Starting phenix.real_space_refine on Fri Jun 27 06:01:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k60_36914/06_2025/8k60_36914.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k60_36914/06_2025/8k60_36914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k60_36914/06_2025/8k60_36914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k60_36914/06_2025/8k60_36914.map" model { file = "/net/cci-nas-00/data/ceres_data/8k60_36914/06_2025/8k60_36914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k60_36914/06_2025/8k60_36914.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 113 5.49 5 Mg 1 5.21 5 S 98 5.16 5 C 19478 2.51 5 N 5666 2.21 5 O 6301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 209 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31659 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1742 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 13, 'TRANS': 212} Chain: "B" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1785 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 219} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 8692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8692 Classifications: {'peptide': 1116} Link IDs: {'PTRANS': 58, 'TRANS': 1057} Chain: "D" Number of atoms: 9812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1259, 9812 Classifications: {'peptide': 1259} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 56, 'TRANS': 1202} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 594 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 72} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2465 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 301} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1148 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "H" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1180 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain: "I" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1904 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 11, 'TRANS': 238} Chain: "J" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1896 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 11, 'TRANS': 237} Chain: "K" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12666 SG CYS D 60 68.579 117.305 60.887 1.00 51.48 S ATOM 12684 SG CYS D 62 69.288 120.672 59.930 1.00 52.09 S ATOM 12793 SG CYS D 75 67.071 118.641 57.198 1.00 57.28 S ATOM 12819 SG CYS D 78 71.063 117.677 58.227 1.00 53.48 S ATOM 19748 SG CYS D 962 72.221 52.024 57.014 1.00 45.14 S ATOM 19796 SG CYS D 969 68.977 50.616 59.275 1.00 40.88 S ATOM 19815 SG CYS D 972 71.840 48.685 58.353 1.00 39.87 S Time building chain proxies: 17.89, per 1000 atoms: 0.57 Number of scatterers: 31659 At special positions: 0 Unit cell: (173.8, 171.6, 152.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 98 16.00 P 113 15.00 Mg 1 11.99 O 6301 8.00 N 5666 7.00 C 19478 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.54 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb=" ZN D1403 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 972 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 969 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 962 " Number of angles added : 6 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6964 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 45 sheets defined 47.8% alpha, 12.7% beta 27 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 11.27 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.984A pdb=" N GLN A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 203 through 225 removed outlier: 3.733A pdb=" N GLU A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 4.069A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 83 removed outlier: 3.578A pdb=" N LEU B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 83 " --> pdb=" O ASN B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 203 through 221 Processing helix chain 'B' and resid 222 through 226 Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.914A pdb=" N SER C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 73 through 81 removed outlier: 3.580A pdb=" N ILE C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE C 78 " --> pdb=" O LEU C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.556A pdb=" N LYS C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 232 through 241 removed outlier: 3.713A pdb=" N GLU C 238 " --> pdb=" O GLU C 234 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU C 239 " --> pdb=" O GLN C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 253 removed outlier: 3.600A pdb=" N ARG C 247 " --> pdb=" O TYR C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'C' and resid 276 through 288 removed outlier: 3.601A pdb=" N LEU C 284 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 309 Processing helix chain 'C' and resid 320 through 336 removed outlier: 3.531A pdb=" N ILE C 325 " --> pdb=" O THR C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 391 removed outlier: 3.549A pdb=" N VAL C 386 " --> pdb=" O MET C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 404 removed outlier: 4.277A pdb=" N ILE C 404 " --> pdb=" O PRO C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 418 removed outlier: 3.885A pdb=" N PHE C 417 " --> pdb=" O ILE C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 439 removed outlier: 3.515A pdb=" N LYS C 438 " --> pdb=" O GLY C 434 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG C 439 " --> pdb=" O LEU C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 460 removed outlier: 3.891A pdb=" N ARG C 459 " --> pdb=" O GLY C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 466 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.637A pdb=" N ARG C 524 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 525' Processing helix chain 'C' and resid 549 through 553 removed outlier: 3.711A pdb=" N GLU C 553 " --> pdb=" O ARG C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 579 Processing helix chain 'C' and resid 582 through 586 Processing helix chain 'C' and resid 587 through 598 removed outlier: 3.532A pdb=" N MET C 593 " --> pdb=" O ASN C 589 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET C 598 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 624 removed outlier: 4.621A pdb=" N ARG C 619 " --> pdb=" O GLY C 615 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 624 " --> pdb=" O SER C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 730 Processing helix chain 'C' and resid 801 through 812 removed outlier: 3.551A pdb=" N GLY C 812 " --> pdb=" O ARG C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 912 removed outlier: 4.548A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 928 Processing helix chain 'C' and resid 937 through 947 removed outlier: 4.082A pdb=" N ARG C 942 " --> pdb=" O GLU C 938 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU C 943 " --> pdb=" O TRP C 939 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL C 945 " --> pdb=" O GLN C 941 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE C 946 " --> pdb=" O ARG C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 976 removed outlier: 3.732A pdb=" N HIS C 976 " --> pdb=" O GLY C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1026 removed outlier: 3.599A pdb=" N LYS C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1054 through 1065 removed outlier: 3.536A pdb=" N TRP C1059 " --> pdb=" O GLU C1055 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C1060 " --> pdb=" O MET C1056 " (cutoff:3.500A) Processing helix chain 'C' and resid 1066 through 1075 removed outlier: 3.591A pdb=" N LEU C1070 " --> pdb=" O ALA C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1080 through 1094 removed outlier: 4.077A pdb=" N VAL C1085 " --> pdb=" O VAL C1081 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS C1086 " --> pdb=" O THR C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1103 through 1115 removed outlier: 3.663A pdb=" N LYS C1107 " --> pdb=" O PRO C1103 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.633A pdb=" N TYR D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 147 through 188 removed outlier: 3.943A pdb=" N ILE D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU D 163 " --> pdb=" O ARG D 159 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 227 Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 283 Processing helix chain 'D' and resid 286 through 305 removed outlier: 4.000A pdb=" N THR D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 303 " --> pdb=" O VAL D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.835A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 338 through 360 removed outlier: 4.203A pdb=" N ASP D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 removed outlier: 3.700A pdb=" N VAL D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 407 removed outlier: 3.688A pdb=" N LYS D 407 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 417 removed outlier: 3.734A pdb=" N LEU D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 480 through 492 removed outlier: 4.217A pdb=" N TYR D 484 " --> pdb=" O ARG D 480 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP D 485 " --> pdb=" O THR D 481 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 580 through 589 Processing helix chain 'D' and resid 606 through 616 Processing helix chain 'D' and resid 636 through 640 removed outlier: 3.561A pdb=" N GLU D 640 " --> pdb=" O ARG D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 672 removed outlier: 3.561A pdb=" N GLU D 670 " --> pdb=" O ALA D 666 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU D 671 " --> pdb=" O LEU D 667 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU D 672 " --> pdb=" O PHE D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 699 Processing helix chain 'D' and resid 700 through 723 removed outlier: 3.627A pdb=" N ASP D 709 " --> pdb=" O