Starting phenix.real_space_refine on Fri Mar 15 05:02:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0m_6698/03_2024/5x0m_6698.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0m_6698/03_2024/5x0m_6698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0m_6698/03_2024/5x0m_6698.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0m_6698/03_2024/5x0m_6698.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0m_6698/03_2024/5x0m_6698.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0m_6698/03_2024/5x0m_6698.pdb" } resolution = 3.8 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 7031 2.51 5 N 1683 2.21 5 O 1878 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 233": "NH1" <-> "NH2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "A ARG 613": "NH1" <-> "NH2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A ARG 957": "NH1" <-> "NH2" Residue "A GLU 977": "OE1" <-> "OE2" Residue "A ARG 1074": "NH1" <-> "NH2" Residue "A ARG 1131": "NH1" <-> "NH2" Residue "A ARG 1138": "NH1" <-> "NH2" Residue "A GLU 1197": "OE1" <-> "OE2" Residue "A ARG 1225": "NH1" <-> "NH2" Residue "A ARG 1274": "NH1" <-> "NH2" Residue "A ARG 1297": "NH1" <-> "NH2" Residue "A GLU 1366": "OE1" <-> "OE2" Residue "A GLU 1416": "OE1" <-> "OE2" Residue "A GLU 1423": "OE1" <-> "OE2" Residue "A GLU 1455": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10654 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1323, 10395 Classifications: {'peptide': 1323} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 45, 'TRANS': 1274} Chain breaks: 2 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 445 Unresolved non-hydrogen angles: 566 Unresolved non-hydrogen dihedrals: 376 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 8, 'GLU:plan': 6, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 247 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.65, per 1000 atoms: 0.53 Number of scatterers: 10654 At special positions: 0 Unit cell: (131.58, 130.29, 125.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1878 8.00 N 1683 7.00 C 7031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 337 " distance=2.24 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 343 " distance=1.72 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 717 " distance=2.02 Simple disulfide: pdb=" SG CYS A1011 " - pdb=" SG CYS A1030 " distance=2.02 Simple disulfide: pdb=" SG CYS A1368 " - pdb=" SG CYS A1381 " distance=1.83 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 BETA1-3 " BMA B 3 " - " BMA B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " BETA1-6 " BMA B 3 " - " BMA B 5 " NAG-ASN " NAG A1606 " - " ASN A1028 " " NAG B 1 " - " ASN A 330 " " NAG C 1 " - " ASN A1034 " " NAG D 1 " - " ASN A1015 " " NAG E 1 " - " ASN A 312 " " NAG F 1 " - " ASN A 308 " " NAG G 1 " - " ASN A 300 " Time building additional restraints: 4.49 Conformation dependent library (CDL) restraints added in 1.6 seconds 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2514 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 69.2% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 47 through 59 Processing helix chain 'A' and resid 94 through 110 Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 139 through 159 removed outlier: 4.053A pdb=" N SER A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET A 159 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 187 removed outlier: 3.764A pdb=" N PHE A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 202 through 215 removed outlier: 3.647A pdb=" N THR A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 241 removed outlier: 3.565A pdb=" N ARG A 230 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 231 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 232 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 238 " --> pdb=" O TRP A 235 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 240 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A 241 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 256 removed outlier: 3.670A pdb=" N THR A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 281 removed outlier: 4.123A pdb=" N LEU A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 360 through 374 removed outlier: 3.703A pdb=" N ALA A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 388 removed outlier: 4.065A pdb=" N LEU A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 403 removed outlier: 3.543A pdb=" N ILE A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 435 removed outlier: 3.581A pdb=" N LEU A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 428 " --> pdb=" O LYS A 424 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 520 through 537 removed outlier: 3.861A pdb=" N THR A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 573 removed outlier: 3.803A pdb=" N ASN A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 560 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 561 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 581 through 604 removed outlier: 3.989A pdb=" N VAL A 591 " --> pdb=" O ASP A 587 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 593 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY A 599 " --> pdb=" O ILE A 595 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 618 removed outlier: 3.617A pdb=" N PHE A 609 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 612 " --> pdb=" O PHE A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 removed outlier: 4.112A pdb=" N PHE A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 635 removed outlier: 3.515A pdb=" N VAL A 633 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 663 removed outlier: 3.613A pdb=" N ILE A 658 " --> pdb=" O ILE A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.742A pdb=" N MET A 671 " --> pdb=" O TYR A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 700 removed outlier: 4.047A pdb=" N VAL A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 714 removed outlier: 3.550A pdb=" N MET A 706 " --> pdb=" O TRP A 702 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A 710 " --> pdb=" O MET A 706 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL A 712 " --> pdb=" O ASP A 708 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP A 714 " --> pdb=" O MET A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 724 Processing helix chain 'A' and resid 728 through 733 Processing helix chain 'A' and resid 734 through 744 removed outlier: 3.582A pdb=" N LEU A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 855 removed outlier: 4.307A pdb=" N GLN A 839 " --> pdb=" O ASP A 835 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN A 855 " --> pdb=" O LEU A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 875 removed outlier: 3.940A pdb=" N PHE A 861 " --> pdb=" O TYR A 857 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 865 " --> pdb=" O PHE A 861 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 875 " --> pdb=" O VAL A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 912 removed outlier: 3.973A pdb=" N LEU A 891 " --> pdb=" O VAL A 887 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A 898 " --> pdb=" O ASP A 894 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 912 " --> pdb=" O MET A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.511A pdb=" N PHE A 918 " --> pdb=" O PHE A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 938 removed outlier: 3.821A pdb=" N ASP A 926 " --> pdb=" O TRP A 922 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 929 " --> pdb=" O LEU A 925 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN A 936 " --> pdb=" O ALA A 932 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 937 " --> pdb=" O TYR