Starting phenix.real_space_refine on Fri Feb 14 00:06:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8izp_35867/02_2025/8izp_35867.cif Found real_map, /net/cci-nas-00/data/ceres_data/8izp_35867/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8izp_35867/02_2025/8izp_35867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8izp_35867/02_2025/8izp_35867.map" model { file = "/net/cci-nas-00/data/ceres_data/8izp_35867/02_2025/8izp_35867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8izp_35867/02_2025/8izp_35867.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.75, per 1000 atoms: 0.61 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: 2.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.08 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: 3.48 Time building geometry restraints manager: 2.88 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: 1.040 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.970 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.600 ------------------------------------------------------------------------------- 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= 0.975 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.040 0.003 TRP A 347 HIS 0.017 0.002 HIS A 372 PHE 0.030 0.003 PHE A 357 TYR 0.036 0.004 TYR A 554 ARG 0.007 0.001 ARG A 601 *********************** 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 : 1.128 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: 0.8445 (mp) REVERT: A 524 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8276 (tt) REVERT: A 562 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8934 (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: 0.5769 (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: 0.8402 (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: 0.5515 (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: 0.7090 (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: 0.6336 (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: 0.6449 (mtp85) outliers start: 156 outliers final: 62 residues processed: 307 average time/residue: 0.2255 time to fit residues: 94.8390 Evaluate side-chains 215 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 138 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 102 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** A1462 ASN A1509 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.176648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.113169 restraints weight = 11488.226| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.35 r_work: 0.3246 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9626 Z= 0.223 Angle : 0.699 8.879 13077 Z= 0.374 Chirality : 0.043 0.171 1526 Planarity : 0.005 0.044 1647 Dihedral : 11.276 84.476 1437 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 6.93 % Allowed : 17.48 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.24), residues: 1200 helix: -0.05 (0.19), residues: 792 sheet: -1.37 (0.66), residues: 50 loop : -0.84 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 347 HIS 0.009 0.001 HIS A1403 PHE 0.016 0.002 PHE A1387 TYR 0.012 0.002 TYR A1490 ARG 0.007 0.001 ARG A1299 *********************** 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 222 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 151 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7990 (tp-100) REVERT: A 261 ARG cc_start: 0.7612 (mmt90) cc_final: 0.6982 (mtm-85) REVERT: A 311 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7149 (t80) REVERT: A 386 MET cc_start: 0.8978 (mtt) cc_final: 0.8605 (mtm) REVERT: A 562 VAL cc_start: 0.8600 (OUTLIER) cc_final: 0.8392 (m) REVERT: A 592 LEU cc_start: 0.8422 (tt) cc_final: 0.8214 (tp) REVERT: A 617 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6841 (tm-30) REVERT: A 620 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7779 (t) REVERT: A 669 SER cc_start: 0.6489 (OUTLIER) cc_final: 0.6221 (t) REVERT: A 688 LYS cc_start: 0.8397 (tttt) cc_final: 0.7857 (tppt) REVERT: A 713 LYS cc_start: 0.8576 (mmtt) cc_final: 0.8326 (mmmm) REVERT: A 720 TYR cc_start: 0.7660 (t80) cc_final: 0.7370 (t80) REVERT: A 832 MET cc_start: 0.6872 (ttt) cc_final: 0.6557 (ttt) REVERT: A 998 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8048 (m-30) REVERT: A 1007 ASN cc_start: 0.7310 (p0) cc_final: 0.6833 (p0) REVERT: A 1290 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6081 (pm20) REVERT: A 1297 ARG cc_start: 0.7057 (ptp-170) cc_final: 0.6316 (ptp-170) REVERT: A 1348 ARG cc_start: 0.6492 (mtt180) cc_final: 0.6030 (mtt180) REVERT: A 1360 HIS cc_start: 0.7087 (OUTLIER) cc_final: 0.6861 (t-90) REVERT: A 1451 GLU cc_start: 0.6159 (OUTLIER) cc_final: 0.5357 (tm-30) outliers start: 71 outliers final: 46 residues processed: 217 average time/residue: 0.2128 time to fit residues: 64.8428 Evaluate side-chains 179 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 123 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 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 657 VAL Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 687 MET 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 1142 VAL 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 35 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 20 optimal weight: 0.0870 chunk 50 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.1364 ------------------------------------------------------------------------------- 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 A1005 GLN A1057 GLN A1360 HIS ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.174054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.109793 restraints weight = 11666.695| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.40 r_work: 0.3203 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9626 Z= 0.229 Angle : 0.619 7.107 13077 Z= 0.323 Chirality : 0.041 0.168 1526 Planarity : 0.004 0.044 1647 Dihedral : 9.367 77.648 1370 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 6.64 % Allowed : 18.75 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.24), residues: 1200 helix: 0.19 (0.19), residues: 792 sheet: -0.97 (0.63), residues: 60 loop : -0.96 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 347 HIS 0.008 0.001 HIS A1403 PHE 0.019 0.001 PHE A 634 TYR 0.023 0.002 TYR A 625 ARG 0.005 0.000 ARG A 474 *********************** 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 201 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 133 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8179 (tp-100) REVERT: A 261 ARG cc_start: 0.7746 (mmt90) cc_final: 0.7157 (mtm-85) REVERT: A 311 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.7347 (t80) REVERT: A 386 MET cc_start: 0.8994 (mtt) cc_final: 0.8491 (mtt) REVERT: A 499 LYS cc_start: 0.8570 (tppt) cc_final: 0.7942 (ttpp) REVERT: A 592 LEU cc_start: 0.8414 (tt) cc_final: 0.8212 (tp) REVERT: A 603 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7711 (tm-30) REVERT: A 617 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6822 (tm-30) REVERT: A 620 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7736 (t) REVERT: A 625 TYR cc_start: 0.6842 (m-80) cc_final: 0.6560 (m-80) REVERT: A 656 LEU cc_start: 0.5569 (OUTLIER) cc_final: 0.5262 (tt) REVERT: A 669 SER cc_start: 0.6252 (OUTLIER) cc_final: 0.5936 (t) REVERT: A 688 LYS cc_start: 0.8426 (tttt) cc_final: 0.7873 (tppt) REVERT: A 713 LYS cc_start: 0.8614 (mmtt) cc_final: 0.8370 (mmmm) REVERT: A 720 TYR cc_start: 0.7767 (t80) cc_final: 0.7363 (t80) REVERT: A 749 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.8038 (pt) REVERT: A 1245 ARG cc_start: 0.6818 (mtt180) cc_final: 0.6449 (mmt180) REVERT: A 1290 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.6003 (pm20) REVERT: A 1348 ARG cc_start: 0.6676 (mtt180) cc_final: 0.6395 (mtt180) REVERT: A 1443 LYS cc_start: 0.7975 (mtmt) cc_final: 0.7669 (tptt) REVERT: A 1451 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.5588 (tm-30) REVERT: A 1479 THR cc_start: 0.8906 (m) cc_final: 0.8655 (t) outliers start: 68 outliers final: 41 residues processed: 192 average time/residue: 0.2203 time to fit residues: 59.9875 Evaluate side-chains 172 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 121 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 395 VAL 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 590 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 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 1476 THR 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 46 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.174695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110625 restraints weight = 11271.458| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.37 r_work: 0.3205 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3613 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= 0.190 Angle : 0.577 8.555 13077 Z= 0.298 Chirality : 0.040 0.166 1526 Planarity : 0.004 0.043 1647 Dihedral : 8.383 70.222 1351 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 5.96 % Allowed : 20.