Starting phenix.real_space_refine on Mon Mar 25 02:16:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5s_26357/03_2024/7u5s_26357.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5s_26357/03_2024/7u5s_26357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5s_26357/03_2024/7u5s_26357.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5s_26357/03_2024/7u5s_26357.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5s_26357/03_2024/7u5s_26357.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5s_26357/03_2024/7u5s_26357.pdb" } resolution = 4.16 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 22792 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 14689 2.51 5 N 3897 2.21 5 O 4408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Residue "A ARG 47": "NH1" <-> "NH2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A ARG 556": "NH1" <-> "NH2" Residue "A GLU 558": "OE1" <-> "OE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A GLU 617": "OE1" <-> "OE2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A GLU 686": "OE1" <-> "OE2" Residue "A GLU 755": "OE1" <-> "OE2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A GLU 895": "OE1" <-> "OE2" Residue "A GLU 911": "OE1" <-> "OE2" Residue "A GLU 916": "OE1" <-> "OE2" Residue "A GLU 942": "OE1" <-> "OE2" Residue "A GLU 989": "OE1" <-> "OE2" Residue "A GLU 1000": "OE1" <-> "OE2" Residue "A GLU 1056": "OE1" <-> "OE2" Residue "A GLU 1084": "OE1" <-> "OE2" Residue "A GLU 1117": "OE1" <-> "OE2" Residue "A GLU 1149": "OE1" <-> "OE2" Residue "A GLU 1170": "OE1" <-> "OE2" Residue "A GLU 1177": "OE1" <-> "OE2" Residue "A GLU 1252": "OE1" <-> "OE2" Residue "A PHE 1274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1361": "OE1" <-> "OE2" Residue "A GLU 1426": "OE1" <-> "OE2" Residue "A GLU 1439": "OE1" <-> "OE2" Residue "A GLU 1442": "OE1" <-> "OE2" Residue "A GLU 1444": "OE1" <-> "OE2" Residue "A GLU 1475": "OE1" <-> "OE2" Residue "A GLU 1494": "OE1" <-> "OE2" Residue "A ARG 1500": "NH1" <-> "NH2" Residue "B GLU 4": "OE1" <-> "OE2" Residue "B ARG 47": "NH1" <-> "NH2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B ARG 241": "NH1" <-> "NH2" Residue "B ARG 257": "NH1" <-> "NH2" Residue "B GLU 277": "OE1" <-> "OE2" Residue "B GLU 326": "OE1" <-> "OE2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "B GLU 477": "OE1" <-> "OE2" Residue "B ARG 556": "NH1" <-> "NH2" Residue "B GLU 558": "OE1" <-> "OE2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B GLU 617": "OE1" <-> "OE2" Residue "B GLU 618": "OE1" <-> "OE2" Residue "B GLU 633": "OE1" <-> "OE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B GLU 755": "OE1" <-> "OE2" Residue "B GLU 876": "OE1" <-> "OE2" Residue "B GLU 894": "OE1" <-> "OE2" Residue "B GLU 911": "OE1" <-> "OE2" Residue "B GLU 942": "OE1" <-> "OE2" Residue "B GLU 986": "OE1" <-> "OE2" Residue "B GLU 1000": "OE1" <-> "OE2" Residue "B GLU 1016": "OE1" <-> "OE2" Residue "B GLU 1084": "OE1" <-> "OE2" Residue "B GLU 1117": "OE1" <-> "OE2" Residue "B GLU 1121": "OE1" <-> "OE2" Residue "B GLU 1252": "OE1" <-> "OE2" Residue "B PHE 1274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1307": "OE1" <-> "OE2" Residue "B GLU 1427": "OE1" <-> "OE2" Residue "B GLU 1439": "OE1" <-> "OE2" Residue "B GLU 1469": "OE1" <-> "OE2" Residue "B GLU 1483": "OE1" <-> "OE2" Residue "B GLU 1509": "OE1" <-> "OE2" Residue "B GLU 1550": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23086 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1501, 11524 Classifications: {'peptide': 1501} Link IDs: {'PTRANS': 67, 'TRANS': 1433} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 11562 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1505, 11553 Classifications: {'peptide': 1505} Link IDs: {'PTRANS': 67, 'TRANS': 1437} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 1505, 11553 Classifications: {'peptide': 1505} Link IDs: {'PTRANS': 67, 'TRANS': 1437} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 11757 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS B 11 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 11 " occ=0.50 Time building chain proxies: 16.47, per 1000 atoms: 0.71 Number of scatterers: 23086 At special positions: 0 Unit cell: (118.703, 181.178, 181.178, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 4408 8.00 N 3897 7.00 C 14689 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 - 3.50 Amino acid : False - 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: 8.14 Conformation dependent library (CDL) restraints added in 5.9 seconds 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5524 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 32 sheets defined 46.0% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.51 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 removed outlier: 3.805A pdb=" N VAL A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU A 27 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA A 30 " --> pdb=" O ARG A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 48 through 60 removed outlier: 3.659A pdb=" N SER A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.598A pdb=" N LYS A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 95 removed outlier: 3.535A pdb=" N ALA A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL A 91 " --> pdb=" O THR A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 123 removed outlier: 3.521A pdb=" N MET A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.504A pdb=" N ARG A 127 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 143 removed outlier: 3.786A pdb=" N VAL A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 178 removed outlier: 4.058A pdb=" N GLU A 178 " --> pdb=" O SER A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 175 through 178' Processing helix chain 'A' and resid 181 through 187 Processing helix chain 'A' and resid 188 through 196 removed outlier: 3.502A pdb=" N VAL A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 193 " --> pdb=" O MET A 189 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 219 removed outlier: 3.722A pdb=" N ASN A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LYS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 248 removed outlier: 3.760A pdb=" N GLU A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.696A pdb=" N PHE A 262 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 274 removed outlier: 3.625A pdb=" N ALA A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 298 removed outlier: 3.795A pdb=" N CYS A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 317 removed outlier: 4.090A pdb=" N VAL A 306 " --> pdb=" O PRO A 302 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A 307 " --> pdb=" O PRO A 303 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 332 Processing helix chain 'A' and resid 333 through 338 removed outlier: 4.103A pdb=" N HIS A 336 " --> pdb=" O PRO A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 346 removed outlier: 3.601A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 346 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 386 removed outlier: 3.596A pdb=" N LEU A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 423 removed outlier: 3.631A pdb=" N ILE A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 448 removed outlier: 3.675A pdb=" N LYS A 439 " --> pdb=" O SER A 435 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 removed outlier: 3.854A pdb=" N THR A 492 " --> pdb=" O ARG A 488 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 496 " --> pdb=" O THR A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'A' and resid 519 through 529 Processing helix chain 'A' and resid 564 through 575 removed outlier: 3.897A pdb=" N VAL A 568 " --> pdb=" O SER A 564 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS A 574 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 578 No H-bonds generated for 'chain 'A' and resid 576 through 578' Processing helix chain 'A' and resid 593 through 607 removed outlier: 3.846A pdb=" N ILE A 597 " --> pdb=" O SER A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 650 removed outlier: 3.770A pdb=" N LEU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 671 removed outlier: 3.716A pdb=" N ALA A 671 " --> pdb=" O GLN A 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 668 through 671' Processing helix chain 'A' and resid 672 through 677 removed outlier: 3.737A pdb=" N VAL A 677 " --> pdb=" O PHE A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 725 Processing helix chain 'A' and resid 738 through 742 removed outlier: 3.965A pdb=" N ARG A 742 " --> pdb=" O ALA A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 760 removed outlier: 3.580A pdb=" N ALA A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 753 " --> pdb=" O ILE A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 806 removed outlier: 3.915A pdb=" N LEU A 804 " --> pdb=" O MET A 800 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 805 " --> pdb=" O SER A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 809 No H-bonds generated for 'chain 'A' and resid 807 through 809' Processing helix chain 'A' and resid 817 through 823 removed outlier: 3.887A pdb=" N THR A 820 " --> pdb=" O GLU A 817 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR A 821 " --> pdb=" O ARG A 818 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY A 822 " --> pdb=" O SER A 819 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS A 823 " --> pdb=" O THR A 820 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 817 through 823' Processing helix chain 'A' and resid 827 through 835 removed outlier: 3.796A pdb=" N HIS A 833 " --> pdb=" O TRP A 829 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 834 " --> pdb=" O ASP A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 883 removed outlier: 3.592A pdb=" N GLU A 876 " --> pdb=" O SER A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 898 removed outlier: 3.971A pdb=" N LEU A 897 " --> pdb=" O LEU A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 906 removed outlier: 3.952A pdb=" N ILE A 905 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 906 " --> pdb=" O LYS A 902 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 901 through 906' Processing helix chain 'A' and resid 909 through 924 removed outlier: 3.669A pdb=" N PHE A 913 " --> pdb=" O GLY A 909 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS A 922 " --> pdb=" O ALA A 918 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU A 923 " --> pdb=" O ILE A 919 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N CYS A 924 " --> pdb=" O VAL A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 957 removed outlier: 3.552A pdb=" N LEU A 950 " --> pdb=" O ALA A 946 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR A 953 " --> pdb=" O GLN A 949 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP A 955 " --> pdb=" O LYS A 951 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN A 956 " --> pdb=" O SER A 952 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A 957 " --> pdb=" O TYR A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 993 removed outlier: 3.601A pdb=" N TRP A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 992 " --> pdb=" O GLN A 988 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ARG A 993 " --> pdb=" O GLU A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 999 Processing helix chain 'A' and resid 1013 through 1023 Processing helix chain 'A' and resid 1024 through 1031 Processing helix chain 'A' and resid 1060 through 1065 Processing helix chain 'A' and resid 1082 through 1095 removed outlier: 3.530A pdb=" N ALA A1087 " --> pdb=" O ALA A1083 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A1093 " --> pdb=" O GLN A1089 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1111 Processing helix chain 'A' and resid 1119 through 1131 removed outlier: 3.645A pdb=" N LEU A1128 " --> pdb=" O SER A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1149 removed outlier: 3.546A pdb=" N GLU A1149 " --> pdb=" O ASN A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1188 removed outlier: 4.050A pdb=" N LYS A1179 " --> pdb=" O ASN A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1213 removed outlier: 3.992A pdb=" N LEU A1206 " --> pdb=" O ILE A1202 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A1213 " --> pdb=" O GLU A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1235 Processing helix chain 'A' and resid 1255 through 1266 removed outlier: 3.501A pdb=" N ASN A1260 " --> pdb=" O ILE A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1298 removed outlier: 3.739A pdb=" N LEU A1289 " --> pdb=" O ARG A1285 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A1293 " --> pdb=" O LEU A1289 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1316 removed outlier: 3.513A pdb=" N TYR A1315 " --> pdb=" O VAL A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1334 removed outlier: 3.707A pdb=" N LYS A1334 " --> pdb=" O MET A1331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1331 through 1334' Processing helix chain 'A' and resid 1335 through 1340 removed outlier: 3.753A pdb=" N MET A1338 " --> pdb=" O LEU A1335 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A1339 " --> pdb=" O ASP A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1345 through 1352 Processing helix chain 'A' and resid 1370 through 1380 removed outlier: 3.790A pdb=" N PHE A1378 " --> pdb=" O ILE A1374 " (cutoff:3.500A) Processing helix chain 'A' and resid 1399 through 1409 Processing helix chain 'A' and resid 1426 through 1431 Processing helix chain 'A' and resid 1445 through 1450 removed outlier: 3.887A pdb=" N LYS A1449 " --> pdb=" O GLN A1445 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1476 