Starting phenix.real_space_refine on Mon Mar 18 08:44:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhf_26513/03_2024/7uhf_26513.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhf_26513/03_2024/7uhf_26513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhf_26513/03_2024/7uhf_26513.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhf_26513/03_2024/7uhf_26513.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhf_26513/03_2024/7uhf_26513.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhf_26513/03_2024/7uhf_26513.pdb" } resolution = 3.1 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= 0.006 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 1 5.49 5 S 112 5.16 5 C 13159 2.51 5 N 3352 2.21 5 O 3753 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A ASP 556": "OD1" <-> "OD2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A GLU 770": "OE1" <-> "OE2" Residue "A PHE 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1157": "OE1" <-> "OE2" Residue "A GLU 1160": "OE1" <-> "OE2" Residue "A PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1431": "OE1" <-> "OE2" Residue "A TYR 1433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1465": "OD1" <-> "OD2" Residue "A PHE 1467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "D PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D ASP 300": "OD1" <-> "OD2" Residue "D GLU 367": "OE1" <-> "OE2" Residue "D TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 654": "OE1" <-> "OE2" Residue "D ASP 665": "OD1" <-> "OD2" Residue "D PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 986": "OD1" <-> "OD2" Residue "D ASP 1057": "OD1" <-> "OD2" Residue "C GLU 53": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 339": "OE1" <-> "OE2" Residue "C TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20379 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 9900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1230, 9900 Classifications: {'peptide': 1230} Link IDs: {'PTRANS': 36, 'TRANS': 1193} Chain breaks: 7 Chain: "D" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7570 Classifications: {'peptide': 948} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 907} Chain breaks: 5 Chain: "C" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2575 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 304} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: 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: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "H" 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: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 123 Unusual residues: {' CA': 1, '3PE': 1, 'N90': 1, 'NAG': 1, 'Y01': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 11.31, per 1000 atoms: 0.55 Number of scatterers: 20379 At special positions: 0 Unit cell: (171.556, 169.328, 183.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 112 16.00 P 1 15.00 O 3753 8.00 N 3352 7.00 C 13159 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1055 " distance=2.03 Simple disulfide: pdb=" SG CYS A1421 " - pdb=" SG CYS A1435 " distance=2.03 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D1044 " distance=2.03 Simple disulfide: pdb=" SG CYS D 404 " - pdb=" SG CYS D1071 " distance=2.03 Simple disulfide: pdb=" SG CYS D 667 " - pdb=" SG CYS D 697 " distance=2.04 Simple disulfide: pdb=" SG CYS D 904 " - pdb=" SG CYS D 974 " distance=2.03 Simple disulfide: pdb=" SG CYS D 996 " - pdb=" SG CYS D1026 " distance=2.03 Simple disulfide: pdb=" SG CYS D 999 " - pdb=" SG CYS D1024 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " NAG B 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " " NAG F 3 " - " NAG F 4 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B 1 " - " ASN D 184 " " NAG D1201 " - " ASN D 92 " " NAG E 1 " - " ASN D 348 " " NAG F 1 " - " ASN D 468 " " NAG G 1 " - " ASN D 613 " " NAG H 1 " - " ASN D 895 " Time building additional restraints: 8.16 Conformation dependent library (CDL) restraints added in 3.6 seconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4736 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 17 sheets defined 53.3% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 126 through 145 Processing helix chain 'A' and resid 155 through 178 removed outlier: 3.802A pdb=" N TYR A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR A 176 " --> pdb=" O PHE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 217 removed outlier: 3.518A pdb=" N GLU A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 217 " --> pdb=" O ILE A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 247 removed outlier: 3.833A pdb=" N PHE A 242 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL A 244 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 248 through 254 removed outlier: 4.298A pdb=" N SER A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 Processing helix chain 'A' and resid 271 through 293 removed outlier: 3.815A pdb=" N ALA A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 362 removed outlier: 3.537A pdb=" N THR A 362 " --> pdb=" O PHE A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 377 Processing helix chain 'A' and resid 381 through 392 removed outlier: 3.709A pdb=" N TYR A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 418 removed outlier: 3.660A pdb=" N PHE A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 428 Processing helix chain 'A' and resid 429 through 445 removed outlier: 3.772A pdb=" N GLU A 433 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TRP A 441 " --> pdb=" O GLY A 437 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA A 445 " --> pdb=" O TRP A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 522 removed outlier: 4.121A pdb=" N LYS A 521 " --> pdb=" O ARG A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 542 removed outlier: 3.500A pdb=" N VAL A 531 " --> pdb=" O TRP A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 557 Processing helix chain 'A' and resid 557 through 578 removed outlier: 3.505A pdb=" N GLY A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 605 removed outlier: 3.848A pdb=" N ARG A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 600 " --> pdb=" O CYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 622 removed outlier: 3.713A pdb=" N SER A 616 " --> pdb=" O PRO A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 626 through 632 removed outlier: 3.787A pdb=" N THR A 630 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N HIS A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 647 Processing helix chain 'A' and resid 650 through 673 Processing helix chain 'A' and resid 690 through 704 Processing helix chain 'A' and resid 706 through 717 removed outlier: 3.545A pdb=" N VAL A 710 " --> pdb=" O ASP A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 729 removed outlier: 3.525A pdb=" N GLY A 725 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N MET A 726 " --> pdb=" O SER A 723 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A 727 " --> pdb=" O SER A 724 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL A 728 " --> pdb=" O GLY A 725 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS A 729 " --> pdb=" O MET A 726 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 722 through 729' Processing helix chain 'A' and resid 730 through 748 removed outlier: 3.584A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 756 removed outlier: 3.948A pdb=" N ASP A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASN A 754 " --> pdb=" O ILE A 750 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 756 " --> pdb=" O VAL A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 761 removed outlier: 3.780A pdb=" N SER A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 768 removed outlier: 3.672A pdb=" N GLU A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 885 Processing helix chain 'A' and resid 887 through 905 removed outlier: 4.299A pdb=" N ILE A 892 " --> pdb=" O PHE A 888 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU A 893 " --> pdb=" O THR A 889 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL A 894 " --> pdb=" O ASN A 890 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET A 897 " --> pdb=" O LEU A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 940 removed outlier: 3.891A pdb=" N LEU A 935 " --> pdb=" O THR A 931 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR A 940 " --> pdb=" O LEU A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 970 removed outlier: 3.626A pdb=" N MET A 960 " --> pdb=" O ASN A 956 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 987 removed outlier: 3.532A pdb=" N ARG A 984 " --> pdb=" O VAL A 980 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 985 " --> pdb=" O LYS A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 998 removed outlier: 4.083A pdb=" N ARG A 997 " --> pdb=" O ARG A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1013 removed outlier: 4.042A pdb=" N LYS A1002 " --> pdb=" O ALA A 998 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG A1013 " --> pdb=" O PHE A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1016 No H-bonds generated for 'chain 'A' and resid 1014 through 1016' Processing helix chain 'A' and resid 1017 through 1037 removed outlier: 3.778A pdb=" N THR A1023 " --> pdb=" O MET A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1066 No H-bonds generated for 'chain 'A' and resid 1064 through 1066' Processing helix chain 'A' and resid 1086 through 1099 Processing helix chain 'A' and resid 1102 through 1112 Processing helix chain 'A' and resid 1125 through 1127 No H-bonds generated for 'chain 'A' and resid 1125 through 1127' Processing helix chain 'A' and resid 1128 through 1144 removed outlier: 4.172A pdb=" N PHE A1132 " --> pdb=" O ILE A1128 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A1142 " --> pdb=" O ILE A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1152 removed outlier: 3.672A pdb=" N VAL A1151 " --> pdb=" O PHE A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1161 Processing helix chain 'A' and resid 1171 through 1181 removed outlier: 4.023A pdb=" N CYS A1175 " --> pdb=" O ASN A1171 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A1176 " --> pdb=" O GLN A1172 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLU A1177 " --> pdb=" O ARG A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1203 removed outlier: 4.263A pdb=" N LYS A1197 " --> pdb=" O PRO A1193 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N PHE A1198 " --> pdb=" O TYR A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1223 removed outlier: 3.865A pdb=" N VAL A1213 " --> pdb=" O TYR A1209 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN A1218 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A1219 " --> pdb=" O ILE A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1260 removed outlier: 3.629A pdb=" N ILE A1257 " --> pdb=" O VAL A1253 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1283 removed outlier: 3.969A pdb=" N SER A1274 " --> pdb=" O ASN A1270 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A1275 " --> pdb=" O THR A1271 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP A1283 " --> pdb=" O GLY A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1321 removed outlier: 3.711A pdb=" N PHE A1321 " --> pdb=" O PHE A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1325 removed outlier: 3.516A pdb=" N ARG A1325 " --> pdb=" O ARG A1322 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1322 through 1325' Processing helix chain 'A' and resid 1326 through 1331 Processing helix chain 'A' and resid 1335 through 1350 removed outlier: 3.568A pdb=" N PHE A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A1350 " --> pdb=" O SER A1346 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1373 removed outlier: 3.673A pdb=" N LEU A1355 " --> pdb=" O PRO A1351 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A1356 " --> pdb=" O TYR A1352 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A1357 " --> pdb=" O VAL A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1404 Processing helix chain 'A' and resid 1407 through 1413 Processing helix chain 'A' and resid 1439 through 1454 Processing helix chain 'A' and resid 1478 through 1492 removed outlier: 4.291A pdb=" N LEU A1482 " --> pdb=" O GLY A1478 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR A1492 " --> pdb=" O ILE A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1511 Processing helix chain 'A' and resid 1522 through 1534 removed outlier: 4.155A pdb=" N VAL A1526 " --> pdb=" O CYS A1522 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N CYS A1528 " --> pdb=" O HIS A1524 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS A1529 " --> pdb=" O ARG A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1558 removed outlier: 3.522A pdb=" N PHE A1551 " --> pdb=" O ASN A1547 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA A1552 " --> pdb=" O ALA A1548 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A1558 " --> pdb=" O VAL A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1576 removed outlier: 4.137A pdb=" N ALA A1569 " --> pdb=" O ASN A1565 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A1570 " --> pdb=" O LEU A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1588 removed outlier: 4.423A pdb=" N LYS A1587 " --> pdb=" O LYS A1583 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 53 removed outlier: 3.520A pdb=" N TRP D 36 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 65 removed outlier: 3.660A pdb=" N TYR D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN D 65 " --> pdb=" O TYR D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 110 removed outlier: 3.583A pdb=" N GLU D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 186 removed outlier: 3.580A pdb=" N TRP D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 4.208A pdb=" N VAL D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU D 199 " --> pdb=" O LYS D 195 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 241 through 249 removed outlier: 3.945A pdb=" N GLY D 247 " --> pdb=" O TRP D 243 