Starting phenix.real_space_refine on Fri Mar 6 12:40:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a43_15135/03_2026/8a43_15135.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a43_15135/03_2026/8a43_15135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a43_15135/03_2026/8a43_15135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a43_15135/03_2026/8a43_15135.map" model { file = "/net/cci-nas-00/data/ceres_data/8a43_15135/03_2026/8a43_15135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a43_15135/03_2026/8a43_15135.cif" } resolution = 4.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 215 5.16 5 C 19760 2.51 5 N 5412 2.21 5 O 5722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 197 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31109 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 12315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1549, 12315 Classifications: {'peptide': 1549} Link IDs: {'PCIS': 4, 'PTRANS': 74, 'TRANS': 1470} Chain breaks: 2 Chain: "B" Number of atoms: 8973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1131, 8973 Classifications: {'peptide': 1131} Link IDs: {'PTRANS': 65, 'TRANS': 1065} Chain: "C" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2450 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 16, 'TRANS': 289} Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 627 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 355 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "J" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 524 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "N" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 832 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 888 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 18, 'TRANS': 103} Time building chain proxies: 6.36, per 1000 atoms: 0.20 Number of scatterers: 31109 At special positions: 0 Unit cell: (164.422, 161.405, 153.863, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 215 16.00 O 5722 8.00 N 5412 7.00 C 19760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 855 " - pdb=" SG CYS B 866 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 39 " 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: 2.61 Conformation dependent library (CDL) restraints added in 1.4 seconds 7772 Ramachandran restraints generated. 3886 Oldfield, 0 Emsley, 3886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7326 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 36 sheets defined 34.8% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 21 through 28 removed outlier: 4.015A pdb=" N LEU A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 92 through 102 Processing helix chain 'A' and resid 113 through 128 Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 159 through 171 Processing helix chain 'A' and resid 181 through 201 removed outlier: 3.553A pdb=" N CYS A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.569A pdb=" N ARG A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 280 removed outlier: 6.735A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TYR A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 296 Processing helix chain 'A' and resid 323 through 346 Processing helix chain 'A' and resid 383 through 403 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 476 through 487 removed outlier: 3.515A pdb=" N LEU A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 523 removed outlier: 4.448A pdb=" N LEU A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 561 removed outlier: 3.667A pdb=" N ILE A 561 " --> pdb=" O ARG A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 585 removed outlier: 3.801A pdb=" N LYS A 583 " --> pdb=" O ALA A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 610 Processing helix chain 'A' and resid 631 through 634 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 649 through 660 Processing helix chain 'A' and resid 683 through 696 removed outlier: 3.659A pdb=" N LEU A 691 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 692 " --> pdb=" O VAL A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 755 removed outlier: 4.332A pdb=" N TYR A 754 " --> pdb=" O ASP A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 770 removed outlier: 3.553A pdb=" N TYR A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 767 " --> pdb=" O HIS A 763 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 768 " --> pdb=" O CYS A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 788 Processing helix chain 'A' and resid 807 through 817 removed outlier: 3.654A pdb=" N LYS A 811 " --> pdb=" O LYS A 807 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN A 813 " --> pdb=" O ASP A 809 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG A 814 " --> pdb=" O VAL A 810 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 817 " --> pdb=" O GLN A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 821 No H-bonds generated for 'chain 'A' and resid 819 through 821' Processing helix chain 'A' and resid 822 through 832 removed outlier: 3.937A pdb=" N ALA A 826 " --> pdb=" O CYS A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 852 Processing helix chain 'A' and resid 855 through 870 Processing helix chain 'A' and resid 872 through 877 Processing helix chain 'A' and resid 894 through 899 removed outlier: 3.535A pdb=" N GLN A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 removed outlier: 4.073A pdb=" N SER A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 948 Processing helix chain 'A' and resid 962 through 993 removed outlier: 4.058A pdb=" N PHE A 966 " --> pdb=" O PRO A 962 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS A 968 " --> pdb=" O PHE A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1033 removed outlier: 4.280A pdb=" N GLN A1033 " --> pdb=" O THR A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1041 removed outlier: 3.793A pdb=" N LEU A1040 " --> pdb=" O GLN A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1050 Processing helix chain 'A' and resid 1063 through 1079 removed outlier: 3.894A pdb=" N PHE A1069 " --> pdb=" O ALA A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1103 removed outlier: 4.555A pdb=" N GLU A1098 " --> pdb=" O GLN A1094 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ALA A1099 " --> pdb=" O LYS A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1127 removed outlier: 3.500A pdb=" N GLN A1118 " --> pdb=" O SER A1114 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU A1119 " --> pdb=" O PRO A1115 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N MET A1120 " --> pdb=" O GLY A1116 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR A1125 " --> pdb=" O LEU A1121 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU A1126 " --> pdb=" O ARG A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1138 removed outlier: 3.643A pdb=" N ARG A1132 " --> pdb=" O ASP A1128 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS A1138 " --> pdb=" O LYS A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1150 Processing helix chain 'A' and resid 1160 through 1180 removed outlier: 4.201A pdb=" N LYS A1166 " --> pdb=" O THR A1162 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ALA A1176 " --> pdb=" O GLN A1172 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN A1177 " --> pdb=" O GLU A1173 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS A1180 " --> pdb=" O ALA A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1204 removed outlier: 3.524A pdb=" N LEU A1204 " --> pdb=" O TRP A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1226 removed outlier: 3.662A pdb=" N LEU A1214 " --> pdb=" O ALA A1210 " (cutoff:3.500A) Proline residue: A1222 - end of helix Processing helix chain 'A' and resid 1243 through 1253 removed outlier: 3.808A pdb=" N ARG A1247 " --> pdb=" O LEU A1243 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A1248 " --> pdb=" O GLY A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1274 through 1285 removed outlier: 4.352A pdb=" N SER A1280 " --> pdb=" O LYS A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1332 removed outlier: 3.880A pdb=" N TYR A1327 " --> pdb=" O PRO A1323 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A1329 " --> pdb=" O ALA A1325 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU A1330 " --> pdb=" O TYR A1326 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS A1332 " --> pdb=" O GLN A1328 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1362 removed outlier: 4.286A pdb=" N PHE A1347 " --> pdb=" O GLU A1343 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS A1348 " --> pdb=" O THR A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1496 