removed outlier: 3.864A pdb=" N LYS A1472 " --> pdb=" O GLY A1468 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A1476 " --> pdb=" O LYS A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1510 Processing helix chain 'A' and resid 1519 through 1536 removed outlier: 3.724A pdb=" N ARG A1529 " --> pdb=" O ASN A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1546 Processing helix chain 'B' and resid 20 through 32 removed outlier: 3.805A pdb=" N VAL B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 28 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B 29 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA B 30 " --> pdb=" O ARG B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 47 Processing helix chain 'B' and resid 48 through 66 removed outlier: 3.658A pdb=" N SER B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 62 " --> pdb=" O PHE B 58 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU B 64 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 95 removed outlier: 3.534A pdb=" N ALA B 89 " --> pdb=" O ARG B 85 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL B 91 " --> pdb=" O THR B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 99 removed outlier: 3.724A pdb=" N GLY B 99 " --> pdb=" O LEU B 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 96 through 99' Processing helix chain 'B' and resid 111 through 123 removed outlier: 3.520A pdb=" N MET B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 137 through 143 removed outlier: 3.786A pdb=" N VAL B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 178 removed outlier: 4.057A pdb=" N GLU B 178 " --> pdb=" O SER B 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 175 through 178' Processing helix chain 'B' and resid 181 through 187 Processing helix chain 'B' and resid 188 through 196 removed outlier: 3.500A pdb=" N VAL B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 193 " --> pdb=" O MET B 189 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 219 removed outlier: 3.721A pdb=" N ASN B 209 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LYS B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 248 removed outlier: 3.691A pdb=" N VAL B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER B 239 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 262 removed outlier: 3.696A pdb=" N PHE B 262 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 274 removed outlier: 3.625A pdb=" N ALA B 269 " --> pdb=" O THR B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 298 removed outlier: 3.796A pdb=" N CYS B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 317 removed outlier: 4.090A pdb=" N VAL B 306 " --> pdb=" O PRO B 302 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 332 Processing helix chain 'B' and resid 333 through 338 removed outlier: 4.105A pdb=" N HIS B 336 " --> pdb=" O PRO B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 346 removed outlier: 3.601A pdb=" N LYS B 345 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 386 removed outlier: 3.595A pdb=" N LEU B 382 " --> pdb=" O SER B 378 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 423 removed outlier: 3.633A pdb=" N ILE B 418 " --> pdb=" O ASN B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 448 removed outlier: 3.675A pdb=" N LYS B 439 " --> pdb=" O SER B 435 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 removed outlier: 3.854A pdb=" N THR B 492 " --> pdb=" O ARG B 488 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 496 " --> pdb=" O THR B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 Processing helix chain 'B' and resid 519 through 529 Processing helix chain 'B' and resid 564 through 575 removed outlier: 3.898A pdb=" N VAL B 568 " --> pdb=" O SER B 564 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS B 574 " --> pdb=" O SER B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 578 No H-bonds generated for 'chain 'B' and resid 576 through 578' Processing helix chain 'B' and resid 593 through 607 removed outlier: 3.908A pdb=" N ILE B 597 " --> pdb=" O SER B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 650 removed outlier: 3.770A pdb=" N LEU B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 671 removed outlier: 3.719A pdb=" N ALA B 671 " --> pdb=" O GLN B 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 668 through 671' Processing helix chain 'B' and resid 672 through 677 removed outlier: 3.738A pdb=" N VAL B 677 " --> pdb=" O PHE B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 725 Processing helix chain 'B' and resid 738 through 742 removed outlier: 3.963A pdb=" N ARG B 742 " --> pdb=" O ALA B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 760 removed outlier: 3.613A pdb=" N ALA B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 753 " --> pdb=" O ILE B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 806 removed outlier: 3.656A pdb=" N ALA B 799 " --> pdb=" O ASP B 795 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 804 " --> pdb=" O MET B 800 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 809 No H-bonds generated for 'chain 'B' and resid 807 through 809' Processing helix chain 'B' and resid 817 through 823 removed outlier: 3.886A pdb=" N THR B 820 " --> pdb=" O GLU B 817 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR B 821 " --> pdb=" O ARG B 818 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY B 822 " --> pdb=" O SER B 819 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS B 823 " --> pdb=" O THR B 820 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 817 through 823' Processing helix chain 'B' and resid 827 through 835 removed outlier: 3.796A pdb=" N HIS B 833 " --> pdb=" O TRP B 829 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER B 834 " --> pdb=" O ASP B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 883 removed outlier: 3.527A pdb=" N TRP B 877 " --> pdb=" O THR B 873 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 896 removed outlier: 3.786A pdb=" N GLU B 894 " --> pdb=" O ASP B 890 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 896 " --> pdb=" O TYR B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 905 removed outlier: 3.586A pdb=" N LEU B 904 " --> pdb=" O ILE B 901 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE B 905 " --> pdb=" O LYS B 902 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 901 through 905' Processing helix chain 'B' and resid 909 through 924 removed outlier: 3.535A pdb=" N PHE B 913 " --> pdb=" O GLY B 909 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 914 " --> pdb=" O TRP B 910 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 918 " --> pdb=" O ARG B 914 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 922 " --> pdb=" O ALA B 918 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU B 923 " --> pdb=" O ILE B 919 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS B 924 " --> pdb=" O VAL B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 956 removed outlier: 4.053A pdb=" N ARG B 947 " --> pdb=" O GLY B 943 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN B 948 " --> pdb=" O GLU B 944 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 949 " --> pdb=" O ASP B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 1002 removed outlier: 3.995A pdb=" N VAL B 990 " --> pdb=" O GLU B 986 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU B 992 " --> pdb=" O GLN B 988 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG B 993 " --> pdb=" O GLU B 989 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 995 " --> pdb=" O TRP B 991 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS B 996 " --> pdb=" O LEU B 992 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N TRP B 997 " --> pdb=" O ARG B 993 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU B1000 " --> pdb=" O LYS B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1032 removed outlier: 3.822A pdb=" N ARG B1021 " --> pdb=" O PHE B1017 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B1025 " --> pdb=" O ARG B1021 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN B1026 " --> pdb=" O ARG B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1060 through 1065 Processing helix chain 'B' and resid 1076 through 1078 No H-bonds generated for 'chain 'B' and resid 1076 through 1078' Processing helix chain 'B' and resid 1082 through 1091 removed outlier: 4.033A pdb=" N VAL B1086 " --> pdb=" O SER B1082 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA B1087 " --> pdb=" O ALA B1083 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA B1091 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1096 Processing helix chain 'B' and resid 1107 through 1111 removed outlier: 3.596A pdb=" N GLY B1111 " --> pdb=" O VAL B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1119 through 1132 removed outlier: 3.539A pdb=" N ARG B1131 " --> pdb=" O LEU B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1152 removed outlier: 3.906A pdb=" N GLU B1150 " --> pdb=" O GLU B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1188 Processing helix chain 'B' and resid 1202 through 1215 removed outlier: 3.613A pdb=" N LEU B1206 " --> pdb=" O ILE B1202 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN B1210 " --> pdb=" O LEU B1206 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS B1213 " --> pdb=" O GLU B1209 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN B1214 " --> pdb=" O ASN B1210 " (cutoff:3.500A) Processing helix chain 'B' and resid 1229 through 1235 removed outlier: 3.707A pdb=" N GLN B1233 " --> pdb=" O GLY B1229 " (cutoff:3.500A) Processing helix chain 'B' and resid 1255 through 1266 Processing helix chain 'B' and resid 1285 through 1297 removed outlier: 3.595A pdb=" N ASN B1291 " --> pdb=" O PRO B1287 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B1292 " --> pdb=" O ASN B1288 " (cutoff:3.500A) Processing helix chain 'B' and resid 1312 through 1317 removed outlier: 3.744A pdb=" N ASP B1316 " --> pdb=" O ASP B1312 " (cutoff:3.500A) Processing helix chain 'B' and resid 1331 through 1335 Processing helix chain 'B' and resid 1336 through 1340 removed outlier: 3.652A pdb=" N LYS B1339 " --> pdb=" O ASP B1336 " (cutoff:3.500A) Processing helix chain 'B' and resid 1345 through 1352 removed outlier: 3.518A pdb=" N GLU B1349 " --> pdb=" O SER B1345 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B1350 " --> pdb=" O ASP B1346 " (cutoff:3.500A) Processing helix chain 'B' and resid 1369 through 1380 removed outlier: 4.225A pdb=" N SER B1377 " --> pdb=" O GLY B1373 " (cutoff:3.500A) Processing helix chain 'B' and resid 1400 through 1410 removed outlier: 3.787A pdb=" N TYR B1405 " --> pdb=" O ARG B1401 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN B1409 " --> pdb=" O TYR B1405 " (cutoff:3.500A) Processing helix chain 'B' and resid 1421 through 1426 Processing helix chain 'B' and resid 1426 through 1431 removed outlier: 3.639A pdb=" N SER B1431 " --> pdb=" O GLU B1427 " (cutoff:3.500A) Processing helix chain 'B' and resid 1443 through 1449 removed outlier: 3.673A pdb=" N ALA B1447 " --> pdb=" O THR B1443 " (cutoff:3.500A) Processing helix chain 'B' and resid 1470 through 1481 removed outlier: 3.766A pdb=" N ILE B1474 " --> pdb=" O VAL B1470 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG B1476 " --> pdb=" O LYS B1472 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER B1479 " --> pdb=" O GLU B1475 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN B1480 " --> pdb=" O ARG B1476 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLY B1481 " --> pdb=" O ILE B1477 " (cutoff:3.500A) Processing helix chain 'B' and resid 1502 through 1510 removed outlier: 3.669A pdb=" N LYS B1506 " --> pdb=" O THR B1502 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU B1507 " --> pdb=" O PRO B1503 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU B1510 " --> pdb=" O LYS B1506 " (cutoff:3.500A) Processing helix chain 'B' and resid 1519 through 1535 removed outlier: 3.682A pdb=" N ASN B1525 " --> pdb=" O GLU B1521 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1548 removed outlier: 3.791A pdb=" N ARG B1546 " --> pdb=" O GLU B1542 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.729A pdb=" N ILE A 8 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU A 12 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N VAL A 170 " --> pdb=" O LYS A 11 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR A 13 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N CYS A 172 " --> pdb=" O THR A 13 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N HIS A 15 " --> pdb=" O CYS A 172 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL A 131 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N PHE A 171 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLN A 133 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ASP A 173 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 134 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL A 38 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL A 109 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL A 40 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N TYR A 37 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N TYR A 74 " --> pdb=" O TYR A 37 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE A 39 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL A 76 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR A 41 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 360 Processing sheet with id=AA4, first strand: chain 'A' and resid 363 through 365 removed outlier: 3.669A pdb=" N LYS A 365 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 813 through 815 Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 456 removed outlier: 3.882A pdb=" N GLY A 425 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N TYR A 634 " --> pdb=" O THR A 426 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ARG A 428 " --> pdb=" O TYR A 634 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 478 through 479 Processing sheet with id=AA8, first strand: chain 'A' and resid 555 through 560 Processing sheet with id=AA9, first strand: chain 'A' and resid 656 through 659 Processing sheet with id=AB1, first strand: chain 'A' and resid 733 through 735 removed outlier: 3.507A pdb=" N GLU A 771 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 863 through 865 Processing sheet with id=AB3, first strand: chain 'A' and resid 885 through 888 removed outlier: 7.072A pdb=" N LYS A 885 " --> pdb=" O VAL A 933 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N SER A 935 " --> pdb=" O LYS A 885 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 887 " --> pdb=" O SER A 935 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1220 through 1223 removed outlier: 6.534A pdb=" N VAL A1193 " --> pdb=" O ILE A1221 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N PHE A1223 " --> pdb=" O VAL A1193 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU A1195 " --> pdb=" O PHE A1223 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL A1160 " --> pdb=" O ILE A1192 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ARG A1194 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY A1162 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL A1196 " --> pdb=" O GLY A1162 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR A1164 " --> pdb=" O VAL A1196 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A1071 " --> pdb=" O ILE A1102 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR A1104 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU A1073 " --> pdb=" O THR A1104 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA A1045 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLU A1072 " --> pdb=" O ALA A1045 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A1047 " --> pdb=" O GLU A1072 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ARG A1074 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU A1049 " --> pdb=" O ARG A1074 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ALA A1046 " --> pdb=" O ILE A1242 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1301 through 1307 removed outlier: 3.534A pdb=" N GLN A1302 " --> pdb=" O LYS A1272 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A1278 " --> pdb=" O PHE A1306 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS A1273 " --> pdb=" O GLY A1325 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A1327 " --> pdb=" O LYS A1273 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N TRP A1275 " --> pdb=" O LEU A1327 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILE A1329 " --> pdb=" O TRP A1275 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE A1277 " --> pdb=" O ILE A1329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1343 through 1344 removed outlier: 6.617A pdb=" N LYS A1343 " --> pdb=" O GLY A1366 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A1363 " --> pdb=" O ILE A1360 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1438 through 1440 removed outlier: 6.274A pdb=" N ILE A1415 " --> pdb=" O GLU A1439 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY A1391 " --> pdb=" O TYR A1416 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL A1418 " --> pdb=" O GLY A1391 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL A1393 " --> pdb=" O VAL A1418 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASN A1390 " --> pdb=" O VAL A1453 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU A1392 " --> pdb=" O LEU A1455 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N SER A1454 " --> pdb=" O THR A1491 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N LEU A1493 " --> pdb=" O SER A1454 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ALA A1456 " --> pdb=" O LEU A1493 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.697A pdb=" N GLU B 4 " --> pdb=" O HIS B 15 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N HIS B 15 " --> pdb=" O GLU B 4 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL B 6 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR B 13 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N VAL B 170 " --> pdb=" O ALYS B 11 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR B 13 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N CYS B 172 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N HIS B 15 " --> pdb=" O CYS B 172 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL B 131 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N PHE B 171 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLN B 133 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASP B 173 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 134 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL B 38 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 109 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL B 40 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR B 37 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N TYR B 74 " --> pdb=" O TYR B 37 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE B 39 " --> pdb=" O TYR B 74 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL B 76 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR B 41 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 149 through 151 Processing sheet with id=AC1, first strand: chain 'B' and resid 359 through 360 Processing sheet with id=AC2, first strand: chain 'B' and resid 363 through 365 removed outlier: 3.669A pdb=" N LYS B 365 " --> pdb=" O LYS B 368 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 813 through 815 Processing sheet with id=AC4, first strand: chain 'B' and resid 424 through 429 removed outlier: 3.883A pdb=" N GLY B 425 " --> pdb=" O GLY B 466 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 478 through 479 Processing sheet with id=AC6, first strand: chain 'B' and resid 555 through 560 Processing sheet with id=AC7, first strand: chain 'B' and resid 656 through 659 Processing sheet with id=AC8, first strand: chain 'B' and resid 733 through 735 removed outlier: 3.509A pdb=" N GLU B 771 " --> pdb=" O ASN B 764 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 861 through 864 removed outlier: 6.461A pdb=" N ILE B 862 " --> pdb=" O LEU B 961 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU B 963 " --> pdb=" O ILE B 862 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE B 864 " --> pdb=" O LEU B 963 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 885 through 886 removed outlier: 6.946A pdb=" N LYS B 885 " --> pdb=" O VAL B 933 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 1220 through 1225 removed outlier: 3.525A pdb=" N PHE B1223 " --> pdb=" O LEU B1195 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL B1160 " --> pdb=" O ILE B1192 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ARG B1194 " --> pdb=" O VAL B1160 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLY B1162 " --> pdb=" O ARG B1194 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL B1196 " --> pdb=" O GLY B1162 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TYR B1164 " --> pdb=" O VAL B1196 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N LYS B1198 " --> pdb=" O TYR B1164 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL B1137 " --> pdb=" O ILE B1161 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N THR B1163 " --> pdb=" O VAL B1137 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU B1139 " --> pdb=" O THR B1163 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N GLN B1165 " --> pdb=" O LEU B1139 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ILE B1102 " --> pdb=" O ASP B1069 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B1071 " --> pdb=" O ILE B1102 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR B1104 " --> pdb=" O VAL B1071 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU B1073 " --> pdb=" O THR B1104 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA B1045 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N GLU B1072 " --> pdb=" O ALA B1045 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B1047 " --> pdb=" O GLU B1072 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ARG B1074 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU B1049 " --> pdb=" O ARG B1074 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1302 through 1307 removed outlier: 3.676A pdb=" N GLY B1278 " --> pdb=" O PHE B1306 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS B1273 " --> pdb=" O GLY B1325 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU B1327 " --> pdb=" O LYS B1273 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TRP B1275 " --> pdb=" O LEU B1327 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE B1329 " --> pdb=" O TRP B1275 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE B1277 " --> pdb=" O ILE B1329 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1343 through 1344 removed outlier: 3.694A pdb=" N GLY B1363 " --> pdb=" O ILE B1360 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1438 through 1440 removed outlier: 6.174A pdb=" N ILE B1415 " --> pdb=" O GLU B1439 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR B1416 " --> pdb=" O GLY B1391 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASN B1390 " --> pdb=" O LEU B1455 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N VAL B1457 " --> pdb=" O ASN B1390 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU B1392 " --> pdb=" O VAL B1457 " (cutoff:3.500A) 798 hydrogen bonds defined for protein. 2205 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.47 Time building geometry restraints manager: 8.91 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: 6654 1.33 - 1.45: 3988 1.45 - 1.57: 12722 1.57 - 1.69: 3 1.69 - 1.82: 148 Bond restraints: 23515 Sorted by residual: bond pdb=" C ASN B 61 " pdb=" N LEU B 62 " ideal model delta sigma weight residual 1.333 1.213 0.120 1.50e-02 4.44e+03 6.37e+01 bond pdb=" C LEU B 62 " pdb=" N SER B 63 " ideal model delta sigma weight residual 1.335 1.419 -0.084 1.38e-02 5.25e+03 3.73e+01 bond pdb=" C SER A 63 " pdb=" N GLU A 64 " ideal model delta sigma weight residual 1.333 1.246 0.087 1.43e-02 4.89e+03 3.71e+01 bond pdb=" C GLU A 64 " pdb=" N LYS A 65 " ideal model delta sigma weight residual 1.333 1.410 -0.077 1.38e-02 5.25e+03 3.15e+01 bond pdb=" C LEU B 536 " pdb=" N ASN B 537 " ideal model delta sigma weight residual 1.332 1.410 -0.078 1.40e-02 5.10e+03 3.10e+01 ... (remaining 23510 not shown) Histogram of bond angle deviations from ideal: 98.08 - 105.47: 491 105.47 - 112.86: 12639 112.86 - 120.25: 9546 120.25 - 127.64: 8980 127.64 - 135.03: 189 Bond angle restraints: 31845 Sorted by residual: angle pdb=" O GLU B 633 " pdb=" C GLU B 633 " pdb=" N TYR B 634 " ideal model delta sigma weight residual 123.31 114.98 8.33 1.17e+00 7.31e-01 5.07e+01 angle pdb=" CA LEU B 536 " pdb=" C LEU B 536 " pdb=" N ASN B 537 " ideal model delta sigma weight residual 116.93 125.64 -8.71 1.26e+00 6.30e-01 4.78e+01 angle pdb=" C LYS B 221 " pdb=" N LYS B 222 " pdb=" CA LYS B 222 " ideal model delta sigma weight residual 121.83 112.03 9.80 1.56e+00 4.11e-01 3.95e+01 angle pdb=" C LYS A 221 " pdb=" N LYS A 222 " pdb=" CA LYS A 222 " ideal model delta sigma weight residual 121.83 112.07 9.76 1.56e+00 4.11e-01 3.92e+01 angle pdb=" N ILE B 777 " pdb=" CA ILE B 777 " pdb=" C ILE B 777 " ideal model delta sigma weight residual 112.35 103.61 8.74 1.41e+00 5.03e-01 3.84e+01 ... (remaining 31840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12751 17.93 - 35.85: 1175 35.85 - 53.77: 219 53.77 - 71.70: 50 71.70 - 89.62: 26 Dihedral angle restraints: 14221 sinusoidal: 5615 harmonic: 8606 Sorted by residual: dihedral pdb=" CA THR A1330 " pdb=" C THR A1330 " pdb=" N MET A1331 " pdb=" CA MET A1331 " ideal model delta harmonic sigma weight residual -180.00 -151.74 -28.26 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA VAL A1038 " pdb=" C VAL A1038 " pdb=" N VAL A1039 " pdb=" CA VAL A1039 " ideal model delta harmonic sigma weight residual 180.00 152.16 27.84 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA VAL A1039 " pdb=" C VAL A1039 " pdb=" N PRO A1040 " pdb=" CA PRO A1040 " ideal model delta harmonic sigma weight residual -180.00 -153.34 -26.66 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 14218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2620 0.060 - 0.119: 861 0.119 - 0.179: 172 0.179 - 0.239: 29 0.239 - 0.298: 11 Chirality restraints: 3693 Sorted by residual: chirality pdb=" CB ILE A1281 " pdb=" CA ILE A1281 " pdb=" CG1 ILE A1281 " pdb=" CG2 ILE A1281 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA MET B1331 " pdb=" N MET B1331 " pdb=" C MET B1331 " pdb=" CB MET B1331 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA ILE B 749 " pdb=" N ILE B 749 " pdb=" C ILE B 749 " pdb=" CB ILE B 749 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 3690 not shown) Planarity restraints: 4070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 633 " 0.025 2.00e-02 2.50e+03 4.66e-02 2.17e+01 pdb=" C GLU B 633 " -0.081 2.00e-02 2.50e+03 pdb=" O GLU B 633 " 0.029 2.00e-02 2.50e+03 pdb=" N TYR B 634 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 63 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.90e+00 pdb=" C SER A 63 " -0.054 2.00e-02 2.50e+03 pdb=" O SER A 63 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU A 64 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 791 