A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 953 Processing helix chain 'A' and resid 954 through 957 removed outlier: 3.556A pdb=" N ARG A 957 " --> pdb=" O ARG A 954 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 954 through 957' Processing helix chain 'A' and resid 958 through 963 removed outlier: 3.791A pdb=" N LEU A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 1002 removed outlier: 3.503A pdb=" N GLU A 977 " --> pdb=" O SER A 973 " (cutoff:3.500A) Proline residue: A 980 - end of helix removed outlier: 3.710A pdb=" N LEU A 987 " --> pdb=" O PHE A 983 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP A 993 " --> pdb=" O GLY A 989 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1032 removed outlier: 3.817A pdb=" N CYS A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1059 removed outlier: 4.148A pdb=" N VAL A1057 " --> pdb=" O SER A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1073 removed outlier: 4.044A pdb=" N ASP A1069 " --> pdb=" O GLN A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1089 Processing helix chain 'A' and resid 1090 through 1101 removed outlier: 3.518A pdb=" N PHE A1094 " --> pdb=" O LEU A1090 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE A1098 " --> pdb=" O PHE A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1124 removed outlier: 4.416A pdb=" N ASP A1113 " --> pdb=" O CYS A1109 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN A1117 " --> pdb=" O ASP A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1146 removed outlier: 4.066A pdb=" N ALA A1146 " --> pdb=" O ARG A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1168 removed outlier: 3.851A pdb=" N MET A1163 " --> pdb=" O PRO A1159 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A1164 " --> pdb=" O GLN A1160 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A1168 " --> pdb=" O TYR A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1188 removed outlier: 3.784A pdb=" N MET A1187 " --> pdb=" O ASN A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1225 removed outlier: 4.275A pdb=" N PHE A1198 " --> pdb=" O GLN A1194 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A1199 " --> pdb=" O SER A1195 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A1201 " --> pdb=" O GLU A1197 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A1210 " --> pdb=" O ASN A1206 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A1211 " --> pdb=" O LEU A1207 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A1218 " --> pdb=" O PHE A1214 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A1223 " --> pdb=" O ILE A1219 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A1224 " --> pdb=" O LYS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1249 removed outlier: 3.821A pdb=" N VAL A1241 " --> pdb=" O ASP A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1271 removed outlier: 4.057A pdb=" N LEU A1264 " --> pdb=" O SER A1260 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A1265 " --> pdb=" O PRO A1261 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A1268 " --> pdb=" O LEU A1264 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A1271 " --> pdb=" O LEU A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1278 removed outlier: 3.662A pdb=" N LEU A1275 " --> pdb=" O VAL A1272 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A1276 " --> pdb=" O GLY A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1319 removed outlier: 3.580A pdb=" N ARG A1293 " --> pdb=" O LEU A1289 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG A1297 " --> pdb=" O ARG A1293 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N THR A1298 " --> pdb=" O LYS A1294 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A1305 " --> pdb=" O ASN A1301 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A1315 " --> pdb=" O PHE A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1351 removed outlier: 3.818A pdb=" N LEU A1346 " --> pdb=" O SER A1342 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A1348 " --> pdb=" O ILE A1344 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A1351 " --> pdb=" O PHE A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1363 removed outlier: 3.605A pdb=" N VAL A1358 " --> pdb=" O GLY A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1396 removed outlier: 3.593A pdb=" N ALA A1389 " --> pdb=" O ALA A1385 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TYR A1390 " --> pdb=" O LEU A1386 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER A1393 " --> pdb=" O ALA A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1401 through 1424 removed outlier: 3.916A pdb=" N ALA A1407 " --> pdb=" O ILE A1403 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE A1410 " --> pdb=" O TYR A1406 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A1418 " --> pdb=" O VAL A1414 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1441 removed outlier: 4.052A pdb=" N TYR A1430 " --> pdb=" O THR A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1459 Processing helix chain 'A' and resid 1470 through 1475 Processing helix chain 'A' and resid 1489 through 1505 Processing helix chain 'A' and resid 1508 through 1521 removed outlier: 3.582A pdb=" N ASP A1512 " --> pdb=" O VAL A1508 " (cutoff:3.500A) Proline residue: A1516 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 67 Processing sheet with id=AA2, first strand: chain 'A' and resid 287 through 290 removed outlier: 3.569A pdb=" N LYS A 287 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 344 " --> pdb=" O LYS A 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1012 through 1013 removed outlier: 3.510A pdb=" N ASP A1013 " --> pdb=" O THR A1017 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1447 through 1449 549 hydrogen bonds defined for protein. 1584 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: 2.97 Time building geometry restraints manager: 4.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1794 1.32 - 1.45: 3059 1.45 - 1.57: 5966 1.57 - 1.69: 3 1.69 - 1.82: 105 Bond restraints: 10927 Sorted by residual: bond pdb=" C ASP A1072 " pdb=" N SER A1073 " ideal model delta sigma weight residual 1.330 1.574 -0.243 1.42e-02 4.96e+03 2.94e+02 bond pdb=" C LEU A 935 " pdb=" N ASN A 936 " ideal model delta sigma weight residual 1.334 1.485 -0.151 1.33e-02 5.65e+03 1.29e+02 bond pdb=" C VAL A1047 " pdb=" N GLY A1048 " ideal model delta sigma weight residual 1.335 1.231 0.104 1.26e-02 6.30e+03 6.77e+01 bond pdb=" C PHE A 674 " pdb=" N PRO A 675 " ideal model delta sigma weight residual 1.334 1.493 -0.160 2.34e-02 1.83e+03 4.65e+01 bond pdb=" C SER A 574 " pdb=" N PRO A 575 " ideal model delta sigma weight residual 1.335 1.421 -0.086 1.30e-02 5.92e+03 4.36e+01 ... (remaining 10922 not shown) Histogram of bond angle deviations from ideal: 99.57 - 108.18: 467 108.18 - 116.79: 7699 116.79 - 125.41: 6535 125.41 - 134.02: 154 134.02 - 142.63: 19 Bond angle restraints: 14874 Sorted by residual: angle pdb=" CA VAL A 503 " pdb=" C VAL A 503 " pdb=" N PRO A 504 " ideal model delta sigma weight residual 120.83 114.03 6.80 6.10e-01 2.69e+00 1.24e+02 angle pdb=" CA ASP A1072 " pdb=" C ASP A1072 " pdb=" N SER A1073 " ideal model delta sigma weight residual 118.36 104.60 13.76 1.33e+00 5.65e-01 1.07e+02 angle pdb=" CA PRO A 519 " pdb=" N PRO A 519 " pdb=" CD PRO A 519 " ideal model delta sigma weight residual 112.00 99.57 12.43 1.40e+00 5.10e-01 7.88e+01 angle pdb=" CA VAL A1047 " pdb=" C VAL A1047 " pdb=" N GLY A1048 " ideal model delta sigma weight residual 117.27 130.68 -13.41 1.51e+00 4.39e-01 7.88e+01 angle pdb=" O ASP A1072 " pdb=" C ASP A1072 " pdb=" N SER A1073 " ideal model delta sigma weight residual 122.41 134.39 -11.98 1.42e+00 4.96e-01 7.12e+01 ... (remaining 