through 1509 Processing helix chain 'A' and resid 1539 through 1549 removed outlier: 4.632A pdb=" N VAL A1545 " --> pdb=" O SER A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1589 removed outlier: 3.744A pdb=" N LEU A1588 " --> pdb=" O ASN A1584 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE A1589 " --> pdb=" O LEU A1585 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1584 through 1589' Processing helix chain 'A' and resid 1606 through 1613 removed outlier: 3.559A pdb=" N ASN A1610 " --> pdb=" O HIS A1606 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A1611 " --> pdb=" O ALA A1607 " (cutoff:3.500A) Processing helix chain 'A' and resid 1614 through 1631 removed outlier: 4.463A pdb=" N ARG A1619 " --> pdb=" O GLU A1615 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL A1620 " --> pdb=" O ALA A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1649 removed outlier: 4.540A pdb=" N ASP A1646 " --> pdb=" O SER A1642 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A1647 " --> pdb=" O LEU A1643 " (cutoff:3.500A) Processing helix chain 'A' and resid 1661 through 1665 Processing helix chain 'A' and resid 1667 through 1673 removed outlier: 4.108A pdb=" N GLN A1671 " --> pdb=" O SER A1667 " (cutoff:3.500A) Processing helix chain 'A' and resid 1676 through 1688 removed outlier: 3.879A pdb=" N PHE A1680 " --> pdb=" O THR A1676 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1703 removed outlier: 3.735A pdb=" N GLY A1703 " --> pdb=" O CYS A1699 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 39 through 57 removed outlier: 3.956A pdb=" N VAL B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 50 " --> pdb=" O PHE B 46 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS B 51 " --> pdb=" O ASN B 47 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 52 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLY B 55 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 106 removed outlier: 3.627A pdb=" N CYS B 103 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 196 through 200 removed outlier: 3.751A pdb=" N THR B 200 " --> pdb=" O LYS B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 261 through 268 Processing helix chain 'B' and resid 277 through 289 Processing helix chain 'B' and resid 296 through 313 removed outlier: 5.377A pdb=" N VAL B 310 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LYS B 311 " --> pdb=" O CYS B 307 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN B 313 " --> pdb=" O ARG B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 329 removed outlier: 3.777A pdb=" N ALA B 323 " --> pdb=" O PRO B 319 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 337 removed outlier: 3.650A pdb=" N LEU B 336 " --> pdb=" O CYS B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 358 Processing helix chain 'B' and resid 376 through 406 removed outlier: 3.905A pdb=" N GLU B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY B 391 " --> pdb=" O GLU B 387 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA B 404 " --> pdb=" O PHE B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 426 through 436 Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 475 through 479 removed outlier: 3.532A pdb=" N PHE B 478 " --> pdb=" O GLY B 475 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 479 " --> pdb=" O ALA B 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 475 through 479' Processing helix chain 'B' and resid 483 through 487 removed outlier: 3.824A pdb=" N VAL B 486 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 536 Processing helix chain 'B' and resid 570 through 584 Processing helix chain 'B' and resid 637 through 640 removed outlier: 4.124A pdb=" N ILE B 640 " --> pdb=" O MET B 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 637 through 640' Processing helix chain 'B' and resid 647 through 651 Processing helix chain 'B' and resid 662 through 667 removed outlier: 3.932A pdb=" N LEU B 666 " --> pdb=" O PRO B 663 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 667 " --> pdb=" O HIS B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 673 Processing helix chain 'B' and resid 681 through 692 Processing helix chain 'B' and resid 693 through 695 No H-bonds generated for 'chain 'B' and resid 693 through 695' Processing helix chain 'B' and resid 724 through 728 Processing helix chain 'B' and resid 731 through 735 removed outlier: 3.523A pdb=" N ASN B 734 " --> pdb=" O ASP B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 766 Processing helix chain 'B' and resid 916 through 920 removed outlier: 4.055A pdb=" N GLY B 919 " --> pdb=" O ASN B 916 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE B 920 " --> pdb=" O PRO B 917 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 916 through 920' Processing helix chain 'B' and resid 926 through 942 Processing helix chain 'B' and resid 957 through 970 removed outlier: 3.611A pdb=" N TYR B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET B 965 " --> pdb=" O TYR B 961 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU B 966 " --> pdb=" O PHE B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1049 removed outlier: 3.510A pdb=" N ARG B1042 " --> pdb=" O GLY B1038 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY B1049 " --> pdb=" O LEU B1045 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1058 Processing helix chain 'B' and resid 1113 through 1126 Processing helix chain 'C' and resid 41 through 47 Processing helix chain 'C' and resid 69 through 84 removed outlier: 3.596A pdb=" N ALA C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 112 removed outlier: 3.678A pdb=" N GLY C 111 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU C 112 " --> pdb=" O HIS C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.813A pdb=" N LEU C 121 " --> pdb=" O ASP C 118 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE C 122 " --> pdb=" O PRO C 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 118 through 122' Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 249 through 257 Processing helix chain 'C' and resid 317 through 344 removed outlier: 3.554A pdb=" N LEU C 321 " --> pdb=" O PRO C 317 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN C 344 " --> pdb=" O LEU C 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.549A pdb=" N LEU E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 44 removed outlier: 4.013A pdb=" N ALA E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN E 43 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER E 44 " --> pdb=" O PHE E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 98 removed outlier: 3.885A pdb=" N ILE E 87 " --> pdb=" O GLY E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 122 removed outlier: 3.539A pdb=" N ASP E 120 " --> pdb=" O GLN E 116 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 removed outlier: 3.547A pdb=" N PHE E 183 " --> pdb=" O VAL E 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 92 through 100 Processing helix chain 'F' and resid 119 through 123 Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.518A pdb=" N ASP H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN H 87 " --> pdb=" O ARG H 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.508A pdb=" N ALA J 20 " --> pdb=" O ASN J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 38 removed outlier: 3.669A pdb=" N ALA J 34 " --> pdb=" O THR J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 47 removed outlier: 3.752A pdb=" N ARG J 46 " --> pdb=" O ARG J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 63 removed outlier: 3.856A pdb=" N TYR J 62 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 62 removed outlier: 4.770A pdb=" N ARG K 56 " --> pdb=" O GLY K 52 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR K 57 " --> pdb=" O ASN K 53 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS K 61 " --> pdb=" O TYR K 57 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASN K 62 " --> pdb=" O MET K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 129 Processing helix chain 'N' and resid 35 through 39 removed outlier: 3.783A pdb=" N MET N 39 " --> pdb=" O PRO N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 84 Processing helix chain 'M' and resid 31 through 36 removed outlier: 3.513A pdb=" N LEU M 35 " --> pdb=" O SER M 31 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR M 36 " --> pdb=" O LEU M 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 31 through 36' Processing helix chain 'M' and resid 52 through 57 removed outlier: 3.974A pdb=" N CYS M 55 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.815A pdb=" N VAL A 87 