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C SER A 791 " 0.053 2.00e-02 2.50e+03 pdb=" O SER A 791 " -0.020 2.00e-02 2.50e+03 pdb=" N SER A 792 " -0.018 2.00e-02 2.50e+03 ... (remaining 4067 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5976 2.79 - 3.32: 20590 3.32 - 3.85: 38357 3.85 - 4.37: 46285 4.37 - 4.90: 76662 Nonbonded interactions: 187870 Sorted by model distance: nonbonded pdb=" O MET B 45 " pdb=" OG1 THR B 48 " model vdw 2.265 2.440 nonbonded pdb=" O MET A 45 " pdb=" OG1 THR A 48 " model vdw 2.265 2.440 nonbonded pdb=" OE2 GLU A1072 " pdb=" OG1 THR A1104 " model vdw 2.265 2.440 nonbonded pdb=" O GLY B 938 " pdb=" OH TYR B 998 " model vdw 2.277 2.440 nonbonded pdb=" O MET A 599 " pdb=" CD1 LEU A 667 " model vdw 2.289 3.460 ... (remaining 187865 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 10 or resid 12 through 634 or resid 639 through \ 1550)) selection = (chain 'B' and (resid 2 through 10 or resid 12 through 250 or resid 256 through \ 634 or resid 639 through 964 or resid 985 through 1550)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.260 Construct map_model_manager: 0.020 Extract box with map and model: 14.600 Check model and map are aligned: 0.310 Set scattering table: 0.220 Process input model: 68.250 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4360 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.120 23515 Z= 0.553 Angle : 1.024 10.029 31845 Z= 0.603 Chirality : 0.061 0.298 3693 Planarity : 0.007 0.072 4070 Dihedral : 14.832 89.625 8697 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.93 (0.12), residues: 2985 helix: -4.22 (0.07), residues: 1274 sheet: -2.24 (0.22), residues: 466 loop : -2.36 (0.15), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B1371 HIS 0.009 0.002 HIS B 707 PHE 0.025 0.003 PHE B 836 TYR 0.027 0.003 TYR A 577 ARG 0.016 0.001 ARG A1546 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 639 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.6778 (tttt) cc_final: 0.6535 (tttt) REVERT: A 117 MET cc_start: 0.6153 (ttp) cc_final: 0.5656 (ttp) REVERT: A 208 GLU cc_start: 0.5450 (mm-30) cc_final: 0.4754 (mm-30) REVERT: A 280 HIS cc_start: 0.5496 (t70) cc_final: 0.5082 (t70) REVERT: A 298 LEU cc_start: 0.7053 (mt) cc_final: 0.6748 (mt) REVERT: A 303 PRO cc_start: 0.7122 (Cg_endo) cc_final: 0.6624 (Cg_exo) REVERT: A 311 LYS cc_start: 0.8213 (tptp) cc_final: 0.7962 (ttmm) REVERT: A 886 MET cc_start: 0.5951 (tmm) cc_final: 0.5497 (tmm) REVERT: A 889 MET cc_start: 0.5590 (mmp) cc_final: 0.4868 (mmp) REVERT: A 932 TYR cc_start: 0.5669 (m-80) cc_final: 0.5439 (m-80) REVERT: A 942 GLU cc_start: 0.6499 (mm-30) cc_final: 0.6230 (tp30) REVERT: A 1009 SER cc_start: 0.8066 (m) cc_final: 0.7431 (t) REVERT: A 1025 VAL cc_start: 0.8239 (t) cc_final: 0.7979 (p) REVERT: A 1043 ARG cc_start: 0.6810 (ttt-90) cc_final: 0.4809 (tmt-80) REVERT: A 1044 SER cc_start: 0.8155 (p) cc_final: 0.7947 (p) REVERT: A 1048 VAL cc_start: 0.8767 (t) cc_final: 0.8474 (m) REVERT: A 1053 ASP cc_start: 0.4810 (t70) cc_final: 0.3516 (t0) REVERT: A 1072 GLU cc_start: 0.6687 (tp30) cc_final: 0.6461 (tp30) REVERT: A 1077 LEU cc_start: 0.7257 (pp) cc_final: 0.6826 (pp) REVERT: A 1078 PHE cc_start: 0.5997 (m-10) cc_final: 0.5785 (m-80) REVERT: A 1093 ILE cc_start: 0.6488 (tt) cc_final: 0.5942 (mm) REVERT: A 1110 GLN cc_start: 0.7330 (mm-40) cc_final: 0.6233 (mp10) REVERT: A 1126 LEU cc_start: 0.8326 (mt) cc_final: 0.7825 (mm) REVERT: A 1128 LEU cc_start: 0.7232 (tp) cc_final: 0.6918 (tp) REVERT: A 1171 LEU cc_start: 0.6886 (mt) cc_final: 0.6537 (mt) REVERT: A 1221 ILE cc_start: 0.7843 (mt) cc_final: 0.7613 (mt) REVERT: A 1224 ASN cc_start: 0.8061 (m-40) cc_final: 0.7831 (m-40) REVERT: A 1231 LEU cc_start: 0.7995 (tp) cc_final: 0.7684 (tt) REVERT: A 1242 ILE cc_start: 0.7554 (pt) cc_final: 0.7000 (mm) REVERT: A 1272 LYS cc_start: 0.8239 (mttp) cc_final: 0.7985 (mmmt) REVERT: A 1286 SER cc_start: 0.7701 (t) cc_final: 0.7492 (p) REVERT: A 1327 LEU cc_start: 0.5504 (mt) cc_final: 0.5288 (mm) REVERT: A 1342 THR cc_start: 0.7414 (p) cc_final: 0.7013 (t) REVERT: A 1356 THR cc_start: 0.7095 (m) cc_final: 0.6745 (p) REVERT: A 1379 ILE cc_start: 0.7512 (mt) cc_final: 0.6979 (tp) REVERT: A 1409 GLN cc_start: 0.6978 (mt0) cc_final: 0.6191 (tt0) REVERT: A 1410 MET cc_start: 0.5121 (tpp) cc_final: 0.4604 (tpp) REVERT: A 1418 VAL cc_start: 0.8262 (t) cc_final: 0.7659 (t) REVERT: A 1424 LYS cc_start: 0.6600 (tttt) cc_final: 0.6277 (tmtt) REVERT: A 1432 PHE cc_start: 0.6745 (m-80) cc_final: 0.6305 (m-80) REVERT: A 1526 GLN cc_start: 0.6431 (tt0) cc_final: 0.6217 (pt0) REVERT: A 1529 ARG cc_start: 0.6949 (tpt90) cc_final: 0.6695 (mmm-85) REVERT: A 1530 GLN cc_start: 0.6669 (mt0) cc_final: 0.5858 (mt0) REVERT: A 1532 LYS cc_start: 0.8659 (tptp) cc_final: 0.7808 (tppt) REVERT: A 1533 LEU cc_start: 0.7951 (mt) cc_final: 0.7728 (mt) REVERT: A 1538 THR cc_start: 0.8734 (m) cc_final: 0.8134 (p) REVERT: B 94 PHE cc_start: 0.4047 (t80) cc_final: 0.1725 (t80) REVERT: B 141 MET cc_start: 0.5388 (mtt) cc_final: 0.4899 (tmm) REVERT: B 180 LEU cc_start: 0.7155 (tp) cc_final: 0.6874 (tp) REVERT: B 198 ILE cc_start: 0.6837 (pt) cc_final: 0.6119 (mt) REVERT: B 243 LYS cc_start: 0.7747 (tttm) cc_final: 0.7363 (tppt) REVERT: B 266 ILE cc_start: 0.7596 (mt) cc_final: 0.6229 (mm) REVERT: B 284 VAL cc_start: 0.6564 (t) cc_final: 0.6094 (t) REVERT: B 798 VAL cc_start: 0.5195 (t) cc_final: 0.4100 (t) REVERT: B 1048 VAL cc_start: 0.7469 (t) cc_final: 0.6792 (p) REVERT: B 1078 PHE cc_start: 0.5674 (m-10) cc_final: 0.5382 (m-80) REVERT: B 1090 ILE cc_start: 0.8399 (mt) cc_final: 0.8192 (tt) REVERT: B 1125 LEU cc_start: 0.8065 (mt) cc_final: 0.7434 (mt) REVERT: B 1126 LEU cc_start: 0.7366 (mt) cc_final: 0.6785 (mt) REVERT: B 1152 SER cc_start: 0.8169 (m) cc_final: 0.7911 (p) REVERT: B 1228 GLN cc_start: 0.7571 (mt0) cc_final: 0.7317 (tt0) REVERT: B 1231 LEU cc_start: 0.8012 (tp) cc_final: 0.7393 (tt) REVERT: B 1233 GLN cc_start: 0.7313 (mt0) cc_final: 0.6979 (tt0) REVERT: B 1235 LEU cc_start: 0.8730 (mt) cc_final: 0.8495 (mm) REVERT: B 1242 ILE cc_start: 0.8143 (pt) cc_final: 0.6568 (mm) REVERT: B 1246 LEU cc_start: 0.8394 (mt) cc_final: 0.8023 (mm) REVERT: B 1256 ILE cc_start: 0.8150 (tp) cc_final: 0.6955 (tp) REVERT: B 1260 ASN cc_start: 0.6760 (m-40) cc_final: 0.6202 (m-40) REVERT: B 1290 HIS cc_start: 0.6069 (m-70) cc_final: 0.4593 (m90) REVERT: B 1342 THR cc_start: 0.7821 (m) cc_final: 0.7483 (p) REVERT: B 1409 GLN cc_start: 0.6850 (mm-40) cc_final: 0.6547 (mm-40) REVERT: B 1437 ASN cc_start: 0.6334 (m110) cc_final: 0.5934 (m110) REVERT: B 1438 LEU cc_start: 0.6807 (mt) cc_final: 0.6495 (tt) REVERT: B 1441 VAL cc_start: 0.8357 (t) cc_final: 0.8093 (p) REVERT: B 1505 MET cc_start: 0.5842 (mtp) cc_final: 0.5216 (mtp) REVERT: B 1522 MET cc_start: 0.6176 (ttp) cc_final: 0.5731 (tpt) REVERT: B 1530 GLN cc_start: 0.6830 (mt0) cc_final: 0.6562 (mt0) REVERT: B 1543 ILE cc_start: 0.8098 (mt) cc_final: 0.7674 (tp) outliers start: 0 outliers final: 0 residues processed: 639 average time/residue: 0.3707 time to fit residues: 358.5403 Evaluate side-chains 512 residues out of total 2537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 512 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 0.5980 chunk 227 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 235 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 272 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS A 431 ASN A 537 ASN A 707 HIS ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1184 GLN ** A1205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 264 HIS B 393 HIS B 440 HIS ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1376 ASN B1484 GLN B1525 ASN B1545 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4831 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 23515 Z= 0.288 Angle : 0.778 15.552 31845 Z= 0.411 Chirality : 0.047 0.215 3693 Planarity : 0.006 0.074 4070 Dihedral : 5.510 22.570 3187 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.28 % Allowed : 3.62 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.14), residues: 2985 helix: -2.32 (0.12), residues: 1320 sheet: -1.53 (0.23), residues: 463 loop : -1.77 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A1514 HIS 0.022 0.002 HIS B 440 PHE 0.034 0.003 PHE A 176 TYR 0.021 0.002 TYR B 634 ARG 0.008 0.001 ARG B1036 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 570 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7030 (mm-30) REVERT: A 117 MET cc_start: 0.6117 (ttp) cc_final: 0.5706 (ttp) REVERT: A 126 MET cc_start: 0.5940 (mmm) cc_final: 0.5443 (mmm) REVERT: A 139 LEU cc_start: 0.7654 (tp) cc_final: 0.7282 (tp) REVERT: A 176 PHE cc_start: 0.6304 (m-10) cc_final: 0.6049 (m-10) REVERT: A 238 GLU cc_start: 0.6983 (mp0) cc_final: 0.6771 (mp0) REVERT: A 262 PHE cc_start: 0.6658 (t80) cc_final: 0.6275 (t80) REVERT: A 264 HIS cc_start: 0.6531 (m-70) cc_final: 0.5659 (m-70) REVERT: A 274 LEU cc_start: 0.7066 (mp) cc_final: 0.6816 (mp) REVERT: A 280 HIS cc_start: 0.5744 (t70) cc_final: 0.5181 (t70) REVERT: A 288 MET cc_start: 0.6327 (mtm) cc_final: 0.6070 (mtm) REVERT: A 294 LEU cc_start: 0.7990 (tp) cc_final: 0.7694 (mt) REVERT: A 298 LEU cc_start: 0.7972 (mt) cc_final: 0.7022 (tp) REVERT: A 311 LYS cc_start: 0.8512 (tptp) cc_final: 0.8176 (ttmm) REVERT: A 327 PHE cc_start: 0.5383 (t80) cc_final: 0.4961 (t80) REVERT: A 831 ILE cc_start: 0.6228 (OUTLIER) cc_final: 0.5998 (mm) REVERT: A 886 MET cc_start: 0.5982 (tmm) cc_final: 0.5525 (tmm) REVERT: A 924 CYS cc_start: 0.7782 (m) cc_final: 0.7326 (t) REVERT: A 932 TYR cc_start: 0.6025 (m-80) cc_final: 0.5622 (m-80) REVERT: A 1009 SER cc_start: 0.7973 (m) cc_final: 0.7200 (t) REVERT: A 1029 LYS cc_start: 0.7931 (ptmt) cc_final: 0.7372 (ptmt) REVERT: A 1043 ARG cc_start: 0.6826 (ttt-90) cc_final: 0.6312 (ttt90) REVERT: A 1048 VAL cc_start: 0.8798 (t) cc_final: 0.8407 (m) REVERT: A 1072 GLU cc_start: 0.6765 (tp30) cc_final: 0.6480 (tp30) REVERT: A 1093 ILE cc_start: 0.7404 (tt) cc_final: 0.6730 (mm) REVERT: A 1125 LEU cc_start: 0.8111 (mt) cc_final: 0.7630 (mp) REVERT: A 1126 LEU cc_start: 0.8549 (mt) cc_final: 0.8311 (mm) REVERT: A 1158 THR cc_start: 0.7402 (m) cc_final: 0.6916 (p) REVERT: A 1171 LEU cc_start: 0.7007 (mt) cc_final: 0.6579 (mt) REVERT: A 1182 TYR cc_start: 0.5428 (t80) cc_final: 0.5222 (t80) REVERT: A 1209 GLU cc_start: 0.7421 (pp20) cc_final: 0.7081 (pp20) REVERT: A 1224 ASN cc_start: 0.7816 (m-40) cc_final: 0.7555 (m110) REVERT: A 1242 ILE cc_start: 0.7615 (pt) cc_final: 0.7170 (mm) REVERT: A 1261 GLN cc_start: 0.7514 (tp40) cc_final: 0.6400 (tp-100) REVERT: A 1262 THR cc_start: 0.7610 (p) cc_final: 0.7287 (t) REVERT: A 1265 ASP cc_start: 0.7767 (m-30) cc_final: 0.6836 (m-30) REVERT: A 1272 LYS cc_start: 0.8476 (mttp) cc_final: 0.8263 (mmmt) REVERT: A 1286 SER cc_start: 0.8140 (t) cc_final: 0.7837 (p) REVERT: A 1290 HIS cc_start: 0.6618 (m-70) cc_final: 0.5937 (m-70) REVERT: A 1297 LEU cc_start: 0.8408 (mt) cc_final: 0.8167 (mm) REVERT: A 1327 LEU cc_start: 0.6214 (mt) cc_final: 0.5783 (mm) REVERT: A 1340 PHE cc_start: 0.5456 (m-80) cc_final: 0.5180 (m-80) REVERT: A 1356 THR cc_start: 0.7417 (m) cc_final: 0.6939 (p) REVERT: A 1376 ASN cc_start: 0.7971 (m-40) cc_final: 0.7675 (m-40) REVERT: A 1410 MET cc_start: 0.5854 (tpp) cc_final: 0.5216 (tpp) REVERT: A 1428 LEU cc_start: 0.8063 (mt) cc_final: 0.7749 (mt) REVERT: A 1429 VAL cc_start: 0.7175 (t) cc_final: 0.6957 (m) REVERT: A 1432 PHE cc_start: 0.6812 (m-80) cc_final: 0.6469 (m-80) REVERT: A 1440 ILE cc_start: 0.6900 (tp) cc_final: 0.6319 (tt) REVERT: A 1529 ARG cc_start: 0.7380 (tpt90) cc_final: 0.7092 (mmm-85) REVERT: A 1530 GLN cc_start: 0.7129 (mt0) cc_final: 0.6347 (mt0) REVERT: A 1532 LYS cc_start: 0.9025 (tptp) cc_final: 0.8384 (tppt) REVERT: A 1534 HIS cc_start: 0.6985 (m170) cc_final: 0.6585 (m170) REVERT: B 94 PHE cc_start: 0.4619 (t80) cc_final: 0.3669 (t80) REVERT: B 141 MET cc_start: 0.5569 (mtt) cc_final: 0.5178 (tmm) REVERT: B 284 VAL cc_start: 0.7248 (t) cc_final: 0.7004 (p) REVERT: B 300 ILE cc_start: 0.7003 (mt) cc_final: 0.6798 (mm) REVERT: B 889 MET cc_start: 0.5921 (mmt) cc_final: 0.5696 (mmp) REVERT: B 1029 LYS cc_start: 0.7965 (mttt) cc_final: 0.7479 (tppt) REVERT: B 1048 VAL cc_start: 0.7640 (t) cc_final: 0.7303 (p) REVERT: B 1090 ILE cc_start: 0.8933 (mt) cc_final: 0.8590 (tp) REVERT: B 1098 ASP cc_start: 0.6526 (p0) cc_final: 0.6319 (p0) REVERT: B 1121 GLU cc_start: 0.6499 (tp30) cc_final: 0.5950 (tp30) REVERT: B 1125 LEU cc_start: 0.8270 (mt) cc_final: 0.7597 (mt) REVERT: B 1126 LEU cc_start: 0.7850 (mt) cc_final: 0.6892 (mt) REVERT: B 1130 ILE cc_start: 0.6388 (mt) cc_final: 0.6076 (mt) REVERT: B 1137 VAL cc_start: 0.5442 (m) cc_final: 0.5227 (p) REVERT: B 1152 SER cc_start: 0.8646 (m) cc_final: 0.8189 (p) REVERT: B 1207 ASP cc_start: 0.6760 (t0) cc_final: 0.6322 (t0) REVERT: B 1233 GLN cc_start: 0.7486 (mt0) cc_final: 0.7061 (tt0) REVERT: B 1235 LEU cc_start: 0.8826 (mt) cc_final: 0.8475 (mm) REVERT: B 1245 LYS cc_start: 0.9000 (pptt) cc_final: 0.8532 (pptt) REVERT: B 1246 LEU cc_start: 0.8308 (mt) cc_final: 0.7311 (mt) REVERT: B 1256 ILE cc_start: 0.8771 (tp) cc_final: 0.8111 (tp) REVERT: B 1289 LEU cc_start: 0.8224 (tt) cc_final: 0.7960 (tt) REVERT: B 1290 HIS cc_start: 0.7529 (m-70) cc_final: 0.6777 (m90) REVERT: B 1297 LEU cc_start: 0.8096 (mt) cc_final: 0.7716 (mt) REVERT: B 1299 LEU cc_start: 0.8863 (mm) cc_final: 0.8438 (mp) REVERT: B 1303 PHE cc_start: 0.7952 (t80) cc_final: 0.7743 (t80) REVERT: B 1312 ASP cc_start: 0.7250 (p0) cc_final: 0.6435 (p0) REVERT: B 1342 THR cc_start: 0.7954 (m) cc_final: 0.7725 (p) REVERT: B 1364 TYR cc_start: 0.7339 (m-80) cc_final: 0.6536 (m-80) REVERT: B 1430 LYS cc_start: 0.8140 (ptpp) cc_final: 0.7838 (mmmm) REVERT: B 1441 VAL cc_start: 0.8394 (t) cc_final: 0.8022 (p) REVERT: B 1505 MET cc_start: 0.6122 (mtp) cc_final: 0.5421 (mtp) REVERT: B 1522 MET cc_start: 0.6883 (ttp) cc_final: 0.6186 (tpt) REVERT: B 1529 ARG cc_start: 0.7980 (mmm-85) cc_final: 0.7655 (mmm160) REVERT: B 1530 GLN cc_start: 0.7835 (mt0) cc_final: 0.7468 (mt0) REVERT: B 1543 ILE cc_start: 0.8327 (mt) cc_final: 0.7935 (mm) outliers start: 7 outliers final: 3 residues processed: 575 average time/residue: 0.3541 time to fit residues: 312.7386 Evaluate side-chains 524 residues out of total 2537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 520 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 226 optimal weight: 0.0070 chunk 185 optimal weight: 0.0970 chunk 75 optimal weight: 4.9990 chunk 272 optimal weight: 0.7980 chunk 294 optimal weight: 0.9980 chunk 243 optimal weight: 5.9990 chunk 270 optimal weight: 0.0870 chunk 93 optimal weight: 3.9990 chunk 218 optimal weight: 0.7980 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 HIS B1096 HIS ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 ASN ** B1302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1484 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4802 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 23515 Z= 0.206 Angle : 0.651 13.521 31845 Z= 0.334 Chirality : 0.044 0.266 3693 Planarity : 0.005 0.107 4070 Dihedral : 5.033 22.845 3187 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.08 % Allowed : 1.97 % Favored : 97.95 % 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: -2.38 (0.15), residues: 2985 helix: -1.54 (0.13), residues: 1330 sheet: -1.25 (0.24), residues: 461 loop : -1.53 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 828 HIS 0.006 0.001 HIS B1408 PHE 0.040 0.002 PHE B 717 TYR 0.019 0.002 TYR B1405 ARG 0.008 0.001 ARG B 748 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 535 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6853 (mm-30) REVERT: A 88 LYS cc_start: 0.6591 (tmmt) cc_final: 0.6337 (tmmt) REVERT: A 117 MET cc_start: 0.5972 (ttp) cc_final: 0.5609 (ttp) REVERT: A 126 MET cc_start: 0.5992 (mmm) cc_final: 0.5545 (mmm) REVERT: A 139 LEU cc_start: 0.6944 (tp) cc_final: 0.6681 (tt) REVERT: A 171 PHE cc_start: 0.7095 (m-80) cc_final: 0.6685 (m-10) REVERT: A 176 PHE cc_start: 0.5956 (m-10) cc_final: 0.5061 (m-10) REVERT: A 192 VAL cc_start: 0.7054 (p) cc_final: 0.6234 (t) REVERT: A 238 GLU cc_start: 0.6859 (mp0) cc_final: 0.6594 (mp0) REVERT: A 280 HIS cc_start: 0.5317 (t70) cc_final: 0.4883 (t70) REVERT: A 288 MET cc_start: 0.6358 (mtm) cc_final: 0.5991 (mtm) REVERT: A 311 LYS cc_start: 0.8417 (tptp) cc_final: 0.8157 (ttmm) REVERT: A 652 MET cc_start: 0.4914 (mpp) cc_final: 0.4695 (mpp) REVERT: A 886 MET cc_start: 0.5988 (tmm) cc_final: 0.5715 (tmm) REVERT: A 924 CYS cc_start: 0.7814 (m) cc_final: 0.7606 (t) REVERT: A 932 TYR cc_start: 0.5882 (m-80) cc_final: 0.5489 (m-80) REVERT: A 1009 SER cc_start: 0.7613 (m) cc_final: 0.7000 (t) REVERT: A 1029 LYS cc_start: 0.7681 (ptmt) cc_final: 0.7094 (ptmm) REVERT: A 1043 ARG cc_start: 0.6734 (ttt-90) cc_final: 0.6203 (ttt90) REVERT: A 1048 VAL cc_start: 0.8753 (t) cc_final: 0.8342 (m) REVERT: A 1054 LEU cc_start: 0.7847 (mm) cc_final: 0.7545 (tp) REVERT: A 1126 LEU cc_start: 0.8547 (mt) cc_final: 0.8309 (mm) REVERT: A 1139 LEU cc_start: 0.7582 (pp) cc_final: 0.7338 (pp) REVERT: A 1158 THR cc_start: 0.7327 (m) cc_final: 0.6831 (p) REVERT: A 1242 ILE cc_start: 0.7539 (pt) cc_final: 0.7048 (mm) REVERT: A 1261 GLN cc_start: 0.7312 (tp40) cc_final: 0.6131 (tp40) REVERT: A 1265 ASP cc_start: 0.7659 (m-30) cc_final: 0.6291 (m-30) REVERT: A 1290 HIS cc_start: 0.6503 (m-70) cc_final: 0.6004 (m90) REVERT: A 1297 LEU cc_start: 0.8438 (mt) cc_final: 0.8153 (mm) REVERT: A 1327 LEU cc_start: 0.5826 (mt) cc_final: 0.5437 (mm) REVERT: A 1356 THR cc_start: 0.7576 (m) cc_final: 0.7054 (p) REVERT: A 1410 MET cc_start: 0.5956 (tpp) cc_final: 0.5250 (tpp) REVERT: A 1418 VAL cc_start: 0.7364 (t) cc_final: 0.7034 (p) REVERT: A 1428 LEU cc_start: 0.7943 (mt) cc_final: 0.7589 (mt) REVERT: A 1432 PHE cc_start: 0.6775 (m-80) cc_final: 0.6428 (m-80) REVERT: A 1440 ILE cc_start: 0.6548 (tp) cc_final: 0.5840 (tt) REVERT: A 1474 ILE cc_start: 0.8490 (pt) cc_final: 0.8263 (pt) REVERT: A 1521 GLU cc_start: 0.7528 (mp0) cc_final: 0.6832 (mp0) REVERT: A 1524 VAL cc_start: 0.7518 (p) cc_final: 0.7117 (p) REVERT: A 1528 ASP cc_start: 0.7462 (m-30) cc_final: 0.6790 (m-30) REVERT: A 1529 ARG cc_start: 0.7332 (tpt90) cc_final: 0.6940 (mmm-85) REVERT: A 1530 GLN cc_start: 0.6994 (mt0) cc_final: 0.6230 (mt0) REVERT: A 1532 LYS cc_start: 0.8939 (tptp) cc_final: 0.8239 (tppt) REVERT: A 1534 HIS cc_start: 0.6966 (m170) cc_final: 0.6541 (m170) REVERT: B 31 ASN cc_start: 0.6191 (p0) cc_final: 0.5986 (p0) REVERT: B 243 LYS cc_start: 0.8126 (ptpt) cc_final: 0.7923 (ptpt) REVERT: B 284 VAL cc_start: 0.7300 (t) cc_final: 0.6821 (p) REVERT: B 288 MET cc_start: 0.7574 (mtm) cc_final: 0.7215 (mtt) REVERT: B 645 TYR cc_start: 0.2293 (m-80) cc_final: 0.2069 (m-10) REVERT: B 798 VAL cc_start: 0.5808 (t) cc_final: 0.4450 (t) REVERT: B 1025 VAL cc_start: 0.7581 (m) cc_final: 0.7366 (p) REVERT: B 1048 VAL cc_start: 0.7572 (t) cc_final: 0.7113 (p) REVERT: B 1090 ILE cc_start: 0.8893 (mt) cc_final: 0.8506 (tp) REVERT: B 1098 ASP cc_start: 0.6456 (p0) cc_final: 0.6154 (p0) REVERT: B 1121 GLU cc_start: 0.6336 (tp30) cc_final: 0.6104 (tp30) REVERT: B 1125 LEU cc_start: 0.8129 (mt) cc_final: 0.7430 (mt) REVERT: B 1126 LEU cc_start: 0.7851 (mt) cc_final: 0.6700 (mt) REVERT: B 1130 ILE cc_start: 0.6505 (mt) cc_final: 0.6194 (mt) REVERT: B 1152 SER cc_start: 0.8585 (m) cc_final: 0.8071 (p) REVERT: B 1171 LEU cc_start: 0.8491 (mt) cc_final: 0.8167 (tp) REVERT: B 1207 ASP cc_start: 0.6728 (t0) cc_final: 0.6254 (t0) REVERT: B 1233 GLN cc_start: 0.7458 (mt0) cc_final: 0.7149 (mt0) REVERT: B 1235 LEU cc_start: 0.8796 (mt) cc_final: 0.8554 (mm) REVERT: B 1256 ILE cc_start: 0.8761 (tp) cc_final: 0.8270 (tp) REVERT: B 1290 HIS cc_start: 0.7477 (m-70) cc_final: 0.7009 (m90) REVERT: B 1312 ASP cc_start: 0.7158 (p0) cc_final: 0.6536 (p0) REVERT: B 1342 THR cc_start: 0.7963 (m) cc_final: 0.7716 (p) REVERT: B 1351 ILE cc_start: 0.8572 (mt) cc_final: 0.8279 (mt) REVERT: B 1372 VAL cc_start: 0.8647 (t) cc_final: 0.8344 (t) REVERT: B 1430 LYS cc_start: 0.8091 (ptpp) cc_final: 0.7793 (mmmm) REVERT: B 1498 LYS cc_start: 0.8280 (mmtt) cc_final: 0.8036 (mmmt) REVERT: B 1505 MET cc_start: 0.6105 (mtp) cc_final: 0.5392 (mtp) REVERT: B 1522 MET cc_start: 0.6762 (ttp) cc_final: 0.6169 (tpt) REVERT: B 1529 ARG cc_start: 0.7966 (mmm-85) cc_final: 0.7596 (mmm160) REVERT: B 1530 GLN cc_start: 0.7813 (mt0) cc_final: 0.7434 (mt0) REVERT: B 1543 ILE cc_start: 0.8146 (mt) cc_final: 0.7707 (tp) outliers start: 2 outliers final: 1 residues processed: 536 average time/residue: 0.3600 time to fit residues: 295.4102 Evaluate side-chains 494 residues out of total 2537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 493 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 273 optimal weight: 0.7980 chunk 289 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 chunk 259 optimal weight: 0.0980 chunk 78 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 HIS ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1205 ASN A1215 ASN ** A1228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1283 HIS ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1437 ASN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 HIS B 668 GLN B 707 HIS ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1165 GLN B1288 ASN ** B1302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1317 ASN B1408 HIS B1484 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4937 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 23515 Z= 0.223 Angle : 0.660 12.806 31845 Z= 0.340 Chirality : 0.045 0.243 3693 Planarity : 0.005 0.087 4070 Dihedral : 4.974 23.432 3187 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.04 % Allowed : 2.36 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.15), residues: 2985 helix: -1.10 (0.14), residues: 1333 sheet: -1.20 (0.24), residues: 472 loop : -1.40 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 828 HIS 0.007 0.001 HIS B 375 PHE 0.035 0.002 PHE B 717 TYR 0.021 0.002 TYR A1512 ARG 0.009 0.001 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 520 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 HIS cc_start: 0.6467 (t70) cc_final: 0.6187 (t70) REVERT: A 37 TYR cc_start: 0.3997 (m-10) cc_final: 0.3751 (m-10) REVERT: A 80 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6918 (mm-30) REVERT: A 88 LYS cc_start: 0.6616 (tmmt) cc_final: 0.6216 (tmmt) REVERT: A 117 MET cc_start: 0.6164 (ttp) cc_final: 0.5908 (ttp) REVERT: A 126 MET cc_start: 0.6062 (mmm) cc_final: 0.5607 (mmm) REVERT: A 168 GLU cc_start: 0.6445 (tm-30) cc_final: 0.5551 (tm-30) REVERT: A 173 ASP cc_start: 0.7056 (t0) cc_final: 0.6267 (t0) REVERT: A 192 VAL cc_start: 0.7274 (p) cc_final: 0.6555 (t) REVERT: A 274 LEU cc_start: 0.7404 (mp) cc_final: 0.7171 (mp) REVERT: A 280 HIS cc_start: 0.5320 (t70) cc_final: 0.4896 (t70) REVERT: A 288 MET cc_start: 0.6435 (mtm) cc_final: 0.6150 (mtm) REVERT: A 311 LYS cc_start: 0.8472 (tptp) cc_final: 0.8188 (tptp) REVERT: A 386 LEU cc_start: 0.6427 (tp) cc_final: 0.5989 (tt) REVERT: A 886 MET cc_start: 0.6106 (tmm) cc_final: 0.5784 (tmm) REVERT: A 994 ARG cc_start: 0.7403 (mtt90) cc_final: 0.6448 (mmt180) REVERT: A 1027 TYR cc_start: 0.6563 (t80) cc_final: 0.6319 (t80) REVERT: A 1029 LYS cc_start: 0.7907 (ptmt) cc_final: 0.7145 (ptmm) REVERT: A 1043 ARG cc_start: 0.6911 (ttt-90) cc_final: 0.5924 (ttt90) REVERT: A 1048 VAL cc_start: 0.8719 (t) cc_final: 0.8277 (m) REVERT: A 1126 LEU cc_start: 0.8633 (mt) cc_final: 0.8424 (mm) REVERT: A 1158 THR cc_start: 0.7388 (m) cc_final: 0.6825 (p) REVERT: A 1261 GLN cc_start: 0.7373 (tp40) cc_final: 0.6162 (tm-30) REVERT: A 1265 ASP cc_start: 0.7716 (m-30) cc_final: 0.6035 (m-30) REVERT: A 1290 HIS cc_start: 0.6618 (m-70) cc_final: 0.4933 (m-70) REVERT: A 1297 LEU cc_start: 0.8453 (mt) cc_final: 0.8176 (mm) REVERT: A 1298 ASN cc_start: 0.7128 (t0) cc_final: 0.6753 (t0) REVERT: A 1327 LEU cc_start: 0.5617 (mt) cc_final: 0.5291 (mm) REVERT: A 1356 THR cc_start: 0.7874 (m) cc_final: 0.6951 (p) REVERT: A 1374 ILE cc_start: 0.8427 (mt) cc_final: 0.8080 (mm) REVERT: A 1410 MET cc_start: 0.6151 (tpp) cc_final: 0.5418 (tpp) REVERT: A 1418 VAL cc_start: 0.7401 (t) cc_final: 0.7005 (p) REVERT: A 1432 PHE cc_start: 0.6819 (m-80) cc_final: 0.6471 (m-80) REVERT: A 1440 ILE cc_start: 0.6509 (tp) cc_final: 0.6052 (tp) REVERT: A 1520 VAL cc_start: 0.7805 (m) cc_final: 0.7495 (m) REVERT: A 1524 VAL cc_start: 0.7457 (p) cc_final: 0.6925 (p) REVERT: A 1526 GLN cc_start: 0.7453 (pt0) cc_final: 0.7016 (pp30) REVERT: A 1528 ASP cc_start: 0.7575 (m-30) cc_final: 0.6726 (m-30) REVERT: A 1529 ARG cc_start: 0.7474 (tpt90) cc_final: 0.7165 (mmm-85) REVERT: A 1530 GLN cc_start: 0.7228 (mt0) cc_final: 0.6312 (mm-40) REVERT: A 1532 LYS cc_start: 0.8956 (tptp) cc_final: 0.8293 (tppt) REVERT: A 1534 HIS cc_start: 0.7016 (m170) cc_final: 0.6644 (m170) REVERT: B 31 ASN cc_start: 0.6309 (p0) cc_final: 0.6089 (p0) REVERT: B 284 VAL cc_start: 0.7444 (t) cc_final: 0.6574 (t) REVERT: B 288 MET cc_start: 0.7539 (mtm) cc_final: 0.7334 (mtm) REVERT: B 301 LEU cc_start: 0.6771 (tp) cc_final: 0.6512 (tp) REVERT: B 1016 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6962 (mt-10) REVERT: B 1025 VAL cc_start: 0.7924 (m) cc_final: 0.7644 (p) REVERT: B 1029 LYS cc_start: 0.8087 (mttt) cc_final: 0.7535 (tttm) REVERT: B 1048 VAL cc_start: 0.7521 (t) cc_final: 0.7132 (p) REVERT: B 1069 ASP cc_start: 0.7652 (m-30) cc_final: 0.7410 (m-30) REVERT: B 1090 ILE cc_start: 0.8960 (mt) cc_final: 0.8637 (tp) REVERT: B 1098 ASP cc_start: 0.6433 (p0) cc_final: 0.6023 (p0) REVERT: B 1121 GLU cc_start: 0.6495 (tp30) cc_final: 0.6269 (tp30) REVERT: B 1125 LEU cc_start: 0.8219 (mt) cc_final: 0.7596 (mt) REVERT: B 1126 LEU cc_start: 0.7887 (mt) cc_final: 0.6830 (mt) REVERT: B 1130 ILE cc_start: 0.6730 (mt) cc_final: 0.6279 (mt) REVERT: B 1152 SER cc_start: 0.8474 (m) cc_final: 0.8034 (p) REVERT: B 1207 ASP cc_start: 0.6759 (t0) cc_final: 0.6296 (t0) REVERT: B 1213 LYS cc_start: 0.7934 (pptt) cc_final: 0.7601 (ttpp) REVERT: B 1233 GLN cc_start: 0.7360 (mt0) cc_final: 0.7013 (tt0) REVERT: B 1235 LEU cc_start: 0.8838 (mt) cc_final: 0.8558 (mm) REVERT: B 1246 LEU cc_start: 0.8635 (mt) cc_final: 0.8349 (mm) REVERT: B 1256 ILE cc_start: 0.8919 (tp) cc_final: 0.8452 (tp) REVERT: B 1301 TYR cc_start: 0.7608 (m-10) cc_final: 0.7398 (m-10) REVERT: B 1312 ASP cc_start: 0.7223 (p0) cc_final: 0.6587 (p0) REVERT: B 1342 THR cc_start: 0.8065 (m) cc_final: 0.7851 (p) REVERT: B 1343 LYS cc_start: 0.8303 (tppt) cc_final: 0.7875 (tppt) REVERT: B 1430 LYS cc_start: 0.8163 (ptpp) cc_final: 0.7877 (mmmm) REVERT: B 1498 LYS cc_start: 0.8403 (mmtt) cc_final: 0.8099 (mmmt) REVERT: B 1505 MET cc_start: 0.6395 (mtp) cc_final: 0.5662 (mtp) REVERT: B 1515 LYS cc_start: 0.7221 (tppt) cc_final: 0.6923 (tppt) REVERT: B 1522 MET cc_start: 0.7098 (ttp) cc_final: 0.6701 (tpt) REVERT: B 1529 ARG cc_start: 0.7903 (mmm-85) cc_final: 0.7530 (mmm160) REVERT: B 1530 GLN cc_start: 0.7940 (mt0) cc_final: 0.7561 (mt0) REVERT: B 1531 PHE cc_start: 0.7380 (t80) cc_final: 0.7123 (t80) REVERT: B 1543 ILE cc_start: 0.8286 (mt) cc_final: 0.7888 (tp) outliers start: 1 outliers final: 0 residues processed: 521 average time/residue: 0.3539 time to fit residues: 286.2805 Evaluate side-chains 483 residues out of total 2537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 483 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 119 optimal weight: 0.4980 chunk 247 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 260 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 HIS A1205 ASN A1224 ASN ** A1228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 HIS ** B 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 GLN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 ASN B1290 HIS B1484 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5149 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 23515 Z= 0.312 Angle : 0.765 15.461 31845 Z= 0.401 Chirality : 0.047 0.253 3693 Planarity : 0.006 0.108 4070 Dihedral : 5.381 24.863 3187 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.08 % Allowed : 2.68 % Favored : 97.24 % 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: -2.03 (0.15), residues: 2985 helix: -1.12 (0.14), residues: 1317 sheet: -1.27 (0.23), residues: 449 loop : -1.45 (0.17), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP B 828 HIS 0.013 0.002 HIS A 268 PHE 0.033 0.003 PHE B 759 TYR 0.034 0.002 TYR B 297 ARG 0.010 0.001 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 522 time to evaluate : 2.