14869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.78: 5871 26.78 - 53.57: 509 53.57 - 80.35: 135 80.35 - 107.13: 58 107.13 - 133.91: 14 Dihedral angle restraints: 6587 sinusoidal: 2692 harmonic: 3895 Sorted by residual: dihedral pdb=" CA TRP A 121 " pdb=" C TRP A 121 " pdb=" N MET A 122 " pdb=" CA MET A 122 " ideal model delta harmonic sigma weight residual -180.00 -46.09 -133.91 0 5.00e+00 4.00e-02 7.17e+02 dihedral pdb=" CA GLY A 605 " pdb=" C GLY A 605 " pdb=" N LEU A 606 " pdb=" CA LEU A 606 " ideal model delta harmonic sigma weight residual 180.00 58.11 121.89 0 5.00e+00 4.00e-02 5.94e+02 dihedral pdb=" CA CYS A1157 " pdb=" C CYS A1157 " pdb=" N HIS A1158 " pdb=" CA HIS A1158 " ideal model delta harmonic sigma weight residual 180.00 75.27 104.73 0 5.00e+00 4.00e-02 4.39e+02 ... (remaining 6584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1707 0.131 - 0.261: 47 0.261 - 0.392: 8 0.392 - 0.522: 2 0.522 - 0.653: 1 Chirality restraints: 1765 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A1015 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA PRO A 719 " pdb=" N PRO A 719 " pdb=" C PRO A 719 " pdb=" CB PRO A 719 " both_signs ideal model delta sigma weight residual False 2.72 2.28 0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CA PRO A 575 " pdb=" N PRO A 575 " pdb=" C PRO A 575 " pdb=" CB PRO A 575 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.53e+00 ... (remaining 1762 not shown) Planarity restraints: 1825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 245 " -1.054 9.50e-02 1.11e+02 4.72e-01 1.35e+02 pdb=" NE ARG A 245 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 245 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 245 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 245 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 935 " 0.041 2.00e-02 2.50e+03 7.35e-02 5.41e+01 pdb=" C LEU A 935 " -0.127 2.00e-02 2.50e+03 pdb=" O LEU A 935 " 0.048 2.00e-02 2.50e+03 pdb=" N ASN A 936 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 330 " 0.049 2.00e-02 2.50e+03 5.50e-02 3.78e+01 pdb=" CG ASN A 330 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN A 330 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 330 " -0.089 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " 0.066 2.00e-02 2.50e+03 ... (remaining 1822 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 144 2.55 - 3.14: 9304 3.14 - 3.73: 15820 3.73 - 4.31: 22555 4.31 - 4.90: 33847 Nonbonded interactions: 81670 Sorted by model distance: nonbonded pdb=" SD MET A1477 " pdb=" OD2 ASP A1499 " model vdw 1.965 3.400 nonbonded pdb=" O LEU A 531 " pdb=" OG1 THR A 534 " model vdw 1.973 2.440 nonbonded pdb=" CE1 PHE A 401 " pdb=" OH TYR A1406 " model vdw 2.009 3.340 nonbonded pdb=" O ILE A1330 " pdb=" N ASP A1332 " model vdw 2.025 2.520 nonbonded pdb=" O GLY A 221 " pdb=" ND1 HIS A 222 " model vdw 2.025 2.520 ... (remaining 81665 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' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 2.440 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 28.910 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5675 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.243 10927 Z= 0.566 Angle : 1.407 17.634 14874 Z= 0.886 Chirality : 0.059 0.653 1765 Planarity : 0.013 0.472 1818 Dihedral : 24.001 133.913 4058 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 54.20 Ramachandran Plot: Outliers : 5.24 % Allowed : 12.91 % Favored : 81.85 % Rotamer: Outliers : 11.48 % Allowed : 12.14 % Favored : 76.38 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 48.94 % Twisted General : 7.70 % 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: -5.95 (0.16), residues: 1317 helix: -3.44 (0.12), residues: 821 sheet: None (None), residues: 0 loop : -4.70 (0.20), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 316 HIS 0.012 0.002 HIS A 291 PHE 0.036 0.001 PHE A 684 TYR 0.081 0.002 TYR A1089 ARG 0.005 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 380 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 PHE cc_start: 0.6576 (t80) cc_final: 0.5715 (m-80) REVERT: A 183 LYS cc_start: 0.8446 (mmtt) cc_final: 0.7788 (mtmt) REVERT: A 219 ASP cc_start: 0.0666 (OUTLIER) cc_final: 0.0054 (t0) REVERT: A 227 ARG cc_start: 0.6226 (mmt90) cc_final: 0.6004 (mmt180) REVERT: A 259 LYS cc_start: 0.2473 (OUTLIER) cc_final: 0.1820 (mtmt) REVERT: A 281 MET cc_start: 0.7065 (ttp) cc_final: 0.6278 (ttm) REVERT: A 331 SER cc_start: 0.6957 (m) cc_final: 0.6741 (t) REVERT: A 379 ASP cc_start: 0.5424 (OUTLIER) cc_final: 0.5114 (t0) REVERT: A 425 ARG cc_start: 0.4644 (OUTLIER) cc_final: 0.4195 (ttm-80) REVERT: A 556 TYR cc_start: 0.8356 (m-80) cc_final: 0.6459 (t80) REVERT: A 557 ILE cc_start: 0.8727 (mt) cc_final: 0.8349 (mt) REVERT: A 590 ILE cc_start: 0.7398 (mm) cc_final: 0.7171 (mt) REVERT: A 613 ARG cc_start: 0.8334 (mtt180) cc_final: 0.7611 (ttm110) REVERT: A 631 MET cc_start: 0.6904 (tpt) cc_final: 0.6377 (tmm) REVERT: A 706 MET cc_start: 0.7510 (ttp) cc_final: 0.6787 (ttp) REVERT: A 711 LEU cc_start: 0.7357 (tm) cc_final: 0.6322 (tm) REVERT: A 735 LEU cc_start: 0.6008 (tp) cc_final: 0.5387 (tt) REVERT: A 854 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.6219 (mmtm) REVERT: A 856 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7333 (ptpt) REVERT: A 905 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.7695 (tpp) REVERT: A 966 ASN cc_start: 0.5686 (OUTLIER) cc_final: 0.5024 (t0) REVERT: A 1003 LEU cc_start: 0.4543 (OUTLIER) cc_final: 0.4294 (pp) REVERT: A 1010 LYS cc_start: 0.7082 (OUTLIER) cc_final: 0.6811 (pttm) REVERT: A 1015 ASN cc_start: 0.6776 (m-40) cc_final: 0.6505 (m-40) REVERT: A 1017 THR cc_start: 0.6255 (p) cc_final: 0.5519 (m) REVERT: A 1032 HIS cc_start: 0.6870 (t70) cc_final: 0.6592 (t70) REVERT: A 1074 ARG cc_start: 0.7304 (pmt-80) cc_final: 0.6546 (pmt-80) REVERT: A 1125 LEU cc_start: 0.4952 (OUTLIER) cc_final: 0.3200 (mt) REVERT: A 1131 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6762 (tpt170) REVERT: A 1134 LEU cc_start: 0.8728 (mt) cc_final: 0.8497 (mt) REVERT: A 1135 ILE cc_start: 0.8360 (mt) cc_final: 0.7973 (mt) REVERT: A 1136 TYR cc_start: 0.7168 (m-80) cc_final: 0.6914 (m-80) REVERT: A 1147 LYS cc_start: 0.8683 (mttt) cc_final: 0.8433 (mmtt) REVERT: A 1149 VAL cc_start: 0.7673 (t) cc_final: 0.7169 (t) REVERT: A 1156 THR cc_start: 0.6576 (OUTLIER) cc_final: 0.6209 (m) REVERT: A 1170 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.6442 (ttp80) REVERT: A 1187 MET cc_start: 0.6390 (mtm) cc_final: 0.5825 (mtm) REVERT: A 1197 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7450 (mt-10) REVERT: A 1258 PHE cc_start: 0.5884 (OUTLIER) cc_final: 0.5517 (m-80) REVERT: A 1268 ARG cc_start: 0.7180 (ttp-170) cc_final: 0.6810 (ttp80) REVERT: A 1276 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7091 (mt) REVERT: A 1277 ARG cc_start: 0.6410 (OUTLIER) cc_final: 0.6157 (mtt180) REVERT: A 1310 MET cc_start: 0.6467 (OUTLIER) cc_final: 0.6109 (mtp) REVERT: A 1316 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.5988 (m-80) REVERT: A 1319 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6715 (mm-30) REVERT: A 1338 THR cc_start: 0.7453 (p) cc_final: 0.7034 (t) REVERT: A 1346 LEU cc_start: 0.5034 (OUTLIER) cc_final: 0.4800 (pp) REVERT: A 1378 PRO cc_start: 0.5105 (Cg_exo) cc_final: 0.4047 (Cg_endo) REVERT: A 1406 TYR cc_start: 0.5478 (OUTLIER) cc_final: 0.4995 (t80) REVERT: A 1416 GLU cc_start: 0.6875 (tt0) cc_final: 0.6467 (tt0) REVERT: A 1429 ASP cc_start: 0.6592 (OUTLIER) cc_final: 0.6388 (t70) REVERT: A 1432 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7805 (ppp) REVERT: A 1438 GLN cc_start: 0.8691 (tt0) cc_final: 0.8180 (tp-100) REVERT: A 1455 