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA D 249 " --> pdb=" O ILE D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 265 Processing helix chain 'D' and resid 266 through 281 removed outlier: 3.697A pdb=" N LYS D 270 " --> pdb=" O GLY D 266 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 323 Processing helix chain 'D' and resid 332 through 345 removed outlier: 3.520A pdb=" N GLN D 343 " --> pdb=" O PHE D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 377 removed outlier: 3.612A pdb=" N PHE D 373 " --> pdb=" O ALA D 369 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS D 375 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN D 377 " --> pdb=" O PHE D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 406 removed outlier: 3.608A pdb=" N ALA D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN D 406 " --> pdb=" O MET D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 417 No H-bonds generated for 'chain 'D' and resid 415 through 417' Processing helix chain 'D' and resid 418 through 423 Processing helix chain 'D' and resid 425 through 431 removed outlier: 4.163A pdb=" N VAL D 429 " --> pdb=" O GLU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 438 removed outlier: 3.902A pdb=" N GLY D 438 " --> pdb=" O MET D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 442 Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 560 through 565 removed outlier: 3.701A pdb=" N GLU D 565 " --> pdb=" O PHE D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 580 removed outlier: 3.631A pdb=" N GLU D 573 " --> pdb=" O ASP D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 647 removed outlier: 3.786A pdb=" N GLN D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR D 644 " --> pdb=" O THR D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 651 removed outlier: 6.021A pdb=" N ASP D 651 " --> pdb=" O LEU D 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 648 through 651' Processing helix chain 'D' and resid 652 through 657 Processing helix chain 'D' and resid 678 through 689 removed outlier: 3.511A pdb=" N ASP D 688 " --> pdb=" O ASN D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 719 removed outlier: 4.046A pdb=" N VAL D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 751 Processing helix chain 'D' and resid 757 through 760 Processing helix chain 'D' and resid 761 through 770 removed outlier: 3.674A pdb=" N ASP D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 827 removed outlier: 3.608A pdb=" N GLU D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 870 Processing helix chain 'D' and resid 874 through 878 Processing helix chain 'D' and resid 879 through 889 removed outlier: 3.524A pdb=" N HIS D 885 " --> pdb=" O SER D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 1042 through 1047 removed outlier: 3.684A pdb=" N MET D1046 " --> pdb=" O ASN D1042 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D1047 " --> pdb=" O PRO D1043 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1042 through 1047' Processing helix chain 'C' and resid 39 through 55 removed outlier: 3.927A pdb=" N GLU C 53 " --> pdb=" O GLN C 49 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG C 54 " --> pdb=" O GLN C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 132 removed outlier: 3.932A pdb=" N GLU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 190 through 208 removed outlier: 3.626A pdb=" N MET C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU C 200 " --> pdb=" O MET C 196 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG C 207 " --> pdb=" O PHE C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 262 removed outlier: 3.721A pdb=" N GLN C 251 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE C 254 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 296 through 308 removed outlier: 3.743A pdb=" N LEU C 300 " --> pdb=" O SER C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 327 removed outlier: 3.533A pdb=" N MET C 320 " --> pdb=" O THR C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 333 Processing helix chain 'C' and resid 341 through 361 removed outlier: 3.519A pdb=" N ALA C 345 " --> pdb=" O GLN C 341 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS C 348 " --> pdb=" O ASP C 344 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR C 352 " --> pdb=" O HIS C 348 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS C 361 " --> pdb=" O TRP C 357 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AA2, first strand: chain 'A' and resid 1058 through 1062 Processing sheet with id=AA3, first strand: chain 'A' and resid 1499 through 1500 Processing sheet with id=AA4, first strand: chain 'D' and resid 68 through 72 Processing sheet with id=AA5, first strand: chain 'D' and resid 142 through 144 removed outlier: 6.369A pdb=" N VAL D 122 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N VAL D 166 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR D 125 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY D 486 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL D 490 " --> pdb=" O GLY D 462 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 142 through 144 removed outlier: 6.369A pdb=" N VAL D 122 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N VAL D 166 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR D 125 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY D 486 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL D 490 " --> pdb=" O GLY D 462 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 150 through 151 Processing sheet with id=AA8, first strand: chain 'D' and resid 298 through 300 removed outlier: 8.400A pdb=" N ALA D 292 " --> pdb=" O MET D 254 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE D 256 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N PHE D 294 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL D 258 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS D 356 " --> pdb=" O ARG D 383 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE D 385 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE D 358 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE D 387 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU D 360 " --> pdb=" O PHE D 387 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL D 389 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR D 362 " --> pdb=" O VAL D 389 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 521 through 523 removed outlier: 6.267A pdb=" N ALA D 514 " --> pdb=" O LEU D 522 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER D 618 " --> pdb=" O ILE D 515 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TYR D 617 " --> pdb=" O VAL D 612 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 658 through 661 removed outlier: 4.513A pdb=" N ILE D 740 " --> pdb=" O THR D 736 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA D 731 " --> pdb=" O LYS D 815 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 800 through 801 Processing sheet with id=AB3, first strand: chain 'D' and resid 859 through 861 removed outlier: 6.733A