Starting phenix.real_space_refine on Thu Feb 15 03:48:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a95_6997/02_2024/6a95_6997_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a95_6997/02_2024/6a95_6997.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a95_6997/02_2024/6a95_6997_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a95_6997/02_2024/6a95_6997_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a95_6997/02_2024/6a95_6997_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a95_6997/02_2024/6a95_6997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a95_6997/02_2024/6a95_6997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a95_6997/02_2024/6a95_6997_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a95_6997/02_2024/6a95_6997_updated.pdb" } resolution = 2.6 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 73 5.16 5 Na 1 4.78 5 C 7262 2.51 5 N 1760 2.21 5 O 1906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 187": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ARG 552": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 613": "NH1" <-> "NH2" Residue "A ARG 619": "NH1" <-> "NH2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A ARG 847": "NH1" <-> "NH2" Residue "A ARG 883": "NH1" <-> "NH2" Residue "A ARG 954": "NH1" <-> "NH2" Residue "A ARG 957": "NH1" <-> "NH2" Residue "A ARG 1074": "NH1" <-> "NH2" Residue "A ARG 1082": "NH1" <-> "NH2" Residue "A ARG 1138": "NH1" <-> "NH2" Residue "A ARG 1268": "NH1" <-> "NH2" Residue "A ARG 1274": "NH1" <-> "NH2" Residue "A ARG 1286": "NH1" <-> "NH2" Residue "A ARG 1293": "NH1" <-> "NH2" Residue "A ARG 1297": "NH1" <-> "NH2" Residue "A ARG 1325": "NH1" <-> "NH2" Residue "A ARG 1369": "NH1" <-> "NH2" Residue "A ARG 1384": "NH1" <-> "NH2" Residue "A ARG 1504": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11002 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 10433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1307, 10433 Classifications: {'peptide': 1307} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 1260} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 7, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 154 Chain: "B" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 447 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {' NA': 1, '9SR': 1, 'NAG': 3} Classifications: {'undetermined': 5, 'water': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.35, per 1000 atoms: 0.49 Number of scatterers: 11002 At special positions: 0 Unit cell: (127.647, 128.738, 120.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 73 16.00 Na 1 11.00 O 1906 8.00 N 1760 7.00 C 7262 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 337 " distance=2.04 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 717 " distance=2.03 Simple disulfide: pdb=" SG CYS A1011 " - pdb=" SG CYS A1030 " distance=2.03 Simple disulfide: pdb=" SG CYS A1368 " - pdb=" SG CYS A1381 " distance=2.04 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 52 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1605 " - " ASN A1015 " " NAG A1606 " - " ASN A 312 " " NAG A1607 " - " ASN A 308 " " NAG C 1 " - " ASN A 330 " " NAG D 1 " - " ASN A1034 " Time building additional restraints: 5.32 Conformation dependent library (CDL) restraints added in 1.9 seconds 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2586 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 4 sheets defined 59.9% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'A' and resid 52 through 55 No H-bonds generated for 'chain 'A' and resid 52 through 55' Processing helix chain 'A' and resid 128 through 137 removed outlier: 3.651A pdb=" N VAL A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 158 removed outlier: 3.711A pdb=" N ILE A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 158 " --> pdb=" O CYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 185 removed outlier: 3.652A pdb=" N ILE A 167 " --> pdb=" O GLN A 163 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 179 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 217 removed outlier: 3.527A pdb=" N VAL A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU A 216 " --> pdb=" O GLY A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.712A pdb=" N ARG A 230 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL A 231 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 232 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG A 233 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 237 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 239 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 240 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 280 removed outlier: 3.536A pdb=" N ASP A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASP A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LEU A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 303 through 310 removed outlier: 3.650A pdb=" N PHE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 361 through 372 Processing helix chain 'A' and resid 377 through 387 removed outlier: 3.648A pdb=" N SER A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.579A pdb=" N ILE A 397 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 399 " --> pdb=" O PHE A 396 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A 401 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR A 402 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 403 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 434 removed outlier: 3.506A pdb=" N LEU A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 519 through 537 removed outlier: 3.597A pdb=" N LEU A 523 " --> pdb=" O PRO A 519 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 568 removed outlier: 3.637A pdb=" N TYR A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 580 No H-bonds generated for 'chain 'A' and resid 578 through 580' Processing helix chain 'A' and resid 584 through 599 Processing helix chain 'A' and resid 609 through 622 removed outlier: 3.615A pdb=" N ARG A 613 " --> pdb=" O ARG A 610 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 614 " --> pdb=" O SER A 611 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 615 " --> pdb=" O PHE A 612 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 618 