PHE 0.012 0.001 PHE A 311 TRP 0.012 0.001 TRP A 347 HIS 0.008 0.001 HIS A1403 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9626) covalent geometry : angle 0.61263 (13077) hydrogen bonds : bond 0.05892 ( 487) hydrogen bonds : angle 4.65143 ( 1416) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 134 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8163 (tp-100) REVERT: A 261 ARG cc_start: 0.7689 (mmt90) cc_final: 0.7080 (mtm-85) REVERT: A 311 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7283 (t80) REVERT: A 386 MET cc_start: 0.8982 (mtt) cc_final: 0.8477 (mtt) REVERT: A 499 LYS cc_start: 0.8529 (tppt) cc_final: 0.7907 (ttpp) REVERT: A 603 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: A 617 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6809 (tm-30) REVERT: A 620 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7726 (t) REVERT: A 625 TYR cc_start: 0.6828 (m-80) cc_final: 0.6560 (m-80) REVERT: A 656 LEU cc_start: 0.5539 (OUTLIER) cc_final: 0.5223 (tt) REVERT: A 669 SER cc_start: 0.6139 (OUTLIER) cc_final: 0.5840 (t) REVERT: A 688 LYS cc_start: 0.8415 (tttt) cc_final: 0.7860 (tppt) REVERT: A 710 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7668 (pp) REVERT: A 713 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8393 (mmmm) REVERT: A 720 TYR cc_start: 0.7785 (t80) cc_final: 0.7321 (t80) REVERT: A 749 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8131 (pt) REVERT: A 1245 ARG cc_start: 0.6796 (mtt180) cc_final: 0.6362 (mmt180) REVERT: A 1262 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7481 (mm-30) REVERT: A 1290 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.6013 (pm20) REVERT: A 1348 ARG cc_start: 0.6641 (mtt180) cc_final: 0.6360 (mtt180) REVERT: A 1443 LYS cc_start: 0.8007 (mtmt) cc_final: 0.7669 (tptt) REVERT: A 1451 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5554 (tm-30) REVERT: A 1479 THR cc_start: 0.8895 (m) cc_final: 0.8659 (t) outliers start: 59 outliers final: 38 residues processed: 186 average time/residue: 0.0993 time to fit residues: 26.0191 Evaluate side-chains 169 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 120 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 788 HIS Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1197 ILE Chi-restraints excluded: chain A residue 1231 SER Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1236 VAL Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1290 GLU Chi-restraints excluded: chain A residue 1293 ASN Chi-restraints excluded: chain A residue 1333 THR Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1360 HIS Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1432 GLN Chi-restraints excluded: chain A residue 1451 GLU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1459 GLU Chi-restraints excluded: chain A residue 1493 VAL Chi-restraints excluded: chain A residue 1501 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 98 optimal weight: 0.0870 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 GLN A1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.174592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.112204 restraints weight = 12022.647| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.63 r_work: 0.3253 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9626 Z= 0.206 Angle : 0.641 9.314 13077 Z= 0.333 Chirality : 0.043 0.176 1526 Planarity : 0.004 0.046 1647 Dihedral : 8.568 72.091 1351 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 6.93 % Allowed : 18.55 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.24), residues: 1200 helix: 0.18 (0.19), residues: 789 sheet: -1.31 (0.58), residues: 61 loop : -0.98 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1299 TYR 0.018 0.002 TYR A1298 PHE 0.018 0.001 PHE A 317 TRP 0.019 0.001 TRP A1283 HIS 0.008 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 9626) covalent geometry : angle 0.64073 (13077) hydrogen bonds : bond 0.06055 ( 487) hydrogen bonds : angle 4.62718 ( 1416) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 138 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7233 (mt-10) REVERT: A 261 ARG cc_start: 0.7868 (mmt90) cc_final: 0.7287 (mtm-85) REVERT: A 311 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7728 (t80) REVERT: A 386 MET cc_start: 0.9095 (mtt) cc_final: 0.8646 (mtt) REVERT: A 419 ARG cc_start: 0.7541 (mmt90) cc_final: 0.7318 (mtt-85) REVERT: A 473 MET cc_start: 0.8197 (tpp) cc_final: 0.7913 (mmm) REVERT: A 603 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.8043 (tm-30) REVERT: A 607 SER cc_start: 0.8356 (t) cc_final: 0.8051 (t) REVERT: A 617 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7294 (tm-30) REVERT: A 625 TYR cc_start: 0.6956 (m-80) cc_final: 0.6679 (m-80) REVERT: A 656 LEU cc_start: 0.6162 (OUTLIER) cc_final: 0.5797 (tt) REVERT: A 688 LYS cc_start: 0.8511 (tttt) cc_final: 0.7999 (tppt) REVERT: A 749 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8189 (pt) REVERT: A 1007 ASN cc_start: 0.7813 (p0) cc_final: 0.7601 (p0) REVERT: A 1245 ARG cc_start: 0.7380 (mtt180) cc_final: 0.6899 (mmt180) REVERT: A 1258 GLU cc_start: 0.8137 (tt0) cc_final: 0.7653 (tp30) REVERT: A 1290 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6668 (pm20) REVERT: A 1307 ARG cc_start: 0.8218 (mtt90) cc_final: 0.7920 (mtt-85) REVERT: A 1348 ARG cc_start: 0.7113 (mtt180) cc_final: 0.6750 (mtt180) REVERT: A 1365 GLN cc_start: 0.8108 (mt0) cc_final: 0.7648 (tp40) REVERT: A 1401 LEU cc_start: 0.7115 (mt) cc_final: 0.6820 (mt) REVERT: A 1443 LYS cc_start: 0.8008 (mtmt) cc_final: 0.7703 (tptt) REVERT: A 1451 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.5695 (tm-30) REVERT: A 1479 THR cc_start: 0.9011 (m) cc_final: 0.8745 (t) outliers start: 71 outliers final: 49 residues processed: 200 average time/residue: 0.1009 time to fit residues: 28.1615 Evaluate side-chains 182 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 126 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 788 HIS Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1197 ILE Chi-restraints excluded: chain A residue 1231 SER Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1236 VAL Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1283 TRP Chi-restraints excluded: chain A residue 1290 GLU Chi-restraints excluded: chain A residue 1293 ASN Chi-restraints excluded: chain A residue 1333 THR Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1360 HIS Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1432 GLN Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1451 GLU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1460 THR Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1493 VAL Chi-restraints excluded: chain A residue 1501 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 33 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1235 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.175022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.110376 restraints weight = 11307.023| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.47 r_work: 0.3119 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9626 Z= 0.152 Angle : 0.595 12.360 13077 Z= 0.303 Chirality : 0.041 0.317 1526 Planarity : 0.004 0.045 1647 Dihedral : 7.979 60.523 1344 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 5.76 % Allowed : 20.41 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.24), residues: 1200 helix: 0.32 (0.19), residues: 790 sheet: -1.38 (0.58), residues: 61 loop : -0.91 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1299 TYR 0.011 0.001 TYR A1298 PHE 0.013 0.001 PHE A 311 TRP 0.014 0.001 TRP A 347 HIS 0.005 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9626) covalent geometry : angle 0.59520 (13077) hydrogen bonds : bond 0.05506 ( 487) hydrogen bonds : angle 4.45341 ( 1416) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 135 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 GLU cc_start: 0.7737 (mm-30) cc_final: 0.6938 (mt-10) REVERT: A 261 ARG cc_start: 0.7733 (mmt90) cc_final: 0.7077 (mtm-85) REVERT: A 311 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.7322 (t80) REVERT: A 386 MET cc_start: 0.8893 (mtt) cc_final: 0.8439 (mtt) REVERT: A 419 ARG cc_start: 0.7083 (mmt90) cc_final: 0.6844 (mtt-85) REVERT: A 429 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8800 (mp) REVERT: A 473 MET cc_start: 0.7806 (tpp) cc_final: 0.7544 (mmm) REVERT: A 607 SER cc_start: 0.8290 (t) cc_final: 0.7965 (t) REVERT: A 617 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6905 (tm-30) REVERT: A 625 TYR cc_start: 0.6805 (m-80) cc_final: 0.6579 (m-80) REVERT: A 656 LEU cc_start: 0.5464 (OUTLIER) cc_final: 0.5165 (tt) REVERT: A 688 LYS cc_start: 0.8377 (tttt) cc_final: 0.7854 (tppt) REVERT: A 710 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7577 (pp) REVERT: A 749 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8097 (pt) REVERT: A 797 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7419 (pt0) REVERT: A 1007 ASN cc_start: 0.7799 (p0) cc_final: 0.7594 (p0) REVERT: A 1245 ARG cc_start: 0.6744 (mtt180) cc_final: 0.6326 (mmt180) REVERT: A 1307 ARG cc_start: 0.8161 (mtt90) cc_final: 0.7846 (mtt-85) REVERT: A 1365 GLN cc_start: 0.8023 (mt0) cc_final: 0.7489 (tp40) REVERT: A 1443 LYS cc_start: 0.8066 (mtmt) cc_final: 0.7767 (tptt) REVERT: A 1451 GLU cc_start: 0.6166 (OUTLIER) cc_final: 0.5215 (tm-30) REVERT: A 1479 THR cc_start: 0.8889 (m) cc_final: 0.8596 (t) REVERT: A 1491 THR cc_start: 0.7062 (OUTLIER) cc_final: 0.6792 (p) outliers start: 59 outliers final: 44 residues processed: 186 average time/residue: 0.0950 time to fit residues: 25.2201 Evaluate side-chains 181 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 128 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 788 HIS Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1197 ILE Chi-restraints excluded: chain A residue 1231 SER Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1236 VAL Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1325 THR Chi-restraints excluded: chain A residue 1333 THR Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1360 HIS Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1432 GLN Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1451 GLU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1459 GLU Chi-restraints excluded: chain A residue 1460 THR Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1493 VAL Chi-restraints excluded: chain A residue 1501 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 117 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 52 optimal weight: 0.0270 chunk 85 optimal weight: 0.5980 chunk 118 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 120 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1235 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.176712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124535 restraints weight = 11448.580| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.81 r_work: 0.3118 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9626 Z= 0.126 Angle : 0.586 14.219 13077 Z= 0.295 Chirality : 0.040 0.352 1526 Planarity : 0.004 0.045 1647 Dihedral : 7.503 59.816 1338 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.18 % Allowed : 20.90 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.24), residues: 1200 helix: 0.55 (0.19), residues: 789 sheet: -1.18 (0.60), residues: 59 loop : -0.91 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1299 TYR 0.010 0.001 TYR A1122 PHE 0.012 0.001 PHE A 311 TRP 0.012 0.001 TRP A 347 HIS 0.003 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9626) covalent geometry : angle 0.58623 (13077) hydrogen bonds : bond 0.04965 ( 487) hydrogen bonds : angle 4.28945 ( 1416) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 132 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 ARG cc_start: 0.7842 (mmt90) cc_final: 0.7112 (mtm-85) REVERT: A 311 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7412 (t80) REVERT: A 386 MET cc_start: 0.8930 (mtt) cc_final: 0.8481 (mtt) REVERT: A 419 ARG cc_start: 0.7275 (mmt90) cc_final: 0.7010 (mtt-85) REVERT: A 429 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8902 (mp) REVERT: A 474 ARG cc_start: 0.8106 (mtt-85) cc_final: 0.7594 (mtm110) REVERT: A 499 LYS cc_start: 0.8704 (tppt) cc_final: 0.7897 (ttpp) REVERT: A 607 SER cc_start: 0.8174 (t) cc_final: 0.7884 (t) REVERT: A 617 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6928 (tm-30) REVERT: A 625 TYR cc_start: 0.6818 (m-80) cc_final: 0.6606 (m-10) REVERT: A 656 LEU cc_start: 0.5667 (OUTLIER) cc_final: 0.5354 (tt) REVERT: A 710 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7682 (pp) REVERT: A 749 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8096 (pt) REVERT: A 1245 ARG cc_start: 0.6946 (mtt180) cc_final: 0.6451 (mmt180) REVERT: A 1307 ARG cc_start: 0.8104 (mtt90) cc_final: 0.7803 (mtt-85) REVERT: A 1348 ARG cc_start: 0.6435 (mtt180) cc_final: 0.6040 (ttm170) REVERT: A 1365 GLN cc_start: 0.8105 (mt0) cc_final: 0.7625 (tp40) REVERT: A 1443 LYS cc_start: 0.7998 (mtmt) cc_final: 0.7741 (tptt) outliers start: 53 outliers final: 39 residues processed: 177 average time/residue: 0.0982 time to fit residues: 24.2586 Evaluate side-chains 171 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 788 HIS Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1236 VAL Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1283 TRP Chi-restraints excluded: chain A residue 1333 THR Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1360 HIS Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1432 GLN Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1459 GLU Chi-restraints excluded: chain A residue 1460 THR Chi-restraints excluded: chain A residue 1493 