pdb=" N ILE D 852 " --> pdb=" O LEU D 860 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY D 992 " --> pdb=" O PHE D1003 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 892 through 904 removed outlier: 3.640A pdb=" N GLN D 980 " --> pdb=" O ASN D 895 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLN D 901 " --> pdb=" O CYS D 974 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N CYS D 974 " --> pdb=" O GLN D 901 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL D 903 " --> pdb=" O GLN D 972 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLN D 972 " --> pdb=" O VAL D 903 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE D 975 " --> pdb=" O SER D1038 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 115 through 119 removed outlier: 3.553A pdb=" N THR C 66 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 93 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL C 64 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 70 through 71 removed outlier: 3.943A pdb=" N TYR C 70 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE C 87 " --> pdb=" O TYR C 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 180 through 183 removed outlier: 3.551A pdb=" N VAL C 292 " --> pdb=" O VAL C 183 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 212 through 215 removed outlier: 3.565A pdb=" N VAL C 268 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR C 215 " --> pdb=" O VAL C 268 " (cutoff:3.500A) 917 hydrogen bonds defined for protein. 2619 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: 7.97 Time building geometry restraints manager: 8.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3809 1.33 - 1.45: 5203 1.45 - 1.57: 11621 1.57 - 1.70: 7 1.70 - 1.82: 176 Bond restraints: 20816 Sorted by residual: bond pdb=" C07 N90 A2201 " pdb=" N14 N90 A2201 " ideal model delta sigma weight residual 1.456 1.288 0.168 2.00e-02 2.50e+03 7.06e+01 bond pdb=" C20 N90 A2201 " pdb=" N17 N90 A2201 " ideal model delta sigma weight residual 1.452 1.336 0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" CAK Y01 A2204 " pdb=" CBD Y01 A2204 " ideal model delta sigma weight residual 1.525 1.639 -0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" CBD Y01 A2204 " pdb=" CBG Y01 A2204 " ideal model delta sigma weight residual 1.520 1.412 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C22 N90 A2201 " pdb=" C23 N90 A2201 " ideal model delta sigma weight residual 1.467 1.570 -0.103 2.00e-02 2.50e+03 2.66e+01 ... (remaining 20811 not shown) Histogram of bond angle deviations from ideal: 92.69 - 100.95: 36 100.95 - 109.22: 1254 109.22 - 117.49: 13827 117.49 - 125.75: 12797 125.75 - 134.02: 273 Bond angle restraints: 28187 Sorted by residual: angle pdb=" CAD Y01 A2204 " pdb=" CBH Y01 A2204 " pdb=" CAT Y01 A2204 " ideal model delta sigma weight residual 109.59 128.45 -18.86 3.00e+00 1.11e-01 3.95e+01 angle pdb=" N ILE A1012 " pdb=" CA ILE A1012 " pdb=" C ILE A1012 " ideal model delta sigma weight residual 110.62 116.77 -6.15 1.14e+00 7.69e-01 2.91e+01 angle pdb=" CAD Y01 A2204 " pdb=" CBH Y01 A2204 " pdb=" CAZ Y01 A2204 " ideal model delta sigma weight residual 108.53 93.63 14.90 3.00e+00 1.11e-01 2.47e+01 angle pdb=" C SER A 723 " pdb=" CA SER A 723 " pdb=" CB SER A 723 " ideal model delta sigma weight residual 115.79 109.99 5.80 1.19e+00 7.06e-01 2.38e+01 angle pdb=" CAK Y01 A2204 " pdb=" CBD Y01 A2204 " pdb=" CBG Y01 A2204 " ideal model delta sigma weight residual 110.32 96.36 13.96 3.00e+00 1.11e-01 2.16e+01 ... (remaining 28182 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.64: 11630 22.64 - 45.29: 913 45.29 - 67.93: 146 67.93 - 90.57: 47 90.57 - 113.21: 19 Dihedral angle restraints: 12755 sinusoidal: 5438 harmonic: 7317 Sorted by residual: dihedral pdb=" CB CYS D 904 " pdb=" SG CYS D 904 " pdb=" SG CYS D 974 " pdb=" CB CYS D 974 " ideal model delta sinusoidal sigma weight residual 93.00 160.63 -67.63 1 1.00e+01 1.00e-02 5.95e+01 dihedral pdb=" CB CYS D 667 " pdb=" SG CYS D 667 " pdb=" SG CYS D 697 " pdb=" CB CYS D 697 " ideal model delta sinusoidal sigma weight residual 93.00 50.21 42.79 1 1.00e+01 1.00e-02 2.56e+01 dihedral pdb=" CA ASN D 613 " pdb=" C ASN D 613 " pdb=" N GLY D 614 " pdb=" CA GLY D 614 " ideal model delta harmonic sigma weight residual 180.00 155.41 24.59 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 12752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 3179 0.127 - 0.255: 28 0.255 - 0.382: 2 0.382 - 0.509: 2 0.509 - 0.636: 1 Chirality restraints: 3212 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN D 613 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN D 184 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CBG Y01 A2204 " pdb=" CAQ Y01 A2204 " pdb=" CBD Y01 A2204 " pdb=" CBI Y01 A2204 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 3209 not shown) Planarity restraints: 3565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2202 " 0.214 2.00e-02 2.50e+03 1.79e-01 3.99e+02 pdb=" C7 NAG A2202 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG A2202 " 0.152 2.00e-02 2.50e+03 pdb=" N2 NAG A2202 " -0.296 2.00e-02 2.50e+03 pdb=" O7 NAG A2202 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 675 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C ASN D 675 " 0.056 2.00e-02 2.50e+03 pdb=" O ASN D 675 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN D 676 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A1428 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO A1429 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A1429 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A1429 " -0.032 5.00e-02 4.00e+02 ... (remaining 3562 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 176 2.62 - 3.19: 17833 3.19 - 3.76: 30154 3.76 - 4.33: 41826 4.33 - 4.90: 68440 Nonbonded interactions: 158429 Sorted by model distance: nonbonded pdb=" O3 NAG A2202 " pdb=" O7 NAG A2202 " model vdw 2.053 2.440 nonbonded pdb=" O TRP A 550 " pdb=" CG2 ILE A 554 " model vdw 2.201 3.460 nonbonded pdb=" OE1 GLN A 359 " pdb=" OH TYR A 712 " model vdw 2.204 2.440 nonbonded pdb=" O4 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.225 2.440 nonbonded pdb=" OD1 ASP D 516 " pdb=" CD PRO D 517 " model vdw 2.233 3.440 ... (remaining 158424 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 'E' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.010 Extract box with map and model: 5.900 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 56.430 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.004 0.168 20816 Z= 0.272 Angle : 0.704 18.864 28187 Z= 0.372 Chirality : 0.047 0.636 3212 Planarity : 0.005 0.179 3559 Dihedral : 16.847 113.215 7989 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.50 % Favored : 94.38 % Rotamer: Outliers : 2.31 % Allowed : 1.22 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.17), residues: 2472 helix: -0.23 (0.15), residues: 1138 sheet: -0.19 (0.34), residues: 252 loop : -1.27 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1341 HIS 0.003 0.001 HIS A 298 PHE 0.030 0.001 PHE A 280 TYR 0.015 0.001 TYR D1068 