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8693 (mm-30) REVERT: A 1473 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8401 (mmtm) REVERT: A 1479 ILE cc_start: 0.8730 (mt) cc_final: 0.8469 (mt) REVERT: A 1494 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8079 (tp30) outliers start: 121 outliers final: 11 residues processed: 455 average time/residue: 0.2554 time to fit residues: 156.3411 Evaluate side-chains 293 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 256 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 521 PHE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 905 MET Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1131 ARG Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1170 ARG Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1227 HIS Chi-restraints excluded: chain A residue 1258 PHE Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1277 ARG Chi-restraints excluded: chain A residue 1310 MET Chi-restraints excluded: chain A residue 1316 PHE Chi-restraints excluded: chain A residue 1346 LEU Chi-restraints excluded: chain A residue 1406 TYR Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1429 ASP Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1473 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS A 286 GLN A 291 HIS A 352 ASN A 382 GLN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 HIS A 661 GLN A 670 ASN A 855 ASN A1002 GLN A1021 HIS ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1079 GLN ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 GLN ** A1341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1446 GLN A1465 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 10927 Z= 0.297 Angle : 1.030 14.491 14874 Z= 0.512 Chirality : 0.053 0.530 1765 Planarity : 0.007 0.070 1818 Dihedral : 17.530 88.396 1936 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 1.97 % Allowed : 11.09 % Favored : 86.94 % Rotamer: Outliers : 6.07 % Allowed : 19.83 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 17.02 % Twisted General : 2.51 % 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: -3.41 (0.22), residues: 1317 helix: -1.34 (0.17), residues: 844 sheet: -4.87 (0.95), residues: 20 loop : -3.85 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 316 HIS 0.008 0.001 HIS A1158 PHE 0.024 0.003 PHE A 996 TYR 0.041 0.003 TYR A1089 ARG 0.011 0.001 ARG A 681 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 309 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 PHE cc_start: 0.6819 (t80) cc_final: 0.6170 (m-80) REVERT: A 156 PHE cc_start: 0.7810 (t80) cc_final: 0.7581 (t80) REVERT: A 189 PHE cc_start: 0.6344 (m-80) cc_final: 0.5983 (m-10) REVERT: A 259 LYS cc_start: 0.1617 (OUTLIER) cc_final: 0.0963 (mtmt) REVERT: A 263 LEU cc_start: 0.6510 (tp) cc_final: 0.6180 (mp) REVERT: A 402 TYR cc_start: 0.6256 (t80) cc_final: 0.5884 (m-80) REVERT: A 548 GLU cc_start: 0.7558 (tp30) cc_final: 0.7053 (pt0) REVERT: A 556 TYR cc_start: 0.7819 (m-10) cc_final: 0.6742 (t80) REVERT: A 557 ILE cc_start: 0.8413 (mt) cc_final: 0.8128 (mt) REVERT: A 580 LYS cc_start: 0.6302 (tptt) cc_final: 0.5787 (tttp) REVERT: A 631 MET cc_start: 0.6904 (tpt) cc_final: 0.6517 (tmm) REVERT: A 735 LEU cc_start: 0.6359 (tp) cc_final: 0.6080 (tt) REVERT: A 737 ILE cc_start: 0.6545 (mt) cc_final: 0.6214 (mt) REVERT: A 856 LYS cc_start: 0.7957 (mttt) cc_final: 0.7602 (pttt) REVERT: A 888 ASN cc_start: 0.8720 (t0) cc_final: 0.8409 (m110) REVERT: A 916 LYS cc_start: 0.8661 (ptpp) cc_final: 0.8405 (tppt) REVERT: A 948 GLN cc_start: 0.8063 (tp40) cc_final: 0.7834 (tp40) REVERT: A 969 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7447 (mp10) REVERT: A 1032 HIS cc_start: 0.6622 (t70) cc_final: 0.6345 (t70) REVERT: A 1052 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.6281 (mp) REVERT: A 1074 ARG cc_start: 0.7355 (pmt-80) cc_final: 0.5749 (tpt170) REVERT: A 1075 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6770 (tt0) REVERT: A 1079 GLN cc_start: 0.8402 (tp40) cc_final: 0.8126 (tp-100) REVERT: A 1094 PHE cc_start: 0.6955 (m-80) cc_final: 0.6654 (t80) REVERT: A 1134 LEU cc_start: 0.8724 (mt) cc_final: 0.8451 (mt) REVERT: A 1135 ILE cc_start: 0.8421 (mt) cc_final: 0.8085 (mt) REVERT: A 1144 MET cc_start: 0.8292 (tmm) cc_final: 0.8081 (tmm) REVERT: A 1147 LYS cc_start: 0.8582 (mttt) cc_final: 0.8275 (mmtm) REVERT: A 1151 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7663 (tpp80) REVERT: A 1170 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.6149 (ttt90) REVERT: A 1197 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7245 (mt-10) REVERT: A 1207 LEU cc_start: 0.8972 (mt) cc_final: 0.8688 (mt) REVERT: A 1288 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7465 (tt) REVERT: A 1310 MET cc_start: 0.6206 (mtp) cc_final: 0.5848 (mtp) REVERT: A 1346 LEU cc_start: 0.5622 (mp) cc_final: 0.5380 (tp) REVERT: A 1432 MET cc_start: 0.8056 (ppp) cc_final: 0.7680 (ppp) REVERT: A 1438 GLN cc_start: 0.8506 (tt0) cc_final: 0.8081 (tt0) REVERT: A 1439 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8003 (tm-30) REVERT: A 1455 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8499 (mm-30) REVERT: A 1458 GLU cc_start: 0.7797 (tt0) cc_final: 0.7562 (mt-10) REVERT: A 1461 GLN cc_start: 0.9193 (mm110) cc_final: 0.8921 (tt0) REVERT: A 1473 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8626 (mmtm) REVERT: A 1494 GLU cc_start: 0.8582 (mt-10) cc_final: 0.7992 (tp30) outliers start: 64 outliers final: 21 residues processed: 346 average time/residue: 0.2252 time to fit residues: 108.3319 Evaluate side-chains 282 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 251 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 892 TYR Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1075 GLU Chi-restraints excluded: chain A residue 1151 ARG Chi-restraints excluded: chain A residue 1170 ARG Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1226 HIS Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1281 SER Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1318 MET Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1473 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 96 optimal weight: 0.0970 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS A 286 GLN A 392 HIS ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10927 Z= 0.245 Angle : 0.908 17.359 14874 Z= 0.445 Chirality : 0.048 0.214 1765 Planarity : 0.007 0.147 1818 Dihedral : 12.180 71.010 1867 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.99 % Allowed : 12.30 % Favored : 86.71 % Rotamer: Outliers : 5.79 % Allowed : 22.30 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 8.51 % Twisted General : 1.