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.7042 (t) cc_final: 0.6776 (m) REVERT: A 80 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7213 (mm-30) REVERT: A 88 LYS cc_start: 0.6942 (tmmt) cc_final: 0.6716 (tmmt) REVERT: A 117 MET cc_start: 0.6570 (ttp) cc_final: 0.6236 (ttp) REVERT: A 264 HIS cc_start: 0.7683 (m170) cc_final: 0.7398 (m170) REVERT: A 284 VAL cc_start: 0.7808 (t) cc_final: 0.7448 (t) REVERT: A 288 MET cc_start: 0.6602 (mtm) cc_final: 0.6259 (mtm) REVERT: A 311 LYS cc_start: 0.8539 (tptp) cc_final: 0.8300 (tptp) REVERT: A 386 LEU cc_start: 0.6480 (tp) cc_final: 0.5873 (tt) REVERT: A 800 MET cc_start: 0.5877 (ptp) cc_final: 0.5567 (ptp) REVERT: A 889 MET cc_start: 0.3224 (tpt) cc_final: 0.2862 (tpt) REVERT: A 1009 SER cc_start: 0.6766 (m) cc_final: 0.6380 (t) REVERT: A 1024 PHE cc_start: 0.6332 (t80) cc_final: 0.5695 (t80) REVERT: A 1029 LYS cc_start: 0.7798 (ptmt) cc_final: 0.7214 (ptmm) REVERT: A 1030 LEU cc_start: 0.6691 (tp) cc_final: 0.6489 (tp) REVERT: A 1044 SER cc_start: 0.8402 (t) cc_final: 0.8199 (p) REVERT: A 1048 VAL cc_start: 0.8682 (t) cc_final: 0.8318 (m) REVERT: A 1072 GLU cc_start: 0.6858 (tp30) cc_final: 0.6499 (tp30) REVERT: A 1103 TYR cc_start: 0.5334 (t80) cc_final: 0.4843 (t80) REVERT: A 1104 THR cc_start: 0.7037 (m) cc_final: 0.6513 (m) REVERT: A 1125 LEU cc_start: 0.8054 (mt) cc_final: 0.7616 (tp) REVERT: A 1126 LEU cc_start: 0.8632 (mt) cc_final: 0.8361 (mm) REVERT: A 1158 THR cc_start: 0.7428 (m) cc_final: 0.6848 (p) REVERT: A 1224 ASN cc_start: 0.8183 (m-40) cc_final: 0.7759 (m110) REVERT: A 1231 LEU cc_start: 0.8387 (tt) cc_final: 0.8176 (tt) REVERT: A 1235 LEU cc_start: 0.8523 (mt) cc_final: 0.7671 (tp) REVERT: A 1261 GLN cc_start: 0.7549 (tp40) cc_final: 0.6631 (tm-30) REVERT: A 1262 THR cc_start: 0.7976 (p) cc_final: 0.7691 (t) REVERT: A 1265 ASP cc_start: 0.7946 (m-30) cc_final: 0.6167 (m-30) REVERT: A 1273 LYS cc_start: 0.8100 (mmmm) cc_final: 0.7718 (mmmt) REVERT: A 1290 HIS cc_start: 0.6661 (m-70) cc_final: 0.4934 (m-70) REVERT: A 1295 LYS cc_start: 0.8708 (pttm) cc_final: 0.8380 (ptmm) REVERT: A 1297 LEU cc_start: 0.8578 (mt) cc_final: 0.8337 (mm) REVERT: A 1298 ASN cc_start: 0.7192 (t0) cc_final: 0.6969 (t0) REVERT: A 1344 LEU cc_start: 0.8367 (tp) cc_final: 0.5976 (tp) REVERT: A 1356 THR cc_start: 0.8228 (m) cc_final: 0.7435 (p) REVERT: A 1374 ILE cc_start: 0.8549 (mt) cc_final: 0.8268 (mm) REVERT: A 1410 MET cc_start: 0.6341 (tpp) cc_final: 0.5641 (tpp) REVERT: A 1440 ILE cc_start: 0.6617 (tp) cc_final: 0.6236 (tt) REVERT: A 1475 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6767 (mt-10) REVERT: A 1520 VAL cc_start: 0.7575 (m) cc_final: 0.7374 (m) REVERT: A 1524 VAL cc_start: 0.7432 (p) cc_final: 0.6654 (p) REVERT: A 1526 GLN cc_start: 0.7532 (pt0) cc_final: 0.7220 (pp30) REVERT: A 1528 ASP cc_start: 0.7536 (m-30) cc_final: 0.6788 (m-30) REVERT: A 1529 ARG cc_start: 0.7693 (tpt90) cc_final: 0.7248 (mmm-85) REVERT: A 1530 GLN cc_start: 0.7319 (mt0) cc_final: 0.6469 (mm-40) REVERT: A 1532 LYS cc_start: 0.9000 (tptp) cc_final: 0.8348 (tppt) REVERT: A 1533 LEU cc_start: 0.8403 (mt) cc_final: 0.8122 (mt) REVERT: A 1534 HIS cc_start: 0.7140 (m170) cc_final: 0.6783 (m170) REVERT: B 102 ARG cc_start: 0.7710 (ptm-80) cc_final: 0.7490 (ptm-80) REVERT: B 179 THR cc_start: 0.7312 (p) cc_final: 0.7098 (t) REVERT: B 189 MET cc_start: 0.7200 (mmt) cc_final: 0.6637 (mmm) REVERT: B 268 HIS cc_start: 0.6620 (t70) cc_final: 0.6244 (t-90) REVERT: B 271 GLU cc_start: 0.6284 (pt0) cc_final: 0.5971 (tp30) REVERT: B 284 VAL cc_start: 0.7539 (t) cc_final: 0.6551 (t) REVERT: B 288 MET cc_start: 0.7656 (mtm) cc_final: 0.7319 (mtm) REVERT: B 311 LYS cc_start: 0.8222 (pttp) cc_final: 0.7991 (pttp) REVERT: B 681 MET cc_start: 0.3809 (tmm) cc_final: 0.3303 (tmm) REVERT: B 800 MET cc_start: 0.4896 (mtp) cc_final: 0.4479 (mtp) REVERT: B 875 SER cc_start: 0.8410 (m) cc_final: 0.7729 (p) REVERT: B 1016 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7122 (mt-10) REVERT: B 1029 LYS cc_start: 0.8386 (mttt) cc_final: 0.7852 (tptp) REVERT: B 1090 ILE cc_start: 0.9053 (mt) cc_final: 0.8792 (tp) REVERT: B 1098 ASP cc_start: 0.6476 (p0) cc_final: 0.6222 (p0) REVERT: B 1121 GLU cc_start: 0.6737 (tp30) cc_final: 0.6434 (tp30) REVERT: B 1125 LEU cc_start: 0.8277 (mt) cc_final: 0.7637 (mt) REVERT: B 1126 LEU cc_start: 0.7994 (mt) cc_final: 0.6824 (mt) REVERT: B 1130 ILE cc_start: 0.7053 (mt) cc_final: 0.6655 (mt) REVERT: B 1152 SER cc_start: 0.8617 (m) cc_final: 0.8168 (p) REVERT: B 1207 ASP cc_start: 0.7063 (t0) cc_final: 0.6621 (t0) REVERT: B 1221 ILE cc_start: 0.8261 (mt) cc_final: 0.8045 (mt) REVERT: B 1233 GLN cc_start: 0.7592 (mt0) cc_final: 0.7246 (mt0) REVERT: B 1238 THR cc_start: 0.7121 (p) cc_final: 0.6898 (p) REVERT: B 1256 ILE cc_start: 0.8921 (tp) cc_final: 0.8555 (tp) REVERT: B 1301 TYR cc_start: 0.7956 (m-10) cc_final: 0.7739 (m-10) REVERT: B 1312 ASP cc_start: 0.7299 (p0) cc_final: 0.6660 (p0) REVERT: B 1364 TYR cc_start: 0.7227 (m-10) cc_final: 0.6750 (m-80) REVERT: B 1379 ILE cc_start: 0.8377 (mt) cc_final: 0.8055 (tp) REVERT: B 1407 LEU cc_start: 0.7807 (pp) cc_final: 0.7127 (pp) REVERT: B 1429 VAL cc_start: 0.8326 (t) cc_final: 0.7844 (p) REVERT: B 1498 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8147 (mmmt) REVERT: B 1505 MET cc_start: 0.6449 (mtp) cc_final: 0.5743 (mtp) REVERT: B 1515 LYS cc_start: 0.7448 (tppt) cc_final: 0.7075 (tppt) REVERT: B 1522 MET cc_start: 0.7457 (ttp) cc_final: 0.6786 (tpt) REVERT: B 1529 ARG cc_start: 0.7976 (mmm-85) cc_final: 0.7623 (mmm160) REVERT: B 1543 ILE cc_start: 0.8353 (mt) cc_final: 0.8091 (tp) outliers start: 2 outliers final: 0 residues processed: 523 average time/residue: 0.3499 time to fit residues: 287.0903 Evaluate side-chains 484 residues out of total 2537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 484 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 0.8980 chunk 261 optimal weight: 0.0170 chunk 57 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 290 optimal weight: 8.9990 chunk 240 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 chunk 96 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1228 GLN ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 ASN B1484 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5088 moved from start: 0.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23515 Z= 0.225 Angle : 0.678 12.418 31845 Z= 0.348 Chirality : 0.046 0.426 3693 Planarity : 0.005 0.117 4070 Dihedral : 5.102 23.699 3187 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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: -1.79 (0.15), residues: 2985 helix: -0.93 (0.14), residues: 1320 sheet: -1.01 (0.24), residues: 452 loop : -1.36 (0.18), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP B1514 HIS 0.009 0.001 HIS A 268 PHE 0.041 0.002 PHE A1024 TYR 0.031 0.002 TYR A1027 ARG 0.013 0.001 ARG A 947 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 516 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6988 (mm-30) REVERT: A 88 LYS cc_start: 0.6921 (tmmt) cc_final: 0.6712 (tmmt) REVERT: A 117 MET cc_start: 0.6450 (ttp) cc_final: 0.6215 (ttp) REVERT: A 241 ARG cc_start: 0.7369 (ptm-80) cc_final: 0.6780 (ptm-80) REVERT: A 264 HIS cc_start: 0.7503 (m170) cc_final: 0.7093 (m170) REVERT: A 284 VAL cc_start: 0.7731 (t) cc_final: 0.7260 (t) REVERT: A 288 MET cc_start: 0.6729 (mtm) cc_final: 0.6120 (mtm) REVERT: A 311 LYS cc_start: 0.8419 (tptp) cc_final: 0.8138 (tptp) REVERT: A 386 LEU cc_start: 0.6385 (tp) cc_final: 0.5847 (tt) REVERT: A 713 MET cc_start: 0.6960 (mmp) cc_final: 0.6614 (mmp) REVERT: A 800 MET cc_start: 0.5868 (ptp) cc_final: 0.5260 (ptp) REVERT: A 886 MET cc_start: 0.5849 (tmm) cc_final: 0.5635 (tmm) REVERT: A 889 MET cc_start: 0.3854 (tpt) cc_final: 0.3497 (tpt) REVERT: A 947 ARG cc_start: 0.6290 (mmp80) cc_final: 0.5441 (mmp80) REVERT: A 994 ARG cc_start: 0.7279 (mpt180) cc_final: 0.6898 (mpt-90) REVERT: A 1009 SER cc_start: 0.6515 (m) cc_final: 0.6205 (t) REVERT: A 1029 LYS cc_start: 0.7853 (ptmt) cc_final: 0.7199 (ptmm) REVERT: A 1048 VAL cc_start: 0.8656 (t) cc_final: 0.8324 (m) REVERT: A 1104 THR cc_start: 0.7018 (m) cc_final: 0.6647 (m) REVERT: A 1126 LEU cc_start: 0.8592 (mt) cc_final: 0.8284 (mm) REVERT: A 1158 THR cc_start: 0.7404 (m) cc_final: 0.6838 (p) REVERT: A 1182 TYR cc_start: 0.6412 (t80) cc_final: 0.5921 (t80) REVERT: A 1224 ASN cc_start: 0.8177 (m-40) cc_final: 0.7683 (m110) REVERT: A 1235 LEU cc_start: 0.8323 (mt) cc_final: 0.7820 (tp) REVERT: A 1261 GLN cc_start: 0.7464 (tp40) cc_final: 0.6573 (tm-30) REVERT: A 1265 ASP cc_start: 0.7735 (m-30) cc_final: 0.5861 (m-30) REVERT: A 1270 THR cc_start: 0.6704 (m) cc_final: 0.6316 (p) REVERT: A 1272 LYS cc_start: 0.8334 (mmpt) cc_final: 0.7763 (mppt) REVERT: A 1273 LYS cc_start: 0.7891 (mmmm) cc_final: 0.7608 (mmmt) REVERT: A 1290 HIS cc_start: 0.6565 (m-70) cc_final: 0.4741 (m-70) REVERT: A 1295 LYS cc_start: 0.8659 (pttm) cc_final: 0.8404 (ptmm) REVERT: A 1298 ASN cc_start: 0.7155 (t0) cc_final: 0.6894 (t0) REVERT: A 1356 THR cc_start: 0.8195 (m) cc_final: 0.7498 (p) REVERT: A 1374 ILE cc_start: 0.8491 (mt) cc_final: 0.8124 (mm) REVERT: A 1376 ASN cc_start: 0.7692 (m-40) cc_final: 0.7221 (m-40) REVERT: A 1410 MET cc_start: 0.6035 (tpp) cc_final: 0.5347 (tpp) REVERT: A 1418 VAL cc_start: 0.7181 (t) cc_final: 0.6843 (p) REVERT: A 1440 ILE cc_start: 0.6473 (tp) cc_final: 0.6063 (tp) REVERT: A 1524 VAL cc_start: 0.7397 (p) cc_final: 0.6601 (p) REVERT: A 1526 GLN cc_start: 0.7416 (pt0) cc_final: 0.7095 (pp30) REVERT: A 1528 ASP cc_start: 0.7460 (m-30) cc_final: 0.6712 (m-30) REVERT: A 1529 ARG cc_start: 0.7633 (tpt90) cc_final: 0.7186 (mmm-85) REVERT: A 1530 GLN cc_start: 0.7258 (mt0) cc_final: 0.6381 (mm-40) REVERT: A 1531 PHE cc_start: 0.7695 (t80) cc_final: 0.7437 (t80) REVERT: A 1532 LYS cc_start: 0.8965 (tptp) cc_final: 0.8260 (tppt) REVERT: A 1533 LEU cc_start: 0.8330 (mt) cc_final: 0.8027 (mt) REVERT: A 1534 HIS cc_start: 0.7132 (m170) cc_final: 0.6660 (m170) REVERT: B 141 MET cc_start: 0.5224 (tmm) cc_final: 0.4863 (tmm) REVERT: B 189 MET cc_start: 0.6930 (mmt) cc_final: 0.6431 (mmm) REVERT: B 268 HIS cc_start: 0.6538 (t70) cc_final: 0.6231 (t-90) REVERT: B 284 VAL cc_start: 0.7664 (t) cc_final: 0.6611 (t) REVERT: B 288 MET cc_start: 0.7529 (mtm) cc_final: 0.7216 (mtm) REVERT: B 311 LYS cc_start: 0.8204 (pttp) cc_final: 0.7949 (pttp) REVERT: B 748 ARG cc_start: 0.6508 (ptt90) cc_final: 0.6192 (tmm160) REVERT: B 800 MET cc_start: 0.4641 (mtp) cc_final: 0.4185 (mtp) REVERT: B 874 LEU cc_start: 0.8461 (mm) cc_final: 0.8246 (mm) REVERT: B 875 SER cc_start: 0.8333 (m) cc_final: 0.7727 (p) REVERT: B 886 MET cc_start: 0.7522 (tmm) cc_final: 0.7046 (tmm) REVERT: B 1016 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7031 (mt-10) REVERT: B 1024 PHE cc_start: 0.6756 (t80) cc_final: 0.6241 (t80) REVERT: B 1025 VAL cc_start: 0.7962 (m) cc_final: 0.7615 (p) REVERT: B 1029 LYS cc_start: 0.7901 (mttt) cc_final: 0.7631 (ttmm) REVERT: B 1090 ILE cc_start: 0.8991 (mt) cc_final: 0.8766 (tp) REVERT: B 1098 ASP cc_start: 0.6329 (p0) cc_final: 0.6037 (p0) REVERT: B 1121 GLU cc_start: 0.6536 (tp30) cc_final: 0.6312 (tp30) REVERT: B 1125 LEU cc_start: 0.8155 (mt) cc_final: 0.7620 (mt) REVERT: B 1126 LEU cc_start: 0.7885 (mt) cc_final: 0.6763 (mt) REVERT: B 1130 ILE cc_start: 0.6906 (mt) cc_final: 0.6571 (mt) REVERT: B 1152 SER cc_start: 0.8557 (m) cc_final: 0.8136 (p) REVERT: B 1207 ASP cc_start: 0.7094 (t0) cc_final: 0.6551 (t0) REVERT: B 1221 ILE cc_start: 0.8190 (mt) cc_final: 0.7989 (mt) REVERT: B 1233 GLN cc_start: 0.7370 (mt0) cc_final: 0.6998 (mt0) REVERT: B 1235 LEU cc_start: 0.8799 (mm) cc_final: 0.8517 (mm) REVERT: B 1238 THR cc_start: 0.7124 (p) cc_final: 0.6870 (p) REVERT: B 1256 ILE cc_start: 0.8897 (tp) cc_final: 0.8461 (tp) REVERT: B 1295 LYS cc_start: 0.9051 (pptt) cc_final: 0.8806 (ptmm) REVERT: B 1301 TYR cc_start: 0.7820 (m-10) cc_final: 0.7332 (m-10) REVERT: B 1312 ASP cc_start: 0.7281 (p0) cc_final: 0.6691 (p0) REVERT: B 1343 LYS cc_start: 0.8272 (tppt) cc_final: 0.8019 (tppt) REVERT: B 1407 LEU cc_start: 0.7610 (pp) cc_final: 0.7300 (pp) REVERT: B 1410 MET cc_start: 0.6150 (mtm) cc_final: 0.5789 (mtm) REVERT: B 1429 VAL cc_start: 0.8289 (t) cc_final: 0.7784 (p) REVERT: B 1498 LYS cc_start: 0.8396 (mmtt) cc_final: 0.8070 (mmmt) REVERT: B 1505 MET cc_start: 0.6585 (mtp) cc_final: 0.5939 (mtp) REVERT: B 1522 MET cc_start: 0.7228 (ttp) cc_final: 0.6714 (tpt) REVERT: B 1529 ARG cc_start: 0.8056 (tpt-90) cc_final: 0.7786 (mmm160) REVERT: B 1543 ILE cc_start: 0.8446 (mt) cc_final: 0.8142 (tp) outliers start: 0 outliers final: 0 residues processed: 516 average time/residue: 0.3415 time to fit residues: 272.5340 Evaluate side-chains 478 