ALA D 705 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG D 721 " --> pdb=" O PHE D 717 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY D 723 " --> pdb=" O ALA D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 757 removed outlier: 3.704A pdb=" N LYS D 750 " --> pdb=" O GLY D 746 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL D 751 " --> pdb=" O GLN D 747 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG D 757 " --> pdb=" O LYS D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 788 removed outlier: 3.521A pdb=" N ASN D 778 " --> pdb=" O THR D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 800 removed outlier: 3.836A pdb=" N VAL D 798 " --> pdb=" O VAL D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 805 through 814 removed outlier: 3.592A pdb=" N ILE D 812 " --> pdb=" O GLN D 808 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA D 813 " --> pdb=" O MET D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 877 removed outlier: 3.911A pdb=" N HIS D 849 " --> pdb=" O PHE D 845 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY D 850 " --> pdb=" O ILE D 846 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS D 853 " --> pdb=" O HIS D 849 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP D 874 " --> pdb=" O ARG D 870 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 915 Processing helix chain 'D' and resid 939 through 950 Processing helix chain 'D' and resid 958 through 962 removed outlier: 3.557A pdb=" N CYS D 962 " --> pdb=" O ILE D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 969 through 974 removed outlier: 3.518A pdb=" N TYR D 973 " --> pdb=" O CYS D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 988 through 999 removed outlier: 3.509A pdb=" N ILE D 992 " --> pdb=" O ALA D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1005 removed outlier: 4.475A pdb=" N THR D1005 " --> pdb=" O GLY D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1022 through 1031 Processing helix chain 'D' and resid 1100 through 1107 removed outlier: 3.604A pdb=" N VAL D1104 " --> pdb=" O ASN D1100 " (cutoff:3.500A) Processing helix chain 'D' and resid 1109 through 1129 removed outlier: 3.834A pdb=" N VAL D1124 " --> pdb=" O GLU D1120 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR D1125 " --> pdb=" O VAL D1121 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN D1128 " --> pdb=" O VAL D1124 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1145 removed outlier: 3.899A pdb=" N ILE D1137 " --> pdb=" O HIS D1133 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE D1140 " --> pdb=" O HIS D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1166 through 1180 Processing helix chain 'D' and resid 1192 through 1199 Processing helix chain 'D' and resid 1202 through 1208 Processing helix chain 'D' and resid 1213 through 1223 Processing helix chain 'D' and resid 1232 through 1237 removed outlier: 3.655A pdb=" N ILE D1237 " --> pdb=" O GLU D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1243 through 1246 removed outlier: 3.882A pdb=" N GLY D1246 " --> pdb=" O ALA D1243 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1243 through 1246' Processing helix chain 'D' and resid 1247 through 1252 Processing helix chain 'D' and resid 1258 through 1265 removed outlier: 3.565A pdb=" N MET D1265 " --> pdb=" O ALA D1261 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 24 removed outlier: 3.697A pdb=" N ALA E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR E 23 " --> pdb=" O LEU E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 45 removed outlier: 3.621A pdb=" N VAL E 30 " --> pdb=" O LYS E 26 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE E 31 " --> pdb=" O TYR E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 78 Processing helix chain 'F' and resid 198 through 208 removed outlier: 4.308A pdb=" N ALA F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA F 208 " --> pdb=" O GLN F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 223 removed outlier: 3.643A pdb=" N GLY F 223 " --> pdb=" O LEU F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 252 Processing helix chain 'F' and resid 257 through 282 Processing helix chain 'F' and resid 282 through 292 removed outlier: 3.745A pdb=" N VAL F 286 " --> pdb=" O ASN F 282 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL F 287 " --> pdb=" O LEU F 283 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG F 292 " --> pdb=" O SER F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 317 removed outlier: 3.516A pdb=" N GLY F 310 " --> pdb=" O GLU F 306 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU F 316 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS F 317 " --> pdb=" O ARG F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 346 removed outlier: 3.798A pdb=" N TYR F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TRP F 332 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TRP F 333 " --> pdb=" O TYR F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 374 Processing helix chain 'F' and resid 378 through 387 removed outlier: 3.608A pdb=" N GLU F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 400 Processing helix chain 'F' and resid 417 through 421 Processing helix chain 'F' and resid 429 through 450 removed outlier: 3.553A pdb=" N THR F 437 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU F 450 " --> pdb=" O VAL F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 463 removed outlier: 3.509A pdb=" N VAL F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 479 removed outlier: 3.776A pdb=" N GLY F 476 " --> pdb=" O LEU F 472 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS F 477 " --> pdb=" O ASP F 473 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL F 478 " --> pdb=" O GLU F 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 499 Processing helix chain 'F' and resid 503 through 510 removed outlier: 4.432A pdb=" N ASP F 508 " --> pdb=" O GLN F 504 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR F 509 " --> pdb=" O VAL F 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 58 Processing helix chain 'I' and resid 65 through 75 Processing helix chain 'I' and resid 81 through 97 removed outlier: 3.542A pdb=" N VAL I 96 " --> pdb=" O ARG I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 137 Processing helix chain 'I' and resid 139 through 152 Processing helix chain 'I' and resid 164 through 192 Processing helix chain 'I' and resid 194 through 209 removed outlier: 3.664A pdb=" N ALA I 198 " --> pdb=" O CYS I 194 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER I 200 " --> pdb=" O ALA I 196 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU I 201 " --> pdb=" O GLU I 197 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA I 204 " --> pdb=" O SER I 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 212 through 226 removed outlier: 3.660A pdb=" N ARG I 216 " --> pdb=" O ARG I 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 247 Processing helix chain 'I' and resid 252 through 264 Processing helix chain 'I' and resid 266 through 270 removed outlier: 3.528A pdb=" N LEU I 269 " --> pdb=" O ASP I 266 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 58 Processing helix chain 'J' and resid 66 through 75 Processing helix chain 'J' and resid 81 through 97 Processing helix chain 'J' and resid 119 through 137 Processing helix chain 'J' and resid 139 through 153 removed outlier: 3.560A pdb=" N LEU J 153 " --> pdb=" O ARG J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 193 removed outlier: 3.542A pdb=" N MET J 188 " --> pdb=" O THR J 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 209 removed outlier: 4.033A pdb=" N SER J 200 " --> pdb=" O ALA J 196 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU J 201 " --> pdb=" O GLU J 197 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA J 204 " --> pdb=" O SER J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 226 removed outlier: 3.835A pdb=" N ARG J 216 " --> pdb=" O ARG J 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 246 removed outlier: 3.570A pdb=" N LEU J 233 " --> pdb=" O GLN J 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 265 Processing helix chain 'J' and resid 266 through 270 Processing helix chain 'K' and resid 250 through 255 Processing helix chain 'K' and resid 257 through 267 Processing helix chain 'K' and resid 271 through 278 Processing helix chain 'K' and resid 279 through 286 Processing helix chain 'K' and resid 290 through 304 removed outlier: 4.013A pdb=" N MET K 304 " --> pdb=" O LYS K 300 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 15 removed outlier: 6.382A pdb=" N ARG A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.782A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.730A pdb=" N ALA A 126 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 13 removed outlier: 3.713A pdb=" N LEU B 192 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR B 187 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ARG B 182 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N PHE B 189 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA B 180 " --> pdb=" O PHE B 189 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LYS B 191 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL B 178 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE B 193 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR B 176 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 99 removed outlier: 7.941A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.563A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.714A pdb=" N VAL B 147 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 166 " --> pdb=" O VAL B 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.506A pdb=" N ILE C 23 " --> pdb=" O ALA C 958 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 100 removed outlier: 6.579A pdb=" N THR C 124 " --> pdb=" O ARG C 96 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N HIS C 98 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N PHE C 122 " --> pdb=" O HIS C 98 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE C 100 " --> pdb=" O PRO C 120 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY C 143 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL C 123 " --> pdb=" O PHE C 141 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N PHE C 141 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA C 125 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N THR C 139 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE C 127 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N SER C 137 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ASN C 129 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE C 135 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB5, first strand: chain 'C' and resid 362 through 364 removed outlier: 6.218A pdb=" N SER C 165 " --> pdb=" O ASN C 442 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY C 484 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 172 through 180 removed outlier: 3.712A pdb=" N LYS C 185 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE C 188 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 200 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN C 220 " --> pdb=" O VAL C 212 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 340 through 342 Processing sheet with id=AB8, first strand: chain 'C' and resid 491 through 492 removed outlier: 5.546A pdb=" N ASP C 513 " --> pdb=" O LYS C 504 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL C 506 " --> pdb=" O THR C 511 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR C 511 " --> pdb=" O VAL C 506 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 491 through 492 Processing sheet with id=AC1, first strand: chain 'C' and resid 628 through 629 removed outlier: 6.740A pdb=" N VAL C 628 " --> pdb=" O LEU C 688 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 634 through 639 removed outlier: 6.551A pdb=" N THR C 645 " --> pdb=" O GLN C 637 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL C 639 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N TYR C 643 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 694 through 695 Processing sheet with id=AC4, first strand: chain 'C' and resid 992 through 993 removed outlier: 7.200A pdb=" N ILE C 721 " --> pdb=" O SER C 882 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE C 884 " --> pdb=" O ILE C 721 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU C 723 " --> pdb=" O ILE C 884 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE C 722 " --> pdb=" O ILE C 902 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ILE C 901 " --> pdb=" O ASN C 704 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU C 706 " --> pdb=" O ILE C 901 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU C 903 " --> pdb=" O LEU C 706 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA C 708 " --> pdb=" O LEU C 903 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER C1009 " --> pdb=" O PHE C 709 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 734 through 746 removed outlier: 3.542A pdb=" N GLN C 853 " --> pdb=" O ALA C 745 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY C 835 " --> pdb=" O TYR C 858 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA C 860 " --> pdb=" O VAL C 833 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL C 833 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N LYS C 862 " --> pdb=" O GLY C 831 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N GLY C 831 " --> pdb=" O LYS C 862 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY C 831 " --> pdb=" O VAL C 782 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 754 through 755 removed outlier: 3.516A pdb=" N GLU C 754 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 787 through 789 removed outlier: 7.045A pdb=" N LEU C 823 " --> pdb=" O LEU C 788 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1027 through 1029 removed outlier: 3.640A pdb=" N SER D 428 " --> pdb=" O MET D 541 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1027 through 1029 removed outlier: 7.558A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ILE D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL D 431 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1052 through 1053 Processing sheet with id=AD2, first strand: chain 'C' and resid 1121 through 1123 Processing sheet with id=AD3, first strand: chain 'D' and resid 94 through 102 removed outlier: 7.033A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 10.848A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.466A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 234 through 235 removed outlier: 5.410A pdb=" N ILE D 136 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 328 through 329 removed outlier: 6.312A pdb=" N PHE D 335 " --> pdb=" O ILE F 404 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 443 through 444 removed outlier: 5.644A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 566 through 567 removed outlier: 3.829A pdb=" N ARG D 572 " --> pdb=" O LYS D 567 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 603 through 604 Processing sheet with id=AD9, first strand: chain 'D' and resid 820 through 821 Processing sheet with id=AE1, first strand: chain 'D' and resid 892 through 894 Processing sheet with id=AE2, first strand: chain 'D' and resid 1038 through 1039 Processing sheet with id=AE3, first strand: chain 'D' and resid 1070 through 1073 removed outlier: 4.038A pdb=" N THR D1070 " --> pdb=" O VAL D1061 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL D1061 " --> pdb=" O THR D1070 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY D1046 " --> pdb=" O VAL D1088 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP D1086 " --> pdb=" O VAL D1048 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1163 through 1165 Processing sheet with id=AE5, first strand: chain 'D' and resid 1254 through 1256 Processing sheet with id=AE6, first strand: chain 'I' and resid 25 through 28 removed outlier: 4.676A pdb=" N ALA I 35 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 102 through 105 Processing sheet with id=AE8, first strand: chain 'J' and resid 25 through 28 removed outlier: 4.700A pdb=" N ALA J 35 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 64 through 65 1371 hydrogen bonds defined for protein. 3906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 67 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 14.77 Time building geometry restraints manager: 9.07 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: 8450 1.33 - 1.45: 6226 1.45 - 1.58: 17328 1.58 - 1.70: 222 1.70 - 1.82: 176 Bond restraints: 32402 Sorted by residual: bond pdb=" C GLU B 24 " pdb=" N PRO B 25 " ideal model delta sigma weight residual 1.334 1.418 -0.084 2.34e-02 1.83e+03 1.30e+01 bond pdb=" O3' DT H 37 " pdb=" P DA H 38 " ideal model delta sigma weight residual 1.607 1.660 -0.053 1.50e-02 4.44e+03 1.24e+01 bond pdb=" O3' DA H 36 " pdb=" P DT H 37 " ideal model delta sigma weight residual 1.607 1.556 0.051 1.50e-02 4.44e+03 1.15e+01 bond pdb=" CB THR D 575 " pdb=" CG2 THR D 575 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.92e+00 bond pdb=" C MET D 576 " pdb=" N PRO D 577 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.44e+00 ... (remaining 32397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 42616 2.52 - 5.04: 1524 5.04 - 7.56: 159 7.56 - 10.08: 35 10.08 - 12.60: 3 Bond angle restraints: 44337 Sorted by residual: angle pdb=" N GLU A 24 " pdb=" CA GLU A 24 " pdb=" C GLU A 24 " ideal model delta sigma weight residual 109.81 122.41 -12.60 2.21e+00 2.05e-01 3.25e+01 angle pdb=" N PHE D 107 " pdb=" CA PHE D 107 " pdb=" C PHE D 107 " ideal model delta sigma weight residual 109.95 103.08 6.87 1.44e+00 4.82e-01 2.28e+01 angle pdb=" CA ARG C 216 " pdb=" CB ARG C 216 " pdb=" CG ARG C 216 " ideal model delta sigma weight residual 114.10 122.99 -8.89 2.00e+00 2.50e-01 1.98e+01 angle pdb=" CA TYR E 32 " pdb=" CB TYR E 32 " pdb=" CG TYR E 32 " ideal model delta sigma weight residual 113.90 121.55 -7.65 1.80e+00 3.09e-01 1.80e+01 angle pdb=" C SER D 592 " pdb=" N GLU D 593 " pdb=" CA GLU D 593 " ideal model delta sigma weight residual 121.54 129.60 -8.06 1.91e+00 2.74e-01 1.78e+01 ... (remaining 44332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 18590 35.94 - 71.88: 921 71.88 - 107.82: 48 107.82 - 143.75: 3 143.75 - 179.69: 6 Dihedral angle restraints: 19568 sinusoidal: 8750 harmonic: 10818 Sorted by residual: dihedral pdb=" CA ASP D 748 " pdb=" C ASP D 748 " pdb=" N GLU D 749 " pdb=" CA GLU D 749 " ideal model delta harmonic sigma weight residual -180.00 -156.90 -23.10 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA PRO D 577 " pdb=" C PRO D 577 " pdb=" N THR D 578 " pdb=" CA THR D 578 " ideal model delta harmonic sigma weight residual 180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA GLU D 682 " pdb=" C GLU D 682 " pdb=" N VAL D 683 " pdb=" CA VAL D 683 " ideal model delta harmonic sigma weight residual -180.00 -158.00 -22.00 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 19565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3821 0.071 - 0.142: 985 0.142 - 0.213: 207 0.213 - 0.284: 30 0.284 - 0.355: 7 Chirality restraints: 5050 Sorted by residual: chirality pdb=" CB VAL C 792 " pdb=" CA VAL C 792 " pdb=" CG1 VAL C 792 " pdb=" CG2 VAL C 792 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CA GLU A 24 " pdb=" N GLU A 24 " pdb=" C GLU A 24 " pdb=" CB GLU A 24 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CB ILE A 193 " pdb=" CA ILE A 193 " pdb=" CG1 ILE A 193 " pdb=" CG2 ILE A 193 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 5047 not shown) Planarity restraints: 