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1200 helix: 0.41 (0.19), residues: 791 sheet: -0.91 (0.61), residues: 62 loop : -0.87 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1283 HIS 0.005 0.001 HIS A1403 PHE 0.015 0.001 PHE A 634 TYR 0.019 0.001 TYR A1298 ARG 0.007 0.000 ARG A1299 *********************** 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 199 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 138 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ARG cc_start: 0.7778 (mmt90) cc_final: 0.7094 (mtm-85) REVERT: A 311 PHE cc_start: 0.7734 (OUTLIER) cc_final: 0.7323 (t80) REVERT: A 386 MET cc_start: 0.8880 (mtt) cc_final: 0.8419 (mtt) REVERT: A 419 ARG cc_start: 0.7085 (mmt90) cc_final: 0.6832 (mtt-85) REVERT: A 603 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7419 (tm-30) REVERT: A 607 SER cc_start: 0.8271 (t) cc_final: 0.7940 (t) REVERT: A 617 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6961 (tm-30) REVERT: A 625 TYR cc_start: 0.6723 (m-80) cc_final: 0.6449 (m-80) REVERT: A 656 LEU cc_start: 0.5551 (OUTLIER) cc_final: 0.5260 (tt) REVERT: A 688 LYS cc_start: 0.8395 (tttt) cc_final: 0.7851 (tppt) REVERT: A 710 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7567 (pp) REVERT: A 713 LYS cc_start: 0.8560 (mmtt) cc_final: 0.8346 (mmmm) REVERT: A 720 TYR cc_start: 0.7692 (t80) cc_final: 0.7279 (t80) REVERT: A 749 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.8002 (pt) REVERT: A 1245 ARG cc_start: 0.6734 (mtt180) cc_final: 0.6334 (mmt180) REVERT: A 1290 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6115 (pm20) REVERT: A 1307 ARG cc_start: 0.8078 (mtt90) cc_final: 0.7651 (mtt-85) REVERT: A 1348 ARG cc_start: 0.6677 (mtt180) cc_final: 0.6187 (mtt180) REVERT: A 1365 GLN cc_start: 0.7975 (mt0) cc_final: 0.7495 (tp40) REVERT: A 1443 LYS cc_start: 0.8071 (mtmt) cc_final: 0.7730 (tptt) REVERT: A 1451 GLU cc_start: 0.6240 (OUTLIER) cc_final: 0.5375 (tm-30) REVERT: A 1479 THR cc_start: 0.8878 (m) cc_final: 0.8594 (t) outliers start: 61 outliers final: 40 residues processed: 189 average time/residue: 0.2142 time to fit residues: 56.8089 Evaluate side-chains 175 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 127 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 405 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 494 ILE 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 590 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 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 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 1247 MET 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 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 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 51 optimal weight: 0.0010 chunk 36 optimal weight: 0.0770 chunk 29 optimal weight: 0.5980 chunk 54 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 86 optimal weight: 0.0370 chunk 44 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 overall best weight: 0.2422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 HIS ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.180574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.116001 restraints weight = 11151.289| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.49 r_work: 0.3213 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9626 Z= 0.142 Angle : 0.538 8.344 13077 Z= 0.275 Chirality : 0.039 0.217 1526 Planarity : 0.004 0.041 1647 Dihedral : 7.481 61.458 1340 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.49 % Allowed : 20.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.24), residues: 1200 helix: 0.76 (0.19), residues: 789 sheet: -0.69 (0.61), residues: 62 loop : -0.76 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1283 HIS 0.005 0.001 HIS A1403 PHE 0.016 0.001 PHE A 634 TYR 0.015 0.001 TYR A 720 ARG 0.003 0.000 ARG A1299 *********************** 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 189 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 ARG cc_start: 0.7705 (mmt90) cc_final: 0.6969 (mtm-85) REVERT: A 311 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.7227 (t80) REVERT: A 386 MET cc_start: 0.8759 (mtt) cc_final: 0.8321 (mtt) REVERT: A 474 ARG cc_start: 0.7933 (mtt-85) cc_final: 0.7450 (mtm180) REVERT: A 499 LYS cc_start: 0.8547 (tppt) cc_final: 0.7870 (ttpp) REVERT: A 603 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7211 (tm-30) REVERT: A 607 SER cc_start: 0.8122 (t) cc_final: 0.7760 (t) REVERT: A 617 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6646 (tm-30) REVERT: A 625 TYR cc_start: 0.6633 (m-80) cc_final: 0.6394 (m-80) REVERT: A 656 LEU cc_start: 0.5296 (OUTLIER) cc_final: 0.5022 (tt) REVERT: A 710 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7705 (pp) REVERT: A 713 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8256 (mmmm) REVERT: A 749 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7934 (pt) REVERT: A 1245 ARG cc_start: 0.6488 (mtt180) cc_final: 0.6074 (mmt180) REVERT: A 1290 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.6165 (pm20) REVERT: A 1307 ARG cc_start: 0.8055 (mtt90) cc_final: 0.7673 (mtt-85) REVERT: A 1348 ARG cc_start: 0.6644 (mtt180) cc_final: 0.6269 (mtt180) REVERT: A 1365 GLN cc_start: 0.7921 (mt0) cc_final: 0.7490 (tp40) REVERT: A 1443 LYS cc_start: 0.7983 (mtmt) cc_final: 0.7740 (tptt) outliers start: 46 outliers final: 34 residues processed: 180 average time/residue: 0.2163 time to fit residues: 54.9569 Evaluate side-chains 172 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 494 ILE Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 603 GLN 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 634 PHE 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 804 THR Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 1008 THR 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 1290 GLU 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 1460 THR Chi-restraints excluded: chain A residue 1487 ILE 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 33 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 114 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.178506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.113622 restraints weight = 11111.847| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.47 r_work: 0.3173 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.4039 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= 0.188 Angle : 0.567 14.892 13077 Z= 0.284 Chirality : 0.039 0.162 1526 Planarity : 0.004 0.041 1647 Dihedral : 7.006 58.857 1335 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.27 % Allowed : 19.73 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.24), residues: 1200 helix: 0.80 (0.19), residues: 790 sheet: -0.51 (0.62), residues: 62 loop : -0.73 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 347 HIS 0.005 0.001 HIS A 372 PHE 0.015 0.001 PHE A 634 TYR 0.013 0.001 TYR A 720 ARG 0.004 0.000 ARG A 419 *********************** 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 186 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 132 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 ARG cc_start: 0.7815 (mmt90) cc_final: 0.7158 (mtm-85) REVERT: A 311 PHE cc_start: 0.7681 (OUTLIER) cc_final: 0.7260 (t80) REVERT: A 386 MET cc_start: 0.8796 (mtt) cc_final: 0.8362 (mtt) REVERT: A 474 ARG cc_start: 0.7939 (mtt-85) cc_final: 0.7443 (mtm180) REVERT: A 603 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7206 (tm-30) REVERT: A 607 SER cc_start: 0.8144 (t) cc_final: 0.7779 (t) REVERT: A 617 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6641 (tm-30) REVERT: A 625 TYR cc_start: 0.6640 (m-80) cc_final: 0.6396 (m-80) REVERT: A 710 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7559 (pp) REVERT: A 713 LYS cc_start: 0.8480 (mmtt) cc_final: 0.8271 (mmmm) REVERT: A 1245 ARG cc_start: 0.6531 (mtt180) cc_final: 0.6105 (mmt180) REVERT: A 1290 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.6037 (pm20) REVERT: A 1307 ARG cc_start: 0.8076 (mtt90) cc_final: 0.7703 (mtt-85) REVERT: A 1348 ARG cc_start: 0.6766 (mtt180) cc_final: 0.6479 (mtt-85) REVERT: A 1365 GLN cc_start: 0.7916 (mt0) cc_final: 0.7636 (tp40) REVERT: A 1443 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7747 (tptt) REVERT: A 1479 THR cc_start: 0.8868 (m) cc_final: 0.8576 (t) outliers start: 54 outliers final: 41 residues processed: 176 average time/residue: 0.2147 time to fit residues: 54.6040 Evaluate side-chains 174 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 128 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 460 VAL Chi-restraints excluded: chain A residue 494 ILE 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 590 SER Chi-restraints excluded: chain A residue 593 THR 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 634 PHE 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 724 LEU 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 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 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 1333 THR Chi-restraints excluded: chain A residue 1360 HIS Chi-restraints excluded: chain A residue 1368 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 1460 THR Chi-restraints excluded: chain A residue 1493 VAL Chi-restraints excluded: chain A residue 1494 LEU 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 