ARG 0.002 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 276 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8098 (tp) REVERT: A 178 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6857 (pt) REVERT: A 363 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7270 (mtp) REVERT: A 395 PHE cc_start: 0.5887 (OUTLIER) cc_final: 0.4689 (m-10) REVERT: A 555 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: A 559 ASN cc_start: 0.7396 (OUTLIER) cc_final: 0.6916 (p0) REVERT: A 765 GLN cc_start: 0.3835 (OUTLIER) cc_final: 0.2744 (mt0) REVERT: A 766 LYS cc_start: 0.4857 (OUTLIER) cc_final: 0.4039 (mtmm) REVERT: A 767 GLU cc_start: 0.4900 (OUTLIER) cc_final: 0.4264 (tp30) REVERT: A 960 MET cc_start: 0.6772 (mpp) cc_final: 0.6134 (ttp) REVERT: A 1013 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6355 (tpt90) REVERT: A 1156 GLN cc_start: 0.7025 (pp30) cc_final: 0.6562 (tm-30) REVERT: A 1162 GLU cc_start: 0.4868 (OUTLIER) cc_final: 0.3727 (mm-30) REVERT: A 1217 LEU cc_start: 0.8187 (tp) cc_final: 0.7501 (mt) REVERT: A 1237 MET cc_start: 0.7101 (mmp) cc_final: 0.6681 (mmt) REVERT: A 1468 ASP cc_start: 0.4461 (OUTLIER) cc_final: 0.4212 (p0) REVERT: D 149 PHE cc_start: 0.8318 (m-10) cc_final: 0.8004 (m-10) REVERT: D 268 THR cc_start: 0.8932 (t) cc_final: 0.8503 (m) REVERT: C 312 MET cc_start: 0.2578 (ptt) cc_final: 0.1763 (ttm) outliers start: 51 outliers final: 33 residues processed: 314 average time/residue: 0.2881 time to fit residues: 144.9075 Evaluate side-chains 281 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 236 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 766 LYS Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1013 ARG Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1162 GLU Chi-restraints excluded: chain A residue 1455 ILE Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1462 VAL Chi-restraints excluded: chain A residue 1463 ILE Chi-restraints excluded: chain A residue 1464 MET Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1467 PHE Chi-restraints excluded: chain A residue 1468 ASP Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 678 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 10.0000 chunk 188 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 226 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN A 359 GLN A 555 GLN A 754 ASN A1017 ASN A1114 ASN A1218 ASN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 HIS D 323 ASN D 770 ASN D 885 HIS D1004 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20816 Z= 0.339 Angle : 0.670 12.622 28187 Z= 0.335 Chirality : 0.048 0.482 3212 Planarity : 0.005 0.059 3559 Dihedral : 12.407 107.248 3273 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.54 % Favored : 94.42 % Rotamer: Outliers : 2.13 % Allowed : 8.55 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.17), residues: 2472 helix: 0.05 (0.15), residues: 1198 sheet: -0.46 (0.31), residues: 262 loop : -1.41 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 185 HIS 0.005 0.001 HIS D 111 PHE 0.018 0.002 PHE A 280 TYR 0.021 0.002 TYR D1068 ARG 0.005 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 244 time to evaluate : 2.528 Fit side-chains revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7222 (pt) REVERT: A 363 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7788 (mtp) REVERT: A 559 ASN cc_start: 0.7516 (OUTLIER) cc_final: 0.7036 (p0) REVERT: A 765 GLN cc_start: 0.3813 (OUTLIER) cc_final: 0.2852 (mt0) REVERT: A 932 VAL cc_start: 0.7989 (p) cc_final: 0.7592 (t) REVERT: A 1156 GLN cc_start: 0.6726 (pp30) cc_final: 0.6485 (tm-30) REVERT: A 1161 LYS cc_start: 0.5064 (OUTLIER) cc_final: 0.4620 (tptp) REVERT: A 1201 VAL cc_start: 0.5155 (t) cc_final: 0.4950 (p) REVERT: A 1211 MET cc_start: 0.6623 (tpt) cc_final: 0.6396 (tpt) REVERT: A 1237 MET cc_start: 0.7084 (mmp) cc_final: 0.6666 (mmt) REVERT: A 1456 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7804 (mp) REVERT: A 1464 MET cc_start: 0.4342 (OUTLIER) cc_final: 0.3951 (tpp) REVERT: A 1468 ASP cc_start: 0.4811 (OUTLIER) cc_final: 0.4497 (p0) REVERT: D 33 ILE cc_start: 0.8580 (tt) cc_final: 0.8375 (mt) REVERT: D 713 ASN cc_start: 0.7663 (t0) cc_final: 0.7438 (t0) REVERT: C 312 MET cc_start: 0.2608 (ptt) cc_final: 0.1710 (ttm) outliers start: 47 outliers final: 29 residues processed: 278 average time/residue: 0.2869 time to fit residues: 129.6177 Evaluate side-chains 263 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 226 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 1114 ASN Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1161 LYS Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1380 ASN Chi-restraints excluded: chain A residue 1425 SER Chi-restraints excluded: chain A residue 1455 ILE Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1462 VAL Chi-restraints excluded: chain A residue 1463 ILE Chi-restraints excluded: chain A residue 1464 MET Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1467 PHE Chi-restraints excluded: chain A residue 1468 ASP Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 678 GLU Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 1021 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 125 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 226 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 chunk 181 optimal weight: 2.9990 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 258 GLN ** A 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1114 ASN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20816 Z= 0.161 Angle : 0.561 11.097 28187 Z= 0.276 Chirality : 0.043 0.422 3212 Planarity : 0.004 0.056 3559 Dihedral : 10.736 105.574 3220 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.85 % Favored : 95.11 % Rotamer: Outliers : 2.40 % Allowed : 10.63 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), residues: 2472 helix: 0.39 (0.15), residues: 1204 sheet: -0.41 (0.32), residues: 260 loop : -1.35 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 185 HIS 0.002 0.000 HIS D 306 PHE 0.017 0.001 PHE A 392 TYR 0.015 0.001 TYR D1068 ARG 0.003 0.000 ARG D 643 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 237 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7089 (pt) REVERT: A 363 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8155 (mtm) REVERT: A 636 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7188 (mt) REVERT: A 765 GLN cc_start: 0.3654 (OUTLIER) cc_final: 0.2726 (mt0) REVERT: A 932 VAL cc_start: 0.7891 (p) cc_final: 0.7629 (t) REVERT: A 963 VAL cc_start: 0.6630 (t) cc_final: 0.6423 (p) REVERT: A 1161 LYS cc_start: 0.5061 (OUTLIER) cc_final: 0.4527 (tptp) REVERT: A 1211 MET cc_start: 0.6518 (tpt) cc_final: 0.6209 (tpt) REVERT: A 1456 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7728 (mp) REVERT: A 1468 ASP cc_start: 0.4778 (OUTLIER) cc_final: 0.4436 (p0) REVERT: D 846 ASP cc_start: 0.7319 (m-30) cc_final: 0.7032 (t0) REVERT: C 255 GLU cc_start: 0.2316 (OUTLIER) cc_final: 0.1524 (pp20) REVERT: C 351 GLU cc_start: 0.1884 (OUTLIER) cc_final: 0.1079 (pm20) outliers start: 53 outliers final: 