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 621 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS A 622 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 634 removed outlier: 3.845A pdb=" N VAL A 633 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 663 removed outlier: 3.519A pdb=" N MET A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 669 No H-bonds generated for 'chain 'A' and resid 666 through 669' Processing helix chain 'A' and resid 671 through 673 No H-bonds generated for 'chain 'A' and resid 671 through 673' Processing helix chain 'A' and resid 675 through 677 No H-bonds generated for 'chain 'A' and resid 675 through 677' Processing helix chain 'A' and resid 687 through 698 removed outlier: 3.622A pdb=" N ALA A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 712 removed outlier: 3.652A pdb=" N ASP A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 712 " --> pdb=" O ASP A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 728 Proline residue: A 719 - end of helix removed outlier: 3.922A pdb=" N VAL A 722 " --> pdb=" O PRO A 719 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL A 724 " --> pdb=" O PHE A 721 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A 727 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY A 728 " --> pdb=" O PHE A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 841 through 854 removed outlier: 3.861A pdb=" N ARG A 846 " --> pdb=" O TRP A 842 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A 847 " --> pdb=" O SER A 843 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 850 " --> pdb=" O ARG A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 874 Processing helix chain 'A' and resid 884 through 911 removed outlier: 3.551A pdb=" N ASN A 888 " --> pdb=" O PRO A 884 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A 894 " --> pdb=" O THR A 890 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL A 902 " --> pdb=" O THR A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 940 removed outlier: 3.670A pdb=" N VAL A 929 " --> pdb=" O LEU A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 959 removed outlier: 3.708A pdb=" N LEU A 952 " --> pdb=" O GLN A 948 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A 953 " --> pdb=" O THR A 949 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ARG A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N VAL A 955 " --> pdb=" O ARG A 951 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N PHE A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARG A 957 " --> pdb=" O LEU A 953 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU A 958 " --> pdb=" O ARG A 954 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE A 959 " --> pdb=" O VAL A 955 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 948 through 959' Processing helix chain 'A' and resid 962 through 964 No H-bonds generated for 'chain 'A' and resid 962 through 964' Processing helix chain 'A' and resid 968 through 976 removed outlier: 3.727A pdb=" N LEU A 975 " --> pdb=" O VAL A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 1004 removed outlier: 3.514A pdb=" N ASN A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 996 " --> pdb=" O PHE A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1032 Processing helix chain 'A' and resid 1047 through 1058 removed outlier: 3.738A pdb=" N GLN A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1071 Processing helix chain 'A' and resid 1086 through 1099 removed outlier: 3.668A pdb=" N ILE A1093 " --> pdb=" O LEU A1090 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A1094 " --> pdb=" O TYR A1091 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A1097 " --> pdb=" O PHE A1094 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY A1099 " --> pdb=" O ILE A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1122 removed outlier: 3.593A pdb=" N CYS A1109 " --> pdb=" O LEU A1106 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A1111 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE A1112 " --> pdb=" O CYS A1109 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A1114 " --> pdb=" O LEU A1111 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A1115 " --> pdb=" O ILE A1112 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG A1116 " --> pdb=" O ASP A1113 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN A1118 " --> pdb=" O PHE A1115 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG A1119 " --> pdb=" O ARG A1116 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A1121 " --> pdb=" O GLN A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1144 removed outlier: 3.785A pdb=" N THR A1143 " --> pdb=" O ALA A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1165 removed outlier: 3.652A pdb=" N LEU A1162 " --> pdb=" O HIS A1158 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N MET A1163 " --> pdb=" O PRO A1159 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A1164 " --> pdb=" O GLN A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1185 removed outlier: 3.640A pdb=" N MET A1177 " --> pdb=" O GLU A1173 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A1179 " --> pdb=" O THR A1175 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A1180 " --> pdb=" O MET A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1189 No H-bonds generated for 'chain 'A' and resid 1187 through 1189' Processing helix chain 'A' and resid 1196 through 1222 removed outlier: 3.502A pdb=" N VAL A1201 " --> pdb=" O GLU A1197 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A1207 " --> pdb=" O ASP A1203 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A1208 " --> pdb=" O TYR A1204 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A1209 " --> pdb=" O LEU A1205 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A1212 " --> pdb=" O ILE A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1226 through 1230 Processing helix chain 'A' and resid 1232 through 1248 removed outlier: 4.316A pdb=" N ILE A1236 " --> pdb=" O PRO A1232 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A1241 " --> pdb=" O ASP A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1280 removed outlier: 3.674A pdb=" N LEU A1267 " --> pdb=" O LEU A1263 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A1269 " --> pdb=" O