Starting phenix.real_space_refine on Tue Aug 26 17:54:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zbj_11156/08_2025/6zbj_11156.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zbj_11156/08_2025/6zbj_11156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zbj_11156/08_2025/6zbj_11156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zbj_11156/08_2025/6zbj_11156.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zbj_11156/08_2025/6zbj_11156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zbj_11156/08_2025/6zbj_11156.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 36 5.16 5 C 12430 2.51 5 N 3176 2.21 5 O 3706 1.98 5 H 19864 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39212 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 11322 Classifications: {'peptide': 666} Link IDs: {'PTRANS': 17, 'TRANS': 648} Chain breaks: 5 Chain: "B" Number of atoms: 8284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 8284 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 12, 'TRANS': 488} Chain breaks: 2 Chain: "C" Number of atoms: 11322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 11322 Classifications: {'peptide': 666} Link IDs: {'PTRANS': 17, 'TRANS': 648} Chain breaks: 5 Chain: "D" Number of atoms: 8284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 8284 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 12, 'TRANS': 488} Chain breaks: 2 Time building chain proxies: 6.07, per 1000 atoms: 0.15 Number of scatterers: 39212 At special positions: 0 Unit cell: (190.629, 154.011, 132.471, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 O 3706 8.00 N 3176 7.00 C 12430 6.00 H 19864 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 813 " - pdb=" SG CYS A 845 " distance=2.03 Simple disulfide: pdb=" SG CYS C 813 " - pdb=" SG CYS C 845 " distance=2.03 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: 2.96 Conformation dependent library (CDL) restraints added in 803.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4564 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 0 sheets defined 83.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 21 through 46 Processing helix chain 'A' and resid 144 through 158 removed outlier: 3.894A pdb=" N LYS A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 174 removed outlier: 3.612A pdb=" N ASP A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.600A pdb=" N TYR A 181 " --> pdb=" O HIS A 177 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 211 removed outlier: 3.867A pdb=" N ILE A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR A 194 " --> pdb=" O ASN A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 219 through 223 removed outlier: 3.845A pdb=" N LYS A 223 " --> pdb=" O PHE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.529A pdb=" N LEU A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 249 through 281 removed outlier: 4.119A pdb=" N ASP A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 321 removed outlier: 3.941A pdb=" N SER A 315 " --> pdb=" O HIS A 311 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 326 through 338 Processing helix chain 'A' and resid 356 through 375 removed outlier: 3.921A pdb=" N THR A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 386 through 400 removed outlier: 4.165A pdb=" N ASN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 443 removed outlier: 3.500A pdb=" N ASN A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 removed outlier: 3.532A pdb=" N ILE A 463 " --> pdb=" O ASN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 494 removed outlier: 3.754A pdb=" N ILE A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A 492 " --> pdb=" O ILE A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 522 removed outlier: 3.833A pdb=" N LEU A 512 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 582 removed outlier: 3.641A pdb=" N LYS A 532 " --> pdb=" O ASP A 528 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 543 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER A 557 " --> pdb=" O SER A 553 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A 560 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASP A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 615 removed outlier: 3.801A pdb=" N THR A 590 " --> pdb=" O ASN A 586 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP A 598 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 666 removed outlier: 3.901A pdb=" N GLN A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU A 649 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 652 " --> pdb=" O ILE A 648 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 656 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU A 663 " --> pdb=" O LYS A 659 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS A 664 " --> pdb=" O ASN A 660 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 693 removed outlier: 4.471A pdb=" N LYS A 688 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 710 removed outlier: 3.782A pdb=" N LYS A 700 " --> pdb=" O GLU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 822 removed outlier: 3.893A pdb=" N LYS A 809 " --> pdb=" O GLU A 805 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 812 " --> pdb=" O THR A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 832 Processing helix chain 'A' and resid 835 through 840 Processing helix chain 'A' and resid 841 through 845 removed outlier: 3.800A pdb=" N CYS A 845 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 856 removed outlier: 3.796A pdb=" N ASN A 856 " --> pdb=" O PHE A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 891 removed outlier: 4.244A pdb=" N ASP A 871 " --> pdb=" O SER A 867 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N HIS A 874 " --> pdb=" O ASN A 870 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE A 877 " --> pdb=" O GLN A 873 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR A 880 " --> pdb=" O PHE A 876 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 882 " --> pdb=" O