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 218 removed outlier: 3.829A pdb=" N LYS A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 575 through 577 removed outlier: 8.518A pdb=" N LEU A 575 " --> pdb=" O ARG A 442 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL A 444 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N LEU A 577 " --> pdb=" O VAL A 444 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N CYS A 446 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 575 through 577 removed outlier: 8.518A pdb=" N LEU A 575 " --> pdb=" O ARG A 442 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL A 444 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N LEU A 577 " --> pdb=" O VAL A 444 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N CYS A 446 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 440 " --> pdb=" O ARG B1013 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG B1013 " --> pdb=" O ALA A 440 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG A 442 " --> pdb=" O GLN B1011 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN B1011 " --> pdb=" O ARG A 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 455 through 458 removed outlier: 3.803A pdb=" N ARG A 567 " --> pdb=" O ILE A 456 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 467 through 468 removed outlier: 4.033A pdb=" N MET A 496 " --> pdb=" O CYS A 539 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 917 through 918 removed outlier: 3.976A pdb=" N GLY A 917 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL A 951 " --> pdb=" O GLY A 917 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 1265 through 1267 removed outlier: 4.202A pdb=" N VAL A1266 " --> pdb=" O LEU A1578 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1288 through 1289 removed outlier: 3.942A pdb=" N VAL A1288 " --> pdb=" O TYR A1554 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR A1554 " --> pdb=" O VAL A1288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 1294 through 1300 removed outlier: 3.557A pdb=" N LEU A1317 " --> pdb=" O VAL A1527 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR A1528 " --> pdb=" O ASP A1514 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 76 through 83 removed outlier: 3.715A pdb=" N THR B 76 " --> pdb=" O ASN B 119 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASP B 117 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA B 80 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B 115 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE B 82 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS B 113 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 170 through 172 removed outlier: 3.972A pdb=" N VAL B 178 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 455 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 182 through 185 removed outlier: 3.668A pdb=" N LEU B 182 " --> pdb=" O LEU B 375 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 191 through 192 Processing sheet with id=AB6, first strand: chain 'B' and resid 213 through 215 Processing sheet with id=AB7, first strand: chain 'B' and resid 235 through 239 removed outlier: 3.617A pdb=" N PHE B 238 " --> pdb=" O PHE B 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 554 through 557 removed outlier: 3.598A pdb=" N VAL B 556 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY B 564 " --> pdb=" O VAL B 556 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 594 through 598 removed outlier: 4.089A pdb=" N GLU B 594 " --> pdb=" O PHE B 613 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE B 613 " --> pdb=" O GLU B 594 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B 609 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 631 through 635 Processing sheet with id=AC2, first strand: chain 'B' and resid 710 through 714 removed outlier: 3.541A pdb=" N SER B 772 " --> pdb=" O ARG B 713 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS B 775 " --> pdb=" O MET B 871 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 893 through 897 removed outlier: 6.831A pdb=" N MET B 757 " --> pdb=" O SER B 894 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B 896 " --> pdb=" O MET B 757 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL B 759 " --> pdb=" O LEU B 896 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 758 " --> pdb=" O LEU B 914 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 824 through 826 removed outlier: 6.813A pdb=" N MET B 839 " --> pdb=" O TYR B 825 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 883 through 884 Processing sheet with id=AC6, first strand: chain 'B' and resid 1066 through 1070 Processing sheet with id=AC7, first strand: chain 'C' and resid 52 through 55 removed outlier: 6.973A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AC9, first strand: chain 'C' and resid 173 through 175 removed outlier: 3.725A pdb=" N LEU C 142 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 93 " --> pdb=" O LEU C 211 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 228 through 231 removed outlier: 6.762A pdb=" N GLU C 311 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 262 through 266 removed outlier: 3.504A pdb=" N ARG C 274 " --> pdb=" O GLU C 263 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 61 through 62 removed outlier: 4.301A pdb=" N LEU E 61 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.987A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 148 through 150 removed outlier: 3.804A pdb=" N VAL E 149 " --> pdb=" O LYS E 192 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS E 192 " --> pdb=" O VAL E 149 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 90 through 92 removed outlier: 3.535A pdb=" N VAL H 59 " --> pdb=" O LEU H 144 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE H 6 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP H 14 " --> pdb=" O HIS H 29 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS H 29 " --> pdb=" O ASP H 14 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER H 26 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP H 38 " --> pdb=" O GLN H 126 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 27 through 30 removed outlier: 4.095A pdb=" N THR K 41 " --> pdb=" O VAL K 30 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASN K 81 " --> pdb=" O TYR K 70 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR K 70 " --> pdb=" O ASN K 81 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG K 83 " --> pdb=" O CYS K 68 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N CYS K 68 " --> pdb=" O ARG K 83 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLN K 85 " --> pdb=" O GLU K 66 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 10 through 13 removed outlier: 5.989A pdb=" N ARG N 10 " --> pdb=" O MET N 99 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL N 101 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLN N 12 " --> pdb=" O VAL N 101 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N ASP N 103 " --> pdb=" O GLN N 12 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ALA N 23 " --> pdb=" O GLU N 105 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 23 through 28 current: chain 'M' and resid 40 through 48 removed outlier: 3.637A pdb=" N GLY M 113 " --> pdb=" O LEU M 42 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER M 85 " --> pdb=" O THR M 114 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 42 through 45 removed outlier: 3.606A pdb=" N THR N 42 " --> pdb=" O ALA N 61 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN N 72 " --> pdb=" O ASN N 108 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASN N 108 " --> pdb=" O ASN N 72 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N MET N 109 " --> pdb=" O LEU N 25 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N GLN N 27 " --> pdb=" O MET N 109 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ALA N 23 " --> pdb=" O GLU N 105 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 98 through 105 current: chain 'M' and resid 106 through 107 935 hydrogen bonds defined for protein. 