Starting phenix.real_space_refine on Tue May 13 18:54:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxc_36696/05_2025/8jxc_36696.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxc_36696/05_2025/8jxc_36696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jxc_36696/05_2025/8jxc_36696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxc_36696/05_2025/8jxc_36696.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxc_36696/05_2025/8jxc_36696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxc_36696/05_2025/8jxc_36696.cif" } resolution = 3.7 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 17 9.91 5 S 132 5.16 5 C 6507 2.51 5 N 1868 2.21 5 O 2180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10704 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10352 Classifications: {'peptide': 1337} Link IDs: {'PCIS': 1, 'PTRANS': 64, 'TRANS': 1271} Chain breaks: 1 Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 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: "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: "A" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 199 Unusual residues: {' CA': 17, 'A2G': 8, 'NAG': 5} Classifications: {'undetermined': 30} Link IDs: {None: 29} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 6.72, per 1000 atoms: 0.63 Number of scatterers: 10704 At special positions: 0 Unit cell: (142.511, 117.113, 128.401, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 17 19.99 S 132 16.00 O 2180 8.00 N 1868 7.00 C 6507 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=55, symmetry=0 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 208 " distance=2.03 Simple disulfide: pdb=" SG CYS A 222 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 272 " - pdb=" SG CYS A 291 " distance=2.04 Simple disulfide: pdb=" SG CYS A 285 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 351 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 357 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 384 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 673 " distance=2.03 Simple disulfide: pdb=" SG CYS A 669 " - pdb=" SG CYS A 688 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 703 " distance=2.03 Simple disulfide: pdb=" SG CYS A 973 " - pdb=" SG CYS A 987 " distance=2.03 Simple disulfide: pdb=" SG CYS A 983 " - pdb=" SG CYS A 997 " distance=2.03 Simple disulfide: pdb=" SG CYS A 999 " - pdb=" SG CYS A1012 " distance=2.03 Simple disulfide: pdb=" SG CYS A1025 " - pdb=" SG CYS A1037 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1050 " distance=2.03 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1059 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1079 " distance=2.03 Simple disulfide: pdb=" SG CYS A1073 " - pdb=" SG CYS A1092 " distance=2.03 Simple disulfide: pdb=" SG CYS A1086 " - pdb=" SG CYS A1101 " distance=2.03 Simple disulfide: pdb=" SG CYS A1110 " - pdb=" SG CYS A1122 " distance=2.03 Simple disulfide: pdb=" SG CYS A1117 " - pdb=" SG CYS A1135 " distance=2.03 Simple disulfide: pdb=" SG CYS A1129 " - pdb=" SG CYS A1144 " distance=2.03 Simple disulfide: pdb=" SG CYS A1150 " - pdb=" SG CYS A1162 " distance=2.03 Simple disulfide: pdb=" SG CYS A1157 " - pdb=" SG CYS A1175 " distance=2.03 Simple disulfide: pdb=" SG CYS A1169 " - pdb=" SG CYS A1184 " distance=2.03 Simple disulfide: pdb=" SG CYS A1188 " - pdb=" SG CYS A1201 " distance=2.03 Simple disulfide: pdb=" SG CYS A1195 " - pdb=" SG CYS A1214 " distance=2.03 Simple disulfide: pdb=" SG CYS A1208 " - pdb=" SG CYS A1223 " distance=2.03 Simple disulfide: pdb=" SG CYS A1231 " - pdb=" SG CYS A1244 " distance=2.03 Simple disulfide: pdb=" SG CYS A1238 " - pdb=" SG CYS A1257 " distance=2.03 Simple disulfide: pdb=" SG CYS A1251 " - pdb=" SG CYS A1267 " distance=2.03 Simple disulfide: pdb=" SG CYS A1272 " - pdb=" SG CYS A1284 " distance=2.03 Simple disulfide: pdb=" SG CYS A1279 " - pdb=" SG CYS A1297 " distance=2.03 Simple disulfide: pdb=" SG CYS A1291 " - pdb=" SG CYS A1306 " distance=2.03 Simple disulfide: pdb=" SG CYS A2701 " - pdb=" SG CYS A2713 " distance=2.03 Simple disulfide: pdb=" SG CYS A2708 " - pdb=" SG CYS A2726 " distance=2.03 Simple disulfide: pdb=" SG CYS A2720 " - pdb=" SG CYS A2737 " distance=2.03 Simple disulfide: pdb=" SG CYS A2742 " - pdb=" SG CYS A2754 " distance=2.03 Simple disulfide: pdb=" SG CYS A2749 " - pdb=" SG CYS A2767 " distance=2.03 Simple disulfide: pdb=" SG CYS A2761 " - pdb=" SG CYS A2776 " distance=2.03 Simple disulfide: pdb=" SG CYS A2781 " - pdb=" SG CYS A2794 " distance=2.03 Simple disulfide: pdb=" SG CYS A2789 " - pdb=" SG CYS A2807 " distance=2.03 Simple disulfide: pdb=" SG