GLU A 878 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE A 885 " --> pdb=" O GLN A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 906 Processing helix chain 'B' and resid 964 through 968 Processing helix chain 'B' and resid 973 through 980 removed outlier: 3.761A pdb=" N VAL B 977 " --> pdb=" O LEU B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1008 Processing helix chain 'B' and resid 1011 through 1014 removed outlier: 3.625A pdb=" N PHE B1014 " --> pdb=" O ASP B1011 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1011 through 1014' Processing helix chain 'B' and resid 1015 through 1022 Processing helix chain 'B' and resid 1025 through 1032 Processing helix chain 'B' and resid 1033 through 1100 removed outlier: 4.269A pdb=" N ASP B1056 " --> pdb=" O GLN B1052 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B1057 " --> pdb=" O LEU B1053 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS B1083 " --> pdb=" O LYS B1079 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B1090 " --> pdb=" O THR B1086 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B1100 " --> pdb=" O LEU B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1146 removed outlier: 3.752A pdb=" N PHE B1113 " --> pdb=" O PHE B1109 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B1119 " --> pdb=" O LYS B1115 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B1122 " --> pdb=" O GLU B1118 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN B1130 " --> pdb=" O ASN B1126 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR B1144 " --> pdb=" O GLY B1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 1156 through 1178 removed outlier: 3.888A pdb=" N THR B1162 " --> pdb=" O VAL B1158 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR B1166 " --> pdb=" O THR B1162 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA B1167 " --> pdb=" O GLU B1163 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1211 removed outlier: 3.529A pdb=" N LEU B1182 " --> pdb=" O ILE B1178 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP B1184 " --> pdb=" O GLY B1180 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B1192 " --> pdb=" O LEU B1188 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1234 removed outlier: 3.517A pdb=" N ASN B1224 " --> pdb=" O SER B1220 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS B1226 " --> pdb=" O SER B1222 " (cutoff:3.500A) Processing helix chain 'B' and resid 1347 through 1392 removed outlier: 3.653A pdb=" N LEU B1351 " --> pdb=" O TYR B1347 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B1357 " --> pdb=" O GLY B1353 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE B1367 " --> pdb=" O GLU B1363 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG B1384 " --> pdb=" O ARG B1380 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B1390 " --> pdb=" O TYR B1386 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B1391 " --> pdb=" O PHE B1387 " (cutoff:3.500A) Processing helix chain 'B' and resid 1393 through 1399 removed outlier: 3.969A pdb=" N MET B1396 " --> pdb=" O SER B1393 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN B1397 " --> pdb=" O ASP B1394 " (cutoff:3.500A) Processing helix chain 'B' and resid 1410 through 1415 removed outlier: 4.117A pdb=" N LYS B1413 " --> pdb=" O ASP B1410 " (cutoff:3.500A) Processing helix chain 'B' and resid 1416 through 1473 removed outlier: 3.957A pdb=" N PHE B1440 " --> pdb=" O ASN B1436 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU B1443 " --> pdb=" O LYS B1439 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B1450 " --> pdb=" O SER B1446 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B1464 " --> pdb=" O GLU B1460 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B1465 " --> pdb=" O SER B1461 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE B1473 " --> pdb=" O GLU B1469 " (cutoff:3.500A) Processing helix chain 'B' and resid 1496 through 1555 removed outlier: 3.627A pdb=" N LEU B1500 " --> pdb=" O PHE B1496 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE B1519 " --> pdb=" O ASP B1515 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B1530 " --> pdb=" O ASN B1526 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B1531 " --> pdb=" O ASP B1527 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS B1538 " --> pdb=" O GLU B1534 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B1555 " --> pdb=" O LYS B1551 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 46 Processing helix chain 'C' and resid 144 through 158 removed outlier: 3.894A pdb=" N LYS C 158 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 174 removed outlier: 3.612A pdb=" N ASP C 164 " --> pdb=" O PRO C 160 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU C 165 " --> pdb=" O GLU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.600A pdb=" N TYR C 181 " --> pdb=" O HIS C 177 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 182 " --> pdb=" O GLY C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 211 removed outlier: 3.867A pdb=" N ILE C 189 " --> pdb=" O GLY C 185 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR C 194 " --> pdb=" O ASN C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 215 Processing helix chain 'C' and resid 219 through 223 removed outlier: 3.845A pdb=" N LYS C 223 " --> pdb=" O PHE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 238 removed outlier: 3.529A pdb=" N LEU C 229 " --> pdb=" O ARG C 225 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 231 " --> pdb=" O ASN C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 247 Processing helix chain 'C' and resid 249 through 281 removed outlier: 4.119A pdb=" N ASP C 255 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 321 removed outlier: 3.941A pdb=" N SER C 315 " --> pdb=" O HIS C 311 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 324 No H-bonds generated for 'chain 'C' and resid 322 through 324' Processing helix chain 'C' and resid 326 through 338 Processing helix chain 'C' and