Starting phenix.real_space_refine on Sat Dec 9 09:36:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0m_6698/12_2023/5x0m_6698.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0m_6698/12_2023/5x0m_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_6698/12_2023/5x0m_6698.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0m_6698/12_2023/5x0m_6698.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0m_6698/12_2023/5x0m_6698.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0m_6698/12_2023/5x0m_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 6 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: 6 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: 6 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: 6 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: 6 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: 6.32, per 1000 atoms: 0.59 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: 4.52 Conformation dependent library (CDL) restraints added in 1.8 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: 1.00 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: 3.29 Time building geometry restraints manager: 4.89 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: 5823 26.78 - 53.57: 495 53.57 - 80.35: 112 80.35 - 107.13: 22 107.13 - 133.91: 2 Dihedral angle restraints: 6454 sinusoidal: 2559 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 6451 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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.410 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 31.000 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.550 ------------------------------------------------------------------------------- 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 : 21.025 133.913 3925 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 : 1.151 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 outliers start: 121 outliers final: 11 residues processed: 455 average time/residue: 0.2654 time to fit residues: 162.8139 Evaluate side-chains 257 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 246 time to evaluate : 1.158 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1081 time to fit residues: 3.7878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 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 153 HIS A 286 GLN A 291 HIS A 352 ASN A 382 GLN A 392 HIS ** 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 ** A1348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1446 GLN A1465 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5900 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 10927 Z= 0.303 Angle : 1.038 14.529 14874 Z= 0.517 Chirality : 0.053 0.634 1765 Planarity : 0.007 0.069 1818 Dihedral : 11.664 75.731 1708 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 2.05 % Allowed : 10.71 % Favored : 87.24 % Rotamer: Outliers : 4.55 % Allowed : 19.92 % Favored : 75.52 % 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: -3.46 (0.22), residues: 1317 helix: -1.38 (0.17), residues: 848 sheet: -4.88 (0.90), residues: 20 loop : -3.89 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 316 HIS 0.007 0.001 HIS A1158 PHE 0.046 0.003 PHE A 189 TYR 0.040 0.003 TYR A1089 ARG 0.007 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 352 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 304 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 18 residues processed: 331 average time/residue: 0.2277 time to fit residues: 106.5293 Evaluate side-chains 256 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 238 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1031 time to fit residues: 5.0538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 99 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 119 optimal weight: 0.0980 chunk 40 optimal weight: 8.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 GLN ** 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 A1183 ASN ** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6050 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10927 Z= 0.245 Angle : 0.879 16.276 14874 Z= 0.440 Chirality : 0.049 0.689 1765 Planarity : 0.006 0.106 1818 Dihedral : 9.958 64.882 1708 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 1.14 % Allowed : 12.07 % Favored : 86.79 % Rotamer: Outliers : 3.98 % Allowed : 22.11 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 8.51 % Twisted General : 1.57 % 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: -2.64 (0.22), residues: 1317 helix: -0.75 (0.17), residues: 863 sheet: None (None), residues: 0 loop : -3.72 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A1063 HIS 0.008 0.001 HIS A1158 PHE 0.030 0.002 PHE A 189 TYR 0.028 0.002 TYR A1089 ARG 0.007 0.001 ARG A1268 *********************** 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 308 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 266 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 20 residues processed: 282 average time/residue: 0.2224 time to fit residues: 89.9792 Evaluate side-chains 261 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 241 time to evaluate : 1.291 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 20 outliers final: 1 residues processed: 20 average time/residue: 0.1083 time to fit residues: 5.7516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1301 ASN ** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1470 