31 residues processed: 276 average time/residue: 0.2828 time to fit residues: 127.8463 Evaluate side-chains 263 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 223 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1161 LYS Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1371 MET Chi-restraints excluded: chain A residue 1380 ASN Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1462 VAL Chi-restraints excluded: chain A residue 1463 ILE Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1467 PHE Chi-restraints excluded: chain A residue 1468 ASP Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 822 ILE Chi-restraints excluded: chain D residue 1021 LYS Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 351 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 223 optimal weight: 20.0000 chunk 170 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 227 optimal weight: 0.0060 chunk 240 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN A1114 ASN A1457 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20816 Z= 0.149 Angle : 0.538 10.085 28187 Z= 0.264 Chirality : 0.042 0.419 3212 Planarity : 0.004 0.054 3559 Dihedral : 9.758 104.993 3209 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.61 % Favored : 95.35 % Rotamer: Outliers : 2.49 % Allowed : 12.67 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.17), residues: 2472 helix: 0.57 (0.15), residues: 1209 sheet: -0.26 (0.32), residues: 250 loop : -1.32 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 185 HIS 0.002 0.000 HIS D 306 PHE 0.020 0.001 PHE A 280 TYR 0.015 0.001 TYR D1068 ARG 0.003 0.000 ARG A1013 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 233 time to evaluate : 2.310 Fit side-chains revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6966 (pt) REVERT: A 765 GLN cc_start: 0.3865 (OUTLIER) cc_final: 0.2839 (mt0) REVERT: A 929 ILE cc_start: 0.7377 (mt) cc_final: 0.7054 (mt) REVERT: A 932 VAL cc_start: 0.7878 (OUTLIER) cc_final: 0.7654 (t) REVERT: A 1211 MET cc_start: 0.6539 (tpt) cc_final: 0.6294 (tpt) REVERT: A 1456 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7765 (mp) REVERT: A 1534 MET cc_start: 0.2522 (mmm) cc_final: 0.2265 (mmm) REVERT: D 846 ASP cc_start: 0.7280 (m-30) cc_final: 0.6981 (t0) REVERT: D 1044 CYS cc_start: 0.6378 (m) cc_final: 0.6157 (m) REVERT: C 255 GLU cc_start: 0.2013 (OUTLIER) cc_final: 0.1637 (pp20) REVERT: C 351 GLU cc_start: 0.1923 (OUTLIER) cc_final: 0.1260 (pm20) outliers start: 55 outliers final: 32 residues processed: 273 average time/residue: 0.2794 time to fit residues: 124.2638 Evaluate side-chains 258 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 220 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1380 ASN Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1462 VAL Chi-restraints excluded: chain A residue 1463 ILE Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1467 PHE Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 822 ILE Chi-restraints excluded: chain D residue 1021 LYS Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 351 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 200 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 205 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 216 optimal weight: 0.0470 chunk 60 optimal weight: 0.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN A1114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20816 Z= 0.190 Angle : 0.553 12.418 28187 Z= 0.270 Chirality : 0.043 0.433 3212 Planarity : 0.004 0.054 3559 Dihedral : 9.405 104.305 3202 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.89 % Favored : 95.06 % Rotamer: Outliers : 2.31 % Allowed : 14.25 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.17), residues: 2472 helix: 0.61 (0.15), residues: 1211 sheet: -0.30 (0.32), residues: 251 loop : -1.36 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 185 HIS 0.002 0.000 HIS D 306 PHE 0.019 0.001 PHE A 392 TYR 0.016 0.001 TYR D1068 ARG 0.003 0.000 ARG A1013 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 228 time to evaluate : 2.368 Fit side-chains revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6914 (pt) REVERT: A 411 LYS cc_start: 0.7549 (tmmt) cc_final: 0.6480 (mmmt) REVERT: A 765 GLN cc_start: 0.4058 (OUTLIER) cc_final: 0.3026 (mt0) REVERT: A 891 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6359 (mm) REVERT: A 932 VAL cc_start: 0.7823 (p) cc_final: 0.7566 (t) REVERT: A 937 LYS cc_start: 0.6599 (mtpt) cc_final: 0.6207 (tmtt) REVERT: A 1161 LYS cc_start: 0.5004 (OUTLIER) cc_final: 0.4444 (tptp) REVERT: A 1456 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7704 (mp) REVERT: A 1468 ASP cc_start: 0.4521 (OUTLIER) cc_final: 0.4191 (p0) REVERT: D 846 ASP cc_start: 0.7377 (m-30) cc_final: 0.7153 (t0) REVERT: D 1044 CYS cc_start: 0.6435 (m) cc_final: 0.6215 (m) REVERT: C 255 GLU cc_start: 0.2106 (OUTLIER) cc_final: 0.1701 (pp20) REVERT: C 351 GLU cc_start: 0.1931 (OUTLIER) cc_final: 0.1275 (pm20) outliers start: 51 outliers final: 32 residues processed: 268 average time/residue: 0.2894 time to fit residues: 126.6411 Evaluate side-chains 260 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 220 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1161 LYS Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1380 ASN Chi-restraints excluded: chain A residue 1425 SER Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1462 VAL Chi-restraints excluded: chain A residue 1463 ILE Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1467 PHE Chi-restraints excluded: chain A residue 1468 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 822 ILE Chi-restraints excluded: chain D residue 1021 LYS Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 351 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 80 optimal weight: 0.7980 chunk 216 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 240 optimal weight: 6.9990 chunk 199 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN A1114 ASN A1124 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20816 Z= 0.178 Angle : 0.544 10.550 28187 Z= 0.266 Chirality : 0.043 0.435 3212 Planarity : 0.004 0.053 3559 Dihedral : 8.921 104.038 3198 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.69 % Favored : 95.23 % Rotamer: Outliers : 2.40 % Allowed : 15.29 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.17), residues: 2472 helix: 0.73 (0.15), residues: 1205 sheet: -0.17 (0.32), residues: 245 loop : -1.35 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1103 HIS 0.002 0.000 HIS D 306 PHE 0.034 0.001 PHE A1147 TYR 0.015 0.001 TYR D1068 ARG 0.004 0.000 ARG A1013 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 228 time to evaluate : 2.202 Fit side-chains revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6911 (pt) REVERT: A 411 LYS cc_start: 0.7459 (tmmt) cc_final: 0.6552 (mmmt) REVERT: A 765 GLN cc_start: 0.4107 (OUTLIER) cc_final: 0.2991 (mt0) REVERT: A 891 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6307 (mm) REVERT: A 932 VAL cc_start: 0.7836 (OUTLIER) cc_final: 0.7511 (t) REVERT: A 937 LYS cc_start: 