resid 356 through 375 removed outlier: 3.921A pdb=" N THR C 375 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 Processing helix chain 'C' and resid 386 through 400 removed outlier: 4.165A pdb=" N ASN C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 443 removed outlier: 3.500A pdb=" N ASN C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 465 removed outlier: 3.532A pdb=" N ILE C 463 " --> pdb=" O ASN C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 494 removed outlier: 3.754A pdb=" N ILE C 472 " --> pdb=" O LYS C 468 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS C 492 " --> pdb=" O ILE C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 522 removed outlier: 3.833A pdb=" N LEU C 512 " --> pdb=" O ASP C 508 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS C 515 " --> pdb=" O GLU C 511 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU C 518 " --> pdb=" O GLU C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 582 removed outlier: 3.641A pdb=" N LYS C 532 " --> pdb=" O ASP C 528 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU C 543 " --> pdb=" O THR C 539 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS C 550 " --> pdb=" O ARG C 546 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER C 553 " --> pdb=" O ASN C 549 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER C 554 " --> pdb=" O LYS C 550 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER C 557 " --> pdb=" O SER C 553 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN C 560 " --> pdb=" O ASN C 556 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASP C 573 " --> pdb=" O SER C 569 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU C 576 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY C 579 " --> pdb=" O SER C 575 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE C 580 " --> pdb=" O LEU C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 615 removed outlier: 3.801A pdb=" N THR C 590 " --> pdb=" O ASN C 586 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 595 " --> pdb=" O LEU C 591 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP C 598 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU C 604 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS C 607 " --> pdb=" O THR C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 666 removed outlier: 3.901A pdb=" N GLN C 638 " --> pdb=" O ILE C 634 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 644 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU C 649 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG C 652 " --> pdb=" O ILE C 648 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 656 " --> pdb=" O ARG C 652 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU C 663 " --> pdb=" O LYS C 659 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS C 664 " --> pdb=" O ASN C 660 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP C 665 " --> pdb=" O ALA C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 693 removed outlier: 4.471A pdb=" N LYS C 688 " --> pdb=" O LEU C 684 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL C 691 " --> pdb=" O LEU C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 710 removed outlier: 3.782A pdb=" N LYS C 700 " --> pdb=" O GLU C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 822 removed outlier: 3.893A pdb=" N LYS C 809 " --> pdb=" O GLU C 805 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C 812 " --> pdb=" O THR C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 832 Processing helix chain 'C' and resid 835 through 840 Processing helix chain 'C' and resid 841 through 845 removed outlier: 3.800A pdb=" N CYS C 845 " --> pdb=" O LEU C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 856 removed outlier: 3.796A pdb=" N ASN C 856 " --> pdb=" O PHE C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 891 removed outlier: 4.244A pdb=" N ASP C 871 " --> pdb=" O SER C 867 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N HIS C 874 " --> pdb=" O ASN C 870 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE C 877 " --> pdb=" O GLN C 873 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR C 880 " --> pdb=" O PHE C 876 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS C 882 " --> pdb=" O GLU C 878 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE C 885 " --> pdb=" O GLN C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 973 through 980 removed outlier: 3.761A pdb=" N VAL D 977 " --> pdb=" O LEU D 973 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1008 Processing helix chain 'D' and resid 1011 through 1014 removed outlier: 3.625A pdb=" N PHE D1014 " --> pdb=" O ASP D1011 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1011 through 1014' Processing helix chain 'D' and resid 1015 through 1022 Processing helix chain 'D' and resid 1025 through 1032 Processing helix chain 'D' and resid 1033 through 1100 removed outlier: 4.269A pdb=" N ASP D1056 " --> pdb=" O GLN D1052 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D1057 " --> pdb=" O LEU D1053 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS D1083 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU D1090 " --> pdb=" O THR D1086 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN D1100 " --> pdb=" O LEU D1096 " (cutoff:3.500A) Processing helix chain 'D' and resid 1109 through 1146 removed outlier: 3.752A pdb=" N PHE D1113 " --> pdb=" O PHE D1109 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D1119 " --> pdb=" O LYS D1115 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA D1122 " --> pdb=" O GLU D1118 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN D1130 " --> pdb=" O ASN D1126 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR D1144 " --> pdb=" O GLY D1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 1156 through 1178 removed outlier: 3.888A pdb=" N THR D1162 " --> pdb=" O VAL D1158 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR D1166 " --> pdb=" O THR D1162 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA D1167 " --> pdb=" O GLU D1163 " (cutoff:3.500A) Processing helix chain 'D' and resid 1178 through 1211 removed outlier: 3.529A pdb=" N LEU D1182 " --> pdb=" O ILE D1178 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP D1184 " --> pdb=" O GLY D1180 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS D1192 " --> pdb=" O LEU D1188 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1234 removed outlier: 3.517A pdb=" N ASN D1224 " --> pdb=" O SER D1220 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS D1226 " --> pdb=" O SER D1222 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1392 removed outlier: 3.653A pdb=" N LEU D1351 " --> pdb=" O TYR D1347 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER D1357 " --> pdb=" O GLY D1353 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE D1367 " --> pdb=" O GLU D1363 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG D1384 " --> pdb=" O ARG D1380 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL D1390 " --> pdb=" O TYR D1386 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D1391 " --> pdb=" O PHE D1387 " (cutoff:3.500A) Processing helix chain 'D' and resid 1393 through 1399 removed outlier: 3.969A pdb=" N MET D1396 " --> pdb=" O SER D1393 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN D1397 " --> pdb=" O ASP D1394 " (cutoff:3.500A) Processing helix chain 'D' and resid 1410 through 1415 removed outlier: 4.117A pdb=" N LYS D1413 " --> pdb=" O ASP D1410 " (cutoff:3.500A) Processing helix chain 'D' and resid 1416 through 1473 removed outlier: 3.957A pdb=" N PHE D1440 " --> pdb=" O ASN D1436 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU D1443 " --> pdb=" O LYS D1439 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS D1450 " --> pdb=" O SER D1446 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS D1464 " --> pdb=" O GLU D1460 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL D1465 " --> pdb=" O SER D1461 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE D1473 " --> pdb=" O GLU D1469 " (cutoff:3.500A) Processing helix chain 'D' and resid 1496 through 1555 removed outlier: 3.627A pdb=" N LEU D1500 " --> pdb=" O PHE D1496 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE D1519 " --> pdb=" O ASP D1515 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D1530 " --> pdb=" O ASN D1526 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU D1531 " --> pdb=" O ASP D1527 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS D1538 " --> pdb=" O GLU D1534 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE D1555 " --> pdb=" O LYS D1551 " (cutoff:3.500A) 1382 hydrogen bonds defined for protein. 4068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.22 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 19856 1.03 - 1.23: 122 1.23 - 1.42: 7750 1.42 - 1.62: 11728 1.62 - 1.81: 60 Bond restraints: 39516 Sorted by residual: bond pdb=" N VAL C 29 " pdb=" CA VAL C 29 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.28e-02 6.10e+03 9.95e+00 bond pdb=" N VAL A 29 " pdb=" CA VAL A 29 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.28e-02 6.10e+03 9.95e+00 bond pdb=" N LYS A 223 " pdb=" CA LYS A 223 " ideal model delta sigma weight residual 1.454 1.494 -0.039 1.27e-02 6.20e+03 9.63e+00 bond pdb=" N LYS C 223 " pdb=" CA LYS C 223 " ideal model delta sigma weight residual 1.454 1.494 -0.039 1.27e-02 6.20e+03 9.63e+00 bond pdb=" N ILE A 224 " pdb=" CA ILE A 224 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.27e-02 6.20e+03 9.18e+00 ... (remaining 39511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 62148 1.70 - 3.39: 9088 3.39 - 5.09: 598 5.09 - 6.78: 138 6.78 - 8.48: 18 Bond angle restraints: 71990 Sorted by residual: angle pdb=" CA LEU C 644 " pdb=" C LEU C 644 " pdb=" O LEU C 644 " ideal model delta sigma weight residual 120.42 114.29 6.13 1.06e+00 8.90e-01 3.35e+01 angle pdb=" CA LEU A 644 " pdb=" C LEU A 644 " pdb=" O LEU A 644 " ideal model delta sigma weight residual 120.42 114.29 6.13 1.06e+00 8.90e-01 3.35e+01 angle pdb=" N ILE C 321 " pdb=" CA ILE C 321 " pdb=" C ILE C 321 " ideal model delta sigma weight residual 113.00 105.76 7.24 1.30e+00 5.92e-01 3.10e+01 angle pdb=" N ILE A 321 " pdb=" CA ILE A 321 " pdb=" C ILE A 321 " ideal model delta sigma weight residual 113.00 105.76 7.24 1.30e+00 5.92e-01 3.10e+01 angle pdb=" C LYS D1470 " pdb=" CA LYS D1470 " pdb=" CB LYS D1470 " ideal model delta sigma weight residual 110.85 102.72 8.13 1.70e+00 3.46e-01 2.29e+01 ... (remaining 71985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 16798 17.93 - 35.86: 1111 35.86 - 53.80: 279 53.80 - 71.73: 54 71.73 - 89.66: 38 Dihedral angle restraints: 18280 sinusoidal: 10170 harmonic: 8110 Sorted by residual: dihedral pdb=" CB CYS C 813 " pdb=" SG CYS C 813 " pdb=" SG CYS C 845 " pdb=" CB CYS C 845 " ideal model delta sinusoidal sigma weight residual 93.00 144.91 -51.91 1 1.00e+01 1.00e-02 3.68e+01 dihedral pdb=" CB CYS A 813 " pdb=" SG CYS A 813 " pdb=" SG CYS A 845 " pdb=" CB CYS A 845 " ideal model delta sinusoidal sigma weight residual 93.00 144.91 -51.91 1 1.00e+01 1.00e-02 3.68e+01 dihedral pdb=" CA GLN C 855 " pdb=" C GLN C 855 " pdb=" N ASN C 856 " pdb=" CA ASN C 856 " ideal model delta harmonic sigma weight residual -180.00 -152.43 -27.57 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 18277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1872 0.048 - 0.095: 726 0.095 - 0.143: 288 0.143 - 0.190: 60 0.190 - 0.238: 16 Chirality restraints: 2962 Sorted by residual: chirality pdb=" CB VAL A 669 " pdb=" CA VAL A 669 " pdb=" CG1 VAL A 669 " pdb=" CG2 VAL A 669 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL C 669 " pdb=" CA VAL C 669 " pdb=" CG1 VAL C 669 " pdb=" CG2 VAL C 669 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ILE A 380 " pdb=" N ILE A 380 " pdb=" C ILE A 380 " pdb=" CB ILE A 380 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 2959 not shown) Planarity restraints: 5584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 574 " -0.019 