5436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 110 " 0.075 5.00e-02 4.00e+02 1.14e-01 2.10e+01 pdb=" N PRO D 111 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO D 111 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO D 111 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET C 579 " -0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C MET C 579 " 0.065 2.00e-02 2.50e+03 pdb=" O MET C 579 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE C 580 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 225 " 0.058 5.00e-02 4.00e+02 8.73e-02 1.22e+01 pdb=" N PRO F 226 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO F 226 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO F 226 " 0.048 5.00e-02 4.00e+02 ... (remaining 5433 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4150 2.76 - 3.29: 30547 3.29 - 3.83: 51985 3.83 - 4.36: 60148 4.36 - 4.90: 102452 Nonbonded interactions: 249282 Sorted by model distance: nonbonded pdb=" OG SER D1202 " pdb=" OE1 GLU D1233 " model vdw 2.223 3.040 nonbonded pdb=" N2 DG G 16 " pdb=" O2 DC H 41 " model vdw 2.257 3.120 nonbonded pdb=" OG1 THR F 389 " pdb=" OE1 GLU F 391 " model vdw 2.257 3.040 nonbonded pdb=" O LEU F 285 " pdb=" OG SER F 288 " model vdw 2.268 3.040 nonbonded pdb=" OG SER D1153 " pdb=" O LEU D1158 " model vdw 2.277 3.040 ... (remaining 249277 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB )) or resid 27 through 152 or (resid 153 and (name N or na \ me CA or name C or name O or name CB )) or resid 154 through 227)) selection = (chain 'B' and resid 2 through 227) } ncs_group { reference = (chain 'I' and resid 23 through 271) selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.030 Extract box with map and model: 1.220 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 85.090 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.140 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 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 : 0.009 0.123 32409 Z= 0.384 Angle : 1.103 14.799 44343 Z= 0.627 Chirality : 0.068 0.355 5050 Planarity : 0.009 0.114 5436 Dihedral : 18.954 179.693 12604 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.02 % Allowed : 13.32 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.13), residues: 3764 helix: 0.66 (0.12), residues: 1542 sheet: -1.10 (0.26), residues: 361 loop : -0.68 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 773 HIS 0.018 0.003 HIS D1010 PHE 0.035 0.004 PHE C 709 TYR 0.031 0.003 TYR D 106 ARG 0.014 0.001 ARG D 113 Details of bonding type rmsd hydrogen bonds : bond 0.26644 ( 1432) hydrogen bonds : angle 7.22214 ( 4028) metal coordination : bond 0.10787 ( 7) metal coordination : angle 10.51659 ( 6) covalent geometry : bond 0.00915 (32402) covalent geometry : angle 1.09634 (44337) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 571 time to evaluate : 3.201 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 82 GLN cc_start: 0.7136 (pt0) cc_final: 0.6913 (pt0) REVERT: B 13 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8370 (m) REVERT: C 281 GLN cc_start: 0.7439 (tp40) cc_final: 0.6963 (mt0) REVERT: C 359 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8943 (m-10) REVERT: C 366 ASN cc_start: 0.7308 (OUTLIER) cc_final: 0.6864 (p0) REVERT: C 642 ASP cc_start: 0.7652 (t70) cc_final: 0.7262 (t0) REVERT: C 725 GLN cc_start: 0.8318 (tt0) cc_final: 0.7913 (tt0) REVERT: C 781 GLU cc_start: 0.8214 (tm-30) cc_final: 0.8002 (tm-30) REVERT: C 1056 MET cc_start: 0.8711 (mtt) cc_final: 0.8332 (mtp) REVERT: C 1104 GLU cc_start: 0.7750 (tp30) cc_final: 0.7529 (tp30) REVERT: D 8 ASP cc_start: 0.7923 (t0) cc_final: 0.7631 (t0) REVERT: D 581 MET cc_start: 0.8692 (mtm) cc_final: 0.8472 (mtt) REVERT: D 971 MET cc_start: 0.7303 (mmt) cc_final: 0.6884 (mmt) REVERT: D 1210 GLN cc_start: 0.8017 (mt0) cc_final: 0.7741 (pt0) REVERT: E 41 ASN cc_start: 0.8724 (t0) cc_final: 0.8508 (t0) REVERT: F 241 GLU cc_start: 0.6732 (mp0) cc_final: 0.6482 (mp0) REVERT: F 296 ARG cc_start: 0.5840 (mmm-85) cc_final: 0.5554 (tpp80) REVERT: F 404 ILE cc_start: 0.8591 (pt) cc_final: 0.8355 (pt) REVERT: F 508 ASP cc_start: 0.7237 (p0) cc_final: 0.6779 (p0) REVERT: I 62 ARG cc_start: 0.6970 (mtm180) cc_final: 0.6726 (mtp180) REVERT: I 209 HIS cc_start: 0.8382 (m-70) cc_final: 0.7799 (m90) REVERT: I 241 ARG cc_start: 0.7769 (ttp80) cc_final: 0.7225 (ttp-110) REVERT: I 261 ARG cc_start: 0.6567 (mtp180) cc_final: 0.6304 (ttm170) REVERT: J 236 TYR cc_start: 0.4499 (t80) cc_final: 0.4235 (t80) outliers start: 32 outliers final: 14 residues processed: 599 average time/residue: 0.5492 time to fit residues: 486.0216 Evaluate side-chains 378 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 361 time to evaluate : 3.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 366 ASN Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1126 ASP Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 443 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 323 optimal weight: 10.0000 chunk 290 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 182 optimal weight: 6.9990 chunk 223 optimal weight: 6.9990 chunk 347 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN A 226 ASN B 5 GLN B 226 ASN C 157 ASN C 235 GLN C 258 GLN C 358 HIS C 509 GLN C 600 GLN C 686 GLN C 729 GLN C 852 ASN C 861 GLN D 232 GLN D 396 ASN D 440 GLN D 494 HIS D 669 ASN D 799 ASN D 935 ASN ** D1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 276 ASN F 282 ASN F 368 GLN F 371 GLN I 170 GLN J 192 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.146150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.107469 restraints weight = 54795.434| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.40 r_work: 0.3207 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32409 Z= 0.174 Angle : 0.638 12.627 44343 Z= 0.347 Chirality : 0.043 0.157 5050 Planarity : 0.006 0.073 5436 Dihedral : 17.709 179.930 5403 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.59 % Allowed : 17.73 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.13), residues: 3764 helix: 1.28 (0.12), residues: 1594 sheet: -0.66 (0.27), residues: 352 loop : -0.49 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 718 HIS 0.005 0.001 HIS D 505 PHE 0.021 0.002 PHE D 226 TYR 0.023 0.001 TYR E 32 ARG 0.009 0.001 ARG D 906 Details of bonding type rmsd hydrogen bonds : bond 0.06330 ( 1432) hydrogen bonds : angle 4.85192 ( 4028) metal coordination : bond 0.00532 ( 7) metal coordination : angle 3.18874 ( 6) covalent geometry : bond 0.00380 (32402) covalent geometry : angle 0.63687 (44337) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 423 time to evaluate : 3.120 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 6 ARG cc_start: 0.6885 (mpt180) cc_final: 0.6577 (mmt-90) REVERT: A 82 GLN cc_start: 0.8002 (pt0) cc_final: 0.7740 (pt0) REVERT: B 82 GLN cc_start: 0.8802 (tp40) cc_final: 0.8343 (tt0) REVERT: B 203 ARG cc_start: 0.7751 (ptt-90) cc_final: 0.7379 (ptt-90) REVERT: C 109 GLU cc_start: 0.7790 (tp30) cc_final: 0.7243 (tp30) REVERT: C 642 ASP cc_start: 0.8208 (t70) cc_final: 0.7786 (t0) REVERT: C 739 GLU cc_start: 0.7181 (mp0) cc_final: 0.6874 (mp0) REVERT: C 781 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8518 (tm-30) REVERT: C 986 MET cc_start: 0.8261 (mtm) cc_final: 0.8033 (mtm) REVERT: D 7 PHE cc_start: 0.7819 (m-80) cc_final: 0.7516 (m-80) REVERT: D 126 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8149 (mm-30) REVERT: D 135 MET cc_start: 0.8152 (ttm) cc_final: 0.7883 (ttt) REVERT: D 389 ARG cc_start: 0.7702 (mtp85) cc_final: 0.7424 (mtt90) REVERT: D 919 MET cc_start: 0.6997 (ptm) cc_final: 0.6591 (ptp) REVERT: D 971 MET cc_start: 0.8242 (mmt) cc_final: 0.7890 (mmt) REVERT: D 1254 ARG cc_start: 0.8212 (mmt180) cc_final: 0.7995 (mpt-90) REVERT: E 41 ASN cc_start: 0.8742 (t0) cc_final: 0.8438 (t0) REVERT: F 293 TYR cc_start: 0.8864 (m-80) cc_final: 0.7933 (m-80) REVERT: F 296 ARG cc_start: 0.6528 (mmm-85) cc_final: 0.5982 (tpp80) REVERT: I 209 HIS cc_start: 0.7974 (m-70) cc_final: 0.7613 (m90) REVERT: I 241 ARG cc_start: 0.7864 (ttp80) cc_final: 0.7350 (ttp-110) REVERT: I 257 GLU cc_start: 0.7327 (tp30) cc_final: 0.7084 (pt0) REVERT: J 148 ARG cc_start: 0.7426 (mtt90) cc_final: 0.7159 (mtm180) REVERT: J 236 TYR cc_start: 0.4608 (t80) cc_final: 0.4401 (t80) REVERT: K 300 LYS cc_start: 0.7850 (mmtt) cc_final: 0.7375 (tptp) REVERT: K 304 MET cc_start: 0.5211 (tmm) cc_final: 0.4849 (tmm) outliers start: 81 outliers final: 37 residues processed: 489 average time/residue: 0.5670 time to fit residues: 436.9151 Evaluate side-chains 399 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 361 time to evaluate : 5.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 366 ASN Chi-restraints excluded: chain C residue 509 GLN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 935 ASN Chi-restraints excluded: chain D residue 944 ASP Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 405 SER Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain K residue 295 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 200 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 162 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 chunk 248 optimal weight: 0.8980 chunk 367 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN C 258 GLN C 428 GLN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 GLN C 729 GLN ** D1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1210 GLN E 64 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.144128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.106002 restraints weight = 55050.977| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.30 r_work: 0.3184 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32409 Z= 0.184 Angle : 0.609 8.966 44343 Z= 0.328 Chirality : 0.042 0.166 5050 Planarity : 0.005 0.056 5436 Dihedral : 17.589 179.573 5396 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.55 % Allowed : 19.91 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.13), residues: 3764 helix: 1.44 (0.13), residues: 1598 sheet: -0.50 (0.26), residues: 373 loop : -0.50 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 177 HIS 0.007 0.001 HIS E 64 PHE 0.014 0.002 PHE C 127 TYR 0.023 0.002 TYR E 32 ARG 0.012 0.000 ARG D 209 Details of bonding type rmsd hydrogen bonds : bond 0.05766 ( 1432) hydrogen bonds : angle 4.59033 ( 4028) metal coordination : bond 0.00630 ( 7) metal coordination : angle 2.37603 ( 6) covalent geometry : bond 0.00434 (32402) covalent geometry : angle 0.60792 (44337) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 376 time to evaluate : 4.