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.22), residues: 1317 helix: -0.68 (0.17), residues: 866 sheet: None (None), residues: 0 loop : -3.69 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1063 HIS 0.009 0.002 HIS A1227 PHE 0.019 0.002 PHE A 653 TYR 0.027 0.002 TYR A1240 ARG 0.022 0.001 ARG A1074 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 287 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 PHE cc_start: 0.6870 (t80) cc_final: 0.6129 (m-80) REVERT: A 259 LYS cc_start: 0.1545 (OUTLIER) cc_final: 0.0888 (mtmt) REVERT: A 260 ASP cc_start: 0.4303 (t70) cc_final: 0.4035 (t70) REVERT: A 263 LEU cc_start: 0.6934 (tp) cc_final: 0.6622 (mp) REVERT: A 281 MET cc_start: 0.6772 (ttp) cc_final: 0.6408 (ttt) REVERT: A 306 TRP cc_start: 0.8127 (t60) cc_final: 0.7805 (t60) REVERT: A 336 MET cc_start: 0.6550 (mpp) cc_final: 0.6324 (mpp) REVERT: A 355 TYR cc_start: 0.6111 (m-80) cc_final: 0.5720 (m-80) REVERT: A 427 ASP cc_start: 0.6432 (t0) cc_final: 0.6117 (t70) REVERT: A 542 ASP cc_start: 0.7114 (m-30) cc_final: 0.6432 (p0) REVERT: A 548 GLU cc_start: 0.7541 (tp30) cc_final: 0.6945 (pt0) REVERT: A 556 TYR cc_start: 0.7718 (m-10) cc_final: 0.6508 (t80) REVERT: A 557 ILE cc_start: 0.8284 (mt) cc_final: 0.8036 (mt) REVERT: A 580 LYS cc_start: 0.6180 (tptt) cc_final: 0.5672 (tttp) REVERT: A 631 MET cc_start: 0.7037 (tpt) cc_final: 0.6506 (tmm) REVERT: A 660 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7910 (mtm) REVERT: A 662 LEU cc_start: 0.7663 (tt) cc_final: 0.7370 (tp) REVERT: A 692 MET cc_start: 0.8102 (tpp) cc_final: 0.7702 (tpp) REVERT: A 856 LYS cc_start: 0.8062 (mttt) cc_final: 0.7587 (pttt) REVERT: A 883 ARG cc_start: 0.6636 (OUTLIER) cc_final: 0.6341 (tmm-80) REVERT: A 904 GLU cc_start: 0.8281 (tm-30) cc_final: 0.8000 (tm-30) REVERT: A 908 MET cc_start: 0.7977 (tpp) cc_final: 0.7416 (tpp) REVERT: A 926 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8245 (t70) REVERT: A 1032 HIS cc_start: 0.6542 (t70) cc_final: 0.6290 (t70) REVERT: A 1094 PHE cc_start: 0.7535 (m-80) cc_final: 0.7289 (t80) REVERT: A 1135 ILE cc_start: 0.8322 (mt) cc_final: 0.8084 (mt) REVERT: A 1144 MET cc_start: 0.8545 (tmm) cc_final: 0.8220 (tmm) REVERT: A 1170 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6136 (ttt90) REVERT: A 1197 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: A 1207 LEU cc_start: 0.8921 (mt) cc_final: 0.8676 (mt) REVERT: A 1231 ASP cc_start: 0.6934 (OUTLIER) cc_final: 0.6725 (m-30) REVERT: A 1318 MET cc_start: 0.5932 (OUTLIER) cc_final: 0.5731 (ptm) REVERT: A 1432 MET cc_start: 0.8141 (ppp) cc_final: 0.7927 (ppp) REVERT: A 1455 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8527 (mm-30) REVERT: A 1458 GLU cc_start: 0.7771 (tt0) cc_final: 0.7515 (mt-10) REVERT: A 1461 GLN cc_start: 0.9255 (mm110) cc_final: 0.8940 (tt0) REVERT: A 1473 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8583 (mptt) REVERT: A 1494 GLU cc_start: 0.8645 (mt-10) cc_final: 0.7982 (tp30) outliers start: 61 outliers final: 26 residues processed: 314 average time/residue: 0.2141 time to fit residues: 95.7231 Evaluate side-chains 283 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 247 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 883 ARG Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 892 TYR Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1143 THR Chi-restraints excluded: chain A residue 1151 ARG Chi-restraints excluded: chain A residue 1170 ARG Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1226 HIS Chi-restraints excluded: chain A residue 1231 ASP Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1281 SER Chi-restraints excluded: chain A residue 1318 MET Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1473 LYS Chi-restraints excluded: chain A residue 1492 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 120 optimal weight: 0.3980 chunk 127 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 ASN ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.7629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 10927 Z= 0.355 Angle : 0.917 21.096 14874 Z= 0.455 Chirality : 0.049 0.243 1765 Planarity : 0.005 0.072 1818 Dihedral : 9.881 65.647 1863 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 1.06 % Allowed : 11.24 % Favored : 87.70 % Rotamer: Outliers : 6.36 % Allowed : 23.81 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 4.26 % Twisted General : 1.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.22), residues: 1317 helix: -0.60 (0.16), residues: 874 sheet: None (None), residues: 0 loop : -3.46 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 715 HIS 0.006 0.001 HIS A 192 PHE 0.027 0.002 PHE A 687 TYR 0.029 0.003 TYR A1089 ARG 0.007 0.001 ARG A1268 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 266 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 LYS cc_start: 0.8691 (mmtt) cc_final: 0.8065 (pttp) REVERT: A 244 TRP cc_start: 0.7700 (t60) cc_final: 0.7422 (t60) REVERT: A 259 LYS cc_start: 0.2953 (OUTLIER) cc_final: 0.2167 (mtmt) REVERT: A 260 ASP cc_start: 0.4937 (t70) cc_final: 0.4497 (t70) REVERT: A 263 LEU cc_start: 0.7734 (tp) cc_final: 0.7439 (mp) REVERT: A 281 MET cc_start: 0.7222 (ttp) cc_final: 0.6578 (tpp) REVERT: A 321 ASP cc_start: 0.7811 (m-30) cc_final: 0.7405 (p0) REVERT: A 347 TYR cc_start: 0.7358 (m-80) cc_final: 0.7125 (m-10) REVERT: A 548 GLU cc_start: 0.7795 (tp30) cc_final: 0.7206 (pt0) REVERT: A 555 ASN cc_start: 0.8486 (t0) cc_final: 0.8278 (t0) REVERT: A 556 TYR cc_start: 0.7887 (m-10) cc_final: 0.6614 (t80) REVERT: A 577 PHE cc_start: 0.7082 (t80) cc_final: 0.6877 (t80) REVERT: A 580 LYS cc_start: 0.6246 (tptt) cc_final: 0.5621 (ttmm) REVERT: A 609 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7739 (t80) REVERT: A 631 MET cc_start: 0.7583 (tpt) cc_final: 0.6965 (tmm) REVERT: A 660 MET cc_start: 0.7986 (mtm) cc_final: 0.7703 (mtm) REVERT: A 856 LYS cc_start: 0.8046 (mttt) cc_final: 0.7563 (pttt) REVERT: A 872 LEU cc_start: 0.8264 (tt) cc_final: 0.8007 (tt) REVERT: A 883 ARG cc_start: 0.6868 (tmt170) cc_final: 0.6523 (tmm-80) REVERT: A 905 MET cc_start: 0.8587 (tpp) cc_final: 0.8161 (tpt) REVERT: A 969 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7752 (mp10) REVERT: A 1074 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.5847 (tpp-160) REVERT: A 1094 PHE cc_start: 0.8210 (m-80) cc_final: 0.7738 (t80) REVERT: A 1147 LYS cc_start: 0.8710 (mttt) cc_final: 0.8429 (mmtt) REVERT: A 1151 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7757 (tpp80) REVERT: A 1163 MET cc_start: 0.8205 (mtp) cc_final: 0.7878 (mtp) REVERT: A 1170 ARG cc_start: 0.7591 (mmt90) cc_final: 0.6246 (ttt90) REVERT: A 1197 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: A 1373 HIS cc_start: 0.7474 (t-90) cc_final: 0.6703 (p-80) REVERT: A 1418 TYR cc_start: 0.7616 (m-80) cc_final: 0.7248 (m-80) REVERT: A 1439 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8149 (tm-30) REVERT: A 1455 GLU cc_start: 0.8950 (tp30) cc_final: 0.8558 (mm-30) REVERT: A 1458 GLU cc_start: 0.7739 (tt0) cc_final: 0.7467 (tt0) REVERT: A 1494 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8078 (tp30) outliers start: 67 outliers final: 25 residues processed: 303 average time/residue: 0.2090 time to fit residues: 91.5719 Evaluate side-chains 269 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 238 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 892 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1074 ARG Chi-restraints excluded: chain A residue 1109 CYS Chi-restraints excluded: chain A residue 1151 ARG Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1200 GLU Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1226 HIS Chi-restraints excluded: chain A residue 1281 SER Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1456 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 5.9990 chunk 1 optimal weight: 30.0000 chunk 95 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 108 optimal weight: 0.0470 chunk 88 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS A 352 ASN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 743 ASN ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.8320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10927 Z= 0.256 Angle : 0.829 19.935 14874 Z= 0.407 Chirality : 0.046 0.229 1765 Planarity : 0.005 0.063 1818 Dihedral : 8.557 63.661 1848 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.76 % Allowed : 10.93 % Favored : 88.31 % Rotamer: Outliers : 5.03 % Allowed : 26.85 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 2.13 % Twisted General : 0.86 % 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: -1.92 (0.23), residues: 1317 helix: -0.21 (0.17), residues: 874 sheet: None (None), residues: 0 loop : -3.47 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 203 HIS 0.005 0.001 HIS A 