CYS A2801 " - pdb=" SG CYS A2818 " distance=2.03 Simple disulfide: pdb=" SG CYS A2823 " - pdb=" SG CYS A2836 " distance=2.03 Simple disulfide: pdb=" SG CYS A2830 " - pdb=" SG CYS A2849 " distance=2.03 Simple disulfide: pdb=" SG CYS A2843 " - pdb=" SG CYS A2860 " distance=2.04 Simple disulfide: pdb=" SG CYS A2865 " - pdb=" SG CYS A2878 " distance=2.03 Simple disulfide: pdb=" SG CYS A2872 " - pdb=" SG CYS A2891 " distance=2.03 Simple disulfide: pdb=" SG CYS A2885 " - pdb=" SG CYS A2901 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=8, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A4701 " - " ASN A 340 " " NAG A4702 " - " ASN A 462 " " NAG A4703 " - " ASN A1187 " " NAG A4728 " - " ASN A2782 " " NAG A4729 " - " ASN A2810 " " NAG C 1 " - " ASN A 657 " " NAG D 1 " - " ASN A 865 " " NAG E 1 " - " ASN A1063 " Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 1.5 seconds 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 34 sheets defined 8.6% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 211 through 215 removed outlier: 3.634A pdb=" N ARG A 215 " --> pdb=" O SER A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 660 through 664 removed outlier: 4.122A pdb=" N SER A 664 " --> pdb=" O PRO A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 749 through 751 No H-bonds generated for 'chain 'A' and resid 749 through 751' Processing helix chain 'A' and resid 979 through 983 Processing helix chain 'A' and resid 1041 through 1043 No H-bonds generated for 'chain 'A' and resid 1041 through 1043' Processing helix chain 'A' and resid 1053 through 1057 removed outlier: 3.906A pdb=" N HIS A1057 " --> pdb=" O SER A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1085 Processing helix chain 'A' and resid 1095 through 1099 removed outlier: 3.924A pdb=" N GLN A1099 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1128 No H-bonds generated for 'chain 'A' and resid 1126 through 1128' Processing helix chain 'A' and resid 1138 through 1142 removed outlier: 3.502A pdb=" N LYS A1142 " --> pdb=" O SER A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1168 Processing helix chain 'A' and resid 1205 through 1207 No H-bonds generated for 'chain 'A' and resid 1205 through 1207' Processing helix chain 'A' and resid 1246 through 1250 Processing helix chain 'A' and resid 1260 through 1264 removed outlier: 3.608A pdb=" N GLU A1263 " --> pdb=" O GLY A1260 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS A1264 " --> pdb=" O SER A1261 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1260 through 1264' Processing helix chain 'A' and resid 1288 through 1290 No H-bonds generated for 'chain 'A' and resid 1288 through 1290' Processing helix chain 'A' and resid 1300 through 1305 removed outlier: 3.923A pdb=" N ASP A1305 " --> pdb=" O SER A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 2717 through 2719 No H-bonds generated for 'chain 'A' and resid 2717 through 2719' Processing helix chain 'A' and resid 2729 through 2733 removed outlier: 3.523A pdb=" N LEU A2733 " --> pdb=" O SER A2730 " (cutoff:3.500A) Processing helix chain 'A' and resid 2735 through 2740 removed outlier: 4.389A pdb=" N PHE A2739 " --> pdb=" O THR A2735 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS A2740 " --> pdb=" O VAL A2736 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2735 through 2740' Processing helix chain 'A' and resid 2758 through 2760 No H-bonds generated for 'chain 'A' and resid 2758 through 2760' Processing helix chain 'A' and resid 2798 through 2800 No H-bonds generated for 'chain 'A' and resid 2798 through 2800' Processing helix chain 'A' and resid 2838 through 2842 Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 189 Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 228 Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 271 Processing sheet with id=AA4, first strand: chain 'A' and resid 319 through 323 removed outlier: 3.524A pdb=" N GLN A 319 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 338 removed outlier: 6.874A pdb=" N THR A 344 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 360 through 362 Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 379 Processing sheet with id=AA8, first strand: chain 'A' and resid 413 through 417 removed outlier: 6.956A pdb=" N LEU A 403 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 428 through 431 removed outlier: 6.791A pdb=" N VAL A 447 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 471 through 474 removed outlier: 6.788A pdb=" N ILE A 490 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 511 through 517 removed outlier: 4.189A pdb=" N GLY A 513 