VAL Chi-restraints excluded: chain A residue 1501 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.173333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107853 restraints weight = 11708.874| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.37 r_work: 0.3177 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9626 Z= 0.188 Angle : 0.616 13.788 13077 Z= 0.312 Chirality : 0.043 0.384 1526 Planarity : 0.004 0.047 1647 Dihedral : 7.172 58.592 1335 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.76 % Allowed : 20.51 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.24), residues: 1200 helix: 0.50 (0.19), residues: 788 sheet: -1.06 (0.62), residues: 59 loop : -0.93 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1381 TYR 0.011 0.001 TYR A1122 PHE 0.014 0.001 PHE A 317 TRP 0.012 0.001 TRP A 347 HIS 0.007 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 9626) covalent geometry : angle 0.61554 (13077) hydrogen bonds : bond 0.05559 ( 487) hydrogen bonds : angle 4.36488 ( 1416) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 124 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7030 (mt-10) REVERT: A 261 ARG cc_start: 0.7827 (mmt90) cc_final: 0.7161 (mtm-85) REVERT: A 311 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7351 (t80) REVERT: A 386 MET cc_start: 0.8946 (mtt) cc_final: 0.8530 (mtt) REVERT: A 419 ARG cc_start: 0.7227 (mmt90) cc_final: 0.6973 (mtt-85) REVERT: A 429 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8923 (mp) REVERT: A 474 ARG cc_start: 0.8174 (mtt-85) cc_final: 0.7670 (mtm110) REVERT: A 607 SER cc_start: 0.8144 (t) cc_final: 0.7842 (t) REVERT: A 617 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6904 (tm-30) REVERT: A 625 TYR cc_start: 0.6894 (m-80) cc_final: 0.6661 (m-80) REVERT: A 656 LEU cc_start: 0.5600 (OUTLIER) cc_final: 0.5295 (tt) REVERT: A 710 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7653 (pp) REVERT: A 749 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8107 (pt) REVERT: A 1245 ARG cc_start: 0.6968 (mtt180) cc_final: 0.6515 (mmt180) REVERT: A 1307 ARG cc_start: 0.8082 (mtt90) cc_final: 0.7774 (mtt-85) REVERT: A 1348 ARG cc_start: 0.6669 (mtt180) cc_final: 0.6389 (ttm170) REVERT: A 1365 GLN cc_start: 0.8063 (mt0) cc_final: 0.7664 (tp40) REVERT: A 1443 LYS cc_start: 0.7976 (mtmt) cc_final: 0.7742 (tptt) outliers start: 59 outliers final: 47 residues processed: 175 average time/residue: 0.0993 time to fit residues: 24.4865 Evaluate side-chains 175 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 122 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 788 HIS Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1231 SER Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1236 VAL Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1263 TYR Chi-restraints excluded: chain A residue 1283 TRP Chi-restraints excluded: chain A residue 1325 THR Chi-restraints excluded: chain A residue 1333 THR Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1360 HIS Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1374 ILE Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1432 GLN Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1459 GLU Chi-restraints excluded: chain A residue 1460 THR Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1493 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 104 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 GLN A1235 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.175334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.109996 restraints weight = 11732.915| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.43 r_work: 0.3199 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9626 Z= 0.127 Angle : 0.594 13.603 13077 Z= 0.295 Chirality : 0.041 0.369 1526 Planarity : 0.004 0.047 1647 Dihedral : 6.730 58.207 1331 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.08 % Allowed : 21.19 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.24), residues: 1200 helix: 0.71 (0.19), residues: 788 sheet: -0.89 (0.63), residues: 59 loop : -0.83 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1299 TYR 0.010 0.001 TYR A1490 PHE 0.012 0.001 PHE A 311 TRP 0.013 0.001 TRP A 347 HIS 0.003 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9626) covalent geometry : angle 0.59372 (13077) hydrogen bonds : bond 0.04872 ( 487) hydrogen bonds : angle 4.20266 ( 1416) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 125 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 ARG cc_start: 0.7799 (mmt90) cc_final: 0.7122 (mtm-85) REVERT: A 311 