192 PHE 0.016 0.001 PHE A 521 TYR 0.028 0.002 TYR A1089 ARG 0.009 0.001 ARG A 386 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 270 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 TRP cc_start: 0.7730 (t60) cc_final: 0.7384 (t60) REVERT: A 252 SER cc_start: 0.7884 (t) cc_final: 0.7356 (m) REVERT: A 281 MET cc_start: 0.7516 (ttp) cc_final: 0.6939 (tpp) REVERT: A 292 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.7935 (m-10) REVERT: A 321 ASP cc_start: 0.7726 (m-30) cc_final: 0.7428 (p0) REVERT: A 336 MET cc_start: 0.6865 (mpp) cc_final: 0.6582 (mpp) REVERT: A 556 TYR cc_start: 0.7767 (m-10) cc_final: 0.6395 (t80) REVERT: A 577 PHE cc_start: 0.6922 (t80) cc_final: 0.6719 (t80) REVERT: A 580 LYS cc_start: 0.6296 (tptt) cc_final: 0.5655 (ttmm) REVERT: A 597 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8034 (mt-10) REVERT: A 609 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7538 (t80) REVERT: A 631 MET cc_start: 0.7623 (tpt) cc_final: 0.6948 (tmm) REVERT: A 724 VAL cc_start: 0.8212 (p) cc_final: 0.7995 (p) REVERT: A 856 LYS cc_start: 0.8028 (mttt) cc_final: 0.7543 (pttt) REVERT: A 890 THR cc_start: 0.8264 (t) cc_final: 0.8059 (t) REVERT: A 908 MET cc_start: 0.8061 (tpp) cc_final: 0.7484 (tpp) REVERT: A 1074 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.5311 (tpp-160) REVERT: A 1085 ASN cc_start: 0.6792 (t0) cc_final: 0.6443 (t0) REVERT: A 1094 PHE cc_start: 0.8129 (m-80) cc_final: 0.7726 (t80) REVERT: A 1096 ILE cc_start: 0.7416 (tt) cc_final: 0.7172 (tt) REVERT: A 1144 MET cc_start: 0.8680 (tmm) cc_final: 0.8421 (mmp) REVERT: A 1147 LYS cc_start: 0.8647 (mttt) cc_final: 0.8349 (mmtt) REVERT: A 1151 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7715 (tpp80) REVERT: A 1170 ARG cc_start: 0.7709 (mmt90) cc_final: 0.6332 (ttt90) REVERT: A 1177 MET cc_start: 0.7031 (mmm) cc_final: 0.6752 (mmm) REVERT: A 1197 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: A 1373 HIS cc_start: 0.7441 (t-90) cc_final: 0.6724 (p-80) REVERT: A 1418 TYR cc_start: 0.7576 (m-80) cc_final: 0.7101 (m-80) REVERT: A 1439 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8397 (tm-30) REVERT: A 1455 GLU cc_start: 0.8938 (tp30) cc_final: 0.8564 (mm-30) REVERT: A 1458 GLU cc_start: 0.7779 (tt0) cc_final: 0.7437 (tt0) REVERT: A 1461 GLN cc_start: 0.9218 (mm110) cc_final: 0.9003 (tt0) REVERT: A 1494 GLU cc_start: 0.8740 (mt-10) cc_final: 0.7985 (tp30) outliers start: 53 outliers final: 31 residues processed: 301 average time/residue: 0.2091 time to fit residues: 90.5074 Evaluate side-chains 286 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 250 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 892 TYR Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 1074 ARG Chi-restraints excluded: chain A residue 1091 TYR Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1109 CYS Chi-restraints excluded: chain A residue 1143 THR Chi-restraints excluded: chain A residue 1151 ARG Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1200 GLU Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1226 HIS Chi-restraints excluded: chain A residue 1231 ASP Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1500 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.9099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10927 Z= 0.246 Angle : 0.824 19.558 14874 Z= 0.404 Chirality : 0.045 0.240 1765 Planarity : 0.005 0.116 1818 Dihedral : 7.647 61.285 1844 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.68 % Allowed : 11.01 % Favored : 88.31 % Rotamer: Outliers : 4.74 % Allowed : 29.22 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 4.26 % Twisted General : 0.86 % 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: -1.71 (0.23), residues: 1317 helix: -0.03 (0.17), residues: 878 sheet: -4.27 (0.96), residues: 10 loop : -3.41 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 316 HIS 0.005 0.001 HIS A 153 PHE 0.023 0.001 PHE A 145 TYR 0.028 0.002 TYR A1089 ARG 0.007 0.001 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 273 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 TRP cc_start: 0.7652 (t60) cc_final: 0.7265 (t60) REVERT: A 281 MET cc_start: 0.7429 (ttp) cc_final: 0.6988 (tpp) REVERT: A 292 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.8006 (m-10) REVERT: A 548 GLU cc_start: 0.7566 (tp30) cc_final: 0.7116 (pt0) REVERT: A 556 TYR cc_start: 0.7865 (m-10) cc_final: 0.6525 (t80) REVERT: A 580 LYS cc_start: 0.6549 (tptt) cc_final: 0.5928 (ttmm) REVERT: A 597 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7911 (mt-10) REVERT: A 609 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7579 (t80) REVERT: A 623 PHE cc_start: 0.7358 (t80) cc_final: 0.7096 (t80) REVERT: A 631 MET cc_start: 0.7677 (tpt) cc_final: 0.7072 (tmm) REVERT: A 692 MET cc_start: 0.8152 (mmt) cc_final: 0.7927 (mmt) REVERT: A 856 LYS cc_start: 0.8012 (mttt) cc_final: 0.7577 (pttt) REVERT: A 908 MET cc_start: 0.8373 (tpp) cc_final: 0.7813 (tpp) REVERT: A 1042 MET cc_start: 0.7929 (mmm) cc_final: 0.7637 (tpt) REVERT: A 1067 MET cc_start: 0.7254 (mtt) cc_final: 0.6963 (mtt) REVERT: A 1074 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.5359 (tpp-160) REVERT: A 1094 PHE cc_start: 0.8755 (m-80) cc_final: 0.8264 (t80) REVERT: A 1144 MET cc_start: 0.8855 (tmm) cc_final: 0.8608 (mmt) REVERT: A 1151 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7705 (tpp80) REVERT: A 1170 ARG cc_start: 0.7757 (mmt90) cc_final: 0.6352 (ttt90) REVERT: A 1197 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: A 1198 PHE cc_start: 0.6948 (m-10) cc_final: 0.6705 (m-10) REVERT: A 1337 LYS cc_start: 0.7084 (mttt) cc_final: 0.6811 (mtmm) REVERT: A 1373 HIS cc_start: 0.7420 (t-90) cc_final: 0.6687 (p-80) REVERT: A 1418 TYR cc_start: 0.7485 (m-80) cc_final: 0.6905 (m-80) REVERT: A 1423 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7081 (mm-30) REVERT: A 1439 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8311 (tm-30) REVERT: A 1455 GLU cc_start: 0.8950 (tp30) cc_final: 0.8633 (mm-30) REVERT: A 1494 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8064 (tp30) outliers start: 50 outliers final: 33 residues processed: 297 average time/residue: 0.1993 time to fit residues: 86.3041 Evaluate side-chains 281 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 243 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 892 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1074 ARG Chi-restraints excluded: chain A residue 1109 CYS Chi-restraints excluded: chain A residue 1143 THR Chi-restraints excluded: chain A residue 1151 ARG Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1200 GLU Chi-restraints excluded: chain A residue 1226 HIS Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1346 LEU Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1497 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 127 optimal weight: 20.0000 chunk 79 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.9543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10927 Z= 0.250 Angle : 0.811 21.372 14874 Z= 0.395 Chirality : 0.044 0.240 1765 Planarity : 0.005 0.120 1818 Dihedral : 7.352 61.209 1844 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.68 % Allowed : 11.47 % Favored : 87.85 % Rotamer: Outliers : 4.65 % Allowed : 30.27 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 2.13 % Twisted General : 0.71 % 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: -1.50 (0.23), residues: 1317 helix: 0.10 (0.17), residues: 881 sheet: -3.54 (0.97), residues: 10 loop : -3.32 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 316 HIS 0.004 0.001 HIS A 541 PHE 0.027 0.001 PHE A 521 TYR 0.021 0.002 TYR A1089 ARG 0.007 0.001 ARG A1268 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 