45 optimal weight: 6.9990 chunk 1 optimal weight: 0.0470 chunk 46 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.178387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126353 restraints weight = 11198.623| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.73 r_work: 0.3131 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4145 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= 0.184 Angle : 0.561 14.971 13077 Z= 0.280 Chirality : 0.039 0.165 1526 Planarity : 0.004 0.042 1647 Dihedral : 6.675 57.733 1332 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.88 % Allowed : 20.02 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.24), residues: 1200 helix: 0.87 (0.19), residues: 790 sheet: -0.32 (0.65), residues: 61 loop : -0.68 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 347 HIS 0.004 0.001 HIS A 372 PHE 0.015 0.001 PHE A 634 TYR 0.010 0.001 TYR A1122 ARG 0.005 0.000 ARG A 419 *********************** 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 181 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 131 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 ARG cc_start: 0.7884 (mmt90) cc_final: 0.7252 (mtm-85) REVERT: A 311 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7428 (t80) REVERT: A 386 MET cc_start: 0.8904 (mtt) cc_final: 0.8472 (mtt) REVERT: A 474 ARG cc_start: 0.8026 (mtt-85) cc_final: 0.7530 (mtm180) REVERT: A 499 LYS cc_start: 0.8707 (tppt) cc_final: 0.7902 (ttpp) REVERT: A 603 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7435 (tm-30) REVERT: A 607 SER cc_start: 0.8185 (t) cc_final: 0.7821 (t) REVERT: A 617 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7048 (tm-30) REVERT: A 625 TYR cc_start: 0.6828 (m-80) cc_final: 0.6528 (m-80) REVERT: A 687 MET cc_start: 0.7437 (ttp) cc_final: 0.6913 (ttm) REVERT: A 713 LYS cc_start: 0.8545 (mmtt) cc_final: 0.8343 (mmmm) REVERT: A 749 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8029 (pt) REVERT: A 1245 ARG cc_start: 0.6836 (mtt180) cc_final: 0.6329 (mmt180) REVERT: A 1290 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6365 (pm20) REVERT: A 1307 ARG cc_start: 0.8093 (mtt90) cc_final: 0.7725 (mtt-85) REVERT: A 1365 GLN cc_start: 0.8033 (mt0) cc_final: 0.7720 (tp40) REVERT: A 1443 LYS cc_start: 0.7966 (mtmt) cc_final: 0.7743 (tptt) outliers start: 50 outliers final: 38 residues processed: 172 average time/residue: 0.2006 time to fit residues: 49.2217 Evaluate side-chains 173 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 460 VAL Chi-restraints excluded: chain A residue 494 ILE 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 590 SER Chi-restraints excluded: chain A residue 593 THR 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 634 PHE 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 1005 GLN Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1231 SER Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1248 SER 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 1368 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 1460 THR 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 100 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 98 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.178509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.113647 restraints weight = 11341.758| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.60 r_work: 0.3160 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4285 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= 0.175 Angle : 0.576 16.296 13077 Z= 0.283 Chirality : 0.039 0.206 1526 Planarity : 0.004 0.044 1647 Dihedral : 6.392 56.540 1330 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.59 % Allowed : 21.00 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.24), residues: 1200 helix: 1.03 (0.19), residues: 790 sheet: -0.10 (0.66), residues: 59 loop : -0.72 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 347 HIS 0.004 0.001 HIS A 372 PHE 0.015 0.001 PHE A 634 TYR 0.010 0.001 TYR A1122 ARG 0.003 0.000 ARG A 419 *********************** 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 173 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 126 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 ARG cc_start: 0.7825 (mmt90) cc_final: 0.7211 (mtm-85) REVERT: A 311 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7227 (t80) REVERT: A 386 MET cc_start: 0.8789 (mtt) cc_final: 0.8374 (mtt) REVERT: A 474 ARG cc_start: 0.7925 (mtt-85) cc_final: 0.7425 (mtm180) REVERT: A 499 LYS cc_start: 0.8572 (tppt) cc_final: 0.7745 (ttpp) REVERT: A 603 