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.7964 (pt0) cc_final: 0.7717 (pt0) REVERT: A 213 LYS cc_start: 0.8674 (tptp) cc_final: 0.8338 (ttpt) REVERT: C 199 TRP cc_start: 0.6097 (OUTLIER) cc_final: 0.4530 (p-90) REVERT: C 246 MET cc_start: 0.7171 (mmm) cc_final: 0.6886 (mmm) REVERT: C 390 MET cc_start: 0.6119 (mmp) cc_final: 0.5699 (mmp) REVERT: C 647 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.8085 (t) REVERT: C 653 TYR cc_start: 0.7221 (m-10) cc_final: 0.6840 (m-10) REVERT: C 744 ASP cc_start: 0.8143 (p0) cc_final: 0.7834 (p0) REVERT: C 969 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8192 (mt-10) REVERT: D 117 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8831 (tt) REVERT: D 389 ARG cc_start: 0.7816 (mtp85) cc_final: 0.7383 (mtt90) REVERT: D 447 MET cc_start: 0.8966 (tpp) cc_final: 0.8438 (ttp) REVERT: D 919 MET cc_start: 0.7057 (ptm) cc_final: 0.6603 (ptp) REVERT: D 971 MET cc_start: 0.8270 (mmt) cc_final: 0.7922 (mmt) REVERT: D 1254 ARG cc_start: 0.8239 (mmt180) cc_final: 0.8031 (mpt-90) REVERT: E 41 ASN cc_start: 0.8714 (t0) cc_final: 0.8421 (t0) REVERT: F 241 GLU cc_start: 0.8373 (tp30) cc_final: 0.8140 (tp30) REVERT: F 293 TYR cc_start: 0.8873 (m-80) cc_final: 0.8148 (m-80) REVERT: F 296 ARG cc_start: 0.6202 (mmm-85) cc_final: 0.5501 (tpp80) REVERT: I 209 HIS cc_start: 0.7910 (m-70) cc_final: 0.7577 (m90) REVERT: I 241 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7404 (ttp-110) REVERT: J 83 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7601 (pp) REVERT: J 147 LEU cc_start: 0.7914 (tt) cc_final: 0.7641 (tt) REVERT: J 177 TRP cc_start: 0.7542 (t-100) cc_final: 0.7281 (t-100) REVERT: J 242 LEU cc_start: 0.4956 (tp) cc_final: 0.4670 (tt) REVERT: K 300 LYS cc_start: 0.7853 (mmtt) cc_final: 0.7629 (mmtt) REVERT: K 304 MET cc_start: 0.5195 (tmm) cc_final: 0.4865 (tmm) outliers start: 111 outliers final: 69 residues processed: 464 average time/residue: 0.5207 time to fit residues: 390.2078 Evaluate side-chains 419 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 345 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 647 THR Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1113 MET Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1082 VAL Chi-restraints excluded: chain D residue 1090 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1123 LYS Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1168 LYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 405 SER Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 195 HIS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 295 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 315 optimal weight: 20.0000 chunk 135 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 24 optimal weight: 8.9990 chunk 240 optimal weight: 6.9990 chunk 298 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 352 optimal weight: 8.9990 chunk 86 optimal weight: 0.2980 chunk 282 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN A 200 GLN D 232 GLN D 416 ASN D 564 ASN D 752 GLN D1210 GLN E 64 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.146651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.109323 restraints weight = 54646.232| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.27 r_work: 0.3234 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32409 Z= 0.121 Angle : 0.536 7.739 44343 Z= 0.289 Chirality : 0.040 0.175 5050 Planarity : 0.004 0.048 5436 Dihedral : 17.369 179.050 5394 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.85 % Allowed : 21.80 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.13), residues: 3764 helix: 1.67 (0.13), residues: 1592 sheet: -0.20 (0.27), residues: 354 loop : -0.46 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 718 HIS 0.009 0.001 HIS E 64 PHE 0.011 0.001 PHE D 226 TYR 0.024 0.001 TYR F 509 ARG 0.030 0.000 ARG J 148 Details of bonding type rmsd hydrogen bonds : bond 0.04734 ( 1432) hydrogen bonds : angle 4.26544 ( 4028) metal coordination : bond 0.00321 ( 7) metal coordination : angle 1.91745 ( 6) covalent geometry : bond 0.00263 (32402) covalent geometry : angle 0.53558 (44337) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 390 time to evaluate : 3.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.7851 (pt0) cc_final: 0.7500 (pt0) REVERT: A 213 LYS cc_start: 0.8664 (tptp) cc_final: 0.8391 (ttpt) REVERT: B 203 ARG cc_start: 0.7431 (ptt-90) cc_final: 0.7158 (ptt-90) REVERT: C 76 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8221 (tt0) REVERT: C 109 GLU cc_start: 0.7578 (tp30) cc_final: 0.7283 (tp30) REVERT: C 199 TRP cc_start: 0.5963 (OUTLIER) cc_final: 0.4466 (p-90) REVERT: C 246 MET cc_start: 0.7363 (mmm) cc_final: 0.7109 (mmm) REVERT: C 390 MET cc_start: 0.5931 (mmp) cc_final: 0.5640 (mmp) REVERT: C 642 ASP cc_start: 0.8485 (t0) cc_final: 0.8243 (t70) REVERT: C 647 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7872 (t) REVERT: C 653 TYR cc_start: 0.7104 (m-10) cc_final: 0.6728 (m-10) REVERT: C 744 ASP cc_start: 0.7964 (p0) cc_final: 0.7691 (p0) REVERT: D 276 ARG cc_start: 0.7783 (mpt180) cc_final: 0.7505 (tpm170) REVERT: D 359 ASP cc_start: 0.7006 (OUTLIER) cc_final: 0.6771 (t0) REVERT: D 389 ARG cc_start: 0.7778 (mtp85) cc_final: 0.7396 (mtt90) REVERT: D 401 SER cc_start: 0.8461 (t) cc_final: 0.8042 (p) REVERT: D 893 LYS cc_start: 0.7822 (tttt) cc_final: 0.7597 (tttm) REVERT: D 919 MET cc_start: 0.6910 (ptm) cc_final: 0.6543 (ptp) REVERT: D 971 MET cc_start: 0.8295 (mmt) cc_final: 0.7962 (mmt) REVERT: D 1170 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7648 (pt0) REVERT: D 1254 ARG cc_start: 0.8250 (mmt180) cc_final: 0.8003 (mpt-90) REVERT: E 41 ASN cc_start: 0.8678 (t0) cc_final: 0.8367 (t0) REVERT: F 232 GLN cc_start: 0.8212 (mm-40) cc_final: 0.8011 (mm-40) REVERT: F 241 GLU cc_start: 0.8334 (tp30) cc_final: 0.8124 (tp30) REVERT: F 293 TYR cc_start: 0.8897 (m-80) cc_final: 0.8092 (m-80) REVERT: F 296 ARG cc_start: 0.6245 (mmm-85) cc_final: 0.5639 (tpp80) REVERT: F 344 ASP cc_start: 0.8241 (m-30) cc_final: 0.7916 (t0) REVERT: I 209 HIS cc_start: 0.7877 (m-70) cc_final: 0.7587 (m90) REVERT: I 241 ARG cc_start: 0.8159 (ttp80) cc_final: 0.7472 (ttp-110) REVERT: J 83 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7536 (pp) REVERT: J 147 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7712 (tt) REVERT: J 177 TRP cc_start: 0.7463 (t-100) cc_final: 0.7029 (t-100) REVERT: J 242 LEU cc_start: 0.4934 (tp) cc_final: 0.4603 (tt) REVERT: K 304 MET cc_start: 0.5148 (tmm) cc_final: 0.4845 (tmm) outliers start: 89 outliers final: 46 residues processed: 461 average time/residue: 0.4439 time to fit residues: 324.5852 Evaluate side-chains 405 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 354 time to evaluate : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 647 THR Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1123 LYS Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1158 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain I residue 195 HIS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain K residue 265 LYS Chi-restraints excluded: chain K residue 295 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 282 optimal weight: 5.9990 chunk 381 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 230 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 111 optimal weight: 0.0870 chunk 380 optimal weight: 40.0000 chunk 338 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 258 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 overall best weight: 3.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 GLN D 622 GLN ** D1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1122 GLN E 64 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.142586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.104024 restraints weight = 55075.593| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.35 r_work: 0.3149 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 32409 Z= 0.206 Angle : 0.615 8.524 44343 Z= 0.328 Chirality : 0.043 0.166 5050 Planarity : 0.005 0.051 5436 Dihedral : 17.357 176.405 5392 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.67 % Allowed : 21.35 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.13), residues: 3764 helix: 1.58 (0.13), residues: 1601 sheet: -0.20 (0.27), residues: 358 loop : -0.53 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 939 HIS 0.008 0.001 HIS D 505 PHE 0.027 0.002 PHE D 639 TYR 0.019 0.002 TYR E 32 ARG 0.004 0.000 ARG D 91 Details of bonding type rmsd hydrogen bonds : bond 0.05176 ( 1432) hydrogen bonds : angle 4.36084 ( 4028) metal coordination : bond 0.00913 ( 7) metal coordination : angle 2.04557 ( 6) covalent geometry : bond 0.00491 (32402) covalent geometry : angle 0.61457 (44337) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 360 time to evaluate : 3.