2643 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.44 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9035 1.33 - 1.45: 5362 1.45 - 1.57: 17041 1.57 - 1.70: 0 1.70 - 1.82: 337 Bond restraints: 31775 Sorted by residual: bond pdb=" C CYS B 498 " pdb=" N PRO B 499 " ideal model delta sigma weight residual 1.336 1.293 0.042 9.80e-03 1.04e+04 1.88e+01 bond pdb=" CB ILE B 746 " pdb=" CG2 ILE B 746 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.15e+00 bond pdb=" CB ASN B 461 " pdb=" CG ASN B 461 " ideal model delta sigma weight residual 1.516 1.456 0.060 2.50e-02 1.60e+03 5.68e+00 bond pdb=" CA VAL B 722 " pdb=" CB VAL B 722 " ideal model delta sigma weight residual 1.537 1.510 0.027 1.17e-02 7.31e+03 5.20e+00 bond pdb=" CB PHE B 962 " pdb=" CG PHE B 962 " ideal model delta sigma weight residual 1.502 1.450 0.052 2.30e-02 1.89e+03 5.06e+00 ... (remaining 31770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 41143 2.23 - 4.45: 1610 4.45 - 6.68: 171 6.68 - 8.90: 24 8.90 - 11.13: 9 Bond angle restraints: 42957 Sorted by residual: angle pdb=" N ARG B 802 " pdb=" CA ARG B 802 " pdb=" C ARG B 802 " ideal model delta sigma weight residual 113.88 102.75 11.13 1.23e+00 6.61e-01 8.18e+01 angle pdb=" N ILE A 802 " pdb=" CA ILE A 802 " pdb=" C ILE A 802 " ideal model delta sigma weight residual 113.71 108.48 5.23 9.50e-01 1.11e+00 3.03e+01 angle pdb=" C GLY B 811 " pdb=" N LEU B 812 " pdb=" CA LEU B 812 " ideal model delta sigma weight residual 123.56 113.07 10.49 1.98e+00 2.55e-01 2.80e+01 angle pdb=" C LEU J 55 " pdb=" N ILE J 56 " pdb=" CA ILE J 56 " ideal model delta sigma weight residual 121.71 115.66 6.05 1.20e+00 6.94e-01 2.54e+01 angle pdb=" N HIS A 995 " pdb=" CA HIS A 995 " pdb=" C HIS A 995 " ideal model delta sigma weight residual 108.19 114.69 -6.50 1.29e+00 6.01e-01 2.54e+01 ... (remaining 42952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16944 17.95 - 35.89: 2039 35.89 - 53.84: 334 53.84 - 71.78: 43 71.78 - 89.73: 25 Dihedral angle restraints: 19385 sinusoidal: 8020 harmonic: 11365 Sorted by residual: dihedral pdb=" CA LYS B 270 " pdb=" C LYS B 270 " pdb=" N GLY B 271 " pdb=" CA GLY B 271 " ideal model delta harmonic sigma weight residual -180.00 -127.78 -52.22 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA ARG A 310 " pdb=" C ARG A 310 " pdb=" N PRO A 311 " pdb=" CA PRO A 311 " ideal model delta harmonic sigma weight residual -180.00 -139.14 -40.86 0 5.00e+00 4.00e-02 6.68e+01 dihedral pdb=" CA SER M 136 " pdb=" C SER M 136 " pdb=" N PRO M 137 " pdb=" CA PRO M 137 " ideal model delta harmonic sigma weight residual 180.00 -141.04 -38.96 0 5.00e+00 4.00e-02 6.07e+01 ... (remaining 19382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3150 0.046 - 0.092: 1187 0.092 - 0.138: 353 0.138 - 0.184: 44 0.184 - 0.230: 6 Chirality restraints: 4740 Sorted by residual: chirality pdb=" CG LEU E 61 " pdb=" CB LEU E 61 " pdb=" CD1 LEU E 61 " pdb=" CD2 LEU E 61 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB VAL B 623 " pdb=" CA VAL B 623 " pdb=" CG1 VAL B 623 " pdb=" CG2 VAL B 623 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA CYS B 866 " pdb=" N CYS B 866 " pdb=" C CYS B 866 " pdb=" CB CYS B 866 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.64e-01 ... (remaining 4737 not shown) Planarity restraints: 5573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 310 " 0.060 5.00e-02 4.00e+02 9.10e-02 1.32e+01 pdb=" N PRO A 311 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO A 311 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 311 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS I 23 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.00e+00 pdb=" C CYS I 23 " 0.049 2.00e-02 2.50e+03 pdb=" O CYS I 23 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY I 24 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 236 " -0.044 5.00e-02 4.00e+02 6.66e-02 7.09e+00 pdb=" N PRO C 237 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 237 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 237 " -0.036 5.00e-02 4.00e+02 ... (remaining 5570 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 532 2.60 - 3.18: 29436 3.18 - 3.75: 46347 3.75 - 4.33: 63287 4.33 - 4.90: 100570 Nonbonded interactions: 240172 Sorted by model distance: nonbonded pdb=" OE2 GLU B 162 " pdb=" OH TYR B 735 " model vdw 2.028 3.040 nonbonded pdb=" O GLY B 232 " pdb=" OG SER B 281 " model vdw 2.044 3.040 nonbonded pdb=" NZ LYS A 933 " pdb=" O MET B 642 " model vdw 2.076 3.120 nonbonded pdb=" O GLY A 545 " pdb=" OH TYR A 609 " model vdw 2.080 3.040 nonbonded pdb=" NH2 ARG C 109 " pdb=" O ILE J 3 " model vdw 2.100 3.120 ... (remaining 240167 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 27.330 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 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 : 0.008 0.082 31777 Z= 0.384 Angle : 1.013 11.125 42961 Z= 0.588 Chirality : 0.051 0.230 4740 Planarity : 0.006 0.091 5573 Dihedral : 15.370 89.731 12053 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 24.40 Ramachandran Plot: Outliers : 0.21 % Allowed : 15.16 % Favored : 84.64 % Rotamer: Outliers : 0.41 % Allowed : 10.84 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.94 (0.11), residues: 3886 helix: -3.04 (0.11), residues: 1192 sheet: -2.63 (0.23), residues: 435 loop : -3.72 (0.11), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 802 TYR 0.031 0.003 TYR C 233 PHE 0.026 0.003 PHE B 75 TRP 0.030 0.002 TRP B 494 HIS 0.012 0.002 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00842 (31775) covalent geometry : angle 1.01192 (42957) SS BOND : bond 0.00394 ( 2) SS BOND : angle 4.53008 ( 4) hydrogen bonds : bond 0.20552 ( 935) hydrogen bonds : angle 8.07869 ( 2643) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7772 Ramachandran restraints generated. 3886 Oldfield, 0 Emsley, 3886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7772 Ramachandran restraints generated. 3886 Oldfield, 0 Emsley, 3886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 291 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: 0.4361 (mmm) cc_final: 0.3794 (tmm) REVERT: A 594 MET cc_start: -0.3981 (mmp) cc_final: -0.4481 (mmp) REVERT: A 635 MET cc_start: 0.6359 (mtp) cc_final: 0.6151 (mtt) REVERT: A 751 LYS cc_start: 0.7394 (tmtt) cc_final: 0.7165 (tptt) REVERT: A 759 TYR cc_start: 0.4766 (t80) cc_final: 0.4498 (t80) REVERT: A 846 TRP cc_start: 0.3772 (t-100) cc_final: 0.3450 (t60) REVERT: A 969 MET cc_start: 0.7808 (mtp) cc_final: 0.7515 (mtm) REVERT: A 1259 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7274 (mt) REVERT: A 1342 MET cc_start: 0.8096 (tmm) cc_final: 0.7632 (tmm) REVERT: A 1540 MET cc_start: 0.6599 (mmt) cc_final: 0.6246 (mmm) REVERT: B 193 MET cc_start: 0.8531 (ttm) cc_final: 0.8306 (ttp) REVERT: B 382 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7129 (tt) REVERT: B 600 MET cc_start: 0.6059 (mtp) cc_final: 0.5546 (mtp) REVERT: B 637 MET cc_start: 0.8178 (tpp) cc_final: 0.7715 (tpp) REVERT: B 757 MET cc_start: 0.6666 (mtm) cc_final: 0.6248 (ptp) REVERT: B 965 MET cc_start: 0.7363 (ttm) cc_final: 0.6874 (tpp) REVERT: B 999 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: F 57 MET cc_start: 0.7035 (tpt) cc_final: 0.6814 (tpp) REVERT: F 83 LEU cc_start: 0.4916 (pt) cc_final: 0.4563 (pp) REVERT: H 43 VAL cc_start: 0.8804 (t) cc_final: 0.8570 (m) REVERT: N 25 LEU cc_start: 0.7548 (mt) cc_final: 0.7273 (mt) REVERT: N 39 MET cc_start: 0.3098 (mtp) cc_final: 0.2182 (ttp) REVERT: N 92 LEU cc_start: 0.7986 (mt) cc_final: 0.7453 (mt) REVERT: M 43 TRP cc_start: 0.7419 (m100) cc_final: 0.7040 (m100) REVERT: M 50 ASP cc_start: 0.7452 (p0) cc_final: 0.7135 (p0) REVERT: M 60 HIS cc_start: 0.5672 (m-70) cc_final: 0.3952 (t70) REVERT: M 67 GLN cc_start: 0.3637 (tt0) cc_final: 0.3025 (mt0) REVERT: M 72 LYS cc_start: 0.6424 (mmtp) cc_final: 0.5614 (mmtm) REVERT: M 95 LEU cc_start: 0.6911 (mp) cc_final: 0.5763 (tp) outliers start: 14 outliers final: 4 residues processed: 304 average time/residue: 0.2174 time to fit residues: 103.5427 Evaluate side-chains 203 residues out of total 3423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 196 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN ** A 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 GLN A 652 HIS A 694 ASN A 704 ASN ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 HIS A1030 GLN A1043 ASN A1079 HIS A1081 ASN A1094 GLN A1111 ASN A1240 ASN A1295 GLN A1310 ASN A1313 GLN A1329 GLN A1359 ASN A1579 ASN ** A1683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1690 HIS B 18 HIS B 59 GLN B 97 ASN ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN B 468 HIS ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 ASN B 889 GLN ** B 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1127 ASN C 59 ASN C 97 ASN C 151 HIS C 160 ASN C 305 HIS E 43 GLN ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 HIS K 45 HIS K 81 ASN K 85 GLN K 101 ASN L 13 GLN L 26 ASN ** N 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.151257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.127052 restraints weight = 100453.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.125621 restraints weight = 119372.