ARG A1265 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A1271 " --> pdb=" O LEU A1267 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL A1272 " --> pdb=" O ARG A1268 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLY A1273 " --> pdb=" O ILE A1269 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ARG A1274 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU A1275 " --> pdb=" O ARG A1271 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU A1276 " --> pdb=" O VAL A1272 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG A1277 " --> pdb=" O GLY A1273 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A1278 " --> pdb=" O ARG A1274 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN A1280 " --> pdb=" O LEU A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1294 removed outlier: 3.512A pdb=" N LEU A1288 " --> pdb=" O GLY A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1320 removed outlier: 3.669A pdb=" N PHE A1307 " --> pdb=" O SER A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1351 removed outlier: 3.522A pdb=" N GLN A1348 " --> pdb=" O ILE A1344 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR A1351 " --> pdb=" O PHE A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1362 removed outlier: 3.682A pdb=" N ALA A1361 " --> pdb=" O GLY A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1398 removed outlier: 4.085A pdb=" N SER A1393 " --> pdb=" O ALA A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1422 removed outlier: 4.080A pdb=" N ALA A1407 " --> pdb=" O ILE A1403 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A1416 " --> pdb=" O ASP A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1427 through 1436 removed outlier: 3.775A pdb=" N MET A1432 " --> pdb=" O ASP A1429 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A1434 " --> pdb=" O ASP A1431 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A1435 " --> pdb=" O MET A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1450 through 1458 removed outlier: 3.562A pdb=" N LEU A1453 " --> pdb=" O TYR A1450 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER A1454 " --> pdb=" O ASP A1451 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A1456 " --> pdb=" O LEU A1453 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU A1457 " --> pdb=" O SER A1454 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU A1458 " --> pdb=" O GLU A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1470 through 1474 Processing helix chain 'A' and resid 1483 through 1485 No H-bonds generated for 'chain 'A' and resid 1483 through 1485' Processing helix chain 'A' and resid 1489 through 1503 removed outlier: 3.534A pdb=" N ASP A1499 " --> pdb=" O ALA A1495 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A1503 " --> pdb=" O ASP A1499 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1519 Processing sheet with id= A, first strand: chain 'A' and resid 1009 through 1012 Processing sheet with id= B, first strand: chain 'A' and resid 1447 through 1449 Processing sheet with id= C, first strand: chain 'B' and resid 28 through 30 Processing sheet with id= D, first strand: chain 'B' and resid 38 through 44 463 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.25 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3272 1.34 - 1.46: 2864 1.46 - 1.58: 5034 1.58 - 1.70: 3 1.70 - 1.83: 118 Bond restraints: 11291 Sorted by residual: bond pdb=" C07 9SR A1608 " pdb=" O01 9SR A1608 " ideal model delta sigma weight residual 1.625 1.463 0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" C19 9SR A1608 " pdb=" O20 9SR A1608 " ideal model delta sigma weight residual 1.467 1.335 0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" C11 9SR A1608 " pdb=" N12 9SR A1608 " ideal model delta sigma weight residual 1.508 1.382 0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C15 9SR A1608 " pdb=" C17 9SR A1608 " ideal model delta sigma weight residual 1.624 1.503 0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" C11 9SR A1608 " pdb=" C17 9SR A1608 " ideal model delta sigma weight residual 1.462 1.576 -0.114 2.00e-02 2.50e+03 3.27e+01 ... (remaining 11286 not shown) Histogram of bond angle deviations from ideal: 95.21 - 103.80: 140 103.80 - 112.38: 5337 112.38 - 120.96: 6703 120.96 - 129.55: 3087 129.55 - 138.13: 91 Bond angle restraints: 15358 Sorted by residual: angle pdb=" N THR A1156 " pdb=" CA THR A1156 " pdb=" C THR A1156 " ideal model delta sigma weight residual 113.88 122.86 -8.98 1.23e+00 6.61e-01 5.33e+01 angle pdb=" N LEU A1162 " pdb=" CA LEU A1162 " pdb=" C LEU A1162 " ideal model delta sigma weight residual 111.36 105.30 6.06 1.09e+00 8.42e-01 3.09e+01 angle pdb=" C THR A1156 " pdb=" CA THR A1156 " pdb=" CB THR A1156 " ideal model delta sigma weight residual 109.03 101.56 7.47 1.62e+00 3.81e-01 2.13e+01 angle pdb=" C THR A1426 " pdb=" N ASP A1427 " pdb=" CA ASP A1427 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 angle pdb=" CA HIS A1158 " pdb=" C HIS A1158 " pdb=" N PRO A1159 " ideal model delta sigma weight residual 120.93 116.24 4.69 1.06e+00 8.90e-01 1.96e+01 ... (remaining 15353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.29: 6193 15.29 - 30.59: 353 30.59 - 45.88: 84 45.88 - 61.17: 22 61.17 - 76.47: 7 Dihedral angle restraints: 6659 sinusoidal: 2650 harmonic: 4009 Sorted by residual: dihedral pdb=" CB CYS B 13 " pdb=" SG CYS B 13 " pdb=" SG CYS B 26 " pdb=" CB CYS B 26 " ideal model delta sinusoidal sigma weight residual -86.00 -155.67 69.67 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CA SER A 574 " pdb=" C SER A 574 " pdb=" N PRO A 575 " pdb=" CA PRO A 575 " ideal model delta harmonic sigma weight residual -180.00 -153.80 -26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA TRP A 624 " pdb=" C TRP A 624 " pdb=" N PRO A 625 " pdb=" CA PRO A 625 " ideal model delta harmonic sigma weight residual -180.00 -156.10 -23.90 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 6656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.059: 1763 1.059 - 2.118: 0 2.118 - 3.178: 0 3.178 - 4.237: 0 4.237 - 5.296: 1 Chirality restraints: 1764 Sorted by residual: chirality pdb=" C03 9SR A1608 " pdb=" C02 9SR A1608 " pdb=" C05 9SR A1608 " pdb=" C21 9SR A1608 " both_signs ideal model delta sigma weight residual False 2.67 -2.63 