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8057 (pt0) cc_final: 0.7752 (pt0) REVERT: B 55 ARG cc_start: 0.8027 (tpt90) cc_final: 0.7806 (tpt90) REVERT: C 76 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8263 (tt0) REVERT: C 109 GLU cc_start: 0.7300 (tp30) cc_final: 0.6586 (tm-30) REVERT: C 199 TRP cc_start: 0.6134 (OUTLIER) cc_final: 0.4428 (p-90) REVERT: C 214 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7902 (mm) REVERT: C 246 MET cc_start: 0.7341 (mmm) cc_final: 0.7105 (mmm) REVERT: C 340 GLU cc_start: 0.7729 (tp30) cc_final: 0.7350 (tp30) REVERT: C 390 MET cc_start: 0.6144 (mmp) cc_final: 0.5906 (mmp) REVERT: C 527 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8577 (mt) REVERT: C 653 TYR cc_start: 0.7286 (m-10) cc_final: 0.6995 (m-10) REVERT: C 721 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9089 (mt) REVERT: C 744 ASP cc_start: 0.8044 (p0) cc_final: 0.7769 (p0) REVERT: C 830 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8042 (mt) REVERT: C 1095 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7596 (tt0) REVERT: D 272 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7347 (mm-30) REVERT: D 276 ARG cc_start: 0.7797 (mpt180) cc_final: 0.7473 (tpm170) REVERT: D 389 ARG cc_start: 0.7818 (mtp85) cc_final: 0.7390 (mtt90) REVERT: D 401 SER cc_start: 0.8716 (t) cc_final: 0.8331 (p) REVERT: D 919 MET cc_start: 0.7125 (ptm) cc_final: 0.6892 (ptp) REVERT: D 971 MET cc_start: 0.8358 (mmt) cc_final: 0.7996 (mmt) REVERT: D 1170 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7595 (pt0) REVERT: D 1253 ILE cc_start: 0.9088 (pt) cc_final: 0.8683 (pt) REVERT: D 1254 ARG cc_start: 0.8376 (mmt180) cc_final: 0.8144 (mpt-90) REVERT: E 18 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: E 41 ASN cc_start: 0.8784 (t0) cc_final: 0.8451 (t0) REVERT: F 293 TYR cc_start: 0.8963 (m-80) cc_final: 0.8145 (m-80) REVERT: F 296 ARG cc_start: 0.6452 (mmm-85) cc_final: 0.5852 (tpp80) REVERT: F 344 ASP cc_start: 0.8283 (m-30) cc_final: 0.7880 (t0) REVERT: I 209 HIS cc_start: 0.7874 (m-70) cc_final: 0.7563 (m90) REVERT: I 241 ARG cc_start: 0.8206 (ttp80) cc_final: 0.7487 (ttp-110) REVERT: I 258 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6377 (mm) REVERT: J 83 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7634 (pp) REVERT: J 147 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7744 (tt) REVERT: J 148 ARG cc_start: 0.7248 (mtt90) cc_final: 0.6903 (mtm180) outliers start: 146 outliers final: 105 residues processed: 471 average time/residue: 0.4307 time to fit residues: 324.4034 Evaluate side-chains 459 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 344 time to evaluate : 3.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 801 THR Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 882 SER Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1095 GLU Chi-restraints excluded: chain C residue 1113 MET Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 748 ASP Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 806 MET Chi-restraints excluded: chain D residue 821 ASN Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 944 ASP Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1070 THR Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain D residue 1090 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1123 LYS Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1158 LEU Chi-restraints excluded: chain D residue 1168 LYS Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 405 SER Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 195 HIS Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 265 LYS Chi-restraints excluded: chain K residue 295 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 277 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 134 optimal weight: 0.6980 chunk 197 optimal weight: 0.8980 chunk 194 optimal weight: 0.0040 chunk 17 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 overall best weight: 1.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN C 729 GLN D 579 GLN D 622 GLN ** D1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.143764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.105389 restraints weight = 55168.913| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.35 r_work: 0.3174 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32409 Z= 0.145 Angle : 0.553 7.543 44343 Z= 0.297 Chirality : 0.041 0.203 5050 Planarity : 0.004 0.083 5436 Dihedral : 17.294 178.927 5392 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.39 % Allowed : 22.28 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.13), residues: 3764 helix: 1.66 (0.13), residues: 1602 sheet: -0.19 (0.27), residues: 363 loop : -0.48 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 177 HIS 0.005 0.001 HIS C 741 PHE 0.021 0.001 PHE C 811 TYR 0.014 0.001 TYR E 32 ARG 0.007 0.000 ARG D 459 Details of bonding type rmsd hydrogen bonds : bond 0.04679 ( 1432) hydrogen bonds : angle 4.23848 ( 4028) metal coordination : bond 0.00544 ( 7) metal coordination : angle 1.71340 ( 6) covalent geometry : bond 0.00336 (32402) covalent geometry : angle 0.55285 (44337) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 366 time to evaluate : 3.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 LYS cc_start: 0.7608 (tppt) cc_final: 0.7250 (tppt) REVERT: C 76 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8315 (tt0) REVERT: C 199 TRP cc_start: 0.6092 (OUTLIER) cc_final: 0.4397 (p-90) REVERT: C 214 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7796 (mm) REVERT: C 246 MET cc_start: 0.7409 (mmm) cc_final: 0.6976 (mmp) REVERT: C 340 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7289 (tp30) REVERT: C 390 MET cc_start: 0.6123 (mmp) cc_final: 0.5877 (mmp) REVERT: C 527 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8572 (mt) REVERT: C 744 ASP cc_start: 0.8030 (p0) cc_final: 0.7771 (p0) REVERT: C 830 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7861 (mt) REVERT: D 119 ASP cc_start: 0.6984 (m-30) cc_final: 0.6283 (p0) REVERT: D 248 PHE cc_start: 0.6535 (OUTLIER) cc_final: 0.5223 (p90) REVERT: D 276 ARG cc_start: 0.7758 (mpt180) cc_final: 0.7472 (tpm170) REVERT: D 401 SER cc_start: 0.8608 (t) cc_final: 0.8189 (p) REVERT: D 919 MET cc_start: 0.7005 (ptm) cc_final: 0.6684 (ptp) REVERT: D 971 MET cc_start: 0.8319 (mmt) cc_final: 0.7939 (mmt) REVERT: D 1162 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: D 1170 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7603 (pt0) REVERT: E 18 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: E 41 ASN cc_start: 0.8738 (t0) cc_final: 0.8398 (t0) REVERT: F 293 TYR cc_start: 0.8941 (m-80) cc_final: 0.8101 (m-80) REVERT: F 296 ARG cc_start: 0.6383 (mmm-85) cc_final: 0.5781 (tpp80) REVERT: F 344 ASP cc_start: 0.8288 (m-30) cc_final: 0.7888 (t0) REVERT: F 504 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7780 (pt0) REVERT: I 209 HIS cc_start: 0.7821 (m-70) cc_final: 0.7520 (m90) REVERT: I 241 ARG cc_start: 0.8180 (ttp80) cc_final: 0.7440 (ttp-110) REVERT: I 258 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6013 (mm) REVERT: J 83 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7607 (pp) REVERT: J 147 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7709 (tt) REVERT: J 177 TRP cc_start: 0.7492 (t-100) cc_final: 0.6977 (t-100) outliers start: 137 outliers final: 89 residues processed: 476 average time/residue: 0.4348 time to fit residues: 328.7582 Evaluate side-chains 450 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 350 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 801 THR Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 925 LEU Chi-restraints excluded: chain C residue 1036 MET Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 806 MET Chi-restraints excluded: chain D residue 821 ASN Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 944 ASP Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1070 THR Chi-restraints excluded: chain D residue 1082 VAL Chi-restraints excluded: chain D residue 1090 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1158 LEU Chi-restraints excluded: chain D residue 1162 GLU Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 405 SER Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 195 HIS Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 265 LYS Chi-restraints excluded: chain K residue 295 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 272 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 281 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 332 optimal weight: 8.9990 chunk 309 optimal weight: 10.0000 chunk 279 optimal weight: 0.7980 chunk 327 optimal weight: 10.0000 chunk 331 optimal weight: 0.0370 overall best weight: 1.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.144020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.106054 restraints weight = 54930.113| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.32 r_work: 0.3184 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32409 Z= 0.138 Angle : 0.547 10.764 44343 Z= 0.293 Chirality : 0.040 0.205 5050 Planarity : 0.004 0.049 5436 Dihedral : 17.238 179.650 5392 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.16 % Allowed : 22.50 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.14), residues: 3764 helix: 1.73 (0.13), residues: 1599 sheet: -0.04 (0.27), residues: 362 loop : -0.45 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 177 HIS 0.006 0.001 HIS E 64 PHE 0.025 0.001 PHE D 639 TYR 0.020 0.001 TYR J 224 ARG 0.009 0.000 ARG J 144 Details of bonding type rmsd hydrogen bonds : bond 0.04466 ( 1432) hydrogen bonds : angle 4.15160 ( 4028) metal coordination : bond 0.00502 ( 7) metal coordination : angle 1.77983 ( 6) covalent geometry : bond 0.00318 (32402) covalent geometry : angle 0.54670 (44337) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 362 time to evaluate : 3.