residues out of total 2537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 478 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 chunk 211 optimal weight: 0.0870 chunk 164 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 162 optimal weight: 0.6980 chunk 289 optimal weight: 1.9990 chunk 180 optimal weight: 0.0980 chunk 176 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 HIS A1003 ASN ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1419 ASN ** B 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1018 ASN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 ASN B1484 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5059 moved from start: 0.6247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23515 Z= 0.199 Angle : 0.654 13.686 31845 Z= 0.335 Chirality : 0.045 0.282 3693 Planarity : 0.005 0.065 4070 Dihedral : 4.981 24.141 3187 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: -1.59 (0.15), residues: 2985 helix: -0.78 (0.14), residues: 1302 sheet: -0.84 (0.24), residues: 446 loop : -1.27 (0.18), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B1514 HIS 0.013 0.001 HIS A 15 PHE 0.035 0.002 PHE A1024 TYR 0.028 0.002 TYR B1294 ARG 0.009 0.001 ARG A 947 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.6439 (ttp) cc_final: 0.6143 (ttp) REVERT: A 126 MET cc_start: 0.5540 (tpt) cc_final: 0.5149 (tpt) REVERT: A 168 GLU cc_start: 0.7218 (pp20) cc_final: 0.6784 (tm-30) REVERT: A 169 TYR cc_start: 0.5870 (m-10) cc_final: 0.5044 (m-10) REVERT: A 241 ARG cc_start: 0.7443 (ptm-80) cc_final: 0.7117 (ptm-80) REVERT: A 264 HIS cc_start: 0.7436 (m170) cc_final: 0.7209 (m170) REVERT: A 284 VAL cc_start: 0.7752 (t) cc_final: 0.7342 (t) REVERT: A 288 MET cc_start: 0.6612 (mtm) cc_final: 0.6130 (mtm) REVERT: A 311 LYS cc_start: 0.8366 (tptp) cc_final: 0.8045 (tptp) REVERT: A 603 MET cc_start: 0.2921 (mtm) cc_final: 0.2700 (mtm) REVERT: A 713 MET cc_start: 0.7010 (mmp) cc_final: 0.6747 (mmm) REVERT: A 800 MET cc_start: 0.5770 (ptp) cc_final: 0.5390 (ptp) REVERT: A 886 MET cc_start: 0.5990 (tmm) cc_final: 0.5763 (tmm) REVERT: A 889 MET cc_start: 0.3755 (tpt) cc_final: 0.3518 (tpt) REVERT: A 947 ARG cc_start: 0.6331 (mmp80) cc_final: 0.6076 (mmm160) REVERT: A 1009 SER cc_start: 0.6426 (m) cc_final: 0.6086 (t) REVERT: A 1025 VAL cc_start: 0.8403 (p) cc_final: 0.7875 (p) REVERT: A 1048 VAL cc_start: 0.8667 (t) cc_final: 0.8331 (m) REVERT: A 1126 LEU cc_start: 0.8463 (mt) cc_final: 0.8180 (mm) REVERT: A 1158 THR cc_start: 0.7369 (m) cc_final: 0.6788 (p) REVERT: A 1182 TYR cc_start: 0.6386 (t80) cc_final: 0.5967 (t80) REVERT: A 1209 GLU cc_start: 0.7200 (pp20) cc_final: 0.6969 (pp20) REVERT: A 1224 ASN cc_start: 0.8237 (m-40) cc_final: 0.7784 (m110) REVERT: A 1235 LEU cc_start: 0.8277 (mt) cc_final: 0.7784 (tp) REVERT: A 1261 GLN cc_start: 0.7433 (tp40) cc_final: 0.6520 (tm-30) REVERT: A 1265 ASP cc_start: 0.7685 (m-30) cc_final: 0.5791 (m-30) REVERT: A 1270 THR cc_start: 0.6704 (m) cc_final: 0.6204 (p) REVERT: A 1272 LYS cc_start: 0.8381 (mmpt) cc_final: 0.7705 (mppt) REVERT: A 1290 HIS cc_start: 0.6511 (m-70) cc_final: 0.4735 (m-70) REVERT: A 1298 ASN cc_start: 0.7107 (t0) cc_final: 0.6790 (t0) REVERT: A 1356 THR cc_start: 0.8151 (m) cc_final: 0.7646 (p) REVERT: A 1374 ILE cc_start: 0.8471 (mt) cc_final: 0.8124 (mm) REVERT: A 1376 ASN cc_start: 0.7634 (m-40) cc_final: 0.7303 (m-40) REVERT: A 1410 MET cc_start: 0.6090 (tpp) cc_final: 0.5242 (tpp) REVERT: A 1418 VAL cc_start: 0.7078 (t) cc_final: 0.6781 (p) REVERT: A 1474 ILE cc_start: 0.8513 (pt) cc_final: 0.8298 (pt) REVERT: A 1524 VAL cc_start: 0.7334 (p) cc_final: 0.6390 (p) REVERT: A 1526 GLN cc_start: 0.7373 (pt0) cc_final: 0.7068 (pp30) REVERT: A 1528 ASP cc_start: 0.7357 (m-30) cc_final: 0.6593 (m-30) REVERT: A 1529 ARG cc_start: 0.7591 (tpt90) cc_final: 0.7107 (mmm-85) REVERT: A 1530 GLN cc_start: 0.7243 (mt0) cc_final: 0.6388 (mm-40) REVERT: A 1531 PHE cc_start: 0.7611 (t80) cc_final: 0.7385 (t80) REVERT: A 1532 LYS cc_start: 0.8954 (tptp) cc_final: 0.8292 (tppt) REVERT: A 1533 LEU cc_start: 0.8234 (mt) cc_final: 0.7973 (mt) REVERT: A 1534 HIS cc_start: 0.6842 (m170) cc_final: 0.6451 (m170) REVERT: B 141 MET cc_start: 0.5182 (tmm) cc_final: 0.4978 (tmm) REVERT: B 189 MET cc_start: 0.6631 (mmt) cc_final: 0.6192 (mmm) REVERT: B 192 VAL cc_start: 0.7542 (p) cc_final: 0.6993 (t) REVERT: B 271 GLU cc_start: 0.5971 (tp30) cc_final: 0.5598 (pt0) REVERT: B 284 VAL cc_start: 0.7643 (t) cc_final: 0.6790 (t) REVERT: B 288 MET cc_start: 0.7426 (mtm) cc_final: 0.7216 (mtt) REVERT: B 681 MET cc_start: 0.3521 (tmm) cc_final: 0.3082 (tmm) REVERT: B 748 ARG cc_start: 0.6551 (ptt90) cc_final: 0.6187 (tmm160) REVERT: B 875 SER cc_start: 0.8305 (m) cc_final: 0.7770 (p) REVERT: B 886 MET cc_start: 0.7310 (tmm) cc_final: 0.6712 (tmm) REVERT: B 1016 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6948 (mt-10) REVERT: B 1025 VAL cc_start: 0.7919 (m) cc_final: 0.7543 (p) REVERT: B 1029 LYS cc_start: 0.7935 (mttt) cc_final: 0.7640 (ttmm) REVERT: B 1076 ASP cc_start: 0.7015 (p0) cc_final: 0.6638 (p0) REVERT: B 1090 ILE cc_start: 0.8952 (mt) cc_final: 0.8704 (tp) REVERT: B 1098 ASP cc_start: 0.6335 (p0) cc_final: 0.6037 (p0) REVERT: B 1113 LYS cc_start: 0.7805 (tppt) cc_final: 0.7542 (ttpt) REVERT: B 1126 LEU cc_start: 0.7830 (mt) cc_final: 0.6714 (mt) REVERT: B 1130 ILE cc_start: 0.7026 (mt) cc_final: 0.6722 (mt) REVERT: B 1152 SER cc_start: 0.8586 (m) cc_final: 0.8178 (p) REVERT: B 1207 ASP cc_start: 0.7096 (t0) cc_final: 0.6550 (t0) REVERT: B 1233 GLN cc_start: 0.7379 (mt0) cc_final: 0.6988 (mt0) REVERT: B 1235 LEU cc_start: 0.8788 (mm) cc_final: 0.8478 (mm) REVERT: B 1245 LYS cc_start: 0.8708 (pptt) cc_final: 0.8362 (pptt) REVERT: B 1256 ILE cc_start: 0.8912 (tp) cc_final: 0.8519 (tp) REVERT: B 1312 ASP cc_start: 0.7131 (p0) cc_final: 0.6709 (p0) REVERT: B 1372 VAL cc_start: 0.8265 (t) cc_final: 0.8047 (t) REVERT: B 1401 ARG cc_start: 0.6822 (mtp85) cc_final: 0.6530 (mtp85) REVERT: B 1407 LEU cc_start: 0.7675 (pp) cc_final: 0.7446 (pp) REVERT: B 1410 MET cc_start: 0.6176 (mtm) cc_final: 0.5757 (mtm) REVERT: B 1429 VAL cc_start: 0.8284 (t) cc_final: 0.7799 (p) REVERT: B 1498 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7983 (mmmt) REVERT: B 1505 MET cc_start: 0.6522 (mtp) cc_final: 0.5712 (mtp) REVERT: B 1522 MET cc_start: 0.7235 (ttp) cc_final: 0.6657 (tpt) REVERT: B 1543 ILE cc_start: 0.8381 (mt) cc_final: 0.8098 (tp) outliers start: 0 outliers final: 0 residues processed: 506 average time/residue: 0.3583 time to fit residues: 280.7849 Evaluate side-chains 471 residues out of total 2537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 471 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 87 optimal weight: 0.0470 chunk 56 optimal weight: 4.9990 chunk 183 optimal weight: 0.0270 chunk 196 optimal weight: 20.0000 chunk 142 optimal weight: 0.0170 chunk 26 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 263 optimal weight: 1.9990 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 61 ASN ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 ASN ** A1224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN ** B 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 ASN B1484 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5039 moved from start: 0.6409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23515 Z= 0.184 Angle : 0.646 13.788 31845 Z= 0.327 Chirality : 0.045 0.209 3693 Planarity : 0.005 0.059 4070 Dihedral : 4.840 23.092 3187 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: -1.46 (0.15), residues: 2985 helix: -0.70 (0.14), residues: 1308 sheet: -0.80 (0.24), residues: 456 loop : -1.14 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 829 HIS 0.007 0.001 HIS A1408 PHE 0.035 0.002 PHE A1078 TYR 0.017 0.001 TYR B1541 ARG 0.011 0.001 ARG A1074 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 499 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.6361 (ttp) cc_final: 0.6078 (ttp) REVERT: A 234 LYS cc_start: 0.8185 (mmmt) cc_final: 0.7852 (mmmt) REVERT: A 241 ARG cc_start: 0.7336 (ptm-80) cc_final: 0.7032 (ptm-80) REVERT: A 264 HIS cc_start: 0.7422 (m170) cc_final: 0.7151 (m170) REVERT: A 288 MET cc_start: 0.6614 (mtm) cc_final: 0.6089 (mtm) REVERT: A 311 LYS cc_start: 0.8300 (tptp) cc_final: 0.7979 (tptp) REVERT: A 599 MET cc_start: 0.2375 (pmm) cc_final: 0.1387 (pmm) REVERT: A 800 MET cc_start: 0.5937 (ptp) cc_final: 0.5309 (ptp) REVERT: A 876 GLU cc_start: 0.7858 (pt0) cc_final: 0.7499 (pt0) REVERT: A 889 MET cc_start: 0.3684 (tpt) cc_final: 0.3480 (tpt) REVERT: A 947 ARG cc_start: 0.6307 (mmp80) cc_final: 0.5982 (mmm160) REVERT: A 1009 SER cc_start: 0.6408 (m) cc_final: 0.6050 (t) REVERT: A 1048 VAL cc_start: 0.8632 (t) cc_final: 0.8289 (m) REVERT: A 1126 LEU cc_start: 0.8447 (mt) cc_final: 0.8218 (mm) REVERT: A 1158 THR cc_start: 0.7380 (m) cc_final: 0.6833 (p) REVERT: A 1182 TYR cc_start: 0.6373 (t80) cc_final: 0.5920 (t80) REVERT: A 1224 ASN cc_start: 0.8343 (m-40) cc_final: 0.7842 (m110) REVERT: A 1235 LEU cc_start: 0.8196 (mt) cc_final: 0.7464 (tt) REVERT: A 1245 LYS cc_start: 0.8249 (tmtt) cc_final: 0.7973 (ptmm) REVERT: A 1261 GLN cc_start: 0.7345 (tp40) cc_final: 0.6533 (tm-30) REVERT: A 1262 THR cc_start: 0.7906 (p) cc_final: 0.7542 (p) REVERT: A 1265 ASP cc_start: 0.7620 (m-30) cc_final: 0.5576 (m-30) REVERT: A 1290 HIS cc_start: 0.6458 (m-70) cc_final: 0.4819 (m-70) REVERT: A 1298 ASN cc_start: 0.7143 (t0) cc_final: 0.6857 (t0) REVERT: A 1356 THR cc_start: 0.8094 (m) cc_final: 0.7344 (p) REVERT: A 1374 ILE cc_start: 0.8451 (mt) cc_final: 0.8125 (mm) REVERT: A 1376 ASN cc_start: 0.7594 (m-40) cc_final: 0.7273 (m-40) REVERT: A 1410 MET cc_start: 0.6110 (tpp) cc_final: 0.5304 (tpp) REVERT: A 1418 VAL cc_start: 0.6810 (t) cc_final: 0.6424 (p) REVERT: A 1432 PHE cc_start: 0.6797 (m-80) cc_final: 0.6508 (m-80) REVERT: A 1524 VAL cc_start: 0.7212 (p) cc_final: 0.6254 (p) REVERT: A 1526 GLN cc_start: 0.7311 (pt0) cc_final: 0.7003 (pp30) REVERT: A 1528 ASP cc_start: 0.7312 (m-30) cc_final: 0.6532 (m-30) REVERT: A 1529 ARG cc_start: 0.7557 (tpt90) cc_final: 0.7138 (mmm-85) REVERT: A 1531 PHE cc_start: 0.7598 (t80) cc_final: 0.7280 (t80) REVERT: A 1532 LYS cc_start: 0.8948 (tptp) cc_final: 0.8329 (tppt) REVERT: A 1533 LEU cc_start: 0.8203 (mt) cc_final: 0.7904 (mt) REVERT: B 141 MET cc_start: 0.5266 (tmm) cc_final: 0.4934 (tmm) REVERT: B 189 MET cc_start: 0.6482 (mmt) cc_final: 0.6050 (mmm) REVERT: B 192 VAL cc_start: 0.7510 (p) cc_final: 0.6849 (t) REVERT: B 259 LEU cc_start: 0.8596 (pp) cc_final: 0.8373 (pp) REVERT: B 271 GLU cc_start: 0.5900 (tp30) cc_final: 0.5497 (pt0) REVERT: B 284 VAL cc_start: 0.7522 (t) cc_final: 0.6564 (t) REVERT: B 288 MET cc_start: 0.7407 (mtm) cc_final: 0.7074 (mtt) REVERT: B 573 MET cc_start: 0.1231 (ptm) cc_final: 0.0765 (ptm) REVERT: B 681 MET cc_start: 0.3780 (tmm) cc_final: 0.3265 (tmm) REVERT: B 718 LEU cc_start: 0.5330 (mp) cc_final: 0.5079 (mp) REVERT: B 752 MET cc_start: -0.0910 (mtt) cc_final: -0.1597 (mmm) REVERT: B 875 SER cc_start: 0.8273 (m) cc_final: 0.7615 (p) REVERT: B 1016 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7061 (mt-10) REVERT: B 1024 PHE cc_start: 0.6603 (t80) cc_final: 0.6105 (t80) REVERT: B 1025 VAL cc_start: 0.7823 (m) cc_final: 0.7536 (p) REVERT: B 1076 ASP cc_start: 0.6980 (p0) cc_final: 0.6608 (p0) REVERT: B 1090 ILE cc_start: 0.8937 (mt) cc_final: 0.8693 (tp) REVERT: B 1098 ASP cc_start: 0.6295 (p0) cc_final: 0.6038 (p0) REVERT: B 1113 LYS cc_start: 0.7869 (tppt) cc_final: 0.7637 (ttmt) REVERT: B 1126 LEU cc_start: 0.7830 (mt) cc_final: 0.6789 (mt) REVERT: B 1130 ILE cc_start: 0.7044 (mt) cc_final: 0.6711 (mt) REVERT: B 1152 SER cc_start: 0.8536 (m) cc_final: 0.8238 (p) REVERT: B 1207 ASP cc_start: 0.7092 (t0) cc_final: 0.6552 (t0) REVERT: B 1213 LYS cc_start: 0.7805 (ptmm) cc_final: 0.7602 (ttpp) REVERT: B 1221 ILE cc_start: 0.8008 (mt) cc_final: 0.7791 (mt) REVERT: B 1233 GLN cc_start: 0.7364 (mt0) cc_final: 0.7075 (mt0) REVERT: B 1235 LEU cc_start: 0.8747 (mm) cc_final: 0.8415 (mm) REVERT: B 1238 THR cc_start: 0.7038 (p) cc_final: 0.6807 (p) REVERT: B 1242 ILE cc_start: 0.8220 (pt) cc_final: 0.7504 (mp) REVERT: B 1245 LYS cc_start: 0.8702 (pptt) cc_final: 0.8225 (pptt) REVERT: B 1256 ILE cc_start: 0.8905 (tp) cc_final: 0.8476 (tp) REVERT: B 1301 TYR cc_start: 0.7693 (m-10) cc_final: 0.7463 (m-10) REVERT: B 1312 ASP cc_start: 0.7064 (p0) cc_final: 0.6622 (p0) REVERT: B 1372 VAL cc_start: 0.8707 (t) cc_final: 0.8430 (t) REVERT: B 1409 GLN cc_start: 0.7176 (mp10) cc_final: 0.6945 (mp10) REVERT: B 1410 MET cc_start: 0.6202 (mtm) cc_final: 0.5891 (mtm) REVERT: B 1429 VAL cc_start: 0.8309 (t) cc_final: 0.7850 (p) REVERT: B 1498 LYS cc_start: 0.8326 (mmtt) cc_final: 0.7893 (mmmt) REVERT: B 1505 MET cc_start: 0.6503 (mtp) cc_final: 0.5696 (mtp) REVERT: B 1522 MET cc_start: 0.7151 (ttp) cc_final: 0.6838 (tpt) REVERT: B 1543 ILE cc_start: 0.8355 (mt) cc_final: 0.8079 (tp) outliers start: 0 outliers final: 0 residues processed: 499 average time/residue: 0.3486 time to fit residues: 271.1674 Evaluate side-chains 475 residues out of total 2537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 475 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 0.8980 chunk 252 optimal weight: 2.9990 chunk 269 optimal weight: 0.9980 chunk 276 optimal weight: 0.9990 chunk 162 optimal weight: 0.0970 chunk 117 optimal weight: 0.9980 chunk 211 optimal weight: 0.0470 chunk 82 optimal weight: 10.0000 chunk 243 optimal weight: 4.9990 chunk 254 optimal weight: 0.5980 chunk 268 optimal weight: 2.