2.00e-02 2.50e+03 1.56e-02 7.28e+00 pdb=" CG TYR C 574 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR C 574 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR C 574 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR C 574 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 574 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 574 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR C 574 " 0.009 2.00e-02 2.50e+03 pdb=" HD1 TYR C 574 " 0.024 2.00e-02 2.50e+03 pdb=" HD2 TYR C 574 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 TYR C 574 " -0.018 2.00e-02 2.50e+03 pdb=" HE2 TYR C 574 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 574 " -0.019 2.00e-02 2.50e+03 1.56e-02 7.28e+00 pdb=" CG TYR A 574 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 574 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 574 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 574 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 574 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 574 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 574 " 0.009 2.00e-02 2.50e+03 pdb=" HD1 TYR A 574 " 0.024 2.00e-02 2.50e+03 pdb=" HD2 TYR A 574 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 TYR A 574 " -0.018 2.00e-02 2.50e+03 pdb=" HE2 TYR A 574 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 394 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.01e+00 pdb=" C LEU A 394 " 0.046 2.00e-02 2.50e+03 pdb=" O LEU A 394 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG A 395 " -0.016 2.00e-02 2.50e+03 ... (remaining 5581 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1953 2.21 - 2.81: 83961 2.81 - 3.40: 102754 3.40 - 4.00: 126453 4.00 - 4.60: 204542 Nonbonded interactions: 519663 Sorted by model distance: nonbonded pdb=" HG SER B1197 " pdb=" OH TYR B1455 " model vdw 1.612 2.450 nonbonded pdb=" HZ2 LYS B1192 " pdb=" OD1 ASN B1365 " model vdw 1.617 2.450 nonbonded pdb=" HZ2 LYS D1192 " pdb=" OD1 ASN D1365 " model vdw 1.619 2.450 nonbonded pdb=" OD1 ASN D 971 " pdb=" HZ2 LYS D 974 " model vdw 1.649 2.450 nonbonded pdb=" OD1 ASN B 971 " pdb=" HZ2 LYS B 974 " model vdw 1.658 2.450 ... (remaining 519658 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.150 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 30.240 Find NCS groups from input model: 0.160 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 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 : 0.011 0.089 19654 Z= 0.519 Angle : 1.038 8.477 26376 Z= 0.658 Chirality : 0.059 0.238 2962 Planarity : 0.005 0.035 3326 Dihedral : 14.139 89.660 7726 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.16), residues: 2298 helix: -0.80 (0.11), residues: 1818 sheet: None (None), residues: 0 loop : -0.46 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG A 225 TYR 0.026 0.003 TYR C 683 PHE 0.026 0.003 PHE C 657 HIS 0.015 0.002 HIS A 814 Details of bonding type rmsd covalent geometry : bond 0.01084 (19652) covalent geometry : angle 1.03814 (26372) SS BOND : bond 0.00159 ( 2) SS BOND : angle 2.24823 ( 4) hydrogen bonds : bond 0.14992 ( 1382) hydrogen bonds : angle 5.68745 ( 4068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8903 (tt0) cc_final: 0.8671 (tm-30) REVERT: A 449 ASP cc_start: 0.7823 (t0) cc_final: 0.7153 (t0) REVERT: A 451 MET cc_start: 0.8227 (tpt) cc_final: 0.7986 (tpp) REVERT: A 853 ASN cc_start: 0.8494 (t0) cc_final: 0.8269 (t0) REVERT: C 27 GLU cc_start: 0.8902 (tt0) cc_final: 0.8671 (tm-30) REVERT: C 449 ASP cc_start: 0.7823 (t0) cc_final: 0.7155 (t0) REVERT: C 451 MET cc_start: 0.8226 (tpt) cc_final: 0.7986 (tpp) REVERT: C 853 ASN cc_start: 0.8494 (t0) cc_final: 0.8271 (t0) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.3827 time to fit residues: 114.0685 Evaluate side-chains 100 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN A 489 ASN A 611 ASN ** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 ASN C 489 ASN C 611 ASN ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.078539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.054814 restraints weight = 214013.155| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.67 r_work: 0.3081 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19654 Z= 0.144 Angle : 0.595 6.200 26376 Z= 0.328 Chirality : 0.035 0.160 2962 Planarity : 0.003 0.032 3326 Dihedral : 5.024 21.767 2478 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.90 % Allowed : 5.50 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.17), residues: 2298 helix: 0.45 (0.12), residues: 1832 sheet: None (None), residues: 0 loop : -0.12 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 537 TYR 0.018 0.001 TYR C 559 PHE 0.012 0.001 PHE C 521 HIS 0.006 0.001 HIS C 814 Details of bonding type rmsd covalent geometry : bond 0.00298 (19652) covalent geometry : angle 0.59504 (26372) SS BOND : bond 0.00132 ( 2) SS BOND : angle 0.86986 ( 4) hydrogen bonds : bond 0.05744 ( 1382) hydrogen bonds : angle 4.25975 ( 4068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.8553 (tpt) cc_final: 0.8186 (tpp) REVERT: A 853 ASN cc_start: 0.9081 (t0) cc_final: 0.8673 (t0) REVERT: B 1080 MET cc_start: 0.9186 (tpp) cc_final: 0.8659 (mmp) REVERT: B 1392 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: C 451 MET cc_start: 0.8547 (tpt) cc_final: 0.8182 (tpp) REVERT: C 853 ASN cc_start: 0.9079 (t0) cc_final: 0.8672 (t0) REVERT: D 1080 MET cc_start: 0.9183 (tpp) cc_final: 0.8656 (mmp) REVERT: D 1392 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7985 (mp0) outliers start: 20 outliers final: 14 residues processed: 108 average time/residue: 0.4104 time to fit residues: 61.7444 Evaluate side-chains 88 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain B residue 1392 GLU Chi-restraints excluded: chain B residue 1552 ILE Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 298 TYR Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 507 LYS Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain D residue 1392 GLU Chi-restraints excluded: chain D residue 1552 