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.126222 restraints weight = 105214.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.126645 restraints weight = 72341.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.127020 restraints weight = 65834.692| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31777 Z= 0.184 Angle : 0.773 10.747 42961 Z= 0.400 Chirality : 0.048 0.206 4740 Planarity : 0.006 0.094 5573 Dihedral : 6.634 49.454 4280 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.78 % Favored : 90.17 % Rotamer: Outliers : 0.18 % Allowed : 7.13 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.64 (0.12), residues: 3886 helix: -1.65 (0.14), residues: 1198 sheet: -2.28 (0.22), residues: 490 loop : -3.02 (0.12), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 172 TYR 0.028 0.002 TYR E 90 PHE 0.020 0.002 PHE A1089 TRP 0.022 0.002 TRP B 494 HIS 0.018 0.002 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00417 (31775) covalent geometry : angle 0.77219 (42957) SS BOND : bond 0.00337 ( 2) SS BOND : angle 3.06925 ( 4) hydrogen bonds : bond 0.05676 ( 935) hydrogen bonds : angle 6.08491 ( 2643) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7772 Ramachandran restraints generated. 3886 Oldfield, 0 Emsley, 3886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7772 Ramachandran restraints generated. 3886 Oldfield, 0 Emsley, 3886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 273 time to evaluate : 1.066 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: A 671 LEU cc_start: 0.8527 (mt) cc_final: 0.8290 (mt) REVERT: A 751 LYS cc_start: 0.7476 (tmtt) cc_final: 0.7231 (tptt) REVERT: A 846 TRP cc_start: 0.4215 (t-100) cc_final: 0.3738 (t60) REVERT: A 860 MET cc_start: 0.7640 (tmm) cc_final: 0.6913 (tmm) REVERT: A 1498 MET cc_start: 0.6792 (mtt) cc_final: 0.6425 (mtt) REVERT: A 1534 MET cc_start: 0.5962 (mpp) cc_final: 0.5668 (mpp) REVERT: A 1540 MET cc_start: 0.6121 (mmt) cc_final: 0.5915 (mmm) REVERT: B 285 MET cc_start: 0.8253 (mtm) cc_final: 0.7939 (ptp) REVERT: B 369 LEU cc_start: 0.8839 (tp) cc_final: 0.8592 (tt) REVERT: B 379 GLN cc_start: 0.7733 (tp-100) cc_final: 0.6874 (tm-30) REVERT: B 600 MET cc_start: 0.6276 (mtp) cc_final: 0.5876 (mtp) REVERT: B 604 PRO cc_start: 0.8462 (Cg_exo) cc_final: 0.8196 (Cg_endo) REVERT: B 637 MET cc_start: 0.8079 (tpp) cc_final: 0.7369 (tpp) REVERT: B 757 MET cc_start: 0.6684 (mtm) cc_final: 0.5936 (ptp) REVERT: B 924 MET cc_start: 0.4958 (mmt) cc_final: 0.4630 (mmt) REVERT: B 965 MET cc_start: 0.7155 (ttm) cc_final: 0.6482 (ttm) REVERT: B 1126 MET cc_start: -0.2400 (mpp) cc_final: -0.2803 (mpp) REVERT: C 245 VAL cc_start: 0.7964 (m) cc_final: 0.7481 (p) REVERT: F 57 MET cc_start: 0.6837 (tpt) cc_final: 0.6444 (tpp) REVERT: H 37 MET cc_start: 0.7519 (mmp) cc_final: 0.6953 (mmp) REVERT: H 122 LEU cc_start: 0.6548 (tt) cc_final: 0.6006 (tt) REVERT: K 60 MET cc_start: 0.7369 (tmm) cc_final: 0.7064 (tmm) REVERT: N 25 LEU cc_start: 0.7701 (mt) cc_final: 0.7463 (mt) REVERT: N 39 MET cc_start: 0.2575 (mtp) cc_final: 0.1685 (ttp) REVERT: N 92 LEU cc_start: 0.7808 (mt) cc_final: 0.7527 (mt) REVERT: N 101 VAL cc_start: 0.8592 (t) cc_final: 0.8015 (t) REVERT: M 60 HIS cc_start: 0.5376 (m-70) cc_final: 0.3964 (t70) REVERT: M 95 LEU cc_start: 0.7097 (mp) cc_final: 0.5910 (tp) outliers start: 6 outliers final: 2 residues processed: 279 average time/residue: 0.1955 time to fit residues: 89.3242 Evaluate side-chains 208 residues out of total 3423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 206 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 9 optimal weight: 50.0000 chunk 36 optimal weight: 10.0000 chunk 25 optimal weight: 50.0000 chunk 68 optimal weight: 0.4980 chunk 192 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 chunk 244 optimal weight: 0.7980 chunk 281 optimal weight: 4.9990 chunk 234 optimal weight: 4.9990 chunk 202 optimal weight: 0.5980 chunk 301 optimal weight: 8.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 322 ASN A 395 GLN A 600 GLN ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 918 GLN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1295 GLN ** A1359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1603 ASN A1683 GLN ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 HIS B 512 ASN B 889 GLN ** B 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN K 38 HIS ** N 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.152312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.127338 restraints weight = 99342.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.125413 restraints weight = 109478.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.126305 restraints weight = 84730.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.126509 restraints weight = 63799.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.126649 restraints weight = 60916.081| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31777 Z= 0.142 Angle : 0.694 9.685 42961 Z= 0.356 Chirality : 0.045 0.190 4740 Planarity : 0.005 0.094 5573 Dihedral : 6.106 43.504 4280 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.83 % Favored : 91.15 % Rotamer: Outliers : 0.03 % Allowed : 4.59 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.13), residues: 3886 helix: -0.94 (0.14), residues: 1188 sheet: -2.04 (0.22), residues: 510 loop : -2.69 (0.12), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 128 TYR 0.028 0.002 TYR E 90 PHE 0.028 0.001 PHE B 259 TRP 0.016 0.001 TRP B 494 HIS 0.009 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00319 (31775) covalent geometry : angle 0.69265 (42957) SS BOND : bond 0.01055 ( 2) SS BOND : angle 3.72506 ( 4) hydrogen bonds : bond 0.04897 ( 935) hydrogen bonds : angle 5.60525 ( 2643) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7772 Ramachandran restraints generated. 3886 Oldfield, 0 Emsley, 3886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7772 Ramachandran restraints generated. 3886 Oldfield, 0 Emsley, 3886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 1.231 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: A 594 MET cc_start: -0.3105 (mmp) cc_final: -0.3617 (mmp) REVERT: A 751 LYS cc_start: 0.7490 (tmtt) cc_final: 0.7277 (tptp) REVERT: A 822 CYS cc_start: 0.8287 (t) cc_final: 0.7878 (m) REVERT: A 846 TRP cc_start: 0.4039 (t-100) cc_final: 0.3645 (t60) REVERT: A 860 MET cc_start: 0.7722 (tmm) cc_final: 0.7102 (tmm) REVERT: A 1540 MET cc_start: 0.6267 (mmt) cc_final: 0.5979 (mmm) REVERT: B 253 LEU cc_start: 0.8085 (mm) cc_final: 0.7882 (pp) REVERT: B 285 MET cc_start: 0.8612 (mtm) cc_final: 0.8247 (ptp) REVERT: B 369 LEU cc_start: 0.8842 (tp) cc_final: 0.8522 (tt) REVERT: B 600 MET cc_start: 0.6266 (mtp) cc_final: 0.5795 (mtp) REVERT: B 604 PRO cc_start: 0.8518 (Cg_exo) cc_final: 0.8178 (Cg_endo) REVERT: B 757 MET cc_start: 0.6599 (mtm) cc_final: 0.6224 (ptp) REVERT: B 965 MET cc_start: 0.7097 (ttm) cc_final: 0.6422 (tpp) REVERT: E 130 PHE cc_start: 0.7467 (m-80) cc_final: 0.7110 (m-80) REVERT: H 37 MET cc_start: 0.7435 (mmp) cc_final: 0.7222 (mmp) REVERT: H 145 MET cc_start: 0.7018 (tmm) cc_final: 0.6614 (tmm) REVERT: K 60 MET cc_start: 0.7247 (tmm) cc_final: 0.7044 (tmm) REVERT: N 39 MET cc_start: 0.1674 (mtp) cc_final: 0.1352 (ttp) REVERT: N 92 LEU cc_start: 0.7918 (mt) cc_final: 0.7598 (mm) REVERT: N 99 MET cc_start: 0.7203 (ttt) cc_final: 0.6964 (ttt) REVERT: N 101 VAL cc_start: 0.8602 (t) cc_final: 0.7983 (t) REVERT: N 109 MET cc_start: 0.1667 (mmp) cc_final: 0.1059 (mmp) REVERT: M 55 CYS cc_start: 0.6110 (p) cc_final: 0.5829 (p) REVERT: M 60 HIS cc_start: 0.5588 (m-70) cc_final: 0.4007 (t70) REVERT: M 95 LEU cc_start: 0.7373 (mp) cc_final: 0.6133 (tp) outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.2045 time to fit residues: 91.5423 Evaluate side-chains 201 residues out of total 3423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 295 optimal weight: 2.9990 chunk 340 optimal weight: 9.9990 chunk 34 optimal weight: 50.0000 chunk 93 optimal weight: 6.9990 chunk 275 optimal weight: 0.0370 chunk 148 optimal weight: 8.9990 chunk 255 optimal weight: 0.9990 chunk 86 optimal weight: 0.0870 chunk 246 optimal weight: 3.9990 chunk 2 optimal weight: 50.0000 chunk 94 optimal weight: 20.0000 overall best weight: 1.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 GLN ** A 995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1359 ASN B 219 HIS ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 GLN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 889 GLN ** B 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN N 82 ASN ** N 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.152892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.127266 restraints weight = 98234.