266 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.7636 (ttp) cc_final: 0.7227 (tpp) REVERT: A 292 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8242 (m-10) REVERT: A 542 ASP cc_start: 0.7248 (m-30) cc_final: 0.6585 (p0) REVERT: A 548 GLU cc_start: 0.7615 (tp30) cc_final: 0.7129 (pt0) REVERT: A 555 ASN cc_start: 0.8297 (m-40) cc_final: 0.7958 (t0) REVERT: A 556 TYR cc_start: 0.8018 (m-10) cc_final: 0.6740 (t80) REVERT: A 580 LYS cc_start: 0.6599 (tptt) cc_final: 0.5948 (ttmm) REVERT: A 597 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7869 (mt-10) REVERT: A 609 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7543 (t80) REVERT: A 623 PHE cc_start: 0.7479 (t80) cc_final: 0.7195 (t80) REVERT: A 631 MET cc_start: 0.7790 (tpt) cc_final: 0.7073 (tmm) REVERT: A 856 LYS cc_start: 0.8080 (mttt) cc_final: 0.7640 (pttt) REVERT: A 904 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8631 (tm-30) REVERT: A 1053 SER cc_start: 0.8477 (t) cc_final: 0.8102 (m) REVERT: A 1067 MET cc_start: 0.7472 (mtt) cc_final: 0.7224 (mtt) REVERT: A 1074 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.5272 (tpp-160) REVERT: A 1094 PHE cc_start: 0.8708 (m-80) cc_final: 0.8225 (t80) REVERT: A 1136 TYR cc_start: 0.7312 (m-80) cc_final: 0.7097 (m-80) REVERT: A 1144 MET cc_start: 0.8875 (tmm) cc_final: 0.8628 (mmt) REVERT: A 1170 ARG cc_start: 0.7892 (mmt90) cc_final: 0.6501 (ttt90) REVERT: A 1198 PHE cc_start: 0.6973 (m-10) cc_final: 0.6740 (m-10) REVERT: A 1283 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6913 (tmm-80) REVERT: A 1337 LYS cc_start: 0.7277 (mttt) cc_final: 0.6965 (mtmm) REVERT: A 1373 HIS cc_start: 0.7385 (t-90) cc_final: 0.6611 (p-80) REVERT: A 1418 TYR cc_start: 0.7515 (m-80) cc_final: 0.6914 (m-80) REVERT: A 1423 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7251 (mm-30) REVERT: A 1455 GLU cc_start: 0.8996 (tp30) cc_final: 0.8686 (mm-30) REVERT: A 1494 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8072 (tp30) outliers start: 49 outliers final: 30 residues processed: 290 average time/residue: 0.2049 time to fit residues: 86.7469 Evaluate side-chains 281 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 247 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 892 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 1074 ARG Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1109 CYS Chi-restraints excluded: chain A residue 1143 THR Chi-restraints excluded: chain A residue 1158 HIS Chi-restraints excluded: chain A residue 1200 GLU Chi-restraints excluded: chain A residue 1226 HIS Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1283 ARG Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1497 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 GLN ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1461 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 1.0082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10927 Z= 0.255 Angle : 0.826 20.481 14874 Z= 0.400 Chirality : 0.045 0.248 1765 Planarity : 0.005 0.107 1818 Dihedral : 6.961 47.921 1841 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.68 % Allowed : 11.24 % Favored : 88.08 % Rotamer: Outliers : 4.65 % Allowed : 30.83 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 2.13 % Twisted General : 0.71 % 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: -1.38 (0.23), residues: 1317 helix: 0.22 (0.17), residues: 873 sheet: -2.69 (1.31), residues: 10 loop : -3.30 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 316 HIS 0.004 0.001 HIS A1021 PHE 0.024 0.002 PHE A 577 TYR 0.023 0.002 TYR A 355 ARG 0.010 0.001 ARG A1268 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 262 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.7775 (ttp) cc_final: 0.7351 (tpp) REVERT: A 292 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.8212 (m-10) REVERT: A 324 GLU cc_start: 0.7725 (pt0) cc_final: 0.7445 (pt0) REVERT: A 542 ASP cc_start: 0.7295 (m-30) cc_final: 0.6604 (p0) REVERT: A 548 GLU cc_start: 0.7673 (tp30) cc_final: 0.7170 (pt0) REVERT: A 555 ASN cc_start: 0.8470 (m-40) cc_final: 0.8176 (t0) REVERT: A 556 TYR cc_start: 0.7860 (m-10) cc_final: 0.6617 (t80) REVERT: A 580 LYS cc_start: 0.6630 (tptt) cc_final: 0.5958 (ttmm) REVERT: A 597 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7924 (mt-10) REVERT: A 609 PHE cc_start: 0.8099 (m-80) cc_final: 0.7443 (t80) REVERT: A 615 LEU cc_start: 0.8439 (tp) cc_final: 0.8191 (tp) REVERT: A 623 PHE cc_start: 0.7232 (t80) cc_final: 0.6904 (t80) REVERT: A 631 MET cc_start: 0.7801 (tpt) cc_final: 0.7077 (tmm) REVERT: A 665 MET cc_start: 0.7457 (ptm) cc_final: 0.7176 (ttp) REVERT: A 856 LYS cc_start: 0.8128 (mttt) cc_final: 0.7665 (pttt) REVERT: A 1067 MET cc_start: 0.7446 (mtt) cc_final: 0.7162 (mtt) REVERT: A 1074 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.5034 (tpp-160) REVERT: A 1087 TYR cc_start: 0.7216 (m-10) cc_final: 0.6902 (m-10) REVERT: A 1094 PHE cc_start: 0.8808 (m-80) cc_final: 0.8266 (t80) REVERT: A 1170 ARG cc_start: 0.7867 (mmt90) cc_final: 0.6478 (ttt90) REVERT: A 1198 PHE cc_start: 0.7073 (m-10) cc_final: 0.6869 (m-10) REVERT: A 1283 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6976 (tmm-80) REVERT: A 1337 LYS cc_start: 0.7322 (mttt) cc_final: 0.7014 (mtmm) REVERT: A 1373 HIS cc_start: 0.7423 (t-90) cc_final: 0.6800 (p-80) REVERT: A 1405 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.7147 (ttt) REVERT: A 1406 TYR cc_start: 0.7420 (m-80) cc_final: 0.7083 (m-80) REVERT: A 1418 TYR cc_start: 0.7557 (m-80) cc_final: 0.6929 (m-80) REVERT: A 1455 GLU cc_start: 0.8989 (tp30) cc_final: 0.8673 (mm-30) REVERT: A 1494 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8035 (tp30) outliers start: 49 outliers final: 36 residues processed: 289 average time/residue: 0.1984 time to fit residues: 84.6255 Evaluate side-chains 285 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 245 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 892 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain A residue 1074 ARG Chi-restraints excluded: chain A residue 1079 GLN Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1109 CYS Chi-restraints excluded: chain A residue 1143 THR Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1226 HIS Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1283 ARG Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1405 MET Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1497 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 5.9990 chunk 121 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1227 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 1.0441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10927 Z= 0.257 Angle : 0.824 20.240 14874 Z= 0.398 Chirality : 0.045 0.249 1765 Planarity : 0.005 0.110 1818 Dihedral : 6.821 46.874 1841 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.76 % Allowed : 11.24 % Favored : 88.00 % Rotamer: Outliers : 4.55 % Allowed : 31.88 % Favored : 63.