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7523 (tm-30) REVERT: A 607 SER cc_start: 0.8103 (t) cc_final: 0.7793 (t) REVERT: A 617 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6887 (tm-30) REVERT: A 625 TYR cc_start: 0.6713 (m-80) cc_final: 0.6408 (m-80) REVERT: A 687 MET cc_start: 0.7423 (ttp) cc_final: 0.6868 (ttm) REVERT: A 710 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7616 (pp) REVERT: A 713 LYS cc_start: 0.8464 (mmtt) cc_final: 0.8263 (mmmm) REVERT: A 749 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7952 (pt) REVERT: A 1027 MET cc_start: 0.7802 (mmp) cc_final: 0.7593 (mmp) REVERT: A 1245 ARG cc_start: 0.6595 (mtt180) cc_final: 0.6133 (mmt180) REVERT: A 1290 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.6017 (pm20) REVERT: A 1307 ARG cc_start: 0.8091 (mtt90) cc_final: 0.7721 (mtt-85) REVERT: A 1348 ARG cc_start: 0.6465 (mtt-85) cc_final: 0.6002 (ttm170) REVERT: A 1365 GLN cc_start: 0.8011 (mt0) cc_final: 0.7748 (tp40) REVERT: A 1443 LYS cc_start: 0.7952 (mtmt) cc_final: 0.7731 (tptt) outliers start: 47 outliers final: 35 residues processed: 164 average time/residue: 0.2049 time to fit residues: 48.1522 Evaluate side-chains 165 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 460 VAL Chi-restraints excluded: chain A residue 494 ILE 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 590 SER Chi-restraints excluded: chain A residue 593 THR 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 634 PHE 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 1005 GLN Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1248 SER 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 1368 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 1460 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 4 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 119 optimal weight: 0.0050 chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.178918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.112023 restraints weight = 11225.709| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.31 r_work: 0.3174 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4356 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= 0.171 Angle : 0.557 15.509 13077 Z= 0.276 Chirality : 0.039 0.225 1526 Planarity : 0.004 0.044 1647 Dihedral : 6.306 55.575 1330 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.98 % Allowed : 20.70 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.24), residues: 1200 helix: 1.12 (0.19), residues: 790 sheet: -0.01 (0.67), residues: 59 loop : -0.72 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 347 HIS 0.004 0.001 HIS A 372 PHE 0.015 0.001 PHE A 634 TYR 0.010 0.001 TYR A1122 ARG 0.003 0.000 ARG A 419 *********************** 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 176 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 125 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 ARG cc_start: 0.7806 (mmt90) cc_final: 0.7254 (mtm-85) REVERT: A 311 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7194 (t80) REVERT: A 386 MET cc_start: 0.8708 (mtt) cc_final: 0.8279 (mtt) REVERT: A 474 ARG cc_start: 0.7907 (mtt-85) cc_final: 0.7408 (mtm180) REVERT: A 499 LYS cc_start: 0.8547 (tppt) cc_final: 0.7731 (ttpp) REVERT: A 603 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: A 607 SER cc_start: 0.8059 (t) cc_final: 0.7745 (t) REVERT: A 617 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6846 (tm-30) REVERT: A 625 TYR cc_start: 0.6728 (m-80) cc_final: 0.6420 (m-80) REVERT: A 687 MET cc_start: 0.7442 (ttp) cc_final: 0.6878 (ttm) REVERT: A 710 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7589 (pp) REVERT: A 713 LYS cc_start: 0.8458 (mmtt) cc_final: 0.8258 (mmmm) REVERT: A 749 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7971 (pt) REVERT: A 1027 MET cc_start: 0.7873 (mmp) cc_final: 0.7661 (mmp) REVERT: A 1245 ARG cc_start: 0.6543 (mtt180) cc_final: 0.6099 (mmt180) REVERT: A 1290 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.6019 (pm20) REVERT: A 1307 ARG cc_start: 0.8091 (mtt90) cc_final: 0.7699 (mtt-85) REVERT: A 1365 GLN cc_start: 0.8006 (mt0) cc_final: 0.7745 (tp40) REVERT: A 1382 MET cc_start: 0.7553 (ttp) cc_final: 0.6875 (tmm) outliers start: 51 outliers final: 40 residues processed: 164 average time/residue: 0.2189 time to fit residues: 52.3066 Evaluate side-chains 168 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 494 ILE 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 590 SER Chi-restraints excluded: chain A residue 593 THR 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 634 PHE 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 