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.125470 restraints weight = 102218.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.125702 restraints weight = 96462.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.125964 restraints weight = 77456.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.126376 restraints weight = 63788.690| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31777 Z= 0.135 Angle : 0.666 9.014 42961 Z= 0.342 Chirality : 0.045 0.247 4740 Planarity : 0.005 0.093 5573 Dihedral : 5.828 43.475 4280 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.57 % Favored : 91.41 % Rotamer: Outliers : 0.03 % Allowed : 4.00 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.13), residues: 3886 helix: -0.59 (0.15), residues: 1186 sheet: -1.73 (0.23), residues: 497 loop : -2.49 (0.13), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 106 TYR 0.020 0.002 TYR B 550 PHE 0.024 0.001 PHE B 259 TRP 0.017 0.001 TRP B 494 HIS 0.011 0.001 HIS A 850 Details of bonding type rmsd covalent geometry : bond 0.00309 (31775) covalent geometry : angle 0.66542 (42957) SS BOND : bond 0.00119 ( 2) SS BOND : angle 3.35814 ( 4) hydrogen bonds : bond 0.04461 ( 935) hydrogen bonds : angle 5.31977 ( 2643) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7772 Ramachandran restraints generated. 3886 Oldfield, 0 Emsley, 3886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7772 Ramachandran restraints generated. 3886 Oldfield, 0 Emsley, 3886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 255 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 846 TRP cc_start: 0.4170 (t-100) cc_final: 0.3884 (t60) REVERT: A 860 MET cc_start: 0.7686 (tmm) cc_final: 0.7302 (tmm) REVERT: A 1534 MET cc_start: 0.6356 (mpp) cc_final: 0.5986 (mpp) REVERT: A 1540 MET cc_start: 0.6211 (mmt) cc_final: 0.5936 (mmm) REVERT: B 253 LEU cc_start: 0.8168 (mm) cc_final: 0.7902 (pp) REVERT: B 285 MET cc_start: 0.8734 (mtm) cc_final: 0.8456 (ptp) REVERT: B 369 LEU cc_start: 0.8876 (tp) cc_final: 0.8559 (tt) REVERT: B 511 MET cc_start: 0.7725 (ttm) cc_final: 0.7363 (mtm) REVERT: B 600 MET cc_start: 0.6263 (mtp) cc_final: 0.5951 (mtp) REVERT: B 924 MET cc_start: 0.4684 (mmt) cc_final: 0.4330 (mmt) REVERT: B 965 MET cc_start: 0.7126 (ttm) cc_final: 0.6419 (tpp) REVERT: F 64 ARG cc_start: 0.5290 (tpp80) cc_final: 0.4454 (ttp80) REVERT: H 37 MET cc_start: 0.7500 (mmp) cc_final: 0.7261 (mmp) REVERT: K 73 THR cc_start: 0.7743 (t) cc_final: 0.7483 (t) REVERT: N 25 LEU cc_start: 0.7736 (mt) cc_final: 0.7514 (mt) REVERT: N 98 GLN cc_start: 0.7830 (tt0) cc_final: 0.7433 (pm20) REVERT: N 109 MET cc_start: 0.1738 (mmp) cc_final: 0.1239 (mmp) REVERT: M 55 CYS cc_start: 0.6143 (p) cc_final: 0.5856 (p) REVERT: M 60 HIS cc_start: 0.5437 (m-70) cc_final: 0.4013 (t70) REVERT: M 95 LEU cc_start: 0.7548 (mp) cc_final: 0.6301 (tp) outliers start: 1 outliers final: 0 residues processed: 256 average time/residue: 0.1843 time to fit residues: 78.0125 Evaluate side-chains 200 residues out of total 3423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 222 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 368 optimal weight: 20.0000 chunk 363 optimal weight: 20.0000 chunk 9 optimal weight: 50.0000 chunk 343 optimal weight: 4.9990 chunk 3 optimal weight: 30.0000 chunk 266 optimal weight: 20.0000 chunk 214 optimal weight: 2.9990 chunk 329 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 995 HIS A1016 GLN A1030 GLN A1295 GLN A1584 ASN A1603 ASN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN B 468 HIS ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 820 GLN B 846 ASN ** B 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 HIS ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 HIS K 85 GLN ** N 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.150742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.125531 restraints weight = 100511.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.123186 restraints weight = 120916.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.124081 restraints weight = 99202.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.124536 restraints weight = 68979.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.124716 restraints weight = 67369.097| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 31777 Z= 0.246 Angle : 0.774 10.545 42961 Z= 0.395 Chirality : 0.048 0.211 4740 Planarity : 0.006 0.093 5573 Dihedral : 6.179 48.548 4280 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.78 % Favored : 89.17 % Rotamer: Outliers : 0.09 % Allowed : 3.89 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.13), residues: 3886 helix: -0.76 (0.15), residues: 1192 sheet: -1.96 (0.22), residues: 513 loop : -2.48 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 106 TYR 0.033 0.002 TYR N 102 PHE 0.025 0.002 PHE B 259 TRP 0.023 0.002 TRP B 494 HIS 0.010 0.002 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00574 (31775) covalent geometry : angle 0.77278 (42957) SS BOND : bond 0.00567 ( 2) SS BOND : angle 3.63070 ( 4) hydrogen bonds : bond 0.05230 ( 935) hydrogen bonds : angle 5.52509 ( 2643) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7772 Ramachandran restraints generated. 3886 Oldfield, 0 Emsley, 3886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7772 Ramachandran restraints generated. 3886 Oldfield, 0 Emsley, 3886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 229 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: -0.1559 (ttp) cc_final: -0.2805 (ttp) REVERT: A 671 LEU cc_start: 0.8384 (mt) cc_final: 0.8015 (mt) REVERT: A 822 CYS cc_start: 0.7708 (t) cc_final: 0.7072 (m) REVERT: A 860 MET cc_start: 0.7883 (tmm) cc_final: 0.7472 (tmm) REVERT: B 369 LEU cc_start: 0.8933 (tp) cc_final: 0.8673 (tt) REVERT: B 600 MET cc_start: 0.6078 (mtp) cc_final: 0.5502 (mtp) REVERT: B 637 MET cc_start: 0.8033 (tpp) cc_final: 0.7558 (tpp) REVERT: B 924 MET cc_start: 0.4911 (mmt) cc_final: 0.4490 (mmt) REVERT: B 965 MET cc_start: 0.7356 (ttm) cc_final: 0.6662 (tpp) REVERT: J 31 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7536 (mm-30) REVERT: N 25 LEU cc_start: 0.7774 (mt) cc_final: 0.7551 (mt) REVERT: N 39 MET cc_start: 0.2182 (mtm) cc_final: 0.1484 (ttp) REVERT: N 92 LEU cc_start: 0.7711 (mm) cc_final: 0.7496 (mm) REVERT: N 109 MET cc_start: 0.1933 (mmp) cc_final: 0.1569 (mmp) REVERT: M 55 CYS cc_start: 0.6224 (p) cc_final: 0.5968 (p) REVERT: M 60 HIS cc_start: 0.5301 (m-70) cc_final: 0.3984 (t70) REVERT: M 95 LEU cc_start: 0.7471 (mp) cc_final: 0.6357 (tp) outliers start: 3 outliers final: 1 residues processed: 232 average time/residue: 0.1742 time to fit residues: 67.7455 Evaluate side-chains 196 residues out of total 3423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 320 optimal weight: 20.0000 chunk 275 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 199 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 32 optimal weight: 50.0000 chunk 178 optimal weight: 5.9990 chunk 88 optimal weight: 0.0670 chunk 155 optimal weight: 2.9990 chunk 47 optimal weight: 50.0000 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 GLN B 715 GLN B 846 ASN B 941 HIS ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.152579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.126303 restraints weight = 98917.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.123893 restraints weight = 101534.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.124321 restraints weight = 102701.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.124666 restraints weight = 77302.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.124992 restraints weight = 63774.265| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31777 Z= 0.146 Angle : 0.678 10.893 42961 Z= 0.345 Chirality : 0.045 0.219 4740 Planarity : 0.005 0.093 5573 Dihedral : 5.799 42.178 4280 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.39 % Favored : 91.59 % Rotamer: Outliers : 0.03 % Allowed : 2.28 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.13), residues: 3886 helix: -0.56 (0.15), residues: 1222 sheet: -1.73 (0.23), residues: 510 loop : -2.35 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 128 TYR 0.027 0.002 TYR A1044 PHE 0.020 0.001 PHE B 259 TRP 0.037 0.001 TRP B 494 HIS 0.010 0.001 HIS A 850 Details of bonding type rmsd covalent geometry : bond 0.00337 (31775) covalent geometry : angle 0.67720 (42957) SS BOND : bond 0.01005 ( 2) SS BOND : angle 3.85435 ( 4) hydrogen bonds : bond 0.04368 ( 935) hydrogen bonds : angle 5.20050 ( 2643) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7772 Ramachandran restraints generated. 