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1290 HIS B1484 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5091 moved from start: 0.6697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23515 Z= 0.206 Angle : 0.655 12.814 31845 Z= 0.335 Chirality : 0.045 0.209 3693 Planarity : 0.005 0.065 4070 Dihedral : 4.850 24.264 3187 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -1.36 (0.15), residues: 2985 helix: -0.64 (0.14), residues: 1295 sheet: -0.62 (0.25), residues: 433 loop : -1.12 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP B1514 HIS 0.012 0.001 HIS A 15 PHE 0.026 0.002 PHE A 204 TYR 0.016 0.001 TYR B 297 ARG 0.009 0.001 ARG A 947 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 501 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.6435 (ttp) cc_final: 0.6166 (ttp) REVERT: A 126 MET cc_start: 0.6544 (ttm) cc_final: 0.6058 (ttt) REVERT: A 169 TYR cc_start: 0.5848 (m-10) cc_final: 0.5569 (m-10) REVERT: A 234 LYS cc_start: 0.8240 (mmmt) cc_final: 0.7899 (mmmt) REVERT: A 241 ARG cc_start: 0.7439 (ptm-80) cc_final: 0.7181 (ptm-80) REVERT: A 264 HIS cc_start: 0.7424 (m170) cc_final: 0.7138 (m170) REVERT: A 311 LYS cc_start: 0.8339 (tptp) cc_final: 0.7998 (tptp) REVERT: A 386 LEU cc_start: 0.6088 (tp) cc_final: 0.5696 (tt) REVERT: A 800 MET cc_start: 0.5805 (ptp) cc_final: 0.5543 (ptp) REVERT: A 876 GLU cc_start: 0.7833 (pt0) cc_final: 0.7448 (pt0) REVERT: A 889 MET cc_start: 0.3647 (tpt) cc_final: 0.3417 (tpt) REVERT: A 947 ARG cc_start: 0.6419 (mmp80) cc_final: 0.5760 (mmm160) REVERT: A 1009 SER cc_start: 0.6449 (m) cc_final: 0.6105 (t) REVERT: A 1048 VAL cc_start: 0.8580 (t) cc_final: 0.8258 (m) REVERT: A 1072 GLU cc_start: 0.6442 (tp30) cc_final: 0.5967 (tp30) REVERT: A 1126 LEU cc_start: 0.8442 (mt) cc_final: 0.8239 (mm) REVERT: A 1158 THR cc_start: 0.7423 (m) cc_final: 0.6896 (p) REVERT: A 1224 ASN cc_start: 0.8367 (m-40) cc_final: 0.7866 (m110) REVERT: A 1235 LEU cc_start: 0.8250 (mt) cc_final: 0.7562 (tt) REVERT: A 1238 THR cc_start: 0.7218 (t) cc_final: 0.6800 (p) REVERT: A 1261 GLN cc_start: 0.7427 (tp40) cc_final: 0.6577 (tm-30) REVERT: A 1262 THR cc_start: 0.7997 (p) cc_final: 0.7625 (p) REVERT: A 1265 ASP cc_start: 0.7687 (m-30) cc_final: 0.5751 (m-30) REVERT: A 1273 LYS cc_start: 0.7700 (tptp) cc_final: 0.7464 (tptm) REVERT: A 1290 HIS cc_start: 0.6444 (m-70) cc_final: 0.4801 (m-70) REVERT: A 1298 ASN cc_start: 0.7175 (t0) cc_final: 0.6869 (t0) REVERT: A 1374 ILE cc_start: 0.8486 (mt) cc_final: 0.8165 (mm) REVERT: A 1376 ASN cc_start: 0.7670 (m-40) cc_final: 0.7371 (m-40) REVERT: A 1410 MET cc_start: 0.6185 (tpp) cc_final: 0.5348 (tpp) REVERT: A 1440 ILE cc_start: 0.6513 (tp) cc_final: 0.5956 (tt) REVERT: A 1526 GLN cc_start: 0.7429 (pt0) cc_final: 0.7066 (pp30) REVERT: A 1528 ASP cc_start: 0.7347 (m-30) cc_final: 0.6846 (m-30) REVERT: A 1529 ARG cc_start: 0.7583 (tpt90) cc_final: 0.7196 (mmm-85) REVERT: A 1531 PHE cc_start: 0.7682 (t80) cc_final: 0.7332 (t80) REVERT: A 1532 LYS cc_start: 0.8984 (tptp) cc_final: 0.8417 (tppt) REVERT: A 1533 LEU cc_start: 0.8246 (mt) cc_final: 0.7983 (mt) REVERT: B 141 MET cc_start: 0.5273 (tmm) cc_final: 0.4898 (tmm) REVERT: B 189 MET cc_start: 0.6741 (mmt) cc_final: 0.6327 (mmm) REVERT: B 192 VAL cc_start: 0.7626 (p) cc_final: 0.6990 (t) REVERT: B 259 LEU cc_start: 0.8652 (pp) cc_final: 0.8449 (pp) REVERT: B 271 GLU cc_start: 0.5877 (tp30) cc_final: 0.5363 (pt0) REVERT: B 288 MET cc_start: 0.7409 (mtm) cc_final: 0.7122 (mtt) REVERT: B 290 LYS cc_start: 0.5225 (pttp) cc_final: 0.4945 (pttp) REVERT: B 573 MET cc_start: 0.1230 (ptm) cc_final: 0.0587 (ptm) REVERT: B 681 MET cc_start: 0.3655 (tmm) cc_final: 0.3197 (tmm) REVERT: B 718 LEU cc_start: 0.5460 (mp) cc_final: 0.5173 (mp) REVERT: B 748 ARG cc_start: 0.6501 (ptt90) cc_final: 0.6113 (tmm160) REVERT: B 752 MET cc_start: -0.0730 (mtt) cc_final: -0.1208 (mmm) REVERT: B 875 SER cc_start: 0.8427 (m) cc_final: 0.7709 (p) REVERT: B 878 LEU cc_start: 0.8278 (tp) cc_final: 0.7995 (tp) REVERT: B 1016 GLU cc_start: 0.7341 (mt-10) cc_final: 0.7043 (mt-10) REVERT: B 1024 PHE cc_start: 0.6634 (t80) cc_final: 0.6281 (t80) REVERT: B 1025 VAL cc_start: 0.7892 (m) cc_final: 0.7590 (p) REVERT: B 1029 LYS cc_start: 0.7987 (mttt) cc_final: 0.7509 (ttmm) REVERT: B 1063 SER cc_start: 0.8364 (p) cc_final: 0.7960 (p) REVERT: B 1076 ASP cc_start: 0.7075 (p0) cc_final: 0.6762 (p0) REVERT: B 1090 ILE cc_start: 0.8955 (mt) cc_final: 0.8725 (tp) REVERT: B 1098 ASP cc_start: 0.6354 (p0) cc_final: 0.6023 (p0) REVERT: B 1113 LYS cc_start: 0.7834 (tppt) cc_final: 0.7516 (ttmt) REVERT: B 1126 LEU cc_start: 0.7886 (mt) cc_final: 0.6918 (mt) REVERT: B 1130 ILE cc_start: 0.7068 (mt) cc_final: 0.6762 (mt) REVERT: B 1152 SER cc_start: 0.8578 (m) cc_final: 0.8358 (p) REVERT: B 1154 LYS cc_start: 0.8106 (mmmt) cc_final: 0.7837 (mmmt) REVERT: B 1207 ASP cc_start: 0.7295 (t0) cc_final: 0.6756 (t0) REVERT: B 1217 LEU cc_start: 0.8319 (tp) cc_final: 0.8118 (tp) REVERT: B 1233 GLN cc_start: 0.7376 (mt0) cc_final: 0.6976 (mt0) REVERT: B 1235 LEU cc_start: 0.8764 (mm) cc_final: 0.8458 (mm) REVERT: B 1245 LYS cc_start: 0.8726 (pptt) cc_final: 0.8217 (pptt) REVERT: B 1256 ILE cc_start: 0.8926 (tp) cc_final: 0.8583 (tp) REVERT: B 1312 ASP cc_start: 0.7061 (p0) cc_final: 0.6682 (p0) REVERT: B 1372 VAL cc_start: 0.8726 (t) cc_final: 0.8338 (t) REVERT: B 1409 GLN cc_start: 0.7141 (mp10) cc_final: 0.6919 (mp10) REVERT: B 1410 MET cc_start: 0.6227 (mtm) cc_final: 0.5860 (mtm) REVERT: B 1429 VAL cc_start: 0.8367 (t) cc_final: 0.7875 (p) REVERT: B 1498 LYS cc_start: 0.8342 (mmtt) cc_final: 0.7892 (mmmt) REVERT: B 1505 MET cc_start: 0.6659 (mtp) cc_final: 0.5774 (mtp) REVERT: B 1522 MET cc_start: 0.7221 (ttp) cc_final: 0.6910 (tpt) outliers start: 0 outliers final: 0 residues processed: 501 average time/residue: 0.3418 time to fit residues: 265.0369 Evaluate side-chains 474 residues out of total 2537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 474 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 0.4980 chunk 284 optimal weight: 0.7980 chunk 173 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 198 optimal weight: 0.0470 chunk 298 optimal weight: 0.9990 chunk 275 optimal weight: 0.6980 chunk 237 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A1215 ASN ** A1224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1290 HIS ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 ASN B1484 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5068 moved from start: 0.6863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23515 Z= 0.187 Angle : 0.642 11.539 31845 Z= 0.327 Chirality : 0.045 0.208 3693 Planarity : 0.005 0.055 4070 Dihedral : 4.761 22.557 3187 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.04 % Allowed : 0.12 % Favored : 99.84 % 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: -1.26 (0.15), residues: 2985 helix: -0.53 (0.14), residues: 1308 sheet: -0.71 (0.25), residues: 441 loop : -1.05 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 828 HIS 0.011 0.001 HIS A 15 PHE 0.025 0.002 PHE B1017 TYR 0.016 0.001 TYR B1004 ARG 0.010 0.001 ARG A 818 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 493 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 CYS cc_start: 0.7244 (m) cc_final: 0.6210 (m) REVERT: A 117 MET cc_start: 0.6357 (ttp) cc_final: 0.6120 (ttp) REVERT: A 234 LYS cc_start: 0.8300 (mmmt) cc_final: 0.8000 (mmmt) REVERT: A 241 ARG cc_start: 0.7444 (ptm-80) cc_final: 0.7155 (ptm-80) REVERT: A 264 HIS cc_start: 0.7397 (m170) cc_final: 0.7041 (m170) REVERT: A 311 LYS cc_start: 0.8299 (tptp) cc_final: 0.7942 (tptp) REVERT: A 800 MET cc_start: 0.5975 (ptp) cc_final: 0.5315 (ptp) REVERT: A 876 GLU cc_start: 0.7797 (pt0) cc_final: 0.7385 (pt0) REVERT: A 947 ARG cc_start: 0.6172 (mmp80) cc_final: 0.5460 (mmm160) REVERT: A 1009 SER cc_start: 0.6492 (m) cc_final: 0.6124 (t) REVERT: A 1025 VAL cc_start: 0.8303 (p) cc_final: 0.8099 (p) REVERT: A 1048 VAL cc_start: 0.8548 (t) cc_final: 0.8162 (m) REVERT: A 1072 GLU cc_start: 0.6424 (tp30) cc_final: 0.5955 (tp30) REVERT: A 1126 LEU cc_start: 0.8469 (mt) cc_final: 0.8223 (mm) REVERT: A 1158 THR cc_start: 0.7453 (m) cc_final: 0.6949 (p) REVERT: A 1171 LEU cc_start: 0.7023 (mt) cc_final: 0.6708 (mt) REVERT: A 1224 ASN cc_start: 0.8423 (m-40) cc_final: 0.7758 (m110) REVERT: A 1235 LEU cc_start: 0.8237 (mt) cc_final: 0.7798 (tp) REVERT: A 1238 THR cc_start: 0.7169 (t) cc_final: 0.6832 (p) REVERT: A 1261 GLN cc_start: 0.7373 (tp40) cc_final: 0.6451 (tm-30) REVERT: A 1262 THR cc_start: 0.7968 (p) cc_final: 0.7570 (p) REVERT: A 1265 ASP cc_start: 0.7595 (m-30) cc_final: 0.5651 (m-30) REVERT: A 1290 HIS cc_start: 0.6339 (m90) cc_final: 0.5208 (m90) REVERT: A 1298 ASN cc_start: 0.7141 (t0) cc_final: 0.6878 (t0) REVERT: A 1374 ILE cc_start: 0.8469 (mt) cc_final: 0.8108 (mm) REVERT: A 1376 ASN cc_start: 0.7628 (m-40) cc_final: 0.7396 (m-40) REVERT: A 1410 MET cc_start: 0.6115 (tpp) cc_final: 0.5318 (tpp) REVERT: A 1432 PHE cc_start: 0.6765 (m-80) cc_final: 0.6536 (m-80) REVERT: A 1512 TYR cc_start: 0.5927 (m-80) cc_final: 0.5619 (m-80) REVERT: A 1524 VAL cc_start: 0.7234 (p) cc_final: 0.6225 (p) REVERT: A 1526 GLN cc_start: 0.7371 (pt0) cc_final: 0.7116 (pp30) REVERT: A 1528 ASP cc_start: 0.7338 (m-30) cc_final: 0.6508 (m-30) REVERT: A 1529 ARG cc_start: 0.7541 (tpt90) cc_final: 0.7130 (mmm-85) REVERT: A 1530 GLN cc_start: 0.6607 (tp-100) cc_final: 0.5355 (mm-40) REVERT: A 1531 PHE cc_start: 0.7692 (t80) cc_final: 0.7206 (t80) REVERT: A 1532 LYS cc_start: 0.8974 (tptp) cc_final: 0.8424 (tppt) REVERT: B 141 MET cc_start: 0.5218 (tmm) cc_final: 0.4810 (tmm) REVERT: B 189 MET cc_start: 0.6509 (mmt) cc_final: 0.6081 (mmm) REVERT: B 192 VAL cc_start: 0.7505 (p) cc_final: 0.6830 (t) REVERT: B 288 MET cc_start: 0.7361 (mtm) cc_final: 0.7028 (mtt) REVERT: B 290 LYS cc_start: 0.5264 (pttp) cc_final: 0.5002 (pttp) REVERT: B 385 VAL cc_start: 0.7827 (m) cc_final: 0.7520 (p) REVERT: B 573 MET cc_start: -0.0107 (ptm) cc_final: -0.0667 (ptm) REVERT: B 681 MET cc_start: 0.3756 (tmm) cc_final: 0.3201 (tmm) REVERT: B 718 LEU cc_start: 0.5474 (mp) cc_final: 0.5154 (mp) REVERT: B 748 ARG cc_start: 0.5215 (ptt90) cc_final: 0.4743 (tmm160) REVERT: B 752 MET cc_start: -0.0642 (mtt) cc_final: -0.1144 (mmm) REVERT: B 875 SER cc_start: 0.8390 (m) cc_final: 0.7701 (p) REVERT: B 878 LEU cc_start: 0.8200 (tp) cc_final: 0.7927 (tp) REVERT: B 1016 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7158 (mt-10) REVERT: B 1025 VAL cc_start: 0.7777 (m) cc_final: 0.7529 (p) REVERT: B 1029 LYS cc_start: 0.7973 (mttt) cc_final: 0.7454 (ttmm) REVERT: B 1063 SER cc_start: 0.8329 (p) cc_final: 0.7956 (p) REVERT: B 1069 ASP cc_start: 0.7693 (m-30) cc_final: 0.7481 (m-30) REVERT: B 1076 ASP cc_start: 0.7001 (p0) cc_final: 0.6667 (p0) REVERT: B 1090 ILE cc_start: 0.8945 (mt) cc_final: 0.8680 (tp) REVERT: B 1113 LYS cc_start: 0.7868 (tppt) cc_final: 0.7521 (ttmt) REVERT: B 1126 LEU cc_start: 0.7931 (mt) cc_final: 0.7178 (mt) REVERT: B 1152 SER cc_start: 0.8568 (m) cc_final: 0.8317 (p) REVERT: B 1207 ASP cc_start: 0.7192 (t0) cc_final: 0.6697 (t0) REVERT: B 1213 LYS cc_start: 0.8104 (pttp) cc_final: 0.7693 (ptmm) REVERT: B 1233 GLN cc_start: 0.7335 (mt0) cc_final: 0.7001 (mt0) REVERT: B 1235 LEU cc_start: 0.8772 (mm) cc_final: 0.8395 (mm) REVERT: B 1242 ILE cc_start: 0.8275 (pt) cc_final: 0.7593 (mp) REVERT: B 1245 LYS cc_start: 0.8802 (pptt) cc_final: 0.8349 (pptt) REVERT: B 1256 ILE cc_start: 0.8948 (tp) cc_final: 0.8592 (tp) REVERT: B 1301 TYR cc_start: 0.7736 (m-10) cc_final: 0.7302 (m-80) REVERT: B 1312 ASP cc_start: 0.7051 (p0) cc_final: 0.6730 (p0) REVERT: B 1407 LEU cc_start: 0.7677 (pp) cc_final: 0.7423 (pp) REVERT: B 1410 MET cc_start: 0.6203 (mtm) cc_final: 0.5868 (mtm) REVERT: B 1429 VAL cc_start: 0.8368 (t) cc_final: 0.7892 (p) REVERT: B 1498 LYS cc_start: 0.8328 (mmtt) cc_final: 0.7888 (mmmt) REVERT: B 1505 MET cc_start: 0.6588 (mtp) cc_final: 0.5782 (mtp) REVERT: B 1522 MET cc_start: 0.7077 (ttp) cc_final: 0.6779 (tpt) REVERT: B 1529 ARG cc_start: 0.7867 (mmm160) cc_final: 0.7310 (tpt90) REVERT: B 1543 ILE cc_start: 0.8401 (tp) cc_final: 0.8166 (tp) outliers start: 1 outliers final: 0 residues processed: 494 average time/residue: 0.3443 time to fit residues: 264.2798 Evaluate side-chains 478 residues out of total 2537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 478 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 0.9990 chunk 253 optimal weight: 0.0670 chunk 72 optimal weight: 0.9990 chunk 219 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 238 optimal weight: 0.0970 chunk 99 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 HIS ** A 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1484 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.206119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.156123 restraints weight = 93347.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.164608 restraints weight = 55299.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.169645 restraints weight = 36352.437| |-----------------------------------------------------------------------------| r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4260 r_free = 0.4260 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4260 r_free = 0.4260 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.7077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23515 Z= 0.195 Angle : 0.645 12.461 31845 Z= 0.329 Chirality : 0.045 0.233 3693 Planarity : 0.005 0.053 4070 Dihedral : 4.775 22.628 3187 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -1.27 (0.16), residues: 2985 helix: -0.53 (0.14), residues: 1316 sheet: -0.66 (0.25), residues: 437 loop : -1.08 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP B1514 HIS 0.009 0.001 HIS A1408 PHE 0.026 0.002 PHE B1017 TYR 0.014 0.001 TYR B1004 ARG 0.008 0.001 ARG B1380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5889.82 seconds wall clock time: 106 minutes 40.16 seconds (6400.16 seconds total)