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7304 (t80) REVERT: A 386 MET cc_start: 0.8840 (mtt) cc_final: 0.8426 (mtt) REVERT: A 419 ARG cc_start: 0.7128 (mmt90) cc_final: 0.6872 (mtt-85) REVERT: A 429 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8909 (mp) REVERT: A 474 ARG cc_start: 0.8016 (mtt-85) cc_final: 0.7539 (mtm110) REVERT: A 499 LYS cc_start: 0.8614 (tppt) cc_final: 0.7740 (ttpp) REVERT: A 607 SER cc_start: 0.8025 (t) cc_final: 0.7746 (t) REVERT: A 617 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6812 (tm-30) REVERT: A 625 TYR cc_start: 0.6799 (m-80) cc_final: 0.6524 (m-80) REVERT: A 705 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6811 (tt) REVERT: A 710 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7543 (pp) REVERT: A 749 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8049 (pt) REVERT: A 1245 ARG cc_start: 0.6816 (mtt180) cc_final: 0.6342 (mmt180) REVERT: A 1348 ARG cc_start: 0.6606 (mtt180) cc_final: 0.6336 (ttm170) REVERT: A 1365 GLN cc_start: 0.8028 (mt0) cc_final: 0.7712 (tp40) REVERT: A 1491 THR cc_start: 0.7105 (OUTLIER) cc_final: 0.6823 (p) outliers start: 52 outliers final: 42 residues processed: 168 average time/residue: 0.1016 time to fit residues: 23.6910 Evaluate side-chains 170 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 121 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 788 HIS Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1236 VAL Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1263 TYR Chi-restraints excluded: chain A residue 1293 ASN Chi-restraints excluded: chain A residue 1333 THR Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1360 HIS Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1432 GLN Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1459 GLU Chi-restraints excluded: chain A residue 1460 THR Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1493 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 69 optimal weight: 0.1980 chunk 54 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.173161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.118149 restraints weight = 11720.679| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.63 r_work: 0.3165 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9626 Z= 0.192 Angle : 0.631 13.980 13077 Z= 0.317 Chirality : 0.043 0.373 1526 Planarity : 0.004 0.048 1647 Dihedral : 6.598 57.266 1329 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 5.57 % Allowed : 21.00 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.24), residues: 1200 helix: 0.60 (0.19), residues: 789 sheet: -0.81 (0.65), residues: 59 loop : -0.92 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1299 TYR 0.011 0.001 TYR A 207 PHE 0.015 0.001 PHE A 317 TRP 0.011 0.001 TRP A 347 HIS 0.007 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 9626) covalent geometry : angle 0.63144 (13077) hydrogen bonds : bond 0.05624 ( 487) hydrogen bonds : angle 4.32337 ( 1416) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 122 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7011 (mt-10) REVERT: A 261 ARG cc_start: 0.7860 (mmt90) cc_final: 0.7288 (mtm-85) REVERT: A 311 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7288 (t80) REVERT: A 386 MET cc_start: 0.8969 (mtt) cc_final: 0.8563 (mtt) REVERT: A 474 ARG cc_start: 0.8125 (mtt-85) cc_final: 0.7636 (mtm110) REVERT: A 499 LYS cc_start: 0.8720 (tppt) cc_final: 0.7848 (ttpp) REVERT: A 607 SER cc_start: 0.8130 (t) cc_final: 0.7829 (t) REVERT: A 617 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6939 (tm-30) REVERT: A 625 TYR cc_start: 0.6904 (m-80) cc_final: 0.6685 (m-80) REVERT: A 705 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6933 (tt) REVERT: A 710 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7590 (pp) REVERT: A 1245 ARG cc_start: 0.7027 (mtt180) cc_final: 0.6554 (mmt180) REVERT: A 1307 ARG cc_start: 0.8040 (mtt-85) cc_final: 0.7614 (mtt-85) REVERT: A 1348 ARG cc_start: 0.6770 (mtt180) cc_final: 0.6492 (ttm170) REVERT: A 1365 GLN cc_start: 0.8062 (mt0) cc_final: 0.7644 (tp40) REVERT: A 1491 THR cc_start: 0.7134 (OUTLIER) cc_final: 0.6857 (p) outliers start: 57 outliers final: 47 residues processed: 170 average time/residue: 0.0918 time to fit residues: 22.0767 Evaluate side-chains 173 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 121 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 788 HIS Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1231 SER Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1236 VAL Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1263 TYR Chi-restraints