5.30 2.00e-01 2.50e+01 7.01e+02 chirality pdb=" CG LEU A1054 " pdb=" CB LEU A1054 " pdb=" CD1 LEU A1054 " pdb=" CD2 LEU A1054 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.02e+00 ... (remaining 1761 not shown) Planarity restraints: 1898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1015 " 0.143 2.00e-02 2.50e+03 2.41e-01 7.25e+02 pdb=" CG ASN A1015 " -0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN A1015 " 0.077 2.00e-02 2.50e+03 pdb=" ND2 ASN A1015 " -0.423 2.00e-02 2.50e+03 pdb=" C1 NAG A1605 " 0.281 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 312 " 0.099 2.00e-02 2.50e+03 1.17e-01 1.72e+02 pdb=" CG ASN A 312 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN A 312 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 312 " -0.193 2.00e-02 2.50e+03 pdb=" C1 NAG A1606 " 0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 330 " -0.100 2.00e-02 2.50e+03 1.13e-01 1.59e+02 pdb=" CG ASN A 330 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 330 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 330 " 0.180 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.136 2.00e-02 2.50e+03 ... (remaining 1895 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3790 2.86 - 3.37: 10306 3.37 - 3.88: 17621 3.88 - 4.39: 20477 4.39 - 4.90: 33904 Nonbonded interactions: 86098 Sorted by model distance: nonbonded pdb=" CG PRO A1155 " pdb=" NH1 ARG A1225 " model vdw 2.354 3.520 nonbonded pdb=" O ILE A1152 " pdb=" OH TYR A1164 " model vdw 2.362 2.440 nonbonded pdb=" OD2 ASP A 539 " pdb=" NZ LYS B 44 " model vdw 2.364 2.520 nonbonded pdb=" OD1 ASP A 686 " pdb=" ND1 HIS A 689 " model vdw 2.373 2.520 nonbonded pdb=" O LEU A1346 " pdb=" OH TYR A1394 " model vdw 2.375 2.440 ... (remaining 86093 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 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.260 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 30.600 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 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 : 0.007 0.162 11291 Z= 0.442 Angle : 1.062 13.131 15358 Z= 0.549 Chirality : 0.140 5.296 1764 Planarity : 0.007 0.104 1893 Dihedral : 11.112 76.466 4049 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.15 % Favored : 92.48 % Rotamer: Outliers : 1.05 % Allowed : 5.36 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -5.57 (0.16), residues: 1356 helix: -4.07 (0.09), residues: 829 sheet: -2.33 (0.80), residues: 31 loop : -2.70 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.004 TRP A1063 HIS 0.012 0.003 HIS A 222 PHE 0.035 0.003 PHE A 535 TYR 0.039 0.004 TYR A 933 ARG 0.028 0.002 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 284 time to evaluate : 1.292 Fit side-chains REVERT: A 141 ILE cc_start: 0.8068 (tp) cc_final: 0.7849 (tt) REVERT: A 159 MET cc_start: 0.7000 (mtm) cc_final: 0.6745 (mtp) REVERT: A 259 LYS cc_start: 0.8440 (ttpp) cc_final: 0.8086 (mptt) REVERT: A 424 LYS cc_start: 0.8195 (mmtp) cc_final: 0.7932 (mtpp) REVERT: A 641 PHE cc_start: 0.8045 (m-80) cc_final: 0.7843 (m-80) REVERT: A 645 MET cc_start: 0.8260 (mmt) cc_final: 0.8021 (mmm) REVERT: A 856 LYS cc_start: 0.7736 (tppt) cc_final: 0.6896 (ptmt) REVERT: A 1147 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7580 (mttp) REVERT: A 1169 ASN cc_start: 0.7934 (t0) cc_final: 0.7510 (t0) REVERT: A 1225 ARG cc_start: 0.7567 (mpp-170) cc_final: 0.7170 (mpp80) REVERT: A 1230 LYS cc_start: 0.6800 (mptp) cc_final: 0.6333 (mmpt) REVERT: A 1300 PHE cc_start: 0.8212 (m-10) cc_final: 0.7333 (t80) REVERT: A 1322 MET cc_start: 0.8676 (ttp) cc_final: 0.8468 (ttm) REVERT: A 1369 ARG cc_start: 0.7867 (mtp180) cc_final: 0.7322 (mtp-110) REVERT: A 1431 ASP cc_start: 0.7351 (m-30) cc_final: 0.6847 (m-30) REVERT: A 1486 HIS cc_start: 0.7063 (m-70) cc_final: 0.6761 (m-70) REVERT: B 15 LYS cc_start: 0.8079 (mmtp) cc_final: 0.7749 (mmmt) REVERT: B 28 LYS cc_start: 0.7667 (mttt) cc_final: 0.7459 (mttp) outliers start: 12 outliers final: 4 residues processed: 292 average time/residue: 1.1524 time to fit residues: 363.2430 Evaluate side-chains 187 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 183 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1401 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.0870 chunk 102 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 122 optimal weight: 0.3980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 291 HIS A 532 ASN A 584 ASN A 661 GLN A 743 ASN A 859 GLN A 882 GLN A 888 ASN A 936 ASN A 966 ASN A1077 HIS A1133 GLN ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1301 ASN A1438 GLN ** A1470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 11291 Z= 0.183 Angle : 0.756 29.234 15358 Z= 0.359 Chirality : 0.065 2.005 1764 Planarity : 0.005 0.050 1893 Dihedral : 7.611 58.728 1650 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.19 % Favored : 93.66 % Rotamer: Outliers : 4.13 % Allowed : 10.98 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -3.19 (0.20), residues: 1356 helix: -1.81 (0.15), residues: 826 sheet: -2.41 (0.77), residues: 31 loop : -2.40 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 624 HIS 0.006 0.001 HIS A 222 PHE 0.015 0.001 PHE A 410 TYR 0.017 0.002 TYR A 381 ARG 0.007 0.001 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 200 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 PHE cc_start: 0.6892 (m-10) cc_final: 0.6657 (m-80) REVERT: A 214 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7767 (mt) REVERT: A 219 ASP cc_start: 0.2322 (OUTLIER) cc_final: 0.1893 (m-30) REVERT: A 259 LYS cc_start: 0.8595 (ttpp) cc_final: 0.8152 (mptt) REVERT: A 374 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7132 (mp) REVERT: A 424 LYS cc_start: 0.8000 (mmtp) cc_final: 0.7695 (mtpp) REVERT: A 598 LEU cc_start: 0.8018 (mm) cc_final: 0.7722 (mm) REVERT: A 914 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7761 (t80) REVERT: A 1021 HIS cc_start: 0.7826 (p-80) cc_final: 0.7552 (p-80) REVERT: A 1025 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6344 (mmt) REVERT: A 1136 TYR cc_start: 0.7662 (m-10) cc_final: 0.7437 (m-10) REVERT: A 1137 ARG cc_start: 0.7876 (ttt-90) cc_final: 0.7599 (tmt90) REVERT: A 1147 LYS cc_start: 0.7918 (mtmm) cc_final: 0.7535 (mtmm) REVERT: A 1169 ASN cc_start: 0.7769 (t0) cc_final: 0.7269 (t0) REVERT: A 1177 MET cc_start: 0.7746 (tpt) cc_final: 0.7529 (tpt) REVERT: A 1230 LYS cc_start: 0.7092 (mptp) cc_final: 0.6659 (mmpt) REVERT: A 1369 ARG cc_start: 0.7846 (mtp180) cc_final: 0.7486 (mtp-110) REVERT: A 1431 ASP cc_start: 0.7310 (m-30) cc_final: 0.6882 (m-30) REVERT: A 1443 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6819 (mp0) REVERT: A 1486 HIS cc_start: 0.6940 (m-70) cc_final: 0.6710 (m-70) REVERT: B 15 LYS cc_start: 0.8015 (mmtp) cc_final: 0.7676 (mmmt) REVERT: B 28 LYS cc_start: 0.7623 (mttt) cc_final: 0.7394 (mttp) REVERT: B 34 LYS cc_start: 0.8211 (ptpp) cc_final: 0.7993 (ptpt) REVERT: B 50 SER cc_start: 0.8643 (m) cc_final: 0.8411 (p) outliers start: 47 outliers final: 15 residues processed: 229 average time/residue: 1.0480 time to fit residues: 263.4230 Evaluate side-chains 193 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 172 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 914 PHE Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1443 GLU Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain B residue 52 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 0.0470 chunk 132 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 98 optimal weight: 3.9990 overall best weight: 0.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 936 ASN A1133 GLN ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1227 HIS ** A1470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 11291 Z= 0.169 Angle : 0.734 27.351 15358 Z= 0.344 Chirality : 0.066 2.112 1764 Planarity : 0.004 0.038 1893 Dihedral : 7.334 58.713 1650 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.19 % Favored : 93.66 % Rotamer: Outliers : 4.48 % Allowed : 12.57 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.82 (0.22), residues: 1356 helix: -0.56 (0.17), residues: 830 sheet: -2.31 (0.80), residues: 31 loop : -2.13 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 624 HIS 0.005 0.001 HIS A 392 PHE 0.013 0.001 PHE A1102 TYR 0.018 0.001 TYR A 933 ARG 0.010 0.001 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 181 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7966 (tm) REVERT: A 259 LYS cc_start: 0.8621 (ttpp) cc_final: 0.8130 (mptt) REVERT: A 374 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7511 (mp) REVERT: A 424 LYS cc_start: 0.7913 (mmtp) cc_final: 0.7607 (mtpp) REVERT: A 543 MET cc_start: 0.8913 (ptt) cc_final: 0.8565 (mtm) REVERT: A 598 LEU cc_start: 0.7967 (mm) cc_final: 0.7670 (mm) REVERT: A 665 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7299 (mmm) REVERT: A 914 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7807 (t80) REVERT: A 969 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7335 (tm-30) REVERT: A 1021 HIS cc_start: 0.7825 (p-80) cc_final: 0.7571 (p-80) REVERT: A 1025 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6427 (mmt) REVERT: A 1136 TYR cc_start: 0.7738 (m-10) cc_final: 0.7526 (m-10) REVERT: A 1147 LYS cc_start: 0.7909 (mtmm) cc_final: 0.7464 (mtmm) REVERT: A 1169 ASN cc_start: 0.7648 (t0) cc_final: 0.7253 (t0) REVERT: A 1177 MET cc_start: 0.7761 (tpt) cc_final: 0.7427 (tpt) REVERT: A 1190 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7493 (m-30) REVERT: A 1211 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7666 (mp) REVERT: A 1263 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8302 (tp) REVERT: A 1369 ARG cc_start: 0.7689 (mtp180) cc_final: 0.7406 (mtp-110) REVERT: A 1427 ASP cc_start: 0.7137 (OUTLIER) cc_final: 0.6919 (m-30) REVERT: A 1431 ASP cc_start: 0.7219 (m-30) cc_final: 0.6792 (m-30) REVERT: A 1443 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: B 14 LYS cc_start: 0.7863 (mmmm) cc_final: 0.7500 (mmmt) REVERT: B 15 LYS cc_start: 0.7991 (mmtp) cc_final: 0.7714 (mmmt) REVERT: B 27 GLN cc_start: 0.7757 (mp10) cc_final: 0.7391 (mm110) outliers start: 51 outliers final: 19 residues processed: 214 average time/residue: 0.9861 time to fit residues: 231.7240 Evaluate side-chains 193 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 163 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 914 PHE Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 1443 GLU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 52 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 ASN A1183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 11291 Z= 0.420 Angle : 0.879 25.355 15358 Z= 0.423 Chirality : 0.073 2.206 1764 Planarity : 0.005 0.050 1893 Dihedral : 7.361 55.726 1650 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.52 % Favored : 92.33 % Rotamer: Outliers : 5.36 % Allowed : 12.83 % Favored : 81.81 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.68 (0.22), residues: 1356 helix: -0.42 (0.17), residues: 858 sheet: -2.36 (0.81), residues: 31 loop : -2.21 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 624 HIS 0.007 0.002 HIS A 392 PHE 0.019 0.003 PHE A1115 TYR 0.039 0.003 TYR A 933 ARG 0.006 0.001 ARG A 847 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 173 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 PHE cc_start: 0.8238 (t80) cc_final: 0.7971 (t80) REVERT: A 216 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7468 (tm) REVERT: A 259 LYS cc_start: 0.8698 (ttpp) cc_final: 0.8047 (mptt) REVERT: A 424 LYS cc_start: 0.7941 (mmtp) cc_final: 0.7622 (mtpp) REVERT: A 598 LEU cc_start: 0.8120 (mm) cc_final: 0.7848 (mm) REVERT: A 634 MET cc_start: 0.7222 (mtm) cc_final: 0.6825 (mmt) REVERT: A 860 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7429 (mptp) REVERT: A 914 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7954 (t80) REVERT: A 1147 LYS cc_start: 0.7994 (mtmm) cc_final: 0.7528 (mtmm) REVERT: A 1169 ASN cc_start: 0.7738 (t0) cc_final: 0.7381 (t0) REVERT: A 1177 MET cc_start: 0.7924 (tpt) cc_final: 0.7602 (tpt) REVERT: A 1209 PHE cc_start: 0.8038 (m-10) cc_final: 0.7765 (m-80) REVERT: A 1211 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7795 (mp) REVERT: A 1235 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.8018 (mp) REVERT: A 1274 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7398 (mtt-85) REVERT: A 1369 ARG cc_start: 0.7655 (mtp180) cc_final: 0.7368 (mtp-110) REVERT: A 1431 ASP cc_start: 0.7323 (m-30) cc_final: 0.6869 (m-30) REVERT: A 1443 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: B 8 GLU cc_start: 0.6367 (tm-30) cc_final: 0.6128 (tt0) REVERT: B 15 LYS cc_start: 0.8026 (mmtp) cc_final: 0.7744 (mmmt) REVERT: B 31 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8010 (pp) REVERT: B 41 ARG cc_start: 0.7735 (mtp85) cc_final: 0.7511 (mmm160) outliers start: 61 outliers final: 29 residues processed: 212 average time/residue: 1.0113 time to fit residues: 234.9345 Evaluate side-chains 205 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 168 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 860 LYS Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 914 PHE Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1443 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 52 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 1 optimal weight: 40.0000 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 111 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 66 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 11291 Z= 0.170 Angle : 0.727 28.120 15358 Z= 0.340 Chirality : 0.065 2.066 1764 Planarity : 0.004 0.044 1893 Dihedral : 6.943 59.054 1650 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.42 % Favored : 93.44 % Rotamer: Outliers : 4.04 % Allowed : 14.59 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.02 (0.23), residues: 1356 helix: 0.16 (0.18), residues: 855 sheet: -2.22 (0.97), residues: 21 loop : -2.10 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 PHE 0.011 0.001 PHE A1488 TYR 0.019 0.001 TYR A1228 ARG 0.009 0.001 ARG A 847 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 183 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 THR cc_start: 0.8113 (m) cc_final: 0.7821 (m) REVERT: A 214 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7706 (mt) REVERT: A 259 LYS cc_start: 0.8658 (ttpp) cc_final: 0.8024 (mptt) REVERT: A 424 LYS cc_start: 0.7802 (mmtp) cc_final: 0.7463 (mtpp) REVERT: A 598 LEU cc_start: 0.7956 (mm) cc_final: 0.7627 (mm) REVERT: A 634 MET cc_start: 0.7257 (mtm) cc_final: 0.6920 (mmt) REVERT: A 914 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7972 (t80) REVERT: A 1025 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6514 (mmt) REVERT: A 1147 LYS cc_start: 0.7924 (mtmm) cc_final: 0.7456 (mtmm) REVERT: A 1169 ASN cc_start: 0.7731 (t0) cc_final: 0.7433 (t0) REVERT: A 1177 MET cc_start: 0.7890 (tpt) cc_final: 0.7475 (tpt) REVERT: A 1209 PHE cc_start: 0.7932 (m-10) cc_final: 0.7670 (m-80) REVERT: A 1211 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.7801 (mp) REVERT: A 1286 ARG cc_start: 0.7575 (ttm110) cc_final: 0.7130 (ptp90) REVERT: A 1431 ASP cc_start: 0.7360 (m-30) cc_final: 0.6924 (m-30) REVERT: A 1443 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: B 8 GLU cc_start: 0.6349 (tm-30) cc_final: 0.6116 (tt0) REVERT: B 14 LYS cc_start: 0.7820 (mmmm) cc_final: 0.7496 (mmmt) REVERT: B 15 LYS cc_start: 0.7965 (mmtp) cc_final: 0.7697 (mmmt) REVERT: B 31 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8019 (pp) outliers start: 46 outliers final: 22 residues processed: 207 average time/residue: 1.0370 time to fit residues: 236.2413 Evaluate side-chains 200 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 172 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 914 PHE Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 1443 GLU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 52 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 0.0060 chunk 32 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 125 optimal weight: 0.0270 overall best weight: 0.5054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11291 Z= 0.154 Angle : 0.701 27.892 15358 Z= 0.325 Chirality : 0.065 2.084 1764 Planarity : 0.003 0.043 1893 Dihedral : 6.591 57.607 1650 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.71 % Favored : 93.14 % Rotamer: Outliers : 4.04 % Allowed : 15.99 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.23), residues: 1356 helix: 0.55 (0.18), residues: 850 sheet: -2.45 (1.70), residues: 10 loop : -2.08 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 624 HIS 0.003 0.001 HIS A 153 PHE 0.011 0.001 PHE A1488 TYR 0.019 0.001 TYR A1228 ARG 0.008 0.001 ARG A 847 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 182 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 THR cc_start: 0.8035 (m) cc_final: 0.7732 (m) REVERT: A 259 LYS cc_start: 0.8674 (ttpp) cc_final: 0.8012 (mptt) REVERT: A 424 LYS cc_start: 0.7724 (mmtp) cc_final: 0.7416 (mtpp) REVERT: A 598 LEU cc_start: 0.7905 (mm) cc_final: 0.7666 (mm) REVERT: A 634 MET cc_start: 0.7062 (mtm) cc_final: 0.6791 (mmt) REVERT: A 665 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7346 (mmm) REVERT: A 969 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7413 (tm-30) REVERT: A 1025 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6572 (mmt) REVERT: A 1142 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7676 (mtt180) REVERT: A 1144 MET cc_start: 0.7319 (tpp) cc_final: 0.6123 (tmm) REVERT: A 1147 LYS cc_start: 0.7848 (mtmm) cc_final: 0.7350 (mtmm) REVERT: A 1177 MET cc_start: 0.7776 (tpt) cc_final: 0.7458 (tpt) REVERT: A 1190 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7533 (m-30) REVERT: A 1209 PHE cc_start: 0.7895 (m-10) cc_final: 0.7604 (m-80) REVERT: A 1263 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8252 (tp) REVERT: A 1285 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7383 (mmt) REVERT: A 1286 ARG cc_start: 0.7454 (ttm110) cc_final: 0.7034 (ptp90) REVERT: A 1369 ARG cc_start: 0.7525 (mtp180) cc_final: 0.7133 (mtp-110) REVERT: A 1431 ASP cc_start: 0.7290 (m-30) cc_final: 0.6871 (m-30) REVERT: B 14 LYS cc_start: 0.7814 (mmmm) cc_final: 0.7495 (mmmt) REVERT: B 15 LYS cc_start: 0.7954 (mmtp) cc_final: 0.7687 (mmmt) REVERT: B 31 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.7965 (pp) outliers start: 46 outliers final: 22 residues processed: 210 average time/residue: 1.0258 time to fit residues: 235.8950 Evaluate side-chains 208 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 179 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 55 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 60 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1439 GLN A1452 GLN ** A1470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.149 11291 Z= 