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 moved from start: 0.7313 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= 0.255 Angle : 0.849 18.078 14874 Z= 0.419 Chirality : 0.048 0.619 1765 Planarity : 0.005 0.083 1818 Dihedral : 8.936 59.866 1708 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 1.06 % Allowed : 10.86 % Favored : 88.08 % Rotamer: Outliers : 3.80 % Allowed : 25.43 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 2.13 % Twisted General : 1.18 % 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: -2.25 (0.22), residues: 1317 helix: -0.49 (0.17), residues: 869 sheet: None (None), residues: 0 loop : -3.50 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 715 HIS 0.005 0.001 HIS A1323 PHE 0.029 0.002 PHE A 189 TYR 0.026 0.002 TYR A 355 ARG 0.005 0.001 ARG A 610 *********************** 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 309 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 269 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 14 residues processed: 291 average time/residue: 0.2108 time to fit residues: 88.5932 Evaluate side-chains 248 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 234 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1041 time to fit residues: 4.2311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 3.9990 chunk 1 optimal weight: 30.0000 chunk 95 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 114 optimal weight: 0.0370 chunk 32 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 HIS ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 ASN ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1373 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.8456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10927 Z= 0.290 Angle : 0.861 19.024 14874 Z= 0.430 Chirality : 0.050 0.612 1765 Planarity : 0.006 0.086 1818 Dihedral : 8.529 59.460 1708 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.84 % Allowed : 11.92 % Favored : 87.24 % Rotamer: Outliers : 3.13 % Allowed : 27.61 % Favored : 69.26 % 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: -2.04 (0.23), residues: 1317 helix: -0.33 (0.17), residues: 859 sheet: None (None), residues: 0 loop : -3.36 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 203 HIS 0.013 0.002 HIS A1373 PHE 0.021 0.002 PHE A 189 TYR 0.028 0.002 TYR A1430 ARG 0.007 0.001 ARG A 610 *********************** 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 302 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 269 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 17 residues processed: 284 average time/residue: 0.2092 time to fit residues: 87.1447 Evaluate side-chains 255 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 238 time to evaluate : 1.087 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1089 time to fit residues: 5.0803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 ASN A 743 ASN ** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.8923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10927 Z= 0.237 Angle : 0.831 19.400 14874 Z= 0.407 Chirality : 0.050 0.802 1765 Planarity : 0.005 0.074 1818 Dihedral : 7.997 54.397 1708 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.68 % Allowed : 10.33 % Favored : 88.99 % Rotamer: Outliers : 2.09 % Allowed : 29.79 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 4.26 % Twisted General : 0.79 % 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: -1.77 (0.23), residues: 1317 helix: -0.04 (0.17), residues: 863 sheet: None (None), residues: 0 loop : -3.48 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 316 HIS 0.004 0.001 HIS A1373 PHE 0.020 0.001 PHE A 577 TYR 0.026 0.002 TYR A1334 ARG 0.007 0.001 ARG A1268 *********************** 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 288 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 266 time to evaluate : 1.162 Fit side-chains outliers start: 22 outliers final: 7 residues processed: 279 average time/residue: 0.2097 time to fit residues: 86.1677 Evaluate side-chains 249 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 242 time to evaluate : 1.833 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1403 time to fit residues: 4.0271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 0.0970 chunk 71 optimal weight: 0.8980 chunk 127 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS ** A 345 GLN ** 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** ** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 moved from start: 0.9318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10927 Z= 0.205 Angle : 0.819 18.591 14874 Z= 0.399 Chirality : 0.050 0.890 1765 Planarity : 0.005 0.122 1818 Dihedral : 7.661 49.178 1708 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.68 % Allowed : 10.93 % Favored : 88.38 % Rotamer: Outliers : 2.28 % Allowed : 29.89 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 4.26 % Twisted General : 0.79 % 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: -1.53 (0.23), residues: 1317 helix: 0.18 (0.17), residues: 859 sheet: None (None), residues: 0 loop : -3.44 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 203 HIS 0.009 0.001 HIS A1077 PHE 0.024 0.001 PHE A 189 TYR 0.018 0.001 TYR A1334 ARG 0.006 0.001 ARG A 957 *********************** 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 284 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 260 time to evaluate : 1.753 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 272 average time/residue: 