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 LYS cc_start: 0.7703 (tppt) cc_final: 0.7312 (tppt) REVERT: C 109 GLU cc_start: 0.7457 (tp30) cc_final: 0.7254 (tm-30) REVERT: C 199 TRP cc_start: 0.6036 (OUTLIER) cc_final: 0.4304 (p-90) REVERT: C 246 MET cc_start: 0.7417 (mmm) cc_final: 0.6954 (mmp) REVERT: C 340 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7304 (tp30) REVERT: C 390 MET cc_start: 0.6095 (mmp) cc_final: 0.5850 (mmp) REVERT: C 527 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8568 (mt) REVERT: C 744 ASP cc_start: 0.7962 (p0) cc_final: 0.7692 (p0) REVERT: C 830 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7872 (mt) REVERT: D 119 ASP cc_start: 0.7039 (m-30) cc_final: 0.6354 (p0) REVERT: D 248 PHE cc_start: 0.6508 (OUTLIER) cc_final: 0.5200 (p90) REVERT: D 276 ARG cc_start: 0.7752 (mpt180) cc_final: 0.7466 (tpm170) REVERT: D 389 ARG cc_start: 0.7860 (mtp85) cc_final: 0.7535 (mtt90) REVERT: D 401 SER cc_start: 0.8582 (t) cc_final: 0.8178 (p) REVERT: D 919 MET cc_start: 0.6968 (ptm) cc_final: 0.6651 (ptp) REVERT: D 971 MET cc_start: 0.8312 (mmt) cc_final: 0.7921 (mmt) REVERT: D 1162 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7522 (pm20) REVERT: D 1170 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7617 (pt0) REVERT: D 1175 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7092 (ttp-170) REVERT: E 18 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: E 41 ASN cc_start: 0.8684 (t0) cc_final: 0.8399 (t0) REVERT: F 293 TYR cc_start: 0.8931 (m-80) cc_final: 0.8114 (m-80) REVERT: F 296 ARG cc_start: 0.6398 (mmm-85) cc_final: 0.5793 (tpp80) REVERT: F 344 ASP cc_start: 0.8281 (m-30) cc_final: 0.7880 (t0) REVERT: F 420 ASP cc_start: 0.8058 (t0) cc_final: 0.7729 (t0) REVERT: F 504 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7751 (pt0) REVERT: I 209 HIS cc_start: 0.7807 (m-70) cc_final: 0.7516 (m90) REVERT: I 241 ARG cc_start: 0.8120 (ttp80) cc_final: 0.7391 (ttp-110) REVERT: J 83 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7591 (pp) REVERT: J 147 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7733 (tt) REVERT: J 148 ARG cc_start: 0.7236 (mtt90) cc_final: 0.6925 (mtm180) outliers start: 130 outliers final: 101 residues processed: 464 average time/residue: 0.4511 time to fit residues: 334.0203 Evaluate side-chains 460 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 349 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 882 SER Chi-restraints excluded: chain C residue 925 LEU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1036 MET Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 806 MET Chi-restraints excluded: chain D residue 821 ASN Chi-restraints excluded: chain D residue 926 ILE Chi-restraints excluded: chain D residue 944 ASP Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1070 THR Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain D residue 1082 VAL Chi-restraints excluded: chain D residue 1090 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1123 LYS Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1158 LEU Chi-restraints excluded: chain D residue 1162 GLU Chi-restraints excluded: chain D residue 1175 ARG Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 405 SER Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 141 CYS Chi-restraints excluded: chain I residue 195 HIS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 265 LYS Chi-restraints excluded: chain K residue 295 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 135 optimal weight: 4.9990 chunk 328 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 265 optimal weight: 0.4980 chunk 211 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 214 optimal weight: 0.9990 chunk 316 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 223 optimal weight: 4.9990 chunk 213 optimal weight: 0.7980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 ASN ** J 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.143557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.105491 restraints weight = 55263.132| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.31 r_work: 0.3179 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32409 Z= 0.147 Angle : 0.551 8.312 44343 Z= 0.295 Chirality : 0.041 0.201 5050 Planarity : 0.004 0.047 5436 Dihedral : 17.213 179.273 5392 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.26 % Allowed : 22.79 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.14), residues: 3764 helix: 1.75 (0.13), residues: 1599 sheet: -0.06 (0.27), residues: 376 loop : -0.44 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 177 HIS 0.005 0.001 HIS E 64 PHE 0.011 0.001 PHE D 452 TYR 0.017 0.001 TYR J 224 ARG 0.006 0.000 ARG C 57 Details of bonding type rmsd hydrogen bonds : bond 0.04454 ( 1432) hydrogen bonds : angle 4.11329 ( 4028) metal coordination : bond 0.00584 ( 7) metal coordination : angle 1.61080 ( 6) covalent geometry : bond 0.00346 (32402) covalent geometry : angle 0.55119 (44337) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 367 time to evaluate : 3.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.8130 (ptm160) cc_final: 0.7863 (ptm160) REVERT: C 71 LYS cc_start: 0.7712 (tppt) cc_final: 0.7355 (tppt) REVERT: C 109 GLU cc_start: 0.7495 (tp30) cc_final: 0.7263 (tm-30) REVERT: C 199 TRP cc_start: 0.6041 (OUTLIER) cc_final: 0.4320 (p-90) REVERT: C 340 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7273 (tp30) REVERT: C 390 MET cc_start: 0.6057 (mmp) cc_final: 0.5779 (mmp) REVERT: C 527 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8578 (mt) REVERT: C 721 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.9083 (mt) REVERT: C 744 ASP cc_start: 0.7988 (p0) cc_final: 0.7741 (p0) REVERT: C 830 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7921 (mt) REVERT: C 912 MET cc_start: 0.9043 (tpp) cc_final: 0.8812 (tpp) REVERT: D 119 ASP cc_start: 0.7054 (m-30) cc_final: 0.6434 (p0) REVERT: D 248 PHE cc_start: 0.6394 (OUTLIER) cc_final: 0.5165 (p90) REVERT: D 276 ARG cc_start: 0.7737 (mpt180) cc_final: 0.7482 (tpm170) REVERT: D 389 ARG cc_start: 0.7843 (mtp85) cc_final: 0.7537 (mtt90) REVERT: D 401 SER cc_start: 0.8616 (t) cc_final: 0.8328 (p) REVERT: D 742 LYS cc_start: 0.8116 (mppt) cc_final: 0.7880 (mppt) REVERT: D 1162 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7506 (pm20) REVERT: D 1170 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7642 (pt0) REVERT: D 1175 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7292 (ttp-170) REVERT: E 18 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8030 (mp0) REVERT: E 41 ASN cc_start: 0.8691 (t0) cc_final: 0.8410 (t0) REVERT: F 293 TYR cc_start: 0.8931 (m-80) cc_final: 0.8083 (m-80) REVERT: F 296 ARG cc_start: 0.6466 (mmm-85) cc_final: 0.5842 (tpp80) REVERT: F 344 ASP cc_start: 0.8266 (m-30) cc_final: 0.7854 (t0) REVERT: F 420 ASP cc_start: 0.8114 (t0) cc_final: 0.7735 (t0) REVERT: F 504 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7761 (pt0) REVERT: I 209 HIS cc_start: 0.7820 (m-70) cc_final: 0.7537 (m90) REVERT: I 241 ARG cc_start: 0.8172 (ttp80) cc_final: 0.7443 (ttp-110) REVERT: I 258 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6223 (mm) REVERT: J 83 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7529 (pp) REVERT: J 147 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7766 (tt) REVERT: K 300 LYS cc_start: 0.7423 (mmmm) cc_final: 0.6803 (tptp) outliers start: 133 outliers final: 108 residues processed: 471 average time/residue: 0.4465 time to fit residues: 336.9566 Evaluate side-chains 470 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 350 time to evaluate : 3.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 882 SER Chi-restraints excluded: chain C residue 925 LEU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1036 MET Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 806 MET Chi-restraints excluded: chain D residue 821 ASN Chi-restraints excluded: chain D residue 926 ILE Chi-restraints excluded: chain D residue 944 ASP Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1070 THR Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain D residue 1082 VAL Chi-restraints excluded: chain D residue 1090 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1123 LYS Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1158 LEU Chi-restraints excluded: chain D residue 1162 GLU Chi-restraints excluded: chain D residue 1175 ARG Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 405 SER Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 141 CYS Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 195 HIS Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 265 LYS Chi-restraints excluded: chain K residue 295 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 91 optimal weight: 6.9990 chunk 170 optimal weight: 0.9980 chunk 185 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 238 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 247 optimal weight: 10.0000 chunk 218 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 935 ASN E 62 HIS ** J 195 HIS ** 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 = 0.3942 r_free = 0.3942 target = 0.143084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.105107 restraints weight = 54939.632| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.29 r_work: 0.3171 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32409 Z= 0.160 Angle : 0.567 11.353 44343 Z= 0.303 Chirality : 0.041 0.202 5050 Planarity : 0.004 0.048 5436 Dihedral : 17.222 179.495 5392 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.29 % Allowed : 23.14 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.14), residues: 3764 helix: 1.74 (0.13), residues: 1600 sheet: -0.04 (0.27), residues: 369 loop : -0.48 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 74 HIS 0.005 0.001 HIS E 62 PHE 0.017 0.001 PHE A 189 TYR 0.021 0.001 TYR C 653 ARG 0.015 0.000 ARG J 149 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 1432) hydrogen bonds : angle 4.12766 ( 4028) metal coordination : bond 0.00629 ( 7) metal coordination : angle 1.70694 ( 6) covalent geometry : bond 0.00379 (32402) covalent geometry : angle 0.56669 (44337) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 353 time to evaluate : 3.