0.191 Angle : 0.732 27.647 15358 Z= 0.339 Chirality : 0.066 2.097 1764 Planarity : 0.004 0.048 1893 Dihedral : 6.502 56.310 1649 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.71 % Favored : 93.14 % Rotamer: Outliers : 4.04 % Allowed : 16.08 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.23), residues: 1356 helix: 0.63 (0.18), residues: 856 sheet: -2.54 (1.71), residues: 10 loop : -2.02 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 624 HIS 0.005 0.001 HIS A 392 PHE 0.013 0.001 PHE A1488 TYR 0.017 0.001 TYR A1228 ARG 0.012 0.001 ARG A 847 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 172 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 THR cc_start: 0.7984 (m) cc_final: 0.7683 (m) REVERT: A 214 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7669 (mt) REVERT: A 259 LYS cc_start: 0.8746 (ttpp) cc_final: 0.8032 (mptt) REVERT: A 320 ASP cc_start: 0.6116 (OUTLIER) cc_final: 0.5300 (m-30) REVERT: A 424 LYS cc_start: 0.7668 (mmtp) cc_final: 0.7372 (mtpp) REVERT: A 598 LEU cc_start: 0.7870 (mm) cc_final: 0.7583 (mm) REVERT: A 634 MET cc_start: 0.7073 (mtm) cc_final: 0.6752 (mmt) REVERT: A 665 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7339 (mmm) REVERT: A 969 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: A 1025 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6545 (mmt) REVERT: A 1142 ARG cc_start: 0.8042 (mtm-85) cc_final: 0.7797 (mtt180) REVERT: A 1144 MET cc_start: 0.7336 (tpp) cc_final: 0.6121 (tmm) REVERT: A 1147 LYS cc_start: 0.7863 (mtmm) cc_final: 0.7376 (mtmm) REVERT: A 1169 ASN cc_start: 0.7772 (t0) cc_final: 0.6421 (t0) REVERT: A 1173 GLU cc_start: 0.7204 (mp0) cc_final: 0.6110 (mp0) REVERT: A 1177 MET cc_start: 0.7827 (tpt) cc_final: 0.7423 (tpt) REVERT: A 1209 PHE cc_start: 0.7929 (m-10) cc_final: 0.7637 (m-80) REVERT: A 1235 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7951 (mp) REVERT: A 1263 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8241 (tp) REVERT: A 1285 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7344 (mmt) REVERT: A 1286 ARG cc_start: 0.7526 (ttm110) cc_final: 0.7082 (ptp90) REVERT: A 1369 ARG cc_start: 0.7522 (mtp180) cc_final: 0.7165 (mtp-110) REVERT: A 1405 MET cc_start: 0.8084 (mmm) cc_final: 0.7857 (mmm) REVERT: A 1431 ASP cc_start: 0.7311 (m-30) cc_final: 0.6875 (m-30) REVERT: B 14 LYS cc_start: 0.7817 (mmmm) cc_final: 0.7494 (mmmt) REVERT: B 15 LYS cc_start: 0.7946 (mmtp) cc_final: 0.7669 (mmmt) REVERT: B 31 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8008 (pp) outliers start: 46 outliers final: 24 residues processed: 199 average time/residue: 1.0468 time to fit residues: 227.6921 Evaluate side-chains 203 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 170 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 1502 SER Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 55 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 124 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 11291 Z= 0.168 Angle : 0.710 27.977 15358 Z= 0.328 Chirality : 0.065 2.082 1764 Planarity : 0.003 0.051 1893 Dihedral : 6.363 56.364 1649 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.49 % Favored : 93.36 % Rotamer: Outliers : 3.60 % Allowed : 16.61 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.23), residues: 1356 helix: 0.77 (0.18), residues: 855 sheet: -2.49 (1.71), residues: 10 loop : -1.99 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 PHE 0.012 0.001 PHE A1198 TYR 0.017 0.001 TYR A1228 ARG 0.013 0.001 ARG A 847 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 173 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 THR cc_start: 0.8044 (m) cc_final: 0.7735 (m) REVERT: A 214 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7713 (mt) REVERT: A 259 LYS cc_start: 0.8741 (ttpp) cc_final: 0.8020 (mptt) REVERT: A 320 ASP cc_start: 0.6062 (OUTLIER) cc_final: 0.5287 (m-30) REVERT: A 424 LYS cc_start: 0.7634 (mmtp) cc_final: 0.7377 (mtpp) REVERT: A 598 LEU cc_start: 0.7871 (mm) cc_final: 0.7632 (mm) REVERT: A 634 MET cc_start: 0.7112 (mtm) cc_final: 0.6709 (mmt) REVERT: A 662 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8686 (mt) REVERT: A 665 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7328 (mmm) REVERT: A 969 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7432 (tm-30) REVERT: A 1025 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6542 (mmt) REVERT: A 1142 ARG cc_start: 0.8008 (mtm-85) cc_final: 0.7797 (mtt180) REVERT: A 1144 MET cc_start: 0.7281 (tpp) cc_final: 0.6110 (tmm) REVERT: A 1147 LYS cc_start: 0.7849 (mtmm) cc_final: 0.7338 (mtmm) REVERT: A 1173 GLU cc_start: 0.7197 (mp0) cc_final: 0.6122 (mp0) REVERT: A 1177 MET cc_start: 0.7754 (tpt) cc_final: 0.7424 (tpt) REVERT: A 1277 ARG cc_start: 0.7752 (ttm170) cc_final: 0.7212 (mtm-85) REVERT: A 1285 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7441 (mmt) REVERT: A 1286 ARG cc_start: 0.7464 (ttm110) cc_final: 0.7049 (ptp90) REVERT: A 1369 ARG cc_start: 0.7423 (mtp180) cc_final: 0.7108 (mtp-110) REVERT: A 1431 ASP cc_start: 0.7363 (m-30) cc_final: 0.6940 (m-30) REVERT: B 14 LYS cc_start: 0.7760 (mmmm) cc_final: 0.7449 (mmmt) REVERT: B 15 LYS cc_start: 0.7943 (mmtp) cc_final: 0.7655 (mmmt) REVERT: B 31 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.7988 (pp) outliers start: 41 outliers final: 25 residues processed: 197 average time/residue: 1.0732 time to fit residues: 230.8697 Evaluate side-chains 201 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 168 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1157 CYS Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 1502 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 55 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.0040 chunk 121 optimal weight: 0.8980 chunk 124 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 11291 Z= 0.205 Angle : 0.734 27.366 15358 Z= 0.341 Chirality : 0.066 2.116 1764 Planarity : 0.004 0.053 1893 Dihedral : 6.366 57.147 1649 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.56 % Favored : 93.29 % Rotamer: Outliers : 3.95 % Allowed : 16.34 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.23), residues: 1356 helix: 0.75 (0.18), residues: 853 sheet: -2.39 (1.14), residues: 20 loop : -1.89 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 