0.6507 (mtpt) cc_final: 0.6193 (tmtt) REVERT: A 1013 ARG cc_start: 0.7861 (tpt90) cc_final: 0.7630 (tpt-90) REVERT: A 1161 LYS cc_start: 0.5007 (OUTLIER) cc_final: 0.4430 (tptp) REVERT: A 1234 ASN cc_start: 0.7267 (t0) cc_final: 0.7023 (t0) REVERT: A 1468 ASP cc_start: 0.4465 (OUTLIER) cc_final: 0.4227 (p0) REVERT: D 328 LYS cc_start: 0.7841 (tttp) cc_final: 0.7573 (ttpp) REVERT: D 1044 CYS cc_start: 0.6510 (m) cc_final: 0.6284 (m) REVERT: C 255 GLU cc_start: 0.2157 (OUTLIER) cc_final: 0.1696 (pp20) REVERT: C 351 GLU cc_start: 0.1946 (OUTLIER) cc_final: 0.1276 (pm20) outliers start: 53 outliers final: 41 residues processed: 267 average time/residue: 0.2884 time to fit residues: 124.2365 Evaluate side-chains 270 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 221 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1114 ASN Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1161 LYS Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1380 ASN Chi-restraints excluded: chain A residue 1425 SER Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1462 VAL Chi-restraints excluded: chain A residue 1463 ILE Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1468 ASP Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 370 GLN Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 822 ILE Chi-restraints excluded: chain D residue 1021 LYS Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 351 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 232 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 202 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 239 optimal weight: 40.0000 chunk 150 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 359 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20816 Z= 0.305 Angle : 0.618 11.422 28187 Z= 0.305 Chirality : 0.046 0.497 3212 Planarity : 0.004 0.054 3559 Dihedral : 9.045 103.333 3196 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.62 % Favored : 94.34 % Rotamer: Outliers : 2.71 % Allowed : 16.06 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.17), residues: 2472 helix: 0.60 (0.15), residues: 1203 sheet: -0.22 (0.32), residues: 254 loop : -1.41 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 550 HIS 0.004 0.001 HIS A1124 PHE 0.033 0.002 PHE A1147 TYR 0.019 0.002 TYR D1068 ARG 0.005 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 227 time to evaluate : 2.214 Fit side-chains revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6962 (pt) REVERT: A 411 LYS cc_start: 0.7467 (tmmt) cc_final: 0.6689 (mmtt) REVERT: A 765 GLN cc_start: 0.4164 (OUTLIER) cc_final: 0.3022 (mt0) REVERT: A 891 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6503 (mm) REVERT: A 932 VAL cc_start: 0.7862 (OUTLIER) cc_final: 0.7485 (t) REVERT: A 937 LYS cc_start: 0.6634 (mtpt) cc_final: 0.6299 (tmtt) REVERT: A 1025 LEU cc_start: 0.8477 (mt) cc_final: 0.8213 (mt) REVERT: A 1161 LYS cc_start: 0.5018 (OUTLIER) cc_final: 0.4460 (tptp) REVERT: A 1234 ASN cc_start: 0.7320 (t0) cc_final: 0.7072 (t0) REVERT: A 1438 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.8011 (m-40) REVERT: A 1468 ASP cc_start: 0.4646 (OUTLIER) cc_final: 0.4378 (p0) REVERT: D 328 LYS cc_start: 0.7845 (tttp) cc_final: 0.7466 (ttpp) REVERT: D 846 ASP cc_start: 0.7560 (t0) cc_final: 0.7323 (t0) REVERT: C 118 ILE cc_start: 0.0958 (OUTLIER) cc_final: 0.0716 (mp) REVERT: C 255 GLU cc_start: 0.2250 (OUTLIER) cc_final: 0.1638 (pp20) REVERT: C 351 GLU cc_start: 0.1975 (OUTLIER) cc_final: 0.1203 (pm20) outliers start: 60 outliers final: 41 residues processed: 275 average time/residue: 0.2717 time to fit residues: 120.4664 Evaluate side-chains 272 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 221 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1161 LYS Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1380 ASN Chi-restraints excluded: chain A residue 1425 SER Chi-restraints excluded: chain A residue 1438 ASN Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1462 VAL Chi-restraints excluded: chain A residue 1463 ILE Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1468 ASP Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 370 GLN Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 822 ILE Chi-restraints excluded: chain D residue 1021 LYS Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 351 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 148 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 188 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 ASN A1114 ASN A1466 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20816 Z= 0.155 Angle : 0.541 9.769 28187 Z= 0.265 Chirality : 0.043 0.426 3212 Planarity : 0.004 0.053 3559 Dihedral : 8.585 103.538 3196 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.85 % Favored : 95.06 % Rotamer: Outliers : 2.26 % Allowed : 16.79 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.17), residues: 2472 helix: 0.80 (0.15), residues: 1199 sheet: -0.24 (0.32), residues: 253 loop : -1.37 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 185 HIS 0.002 0.000 HIS D 306 PHE 0.035 0.001 PHE A1147 TYR 0.014 0.001 TYR D1068 ARG 0.004 0.000 ARG A1013 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 221 time to evaluate : 2.236 Fit side-chains revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6848 (pt) REVERT: A 411 LYS cc_start: 0.7640 (tmmt) cc_final: 0.6814 (mmtt) REVERT: A 765 GLN cc_start: 0.4102 (OUTLIER) cc_final: 0.2974 (mt0) REVERT: A 891 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6363 (mm) REVERT: A 932 VAL cc_start: 0.7777 (OUTLIER) cc_final: 0.7426 (t) REVERT: A 1013 ARG cc_start: 0.7828 (tpt90) cc_final: 0.7556 (tpt-90) REVERT: A 1161 LYS cc_start: 0.4985 (OUTLIER) cc_final: 0.4428 (tptp) REVERT: A 1234 ASN cc_start: 0.7444 (t0) cc_final: 0.7181 (t0) REVERT: A 1456 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7857 (mp) REVERT: A 1468 ASP cc_start: 0.4649 (OUTLIER) cc_final: 0.4380 (p0) REVERT: D 328 LYS cc_start: 0.7815 (tttp) cc_final: 0.7529 (ttpp) REVERT: D 846 ASP cc_start: 0.7429 (t0) cc_final: 0.7162 (t0) REVERT: D 1044 CYS cc_start: 0.6547 (m) cc_final: 0.6320 (m) REVERT: C 255 GLU cc_start: 0.2446 (OUTLIER) cc_final: 0.1736 (pp20) REVERT: C 351 GLU cc_start: 0.2017 (OUTLIER) cc_final: 0.1197 (pm20) outliers start: 50 outliers final: 34 residues processed: 258 average time/residue: 0.2903 time to fit residues: 120.2865 Evaluate side-chains 259 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 216 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 1114 ASN Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1161 LYS Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1380 ASN Chi-restraints excluded: chain A residue 1416 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1462 VAL Chi-restraints excluded: chain A residue 1463 ILE Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1468 ASP Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 370 GLN Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 822 ILE Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 351 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 