excluded: chain A residue 1325 THR Chi-restraints excluded: chain A residue 1333 THR Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1360 HIS Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1432 GLN Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1459 GLU Chi-restraints excluded: chain A residue 1460 THR Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1493 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.172678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.108195 restraints weight = 11494.496| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.33 r_work: 0.3166 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9626 Z= 0.170 Angle : 0.620 13.279 13077 Z= 0.310 Chirality : 0.041 0.171 1526 Planarity : 0.004 0.049 1647 Dihedral : 6.504 57.173 1329 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.18 % Allowed : 21.19 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.24), residues: 1200 helix: 0.66 (0.19), residues: 789 sheet: -0.70 (0.65), residues: 59 loop : -0.90 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1381 TYR 0.011 0.001 TYR A 554 PHE 0.014 0.001 PHE A 311 TRP 0.011 0.001 TRP A 347 HIS 0.006 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 9626) covalent geometry : angle 0.62020 (13077) hydrogen bonds : bond 0.05348 ( 487) hydrogen bonds : angle 4.27698 ( 1416) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 120 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 GLU cc_start: 0.7795 (mm-30) cc_final: 0.6987 (mt-10) REVERT: A 261 ARG cc_start: 0.7808 (mmt90) cc_final: 0.7151 (mtm-85) REVERT: A 311 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7180 (t80) REVERT: A 386 MET cc_start: 0.8899 (mtt) cc_final: 0.8494 (mtt) REVERT: A 474 ARG cc_start: 0.8074 (mtt-85) cc_final: 0.7590 (mtm110) REVERT: A 499 LYS cc_start: 0.8676 (tppt) cc_final: 0.7872 (ttpp) REVERT: A 607 SER cc_start: 0.8091 (t) cc_final: 0.7794 (t) REVERT: A 617 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6856 (tm-30) REVERT: A 625 TYR cc_start: 0.6826 (m-80) cc_final: 0.6615 (m-80) REVERT: A 705 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6799 (tt) REVERT: A 710 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7605 (pp) REVERT: A 1245 ARG cc_start: 0.6967 (mtt180) cc_final: 0.6483 (mmt180) REVERT: A 1348 ARG cc_start: 0.6816 (mtt180) cc_final: 0.6538 (ttm170) REVERT: A 1365 GLN cc_start: 0.8033 (mt0) cc_final: 0.7681 (tp40) outliers start: 53 outliers final: 48 residues processed: 164 average time/residue: 0.0981 time to fit residues: 22.7109 Evaluate side-chains 170 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 118 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 788 HIS Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1231 SER Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1263 TYR Chi-restraints excluded: chain A residue 1325 THR Chi-restraints excluded: chain A residue 1333 THR Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1360 HIS Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1374 ILE Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1432 GLN Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1459 GLU Chi-restraints excluded: chain A residue 1460 THR Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1493 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 25 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 57 optimal weight: 0.0030 chunk 22 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 107 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.175529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.109623 restraints weight = 11469.017| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.38 r_work: 0.3195 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9626 Z= 0.142 Angle : 0.592 14.139 13077 Z= 0.296 Chirality : 0.040 0.169 1526 Planarity : 0.004 0.049 1647 Dihedral : 6.318 56.460 1328 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 5.18 % Allowed : 21.78 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.24), residues: 1200 helix: 0.81 (0.19), residues: 788 sheet: -0.73 (0.65), residues: 59 loop : -0.84 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1299 TYR 0.010 0.001 TYR A 554 PHE 0.013 0.001 PHE A 311 TRP 0.012 0.001 TRP A 347 HIS 0.004 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9626) covalent geometry : angle 0.59203 (13077) hydrogen bonds : bond 0.05007 ( 487) hydrogen bonds : angle 4.15438 ( 1416) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2927.38 seconds wall clock time: 50 minutes 42.32 seconds (3042.32 seconds total)