3886 Oldfield, 0 Emsley, 3886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7772 Ramachandran restraints generated. 3886 Oldfield, 0 Emsley, 3886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 246 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 671 LEU cc_start: 0.8206 (mt) cc_final: 0.7806 (mt) REVERT: A 822 CYS cc_start: 0.8276 (t) cc_final: 0.7935 (m) REVERT: A 860 MET cc_start: 0.7741 (tmm) cc_final: 0.7415 (tmm) REVERT: A 1030 GLN cc_start: 0.7782 (pp30) cc_final: 0.7241 (pm20) REVERT: A 1498 MET cc_start: 0.6367 (mtt) cc_final: 0.6166 (mtp) REVERT: B 253 LEU cc_start: 0.8127 (mm) cc_final: 0.7820 (pp) REVERT: B 600 MET cc_start: 0.6279 (mtp) cc_final: 0.5937 (mtp) REVERT: B 965 MET cc_start: 0.7306 (ttm) cc_final: 0.6798 (ttm) REVERT: F 95 LYS cc_start: 0.6815 (mttm) cc_final: 0.6501 (mmtm) REVERT: J 1 MET cc_start: 0.8630 (ttt) cc_final: 0.8141 (ttp) REVERT: J 31 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7477 (mm-30) REVERT: N 39 MET cc_start: 0.1926 (mtm) cc_final: 0.1278 (ttp) REVERT: N 92 LEU cc_start: 0.7696 (mm) cc_final: 0.6988 (mm) REVERT: N 109 MET cc_start: 0.2066 (mmp) cc_final: 0.1717 (mmp) REVERT: M 55 CYS cc_start: 0.6225 (p) cc_final: 0.5963 (p) REVERT: M 60 HIS cc_start: 0.4981 (m-70) cc_final: 0.4164 (t70) REVERT: M 95 LEU cc_start: 0.7479 (mp) cc_final: 0.6269 (tp) outliers start: 1 outliers final: 0 residues processed: 247 average time/residue: 0.1783 time to fit residues: 73.5997 Evaluate side-chains 198 residues out of total 3423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 88 optimal weight: 0.9990 chunk 208 optimal weight: 10.0000 chunk 318 optimal weight: 5.9990 chunk 12 optimal weight: 50.0000 chunk 33 optimal weight: 50.0000 chunk 182 optimal weight: 7.9990 chunk 364 optimal weight: 0.0020 chunk 180 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 846 ASN ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.152207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.127445 restraints weight = 99872.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.125179 restraints weight = 126773.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.126199 restraints weight = 98035.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.126429 restraints weight = 72120.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.126658 restraints weight = 70147.992| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31777 Z= 0.161 Angle : 0.681 10.075 42961 Z= 0.346 Chirality : 0.045 0.192 4740 Planarity : 0.005 0.093 5573 Dihedral : 5.743 44.942 4280 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.26 % Favored : 90.71 % Rotamer: Outliers : 0.03 % Allowed : 1.87 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.13), residues: 3886 helix: -0.41 (0.15), residues: 1212 sheet: -1.67 (0.23), residues: 513 loop : -2.27 (0.13), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 464 TYR 0.023 0.002 TYR B 550 PHE 0.019 0.001 PHE A1303 TRP 0.029 0.001 TRP B 494 HIS 0.008 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00375 (31775) covalent geometry : angle 0.68056 (42957) SS BOND : bond 0.00297 ( 2) SS BOND : angle 3.44863 ( 4) hydrogen bonds : bond 0.04386 ( 935) hydrogen bonds : angle 5.15244 ( 2643) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7772 Ramachandran restraints generated. 3886 Oldfield, 0 Emsley, 3886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7772 Ramachandran restraints generated. 3886 Oldfield, 0 Emsley, 3886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 242 time to evaluate : 1.398 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: A 671 LEU cc_start: 0.8201 (mt) cc_final: 0.7781 (mt) REVERT: A 822 CYS cc_start: 0.7467 (t) cc_final: 0.6959 (m) REVERT: A 860 MET cc_start: 0.7853 (tmm) cc_final: 0.7561 (tmm) REVERT: A 1030 GLN cc_start: 0.8222 (pp30) cc_final: 0.7913 (pp30) REVERT: A 1048 MET cc_start: 0.7405 (mtm) cc_final: 0.6409 (mtm) REVERT: A 1351 MET cc_start: 0.7734 (mmp) cc_final: 0.7212 (mmm) REVERT: A 1498 MET cc_start: 0.6494 (mtt) cc_final: 0.6241 (mtp) REVERT: B 600 MET cc_start: 0.6184 (mtp) cc_final: 0.5617 (mtp) REVERT: B 637 MET cc_start: 0.7848 (tpp) cc_final: 0.7178 (tpp) REVERT: H 37 MET cc_start: 0.7749 (mmp) cc_final: 0.7466 (mmp) REVERT: J 1 MET cc_start: 0.8649 (ttt) cc_final: 0.8193 (ttp) REVERT: N 39 MET cc_start: 0.2122 (mtm) cc_final: 0.1407 (ttm) REVERT: M 55 CYS cc_start: 0.6181 (p) cc_final: 0.5896 (p) REVERT: M 60 HIS cc_start: 0.4878 (m-70) cc_final: 0.4070 (t70) REVERT: M 95 LEU cc_start: 0.7460 (mp) cc_final: 0.6350 (tp) outliers start: 1 outliers final: 1 residues processed: 243 average time/residue: 0.1891 time to fit residues: 77.0395 Evaluate side-chains 195 residues out of total 3423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 82 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 258 optimal weight: 6.9990 chunk 34 optimal weight: 50.0000 chunk 304 optimal weight: 8.9990 chunk 187 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 146 optimal weight: 0.5980 chunk 360 optimal weight: 6.9990 chunk 382 optimal weight: 10.0000 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 GLN ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 846 ASN ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.151059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.124664 restraints weight = 100052.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.120917 restraints weight = 100520.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.121559 restraints weight = 95052.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.121735 restraints weight = 71817.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.122476 restraints weight = 65984.963| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 31777 Z= 0.212 Angle : 0.734 11.394 42961 Z= 0.373 Chirality : 0.047 0.214 4740 Planarity : 0.005 0.093 5573 Dihedral : 5.932 46.196 4280 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.11 % Favored : 89.86 % Rotamer: Outliers : 0.03 % Allowed : 1.67 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.13), residues: 3886 helix: -0.50 (0.15), residues: 1206 sheet: -1.73 (0.23), residues: 505 loop : -2.29 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 187 TYR 0.029 0.002 TYR A 754 PHE 0.023 0.002 PHE A1089 TRP 0.045 0.002 TRP B 494 HIS 0.009 0.002 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00495 (31775) covalent geometry : angle 0.73287 (42957) SS BOND : bond 0.00322 ( 2) SS BOND : angle 3.51448 ( 4) hydrogen bonds : bond 0.04824 ( 935) hydrogen bonds : angle 5.32817 ( 2643) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7772 Ramachandran restraints generated. 3886 Oldfield, 0 Emsley, 3886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7772 Ramachandran restraints generated. 3886 Oldfield, 0 Emsley, 3886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 860 MET cc_start: 0.7780 (tmm) cc_final: 0.7480 (tmm) REVERT: A 1048 MET cc_start: 0.7736 (mtm) cc_final: 0.6578 (mtm) REVERT: A 1253 MET cc_start: 0.7445 (ptp) cc_final: 0.6580 (ptm) REVERT: A 1534 MET cc_start: 0.5412 (mpp) cc_final: 0.4946 (mpp) REVERT: B 600 MET cc_start: 0.6472 (mtp) cc_final: 0.5891 (mtp) REVERT: B 637 MET cc_start: 0.7868 (tpp) cc_final: 0.7288 (tpp) REVERT: B 753 MET cc_start: 0.1834 (tpt) cc_final: 0.1569 (tpt) REVERT: H 37 MET cc_start: 0.7830 (mmp) cc_final: 0.7391 (mmp) REVERT: J 1 MET cc_start: 0.8711 (ttt) cc_final: 0.8316 (ttp) REVERT: N 25 LEU cc_start: 0.8032 (mm) cc_final: 0.7803 (mt) REVERT: N 39 MET cc_start: 0.1929 (mtm) cc_final: 0.1315 (ttm) REVERT: M 55 CYS cc_start: 0.6432 (p) cc_final: 0.6177 (p) REVERT: M 60 HIS cc_start: 0.5448 (m-70) cc_final: 0.4244 (t70) REVERT: M 95 LEU cc_start: 0.7746 (mp) cc_final: 0.6483 (tp) outliers start: 1 outliers final: 0 residues processed: 237 average time/residue: 0.1860 time to fit residues: 73.8506 Evaluate side-chains 193 residues out of total 3423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 255 optimal weight: 1.9990 chunk 356 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 285 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 34 optimal weight: 50.0000 chunk 40 optimal weight: 10.0000 chunk 35 optimal weight: 50.0000 chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 245 optimal weight: 0.0870 overall best weight: 1.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 GLN ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 846 ASN ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1024 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1127 ASN ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS ** N 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 78 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.152839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.127740 restraints weight = 99368.