624 HIS 0.005 0.001 HIS A 392 PHE 0.012 0.001 PHE A1115 TYR 0.016 0.002 TYR A 381 ARG 0.013 0.001 ARG A 847 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 168 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: A 136 THR cc_start: 0.8047 (m) cc_final: 0.7744 (m) REVERT: A 259 LYS cc_start: 0.8725 (ttpp) cc_final: 0.8003 (mptt) REVERT: A 320 ASP cc_start: 0.6223 (OUTLIER) cc_final: 0.5423 (m-30) REVERT: A 424 LYS cc_start: 0.7726 (mmtp) cc_final: 0.7422 (mtpp) REVERT: A 598 LEU cc_start: 0.7852 (mm) cc_final: 0.7566 (mm) REVERT: A 631 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7931 (mtp) REVERT: A 634 MET cc_start: 0.7150 (mtm) cc_final: 0.6822 (mmt) REVERT: A 662 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8712 (mt) REVERT: A 665 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7332 (mmm) REVERT: A 969 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: A 1025 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6539 (mmt) REVERT: A 1142 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7787 (mtt180) REVERT: A 1144 MET cc_start: 0.7319 (tpp) cc_final: 0.6203 (tmm) REVERT: A 1147 LYS cc_start: 0.7874 (mtmm) cc_final: 0.7355 (mtmm) REVERT: A 1173 GLU cc_start: 0.7223 (mp0) cc_final: 0.6138 (mp0) REVERT: A 1177 MET cc_start: 0.7817 (tpt) cc_final: 0.7478 (tpt) REVERT: A 1277 ARG cc_start: 0.7757 (ttm170) cc_final: 0.7205 (mtm-85) REVERT: A 1285 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7393 (mmt) REVERT: A 1286 ARG cc_start: 0.7472 (ttm110) cc_final: 0.7025 (ptp90) REVERT: A 1369 ARG cc_start: 0.7488 (mtp180) cc_final: 0.7184 (mtp-110) REVERT: A 1431 ASP cc_start: 0.7314 (m-30) cc_final: 0.6896 (m-30) REVERT: B 14 LYS cc_start: 0.7797 (mmmm) cc_final: 0.7431 (mmmt) REVERT: B 15 LYS cc_start: 0.7979 (mmtp) cc_final: 0.7674 (mmmt) REVERT: B 31 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8018 (pp) outliers start: 45 outliers final: 29 residues processed: 197 average time/residue: 1.1182 time to fit residues: 240.8329 Evaluate side-chains 201 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 164 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1157 CYS Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 1502 SER Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 55 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 11291 Z= 0.197 Angle : 0.729 27.924 15358 Z= 0.338 Chirality : 0.066 2.083 1764 Planarity : 0.004 0.055 1893 Dihedral : 6.327 57.154 1649 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.42 % Favored : 93.44 % Rotamer: Outliers : 3.51 % Allowed : 16.61 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.23), residues: 1356 helix: 0.78 (0.18), residues: 853 sheet: -2.36 (1.68), residues: 10 loop : -1.90 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 624 HIS 0.005 0.001 HIS A 153 PHE 0.012 0.001 PHE A1488 TYR 0.018 0.001 TYR A1136 ARG 0.013 0.001 ARG A 847 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 170 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 136 THR cc_start: 0.8019 (m) cc_final: 0.7706 (m) REVERT: A 259 LYS cc_start: 0.8708 (ttpp) cc_final: 0.8003 (mptt) REVERT: A 320 ASP cc_start: 0.6216 (OUTLIER) cc_final: 0.5411 (m-30) REVERT: A 424 LYS cc_start: 0.7667 (mmtp) cc_final: 0.7372 (mtpp) REVERT: A 598 LEU cc_start: 0.7843 (mm) cc_final: 0.7557 (mm) REVERT: A 631 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7944 (mtp) REVERT: A 634 MET cc_start: 0.7164 (mtm) cc_final: 0.6796 (mmt) REVERT: A 662 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8710 (mt) REVERT: A 665 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7321 (mmm) REVERT: A 969 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7445 (tm-30) REVERT: A 1025 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6544 (mmt) REVERT: A 1142 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7780 (mtt180) REVERT: A 1144 MET cc_start: 0.7308 (tpp) cc_final: 0.6205 (tmm) REVERT: A 1147 LYS cc_start: 0.7871 (mtmm) cc_final: 0.7395 (mtmm) REVERT: A 1173 GLU cc_start: 0.7247 (mp0) cc_final: 0.6153 (mp0) REVERT: A 1177 MET cc_start: 0.7811 (tpt) cc_final: 0.7467 (tpt) REVERT: A 1277 ARG cc_start: 0.7790 (ttm170) cc_final: 0.7232 (mtm-85) REVERT: A 1285 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7401 (mmt) REVERT: A 1286 ARG cc_start: 0.7488 (ttm110) cc_final: 0.7064 (ptp90) REVERT: A 1288 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8780 (tp) REVERT: A 1369 ARG cc_start: 0.7446 (mtp180) cc_final: 0.7152 (mtp-110) REVERT: A 1431 ASP cc_start: 0.7334 (m-30) cc_final: 0.6896 (m-30) REVERT: B 14 LYS cc_start: 0.7765 (mmmm) cc_final: 0.7404 (mmmt) REVERT: B 15 LYS cc_start: 0.7979 (mmtp) cc_final: 0.7671 (mmmt) REVERT: B 31 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8001 (pp) outliers start: 40 outliers final: 31 residues processed: 195 average time/residue: 1.0459 time to fit residues: 223.3326 Evaluate side-chains 208 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 168 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1157 CYS Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 1502 SER Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 55 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 0.1980 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 110 optimal weight: 0.1980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.163778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.118062 restraints weight = 12193.608| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.81 r_work: 0.3120 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 11291 Z= 0.267 Angle : 0.777 27.354 15358 Z= 0.365 Chirality : 0.067 2.110 1764 Planarity : 0.004 0.048 1893 Dihedral : 6.490 58.565 1649 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.93 % Favored : 92.85 % Rotamer: Outliers : 3.87 % Allowed : 16.34 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.23), residues: 1356 helix: 0.62 (0.18), residues: 857 sheet: -2.44 (1.14), residues: 20 loop : -1.90 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 624 HIS 0.006 0.001 HIS A 153 PHE 0.015 0.002 PHE A 687 TYR 0.017 0.002 TYR A 933 ARG 0.012 0.001 ARG A 847 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4551.32 seconds wall clock time: 82 minutes 3.36 seconds (4923.36 seconds total)