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ILE cc_start: 0.7681 (mm) cc_final: 0.7284 (mt) REVERT: A 203 ARG cc_start: 0.8133 (ptm160) cc_final: 0.7880 (ptm160) REVERT: C 57 ARG cc_start: 0.7401 (tmm160) cc_final: 0.7000 (ttp80) REVERT: C 71 LYS cc_start: 0.7732 (tppt) cc_final: 0.7370 (tppt) REVERT: C 109 GLU cc_start: 0.7366 (tp30) cc_final: 0.7139 (tm-30) REVERT: C 199 TRP cc_start: 0.6070 (OUTLIER) cc_final: 0.4427 (p-90) REVERT: C 340 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7232 (tp30) REVERT: C 527 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8571 (mt) REVERT: C 721 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9094 (mt) REVERT: C 744 ASP cc_start: 0.7995 (p0) cc_final: 0.7750 (p0) REVERT: C 830 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7855 (mt) REVERT: C 912 MET cc_start: 0.9043 (tpp) cc_final: 0.8832 (tpp) REVERT: D 119 ASP cc_start: 0.7033 (m-30) cc_final: 0.6420 (p0) REVERT: D 248 PHE cc_start: 0.6343 (OUTLIER) cc_final: 0.5079 (p90) REVERT: D 276 ARG cc_start: 0.7759 (mpt180) cc_final: 0.7469 (tpm170) REVERT: D 389 ARG cc_start: 0.7835 (mtp85) cc_final: 0.7540 (mtt90) REVERT: D 401 SER cc_start: 0.8670 (t) cc_final: 0.8393 (p) REVERT: D 971 MET cc_start: 0.8198 (mmt) cc_final: 0.7942 (mmt) REVERT: D 1162 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: D 1170 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7619 (pt0) REVERT: D 1175 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7295 (ttp-170) REVERT: E 18 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8009 (mp0) REVERT: E 41 ASN cc_start: 0.8700 (t0) cc_final: 0.8418 (t0) REVERT: F 293 TYR cc_start: 0.8928 (m-80) cc_final: 0.8050 (m-80) REVERT: F 296 ARG cc_start: 0.6525 (mmm-85) cc_final: 0.5899 (tpp80) REVERT: F 344 ASP cc_start: 0.8236 (m-30) cc_final: 0.7826 (t0) REVERT: F 420 ASP cc_start: 0.8149 (t0) cc_final: 0.7761 (t0) REVERT: I 209 HIS cc_start: 0.7830 (m-70) cc_final: 0.7554 (m90) REVERT: I 241 ARG cc_start: 0.8206 (ttp80) cc_final: 0.7487 (ttp-110) REVERT: I 258 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6221 (mm) REVERT: J 83 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7509 (pp) REVERT: J 147 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7682 (tt) outliers start: 134 outliers final: 110 residues processed: 458 average time/residue: 0.4430 time to fit residues: 325.3260 Evaluate side-chains 467 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 345 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 882 SER Chi-restraints excluded: chain C residue 925 LEU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1036 MET Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 806 MET Chi-restraints excluded: chain D residue 821 ASN Chi-restraints excluded: chain D residue 926 ILE Chi-restraints excluded: chain D residue 935 ASN Chi-restraints excluded: chain D residue 944 ASP Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1070 THR Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain D residue 1082 VAL Chi-restraints excluded: chain D residue 1090 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1123 LYS Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1158 LEU Chi-restraints excluded: chain D residue 1162 GLU Chi-restraints excluded: chain D residue 1175 ARG Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 405 SER Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 141 CYS Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 195 HIS Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 265 LYS Chi-restraints excluded: chain K residue 295 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 192 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 176 optimal weight: 7.9990 chunk 343 optimal weight: 0.7980 chunk 239 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 339 optimal weight: 20.0000 chunk 233 optimal weight: 2.9990 chunk 337 optimal weight: 6.9990 chunk 172 optimal weight: 20.0000 chunk 201 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 935 ASN ** J 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.141909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103913 restraints weight = 55089.692| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.30 r_work: 0.3151 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 32409 Z= 0.190 Angle : 0.595 9.516 44343 Z= 0.318 Chirality : 0.042 0.209 5050 Planarity : 0.005 0.053 5436 Dihedral : 17.260 178.633 5392 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.10 % Allowed : 23.40 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.13), residues: 3764 helix: 1.68 (0.13), residues: 1599 sheet: -0.20 (0.26), residues: 381 loop : -0.52 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 231 HIS 0.006 0.001 HIS C 741 PHE 0.021 0.002 PHE D 252 TYR 0.015 0.002 TYR J 224 ARG 0.006 0.000 ARG C 57 Details of bonding type rmsd hydrogen bonds : bond 0.04778 ( 1432) hydrogen bonds : angle 4.19339 ( 4028) metal coordination : bond 0.00772 ( 7) metal coordination : angle 1.81294 ( 6) covalent geometry : bond 0.00454 (32402) covalent geometry : angle 0.59504 (44337) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 336 time to evaluate : 3.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 ILE cc_start: 0.7640 (mm) cc_final: 0.7208 (mt) REVERT: C 57 ARG cc_start: 0.7488 (tmm160) cc_final: 0.7081 (ttp80) REVERT: C 71 LYS cc_start: 0.7902 (tppt) cc_final: 0.7466 (tppt) REVERT: C 199 TRP cc_start: 0.6172 (OUTLIER) cc_final: 0.4435 (p-90) REVERT: C 340 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7258 (tp30) REVERT: C 527 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8584 (mt) REVERT: C 721 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.9118 (mt) REVERT: C 744 ASP cc_start: 0.8002 (p0) cc_final: 0.7765 (p0) REVERT: C 912 MET cc_start: 0.9064 (tpp) cc_final: 0.8854 (tpp) REVERT: D 119 ASP cc_start: 0.7112 (m-30) cc_final: 0.6470 (p0) REVERT: D 248 PHE cc_start: 0.6516 (OUTLIER) cc_final: 0.5179 (p90) REVERT: D 276 ARG cc_start: 0.7738 (mpt180) cc_final: 0.7456 (tpm170) REVERT: D 389 ARG cc_start: 0.7861 (mtp85) cc_final: 0.7583 (mtt90) REVERT: D 401 SER cc_start: 0.8715 (t) cc_final: 0.8374 (p) REVERT: D 935 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7881 (p0) REVERT: D 1162 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7422 (pm20) REVERT: D 1170 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7673 (pt0) REVERT: D 1175 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7309 (ttp-170) REVERT: E 18 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: E 41 ASN cc_start: 0.8746 (t0) cc_final: 0.8442 (t0) REVERT: F 293 TYR cc_start: 0.8945 (m-80) cc_final: 0.8259 (m-80) REVERT: F 296 ARG cc_start: 0.6612 (mmm-85) cc_final: 0.5897 (tpp80) REVERT: F 344 ASP cc_start: 0.8238 (m-30) cc_final: 0.7816 (t0) REVERT: F 420 ASP cc_start: 0.8087 (t0) cc_final: 0.7742 (t0) REVERT: I 209 HIS cc_start: 0.7853 (m-70) cc_final: 0.7580 (m90) REVERT: I 258 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6251 (mm) REVERT: J 83 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7505 (pp) REVERT: J 147 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7699 (tt) outliers start: 128 outliers final: 112 residues processed: 438 average time/residue: 0.4957 time to fit residues: 352.2265 Evaluate side-chains 456 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 332 time to evaluate : 6.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 882 SER Chi-restraints excluded: chain C residue 925 LEU Chi-restraints excluded: chain C residue 1036 MET Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 806 MET Chi-restraints excluded: chain D residue 821 ASN Chi-restraints excluded: chain D residue 926 ILE Chi-restraints excluded: chain D residue 935 ASN Chi-restraints excluded: chain D residue 944 ASP Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1070 THR Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain D residue 1082 VAL Chi-restraints excluded: chain D residue 1090 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1123 LYS Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1158 LEU Chi-restraints excluded: chain D residue 1162 GLU Chi-restraints excluded: chain D residue 1175 ARG Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 405 SER Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 141 CYS Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 195 HIS Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 265 LYS Chi-restraints excluded: chain K residue 295 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 318 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 156 optimal weight: 0.1980 chunk 133 optimal weight: 4.9990 chunk 119 optimal weight: 0.0970 chunk 283 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 179 optimal weight: 0.3980 chunk 128 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN ** D1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.143799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.105999 restraints weight = 55057.261| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.30 r_work: 0.3187 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32409 Z= 0.125 Angle : 0.550 10.547 44343 Z= 0.294 Chirality : 0.040 0.281 5050 Planarity : 0.004 0.048 5436 Dihedral : 17.194 178.670 5392 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.52 % Allowed : 24.04 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.14), residues: 3764 helix: 1.76 (0.13), residues: 1601 sheet: -0.08 (0.27), residues: 379 loop : -0.45 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 718 HIS 0.003 0.001 HIS D 849 PHE 0.017 0.001 PHE D 252 TYR 0.015 0.001 TYR J 224 ARG 0.007 0.000 ARG J 148 Details of bonding type rmsd hydrogen bonds : bond 0.04290 ( 1432) hydrogen bonds : angle 4.06357 ( 4028) metal coordination : bond 0.00516 ( 7) metal coordination : angle 1.46913 ( 6) covalent geometry : bond 0.00283 (32402) covalent geometry : angle 0.54966 (44337) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17217.00 seconds wall clock time: 301 minutes 22.44 seconds (18082.44 seconds total)