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 chunk 221 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN A 611 ASN C 245 ASN C 611 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.076225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.051129 restraints weight = 217988.325| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.66 r_work: 0.2956 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 19654 Z= 0.264 Angle : 0.596 5.979 26376 Z= 0.334 Chirality : 0.036 0.157 2962 Planarity : 0.003 0.027 3326 Dihedral : 4.566 22.729 2478 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.99 % Allowed : 7.30 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.17), residues: 2298 helix: 1.00 (0.12), residues: 1860 sheet: None (None), residues: 0 loop : -0.01 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 577 TYR 0.015 0.001 TYR C 559 PHE 0.010 0.001 PHE C 46 HIS 0.006 0.001 HIS C 814 Details of bonding type rmsd covalent geometry : bond 0.00563 (19652) covalent geometry : angle 0.59568 (26372) SS BOND : bond 0.00603 ( 2) SS BOND : angle 1.20756 ( 4) hydrogen bonds : bond 0.05013 ( 1382) hydrogen bonds : angle 4.25259 ( 4068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.8701 (tpt) cc_final: 0.8411 (tpp) REVERT: A 853 ASN cc_start: 0.9195 (t0) cc_final: 0.8724 (t0) REVERT: B 1080 MET cc_start: 0.9133 (tpp) cc_final: 0.8758 (mmp) REVERT: C 451 MET cc_start: 0.8710 (tpt) cc_final: 0.8424 (tpp) REVERT: C 853 ASN cc_start: 0.9188 (t0) cc_final: 0.8719 (t0) REVERT: D 1080 MET cc_start: 0.9141 (tpp) cc_final: 0.8767 (mmp) outliers start: 22 outliers final: 16 residues processed: 88 average time/residue: 0.3610 time to fit residues: 46.9335 Evaluate side-chains 84 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain B residue 1376 ILE Chi-restraints excluded: chain B residue 1392 GLU Chi-restraints excluded: chain B residue 1552 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 298 TYR Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 507 LYS Chi-restraints excluded: chain D residue 1376 ILE Chi-restraints excluded: chain D residue 1392 GLU Chi-restraints excluded: chain D residue 1552 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 181 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 164 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 189 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.076330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.052119 restraints weight = 215315.039| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.59 r_work: 0.2980 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19654 Z= 0.140 Angle : 0.487 5.073 26376 Z= 0.269 Chirality : 0.033 0.155 2962 Planarity : 0.003 0.027 3326 Dihedral : 4.219 19.574 2478 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.90 % Allowed : 7.21 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.17), residues: 2298 helix: 1.51 (0.12), residues: 1852 sheet: None (None), residues: 0 loop : 0.27 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 577 TYR 0.014 0.001 TYR C 559 PHE 0.009 0.001 PHE A 521 HIS 0.004 0.001 HIS C 814 Details of bonding type rmsd covalent geometry : bond 0.00291 (19652) covalent geometry : angle 0.48730 (26372) SS BOND : bond 0.00412 ( 2) SS BOND : angle 0.80942 ( 4) hydrogen bonds : bond 0.04532 ( 1382) hydrogen bonds : angle 3.77146 ( 4068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.8681 (tpt) cc_final: 0.8386 (tpp) REVERT: A 853 ASN cc_start: 0.9106 (t0) cc_final: 0.8678 (t0) REVERT: C 451 MET cc_start: 0.8670 (tpt) cc_final: 0.8375 (tpp) REVERT: C 853 ASN cc_start: 0.9094 (t0) cc_final: 0.8663 (t0) outliers start: 20 outliers final: 14 residues processed: 98 average time/residue: 0.3417 time to fit residues: 50.6151 Evaluate side-chains 83 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain B residue 1376 ILE Chi-restraints excluded: chain B residue 1552 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 298 TYR Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 507 LYS Chi-restraints excluded: chain D residue 1376 ILE Chi-restraints excluded: chain D residue 1552 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 63 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 157 optimal weight: 0.5980 chunk 144 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 231 optimal weight: 0.7980 chunk 226 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.076410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.051247 restraints weight = 215303.960| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.64 r_work: 0.2991 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19654 Z= 0.147 Angle : 0.472 5.691 26376 Z= 0.259 Chirality : 0.033 0.150 2962 Planarity : 0.002 0.027 3326 Dihedral : 3.943 17.576 2478 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.95 % Allowed : 7.53 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.18), residues: 2298 helix: 1.90 (0.12), residues: 1854 sheet: None (None), residues: 0 loop : 0.55 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 577 TYR 0.013 0.001 TYR A 559 PHE 0.008 0.001 PHE A 521 HIS 0.003 0.001 HIS A 814 Details of bonding type rmsd covalent geometry : bond 0.00316 (19652) covalent geometry : angle 0.47172 (26372) SS BOND : bond 0.00438 ( 2) SS BOND : angle 0.80522 ( 4) hydrogen bonds : bond 0.04157 ( 1382) hydrogen bonds : angle 3.62614 ( 4068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.8680 (tpt) cc_final: 0.8380 (tpp) REVERT: A 851 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8482 (mt) REVERT: A 853 ASN cc_start: 0.9121 (t0) cc_final: 0.8719 (t0) REVERT: C 451 MET cc_start: 0.8667 (tpt) cc_final: 0.8368 (tpp) REVERT: C 851 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8483 (mt) REVERT: C 853 ASN cc_start: 0.9115 (t0) cc_final: 0.8713 (t0) outliers start: 21 outliers final: 14 residues processed: 89 average time/residue: 0.3742 time to fit residues: 51.0986 Evaluate side-chains 87 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1376 ILE