218 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 chunk 209 optimal weight: 0.9990 chunk 223 optimal weight: 20.0000 chunk 134 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 202 optimal weight: 7.9990 chunk 211 optimal weight: 0.8980 chunk 222 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN A1114 ASN C 197 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20816 Z= 0.161 Angle : 0.547 9.648 28187 Z= 0.268 Chirality : 0.043 0.435 3212 Planarity : 0.004 0.053 3559 Dihedral : 8.428 103.258 3196 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.81 % Favored : 95.11 % Rotamer: Outliers : 2.22 % Allowed : 17.06 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2472 helix: 0.91 (0.15), residues: 1190 sheet: -0.25 (0.32), residues: 253 loop : -1.37 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 185 HIS 0.002 0.000 HIS A 298 PHE 0.034 0.001 PHE A 590 TYR 0.015 0.001 TYR D1068 ARG 0.004 0.000 ARG A1013 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 220 time to evaluate : 2.360 Fit side-chains revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6844 (pt) REVERT: A 411 LYS cc_start: 0.7575 (tmmt) cc_final: 0.6793 (mmtt) REVERT: A 765 GLN cc_start: 0.4102 (OUTLIER) cc_final: 0.2957 (mt0) REVERT: A 891 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6439 (mm) REVERT: A 1013 ARG cc_start: 0.7823 (tpt90) cc_final: 0.7570 (tpt-90) REVERT: A 1161 LYS cc_start: 0.4991 (OUTLIER) cc_final: 0.4465 (tptp) REVERT: A 1456 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7834 (mp) REVERT: A 1468 ASP cc_start: 0.4638 (OUTLIER) cc_final: 0.4355 (p0) REVERT: D 149 PHE cc_start: 0.8480 (m-10) cc_final: 0.8162 (m-10) REVERT: D 328 LYS cc_start: 0.7744 (tttp) cc_final: 0.7472 (ttpp) REVERT: D 846 ASP cc_start: 0.7362 (t0) cc_final: 0.7122 (t0) REVERT: D 1044 CYS cc_start: 0.6473 (m) cc_final: 0.6235 (m) REVERT: C 196 MET cc_start: 0.4474 (ppp) cc_final: 0.3395 (mmm) REVERT: C 255 GLU cc_start: 0.2443 (OUTLIER) cc_final: 0.1733 (pp20) REVERT: C 351 GLU cc_start: 0.2056 (OUTLIER) cc_final: 0.1272 (pm20) outliers start: 49 outliers final: 37 residues processed: 254 average time/residue: 0.2922 time to fit residues: 119.8123 Evaluate side-chains 262 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 217 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 1114 ASN Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1161 LYS Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1380 ASN Chi-restraints excluded: chain A residue 1416 LEU Chi-restraints excluded: chain A residue 1425 SER Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1462 VAL Chi-restraints excluded: chain A residue 1463 ILE Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1468 ASP Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 370 GLN Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 822 ILE Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 351 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 146 optimal weight: 2.9990 chunk 236 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 228 optimal weight: 20.0000 chunk 197 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 152 optimal weight: 0.7980 chunk 121 optimal weight: 8.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN A 638 ASN A1114 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20816 Z= 0.256 Angle : 0.588 10.599 28187 Z= 0.289 Chirality : 0.045 0.466 3212 Planarity : 0.004 0.054 3559 Dihedral : 8.473 102.460 3194 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.10 % Favored : 94.86 % Rotamer: Outliers : 2.08 % Allowed : 17.19 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.17), residues: 2472 helix: 0.83 (0.15), residues: 1189 sheet: -0.27 (0.32), residues: 255 loop : -1.38 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1103 HIS 0.003 0.001 HIS D 111 PHE 0.035 0.002 PHE A1147 TYR 0.017 0.001 TYR D1068 ARG 0.003 0.000 ARG A1013 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 222 time to evaluate : 2.215 Fit side-chains revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6853 (pt) REVERT: A 408 GLU cc_start: 0.6445 (tm-30) cc_final: 0.6020 (tm-30) REVERT: A 411 LYS cc_start: 0.7590 (tmmt) cc_final: 0.6809 (mmmt) REVERT: A 579 LEU cc_start: 0.7747 (tp) cc_final: 0.7467 (tt) REVERT: A 765 GLN cc_start: 0.4210 (OUTLIER) cc_final: 0.3030 (mt0) REVERT: A 891 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6498 (mm) REVERT: A 1025 LEU cc_start: 0.8459 (mt) cc_final: 0.8183 (mt) REVERT: A 1161 LYS cc_start: 0.4917 (OUTLIER) cc_final: 0.4370 (tptp) REVERT: A 1456 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7806 (mp) REVERT: A 1468 ASP cc_start: 0.4794 (OUTLIER) cc_final: 0.4521 (p0) REVERT: D 149 PHE cc_start: 0.8534 (m-10) cc_final: 0.8177 (m-10) REVERT: D 328 LYS cc_start: 0.7807 (tttp) cc_final: 0.7428 (ttpp) REVERT: D 671 LYS cc_start: 0.7382 (mmtt) cc_final: 0.7171 (mmtt) REVERT: D 846 ASP cc_start: 0.7340 (t0) cc_final: 0.7112 (t0) REVERT: C 196 MET cc_start: 0.4432 (ppp) cc_final: 0.3291 (mmm) REVERT: C 255 GLU cc_start: 0.2324 (OUTLIER) cc_final: 0.1607 (pp20) REVERT: C 351 GLU cc_start: 0.1980 (OUTLIER) cc_final: 0.1197 (pm20) outliers start: 46 outliers final: 36 residues processed: 254 average time/residue: 0.2845 time to fit residues: 116.2798 Evaluate side-chains 258 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 214 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 1114 ASN Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1161 LYS Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1425 SER Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1462 VAL Chi-restraints excluded: chain A residue 1463 ILE Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1468 ASP Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 370 GLN Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 822 ILE Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 351 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 156 optimal weight: 0.9980 chunk 210 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 0.3980 chunk 197 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 203 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.209384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.138209 restraints weight = 26011.432| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.94 r_work: 0.3277 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20816 Z= 0.149 Angle : 0.549 9.606 28187 Z= 0.269 Chirality : 0.043 0.431 3212 Planarity : 0.004 0.052 3559 Dihedral : 8.224 102.638 3194 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 1.76 % Allowed : 17.56 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.17), residues: 2472 helix: 0.91 (0.15), residues: 1204 sheet: -0.24 (0.32), residues: 255 loop : -1.39 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 185 HIS 0.002 0.000 HIS A 298 PHE 0.035 0.001 PHE A1147 TYR 0.015 0.001 TYR A 146 ARG 0.002 0.000 ARG A1013 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4283.48 seconds wall clock time: 79 minutes 54.82 seconds (4794.82 seconds total)