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 1005 GLN Chi-restraints excluded: chain A residue 1020 ILE 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 1290 GLU Chi-restraints excluded: chain A residue 1333 THR 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 1460 THR Chi-restraints excluded: chain A residue 1493 VAL Chi-restraints excluded: chain A residue 1494 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.178119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.125329 restraints weight = 11325.950| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.75 r_work: 0.3095 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9626 Z= 0.233 Angle : 0.603 15.588 13077 Z= 0.298 Chirality : 0.041 0.204 1526 Planarity : 0.004 0.046 1647 Dihedral : 6.332 54.474 1330 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.39 % Allowed : 21.58 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.24), residues: 1200 helix: 1.03 (0.19), residues: 790 sheet: 0.05 (0.67), residues: 59 loop : -0.73 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 995 HIS 0.006 0.001 HIS A 372 PHE 0.016 0.001 PHE A 634 TYR 0.011 0.001 TYR A 554 ARG 0.003 0.000 ARG A 419 ********************** 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 164 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 119 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 ARG cc_start: 0.7883 (mmt90) cc_final: 0.7380 (mtm-85) REVERT: A 311 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7610 (t80) REVERT: A 386 MET cc_start: 0.9001 (mtt) cc_final: 0.8565 (mtt) REVERT: A 474 ARG cc_start: 0.8136 (mtt-85) cc_final: 0.7651 (mtm180) REVERT: A 499 LYS cc_start: 0.8855 (tppt) cc_final: 0.8562 (tppt) REVERT: A 603 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: A 607 SER cc_start: 0.8251 (t) cc_final: 0.7903 (t) REVERT: A 617 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6904 (tm-30) REVERT: A 625 TYR cc_start: 0.6988 (m-80) cc_final: 0.6696 (m-80) REVERT: A 687 MET cc_start: 0.7745 (ttp) cc_final: 0.7094 (ttm) REVERT: A 710 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7833 (pp) REVERT: A 749 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8095 (pt) REVERT: A 1027 MET cc_start: 0.8380 (mmp) cc_final: 0.8072 (mmp) REVERT: A 1245 ARG cc_start: 0.7411 (mtt180) cc_final: 0.6924 (mmt180) REVERT: A 1290 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6466 (pm20) REVERT: A 1307 ARG cc_start: 0.8175 (mtt90) cc_final: 0.7822 (mtt-85) REVERT: A 1348 ARG cc_start: 0.6953 (mtt180) cc_final: 0.6309 (ttm170) REVERT: A 1365 GLN cc_start: 0.8213 (mt0) cc_final: 0.7902 (tp40) REVERT: A 1382 MET cc_start: 0.7842 (ttp) cc_final: 0.7209 (tmm) outliers start: 45 outliers final: 36 residues processed: 154 average time/residue: 0.2136 time to fit residues: 47.1011 Evaluate side-chains 157 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 115 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 395 VAL 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 590 SER Chi-restraints excluded: chain A residue 593 THR 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 634 PHE 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 1005 GLN Chi-restraints excluded: chain A residue 1020 ILE 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 1290 GLU Chi-restraints excluded: chain A residue 1333 THR 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 1432 GLN Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1460 THR Chi-restraints excluded: chain A residue 1494 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 107 optimal weight: 0.0040 overall best weight: 0.4370 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.181081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.119031 restraints weight = 11816.582| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.65 r_work: 0.3335 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9626 Z= 0.155 Angle : 0.575 13.980 13077 Z= 0.281 Chirality : 0.039 0.198 1526 Planarity : 0.004 0.044 1647 Dihedral : 6.216 55.853 1328 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.10 % Allowed : 22.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.25), residues: 1200 helix: 1.25 (0.19), residues: 791 sheet: 0.14 (0.67), residues: 59 loop : -0.66 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 347 HIS 0.003 0.000 HIS A1403 PHE 0.015 0.001 PHE A 634 TYR 0.010 0.001 TYR A1122 ARG 0.007 0.000 ARG A1381 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5882.29 seconds wall clock time: 104 minutes 37.40 seconds (6277.40 seconds total)