Chi-restraints excluded: chain B residue 1552 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 298 TYR Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1376 ILE Chi-restraints excluded: chain D residue 1552 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 19 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 229 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.074738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.049658 restraints weight = 217296.930| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.70 r_work: 0.2921 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19654 Z= 0.179 Angle : 0.480 4.762 26376 Z= 0.266 Chirality : 0.033 0.154 2962 Planarity : 0.002 0.027 3326 Dihedral : 3.828 17.943 2478 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.72 % Allowed : 7.71 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.66 (0.18), residues: 2298 helix: 2.09 (0.12), residues: 1860 sheet: None (None), residues: 0 loop : 0.47 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 577 TYR 0.012 0.001 TYR C 559 PHE 0.008 0.001 PHE C 521 HIS 0.003 0.001 HIS C 814 Details of bonding type rmsd covalent geometry : bond 0.00380 (19652) covalent geometry : angle 0.48036 (26372) SS BOND : bond 0.00485 ( 2) SS BOND : angle 0.91662 ( 4) hydrogen bonds : bond 0.04109 ( 1382) hydrogen bonds : angle 3.64510 ( 4068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.8690 (tpt) cc_final: 0.8398 (tpp) REVERT: A 851 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8278 (mt) REVERT: A 853 ASN cc_start: 0.9064 (t0) cc_final: 0.8642 (t0) REVERT: A 884 MET cc_start: 0.9129 (mmm) cc_final: 0.8681 (mmm) REVERT: C 451 MET cc_start: 0.8681 (tpt) cc_final: 0.8386 (tpp) REVERT: C 851 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8279 (mt) REVERT: C 853 ASN cc_start: 0.9077 (t0) cc_final: 0.8632 (t0) REVERT: C 884 MET cc_start: 0.9136 (mmm) cc_final: 0.8687 (mmm) outliers start: 16 outliers final: 12 residues processed: 85 average time/residue: 0.4325 time to fit residues: 55.0461 Evaluate side-chains 85 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 1376 ILE Chi-restraints excluded: chain B residue 1552 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 298 TYR Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 489 ASN Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 1376 ILE Chi-restraints excluded: chain D residue 1552 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 91 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 225 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 180 optimal weight: 0.1980 chunk 95 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.077413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.053089 restraints weight = 219060.396| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.55 r_work: 0.2938 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19654 Z= 0.132 Angle : 0.454 6.493 26376 Z= 0.249 Chirality : 0.032 0.150 2962 Planarity : 0.002 0.027 3326 Dihedral : 3.744 18.056 2478 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.72 % Allowed : 8.16 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.96 (0.18), residues: 2298 helix: 2.30 (0.12), residues: 1856 sheet: None (None), residues: 0 loop : 0.61 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 577 TYR 0.012 0.001 TYR D1343 PHE 0.007 0.001 PHE C 521 HIS 0.003 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00281 (19652) covalent geometry : angle 0.45394 (26372) SS BOND : bond 0.00355 ( 2) SS BOND : angle 0.65299 ( 4) hydrogen bonds : bond 0.03979 ( 1382) hydrogen bonds : angle 3.48940 ( 4068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.8668 (tpt) cc_final: 0.8383 (tpp) REVERT: A 851 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8290 (mt) REVERT: A 853 ASN cc_start: 0.8991 (t0) cc_final: 0.8572 (t0) REVERT: C 451 MET cc_start: 0.8662 (tpt) cc_final: 0.8378 (tpp) REVERT: C 851 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8290 (mt) REVERT: C 853 ASN cc_start: 0.8992 (t0) cc_final: 0.8574 (t0) outliers start: 16 outliers final: 12 residues processed: 81 average time/residue: 0.3667 time to fit residues: 45.4939 Evaluate side-chains 83 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1376 ILE Chi-restraints excluded: chain B residue 1552 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 298 TYR Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1376 ILE Chi-restraints excluded: chain D residue 1552 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 13 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 chunk 201 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 220 optimal weight: 2.9990 chunk 202 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 853 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.075324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.050342 restraints weight = 216747.368| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.68 r_work: 0.2943 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19654 Z= 0.107 Angle : 0.435 6.413 26376 Z= 0.236 Chirality : 0.032 0.148 2962 Planarity : 0.002 0.027 3326 Dihedral : 3.617 16.041 2478 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.54 % Allowed : 8.25 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.28 (0.18), residues: 2298 helix: 2.53 (0.12), residues: 1854 sheet: None (None), residues: 0 loop : 0.68 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 537 TYR 0.012 0.001 TYR A 880 PHE 0.007 0.001 PHE C 521 HIS 0.003 0.001 HIS A 889 Details of bonding type rmsd covalent geometry : bond 0.00226 (19652) covalent geometry : angle 0.43472 (26372) SS BOND : bond 0.00300 ( 2) SS BOND : angle 0.55378 ( 4) hydrogen bonds : bond 0.03765 ( 1382) hydrogen bonds : angle 3.33132 ( 4068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.8657 (tpt) cc_final: 0.8367 (tpp) REVERT: A 851 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8203 (mt) REVERT: A 853 ASN cc_start: 0.9012 (t0) cc_final: 0.8604 (t0) REVERT: C 451 MET cc_start: 0.8655 (tpt) cc_final: 0.8365 (tpp) REVERT: C 851 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8210 (mt) REVERT: C 853 ASN cc_start: 0.9036 (t160) cc_final: 0.8678 (t0) REVERT: C 884 MET cc_start: 0.9151 (mmm) cc_final: 0.8745 (mmm) outliers start: 12 outliers final: 10 residues processed: 83 average time/residue: 0.3705 time to fit residues: 47.3857 Evaluate side-chains 83 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1376 ILE Chi-restraints excluded: chain B residue 1552 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 298 TYR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1376 ILE Chi-restraints excluded: chain D residue 1552 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 225 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 151 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1397 GLN D1397 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.075488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.050457 restraints weight = 217222.410| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.70 r_work: 0.2951 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19654 Z= 0.098 Angle : 0.423 6.140 26376 Z= 0.230 Chirality : 0.031 0.146 2962 Planarity : 0.002 0.027 3326 Dihedral : 3.517 15.298 2478 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.63 % Allowed : 8.16 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.52 (0.18), residues: 2298 helix: 2.70 (0.12), residues: 1850 sheet: None (None), residues: 0 loop : 0.79 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 537 TYR 0.011 0.001 TYR A 559 PHE 0.006 0.001 PHE A 521 HIS 0.003 0.001 HIS A 889 Details of bonding type rmsd covalent geometry : bond 0.00209 (19652) covalent geometry : angle 0.42309 (26372) SS BOND : bond 0.00254 ( 2) SS BOND : angle 0.51213 ( 4) hydrogen bonds : bond 0.03660 ( 1382) hydrogen bonds : angle 3.25189 ( 4068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.8645 (tpt) cc_final: 0.8361 (tpp) REVERT: A 824 MET cc_start: 0.7333 (ttp) cc_final: 0.7131 (ttp) REVERT: A 851 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8248 (mt) REVERT: A 853 ASN cc_start: 0.9002 (t0) cc_final: 0.8602 (t0) REVERT: C 451 MET cc_start: 0.8635 (tpt) cc_final: 0.8354 (tpp) REVERT: C 851 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8218 (mt) REVERT: C 884 MET cc_start: 0.9065 (mmm) cc_final: 0.8832 (mmm) outliers start: 14 outliers final: 10 residues processed: 85 average time/residue: 0.3861 time to fit residues: 49.3137 Evaluate side-chains 84 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1376 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 298 TYR Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1376 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 17 optimal weight: 0.4980 chunk 157 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 137 optimal weight: 9.9990 chunk 187 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.074936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.049912 restraints weight = 217406.422| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.68 r_work: 0.2933 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19654 Z= 0.135 Angle : 0.443 7.513 26376 Z= 0.242 Chirality : 0.032 0.148 2962 Planarity : 0.002 0.027 3326 Dihedral : 3.471 15.093 2478 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.63 % Allowed : 8.16 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.62 (0.17), residues: 2298 helix: 2.79 (0.12), residues: 1842 sheet: None (None), residues: 0 loop : 0.73 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 577 TYR 0.012 0.001 TYR A 559 PHE 0.007 0.001 PHE A 521 HIS 0.003 0.001 HIS A 889 Details of bonding type rmsd covalent geometry : bond 0.00289 (19652) covalent geometry : angle 0.44307 (26372) SS BOND : bond 0.00371 ( 2) SS BOND : angle 0.74234 ( 4) hydrogen bonds : bond 0.03647 ( 1382) hydrogen bonds : angle 3.32734 ( 4068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.8663 (tpt) cc_final: 0.8386 (tpp) REVERT: A 851 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8182 (mt) REVERT: A 853 ASN cc_start: 0.9011 (t0) cc_final: 0.8619 (t0) REVERT: C 451 MET cc_start: 0.8654 (tpt) cc_final: 0.8379 (tpp) REVERT: C 851 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8181 (mt) REVERT: C 884 MET cc_start: 0.9084 (mmm) cc_final: 0.8858 (mmm) outliers start: 14 outliers final: 10 residues processed: 82 average time/residue: 0.3733 time to fit residues: 45.2314 Evaluate side-chains 84 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1376 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 298 TYR Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1376 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 116 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 217 optimal weight: 0.8980 chunk 187 optimal weight: 0.9980 chunk 67 optimal weight: 0.0980 chunk 181 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.075540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.050567 restraints weight = 216981.216| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.68 r_work: 0.2951 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19654 Z= 0.091 Angle : 0.417 5.750 26376 Z= 0.226 Chirality : 0.031 0.186 2962 Planarity : 0.002 0.026 3326 Dihedral : 3.434 14.912 2478 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.54 % Allowed : 8.25 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.79 (0.18), residues: 2298 helix: 2.92 (0.12), residues: 1840 sheet: None (None), residues: 0 loop : 0.77 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 537 TYR 0.012 0.001 TYR A 559 PHE 0.006 0.001 PHE B1387 HIS 0.003 0.001 HIS A 889 Details of bonding type rmsd covalent geometry : bond 0.00194 (19652) covalent geometry : angle 0.41720 (26372) SS BOND : bond 0.00230 ( 2) SS BOND : angle 0.41262 ( 4) hydrogen bonds : bond 0.03564 ( 1382) hydrogen bonds : angle 3.18362 ( 4068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8637.84 seconds wall clock time: 147 minutes 15.58 seconds (8835.58 seconds total)