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 2.13 % Twisted General : 0.71 % 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: -1.30 (0.23), residues: 1317 helix: 0.29 (0.17), residues: 874 sheet: -2.51 (1.44), residues: 10 loop : -3.30 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 922 HIS 0.004 0.001 HIS A 192 PHE 0.025 0.002 PHE A 521 TYR 0.022 0.002 TYR A 355 ARG 0.008 0.001 ARG A1268 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 266 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TRP cc_start: 0.8173 (t60) cc_final: 0.7381 (m100) REVERT: A 281 MET cc_start: 0.7758 (ttp) cc_final: 0.7428 (tpp) REVERT: A 292 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8359 (m-80) REVERT: A 316 TRP cc_start: 0.8066 (OUTLIER) cc_final: 0.7214 (p90) REVERT: A 542 ASP cc_start: 0.7433 (m-30) cc_final: 0.6748 (p0) REVERT: A 548 GLU cc_start: 0.7739 (tp30) cc_final: 0.7241 (pt0) REVERT: A 555 ASN cc_start: 0.8467 (m-40) cc_final: 0.8115 (t0) REVERT: A 556 TYR cc_start: 0.7840 (m-10) cc_final: 0.6430 (t80) REVERT: A 580 LYS cc_start: 0.6617 (tptt) cc_final: 0.5938 (ttmm) REVERT: A 615 LEU cc_start: 0.8395 (tp) cc_final: 0.8153 (tp) REVERT: A 631 MET cc_start: 0.7760 (tpt) cc_final: 0.6899 (tmm) REVERT: A 646 TYR cc_start: 0.8290 (t80) cc_final: 0.7956 (t80) REVERT: A 856 LYS cc_start: 0.8241 (mttt) cc_final: 0.7789 (pttt) REVERT: A 905 MET cc_start: 0.8739 (tpp) cc_final: 0.8519 (tpt) REVERT: A 991 PHE cc_start: 0.6970 (t80) cc_final: 0.6751 (t80) REVERT: A 1042 MET cc_start: 0.7995 (mmm) cc_final: 0.7744 (tpp) REVERT: A 1053 SER cc_start: 0.8676 (t) cc_final: 0.8329 (m) REVERT: A 1074 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.4891 (tpp-160) REVERT: A 1087 TYR cc_start: 0.7338 (m-10) cc_final: 0.7045 (m-10) REVERT: A 1094 PHE cc_start: 0.8830 (m-80) cc_final: 0.8229 (t80) REVERT: A 1170 ARG cc_start: 0.7817 (mmt90) cc_final: 0.6403 (ttt90) REVERT: A 1200 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7814 (pt0) REVERT: A 1283 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6576 (tmm-80) REVERT: A 1373 HIS cc_start: 0.7490 (t-90) cc_final: 0.6850 (p-80) REVERT: A 1405 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7227 (ttt) REVERT: A 1418 TYR cc_start: 0.7559 (m-80) cc_final: 0.6898 (m-80) REVERT: A 1455 GLU cc_start: 0.9028 (tp30) cc_final: 0.8720 (mm-30) REVERT: A 1494 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8078 (tp30) outliers start: 48 outliers final: 32 residues processed: 294 average time/residue: 0.1883 time to fit residues: 81.9903 Evaluate side-chains 293 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 255 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain A residue 1074 ARG Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1109 CYS Chi-restraints excluded: chain A residue 1143 THR Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1147 LYS Chi-restraints excluded: chain A residue 1200 GLU Chi-restraints excluded: chain A residue 1226 HIS Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1283 ARG Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1405 MET Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1497 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 121 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 1.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10927 Z= 0.211 Angle : 0.823 19.938 14874 Z= 0.396 Chirality : 0.044 0.240 1765 Planarity : 0.005 0.103 1818 Dihedral : 6.589 45.106 1841 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.68 % Allowed : 11.47 % Favored : 87.85 % Rotamer: Outliers : 3.23 % Allowed : 33.40 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 2.13 % Twisted General : 0.63 % 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: -1.22 (0.23), residues: 1317 helix: 0.37 (0.17), residues: 874 sheet: -2.39 (1.50), residues: 10 loop : -3.31 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 922 HIS 0.003 0.001 HIS A 192 PHE 0.027 0.001 PHE A 535 TYR 0.026 0.002 TYR A1089 ARG 0.006 0.000 ARG A1268 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 282 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TRP cc_start: 0.8170 (t60) cc_final: 0.7390 (m100) REVERT: A 268 SER cc_start: 0.7805 (t) cc_final: 0.7597 (t) REVERT: A 281 MET cc_start: 0.7803 (ttp) cc_final: 0.7483 (tpp) REVERT: A 306 TRP cc_start: 0.8447 (t60) cc_final: 0.8015 (t60) REVERT: A 316 TRP cc_start: 0.7845 (OUTLIER) cc_final: 0.7052 (p90) REVERT: A 347 TYR cc_start: 0.7487 (m-80) cc_final: 0.6838 (m-80) REVERT: A 409 ASN cc_start: 0.6935 (m110) cc_final: 0.6283 (m110) REVERT: A 531 LEU cc_start: 0.8072 (tp) cc_final: 0.7818 (tp) REVERT: A 542 ASP cc_start: 0.7399 (m-30) cc_final: 0.6739 (p0) REVERT: A 548 GLU cc_start: 0.7829 (tp30) cc_final: 0.7232 (pt0) REVERT: A 555 ASN cc_start: 0.8238 (m-40) cc_final: 0.7900 (t0) REVERT: A 556 TYR cc_start: 0.7919 (m-10) cc_final: 0.6459 (t80) REVERT: A 580 LYS cc_start: 0.6600 (tptt) cc_final: 0.5923 (ttmm) REVERT: A 597 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6902 (mm-30) REVERT: A 598 LEU cc_start: 0.6886 (mt) cc_final: 0.6555 (pp) REVERT: A 615 LEU cc_start: 0.8379 (tp) cc_final: 0.8176 (tp) REVERT: A 631 MET cc_start: 0.7862 (tpt) cc_final: 0.6985 (tmm) REVERT: A 692 MET cc_start: 0.8188 (mmt) cc_final: 0.7977 (mmm) REVERT: A 856 LYS cc_start: 0.8260 (mttt) cc_final: 0.7760 (pttt) REVERT: A 905 MET cc_start: 0.8687 (tpp) cc_final: 0.8448 (tpt) REVERT: A 991 PHE cc_start: 0.6977 (t80) cc_final: 0.6728 (t80) REVERT: A 1042 MET cc_start: 0.7748 (mmm) cc_final: 0.7389 (mmm) REVERT: A 1053 SER cc_start: 0.8622 (t) cc_final: 0.8289 (m) REVERT: A 1067 MET cc_start: 0.7756 (mtt) cc_final: 0.7517 (mtt) REVERT: A 1074 ARG cc_start: 0.6515 (OUTLIER) cc_final: 0.5006 (ttm170) REVERT: A 1087 TYR cc_start: 0.7165 (m-10) cc_final: 0.6850 (m-10) REVERT: A 1094 PHE cc_start: 0.8825 (m-80) cc_final: 0.8180 (t80) REVERT: A 1170 ARG cc_start: 0.7903 (mmt90) cc_final: 0.6364 (ttt90) REVERT: A 1283 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6545 (tmm-80) REVERT: A 1287 LEU cc_start: 0.8187 (tt) cc_final: 0.7870 (pp) REVERT: A 1373 HIS cc_start: 0.7579 (t-90) cc_final: 0.7047 (p-80) REVERT: A 1406 TYR cc_start: 0.7412 (m-80) cc_final: 0.7114 (m-80) REVERT: A 1432 MET cc_start: 0.8287 (ppp) cc_final: 0.7811 (ppp) REVERT: A 1455 GLU cc_start: 0.9027 (tp30) cc_final: 0.8712 (mm-30) REVERT: A 1494 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8065 (tp30) outliers start: 34 outliers final: 27 residues processed: 301 average time/residue: 0.2016 time to fit residues: 88.2394 Evaluate side-chains 299 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 269 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1074 ARG Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1109 CYS Chi-restraints excluded: chain A residue 1147 LYS Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1283 ARG Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1497 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 0.0970 chunk 107 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 5 optimal weight: 50.0000 chunk 75 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN A 882 GLN ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1461 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.168401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134909 restraints weight = 16217.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.136912 restraints weight = 10681.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.137856 restraints weight = 7119.199| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 1.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10927 Z= 0.255 Angle : 0.837 20.146 14874 Z= 0.405 Chirality : 0.045 0.251 1765 Planarity : 0.005 0.106 1818 Dihedral : 6.583 44.064 1841 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.76 % Allowed : 11.39 % Favored : 87.85 % Rotamer: Outliers : 3.70 % Allowed : 32.83 % Favored : 63.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 2.13 % Twisted General : 0.63 % 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: -1.20 (0.24), residues: 1317 helix: 0.37 (0.17), residues: 879 sheet: -2.23 (1.50), residues: 10 loop : -3.32 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 624 HIS 0.005 0.001 HIS A 315 PHE 0.021 0.002 PHE A 577 TYR 0.028 0.002 TYR A1089 ARG 0.014 0.001 ARG A1503 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2450.32 seconds wall clock time: 44 minutes 40.61 seconds (2680.61 seconds total)