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.125851 restraints weight = 111526.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.126362 restraints weight = 104616.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.126357 restraints weight = 83936.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.126798 restraints weight = 69221.588| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31777 Z= 0.128 Angle : 0.665 10.858 42961 Z= 0.337 Chirality : 0.044 0.188 4740 Planarity : 0.005 0.093 5573 Dihedral : 5.599 41.365 4280 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.82 % Favored : 92.15 % Rotamer: Outliers : 0.06 % Allowed : 0.82 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.13), residues: 3886 helix: -0.25 (0.15), residues: 1215 sheet: -1.50 (0.24), residues: 493 loop : -2.19 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 436 TYR 0.019 0.001 TYR H 90 PHE 0.024 0.001 PHE A1089 TRP 0.029 0.002 TRP B 494 HIS 0.010 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00292 (31775) covalent geometry : angle 0.66428 (42957) SS BOND : bond 0.00524 ( 2) SS BOND : angle 3.97866 ( 4) hydrogen bonds : bond 0.04082 ( 935) hydrogen bonds : angle 5.00398 ( 2643) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7772 Ramachandran restraints generated. 3886 Oldfield, 0 Emsley, 3886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7772 Ramachandran restraints generated. 3886 Oldfield, 0 Emsley, 3886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 246 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 MET cc_start: -0.5374 (mtp) cc_final: -0.5771 (mtp) REVERT: A 641 MET cc_start: 0.8291 (mtm) cc_final: 0.7833 (mtm) REVERT: A 822 CYS cc_start: 0.7344 (t) cc_final: 0.6897 (m) REVERT: A 860 MET cc_start: 0.7783 (tmm) cc_final: 0.7457 (tmm) REVERT: A 1253 MET cc_start: 0.7408 (ptp) cc_final: 0.6559 (ptm) REVERT: A 1263 MET cc_start: 0.6649 (ttt) cc_final: 0.6254 (ttm) REVERT: A 1305 MET cc_start: 0.3515 (mpp) cc_final: 0.2575 (ptp) REVERT: A 1342 MET cc_start: 0.8756 (tmm) cc_final: 0.8430 (tmm) REVERT: A 1498 MET cc_start: 0.6350 (mtt) cc_final: 0.6124 (mtp) REVERT: B 600 MET cc_start: 0.6196 (mtp) cc_final: 0.5679 (mtp) REVERT: B 691 MET cc_start: 0.7081 (mtm) cc_final: 0.6738 (mtm) REVERT: B 753 MET cc_start: 0.2291 (tpt) cc_final: 0.2020 (tpt) REVERT: H 37 MET cc_start: 0.7869 (mmp) cc_final: 0.7421 (mmp) REVERT: J 1 MET cc_start: 0.8560 (ttt) cc_final: 0.8134 (ttp) REVERT: N 39 MET cc_start: 0.2000 (mtm) cc_final: 0.1304 (ttm) REVERT: N 98 GLN cc_start: 0.7523 (tt0) cc_final: 0.7234 (pp30) REVERT: M 55 CYS cc_start: 0.6214 (p) cc_final: 0.5952 (p) REVERT: M 60 HIS cc_start: 0.4980 (m-70) cc_final: 0.3976 (t70) REVERT: M 95 LEU cc_start: 0.7477 (mp) cc_final: 0.6244 (tp) outliers start: 2 outliers final: 1 residues processed: 248 average time/residue: 0.1859 time to fit residues: 77.9495 Evaluate side-chains 198 residues out of total 3423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 227 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 217 optimal weight: 0.4980 chunk 242 optimal weight: 6.9990 chunk 6 optimal weight: 50.0000 chunk 312 optimal weight: 8.9990 chunk 228 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 249 optimal weight: 6.9990 chunk 375 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 GLN ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 846 ASN ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 HIS ** B1024 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 78 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.152544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.128316 restraints weight = 99199.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.126801 restraints weight = 120005.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.127549 restraints weight = 97877.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.127825 restraints weight = 68918.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.128153 restraints weight = 62198.942| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 31777 Z= 0.136 Angle : 0.672 13.542 42961 Z= 0.339 Chirality : 0.045 0.206 4740 Planarity : 0.005 0.093 5573 Dihedral : 5.510 43.456 4280 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 0.06 % Allowed : 0.38 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.13), residues: 3886 helix: -0.16 (0.15), residues: 1209 sheet: -1.42 (0.23), residues: 497 loop : -2.13 (0.13), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 64 TYR 0.038 0.002 TYR A 450 PHE 0.024 0.001 PHE A1089 TRP 0.033 0.001 TRP B 494 HIS 0.009 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00316 (31775) covalent geometry : angle 0.67113 (42957) SS BOND : bond 0.00334 ( 2) SS BOND : angle 3.56860 ( 4) hydrogen bonds : bond 0.04096 ( 935) hydrogen bonds : angle 4.96849 ( 2643) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7772 Ramachandran restraints generated. 3886 Oldfield, 0 Emsley, 3886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7772 Ramachandran restraints generated. 3886 Oldfield, 0 Emsley, 3886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 239 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 MET cc_start: -0.5239 (mtp) cc_final: -0.5669 (mtp) REVERT: A 641 MET cc_start: 0.8416 (mtm) cc_final: 0.8005 (mtm) REVERT: A 822 CYS cc_start: 0.7299 (t) cc_final: 0.6857 (m) REVERT: A 860 MET cc_start: 0.7793 (tmm) cc_final: 0.7469 (tmm) REVERT: A 1253 MET cc_start: 0.7405 (ptp) cc_final: 0.6534 (ptm) REVERT: A 1263 MET cc_start: 0.6483 (ttt) cc_final: 0.6061 (ttm) REVERT: A 1305 MET cc_start: 0.3067 (mpp) cc_final: 0.2016 (ptp) REVERT: A 1351 MET cc_start: 0.7825 (mmp) cc_final: 0.7484 (mmm) REVERT: A 1498 MET cc_start: 0.6385 (mtt) cc_final: 0.6156 (mtp) REVERT: A 1534 MET cc_start: 0.5494 (mpp) cc_final: 0.5198 (mpp) REVERT: B 600 MET cc_start: 0.6123 (mtp) cc_final: 0.5657 (mtp) REVERT: B 691 MET cc_start: 0.7085 (mtm) cc_final: 0.6750 (mtm) REVERT: B 753 MET cc_start: 0.2389 (tpt) cc_final: 0.2083 (tpt) REVERT: E 61 LEU cc_start: 0.7561 (mm) cc_final: 0.7185 (mt) REVERT: J 1 MET cc_start: 0.8546 (ttt) cc_final: 0.8170 (ttp) REVERT: N 39 MET cc_start: 0.2099 (mtm) cc_final: 0.1359 (ttm) REVERT: M 55 CYS cc_start: 0.6164 (p) cc_final: 0.5883 (p) REVERT: M 60 HIS cc_start: 0.4989 (m-70) cc_final: 0.3970 (t70) REVERT: M 95 LEU cc_start: 0.7456 (mp) cc_final: 0.6335 (tp) outliers start: 2 outliers final: 0 residues processed: 241 average time/residue: 0.1877 time to fit residues: 75.7919 Evaluate side-chains 197 residues out of total 3423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 68 optimal weight: 8.9990 chunk 212 optimal weight: 0.3980 chunk 211 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 369 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 278 optimal weight: 3.9990 chunk 200 optimal weight: 0.4980 chunk 242 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 GLN ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 ASN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 HIS B1024 GLN ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS ** N 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.153514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.128552 restraints weight = 99564.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.126282 restraints weight = 113231.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.127193 restraints weight = 91434.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.127450 restraints weight = 67460.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.127671 restraints weight = 64730.046| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31777 Z= 0.123 Angle : 0.652 11.439 42961 Z= 0.329 Chirality : 0.044 0.185 4740 Planarity : 0.005 0.093 5573 Dihedral : 5.386 40.874 4280 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.06 % Allowed : 0.35 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.14), residues: 3886 helix: -0.01 (0.15), residues: 1205 sheet: -1.21 (0.24), residues: 497 loop : -2.03 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 301 TYR 0.044 0.001 TYR A 450 PHE 0.023 0.001 PHE A1089 TRP 0.029 0.002 TRP B 494 HIS 0.009 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00281 (31775) covalent geometry : angle 0.65173 (42957) SS BOND : bond 0.00370 ( 2) SS BOND : angle 3.08533 ( 4) hydrogen bonds : bond 0.03832 ( 935) hydrogen bonds : angle 4.84571 ( 2643) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4210.40 seconds wall clock time: 74 minutes 45.36 seconds (4485.36 seconds total)