0.2519 time to fit residues: 101.5364 Evaluate side-chains 252 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 244 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1076 time to fit residues: 3.1715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS ** A 345 GLN ** 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** ** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1373 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.9678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10927 Z= 0.231 Angle : 0.827 18.839 14874 Z= 0.403 Chirality : 0.049 0.816 1765 Planarity : 0.005 0.118 1818 Dihedral : 7.430 45.414 1708 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.68 % Allowed : 10.93 % Favored : 88.38 % Rotamer: Outliers : 0.95 % Allowed : 31.50 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 2.13 % Twisted General : 0.79 % 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: -1.41 (0.23), residues: 1317 helix: 0.28 (0.17), residues: 863 sheet: None (None), residues: 0 loop : -3.43 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 316 HIS 0.011 0.001 HIS A1373 PHE 0.027 0.001 PHE A 521 TYR 0.020 0.002 TYR A1240 ARG 0.008 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 269 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 259 time to evaluate : 1.057 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 264 average time/residue: 0.2084 time to fit residues: 80.9313 Evaluate side-chains 242 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 237 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1138 time to fit residues: 2.6753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS ** A 345 GLN ** 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** ** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.9960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10927 Z= 0.208 Angle : 0.823 18.531 14874 Z= 0.397 Chirality : 0.048 0.776 1765 Planarity : 0.005 0.113 1818 Dihedral : 7.283 45.414 1708 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.68 % Allowed : 10.93 % Favored : 88.38 % Rotamer: Outliers : 0.57 % Allowed : 32.83 % Favored : 66.60 % 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: -1.24 (0.23), residues: 1317 helix: 0.40 (0.17), residues: 866 sheet: None (None), residues: 0 loop : -3.35 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 922 HIS 0.004 0.001 HIS A1373 PHE 0.030 0.001 PHE A 521 TYR 0.019 0.002 TYR A 355 ARG 0.010 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 261 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 255 time to evaluate : 1.159 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 257 average time/residue: 0.2066 time to fit residues: 79.0313 Evaluate side-chains 243 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 240 time to evaluate : 1.112 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1173 time to fit residues: 2.1518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 131 optimal weight: 30.0000 chunk 121 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS A 409 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** A1348 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 1.0380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10927 Z= 0.287 Angle : 0.874 19.001 14874 Z= 0.424 Chirality : 0.050 0.778 1765 Planarity : 0.005 0.114 1818 Dihedral : 7.293 45.934 1708 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.68 % Allowed : 11.62 % Favored : 87.70 % Rotamer: Outliers : 0.47 % Allowed : 33.78 % Favored : 65.75 % 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: -1.32 (0.23), residues: 1317 helix: 0.34 (0.17), residues: 864 sheet: None (None), residues: 0 loop : -3.38 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 922 HIS 0.005 0.001 HIS A 315 PHE 0.025 0.002 PHE A 145 TYR 0.034 0.002 TYR A1089 ARG 0.010 0.001 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 266 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 261 time to evaluate : 1.230 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 262 average time/residue: 0.1998 time to fit residues: 77.7531 Evaluate side-chains 253 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 250 time to evaluate : 1.133 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1079 time to fit residues: 2.2738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.171994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.138970 restraints weight = 16030.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.140133 restraints weight = 10329.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.141480 restraints weight = 7894.349| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 1.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10927 Z= 0.252 Angle : 0.853 18.973 14874 Z= 0.413 Chirality : 0.049 0.768 1765 Planarity : 0.005 0.110 1818 Dihedral : 7.209 45.771 1708 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.84 % Allowed : 11.01 % Favored : 88.15 % Rotamer: Outliers : 0.57 % Allowed : 34.35 % 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: -1.28 (0.24), residues: 1317 helix: 0.36 (0.18), residues: 863 sheet: -1.85 (1.59), residues: 10 loop : -3.34 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 203 HIS 0.003 0.001 HIS A 315 PHE 0.028 0.002 PHE A 521 TYR 0.032 0.002 TYR A 347 ARG 0.010 0.001 ARG A1268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2449.42 seconds wall clock time: 45 minutes 18.72 seconds (2718.72 seconds total)