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR A 522 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 537 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 558 through 564 removed outlier: 4.929A pdb=" N GLY A 560 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 573 " --> pdb=" O GLY A 560 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 569 " --> pdb=" O ASP A 564 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR A 579 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE A 580 " --> pdb=" O VAL A 593 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 603 through 608 removed outlier: 4.075A pdb=" N GLY A 605 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 623 " --> pdb=" O TYR A 637 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 672 through 675 Processing sheet with id=AB6, first strand: chain 'A' and resid 694 through 696 Processing sheet with id=AB7, first strand: chain 'A' and resid 732 through 735 removed outlier: 6.660A pdb=" N VAL A 733 " --> pdb=" O GLY A 720 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLY A 720 " --> pdb=" O VAL A 733 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS A 958 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 742 through 748 removed outlier: 4.840A pdb=" N GLY A 744 " --> pdb=" O SER A 757 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE A 764 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 789 through 791 removed outlier: 3.730A pdb=" N ILE A 821 " --> pdb=" O VAL A 807 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL A 809 " --> pdb=" O GLN A 819 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLN A 819 " --> pdb=" O VAL A 809 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ARG A 811 " --> pdb=" O ARG A 817 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG A 817 " --> pdb=" O ARG A 811 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 827 through 833 removed outlier: 4.988A pdb=" N SER A 829 " --> pdb=" O SER A 842 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE A 850 " --> pdb=" O ILE A 863 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 874 through 876 Processing sheet with id=AC3, first strand: chain 'A' and resid 915 through 921 removed outlier: 6.217A pdb=" N THR A 928 " --> pdb=" O PHE A 916 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU A 918 " --> pdb=" O PHE A 926 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE A 926 " --> pdb=" O LEU A 918 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL A 920 " --> pdb=" O ASN A 924 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASN A 924 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 934 " --> pdb=" O ASP A 929 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE A 935 " --> pdb=" O ILE A 949 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 986 through 990 removed outlier: 3.503A pdb=" N PHE A 986 " --> pdb=" O GLY A 998 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1003 through 1005 Processing sheet with id=AC6, first strand: chain 'A' and resid 1029 through 1031 Processing sheet with id=AC7, first strand: chain 'A' and resid 1071 through 1073 removed outlier: 4.587A pdb=" N GLN A1078 " --> pdb=" O CYS A1073 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1114 through 1116 Processing sheet with id=AC9, first strand: chain 'A' and resid 1155 through 1156 Processing sheet with id=AD1, first strand: chain 'A' and resid 1192 through 1194 Processing sheet with id=AD2, first strand: chain 'A' and resid 1236 through 1237 Processing sheet with id=AD3, first strand: chain 'A' and resid 1276 through 1278 Processing sheet with id=AD4, first strand: chain 'A' and resid 2705 through 2706 Processing sheet with id=AD5, first strand: chain 'A' and resid 2746 through 2748 Processing sheet with id=AD6, first strand: chain 'A' and resid 2786 through 2788 Processing sheet with id=AD7, first strand: chain 'A' and resid 2869 through 2871 219 hydrogen bonds defined for protein. 492 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: 4.46 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3672 1.34 - 1.46: 2518 1.46 - 1.58: 4594 1.58 - 1.70: 0 1.70 - 1.83: 150 Bond restraints: 10934 Sorted by residual: bond pdb=" C1 NAG A4703 " pdb=" O5 NAG A4703 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.10e+00 bond pdb=" C1 A2G A4709 " pdb=" O5 A2G A4709 " ideal model delta sigma weight residual 1.385 1.420 -0.035 2.00e-02 2.50e+03 3.06e+00 bond pdb=" C1 A2G A4706 " pdb=" O5 A2G A4706 " ideal model delta sigma weight residual 1.385 1.420 -0.035 2.00e-02 2.50e+03 3.06e+00 bond pdb=" C1 A2G A4707 " pdb=" O5 A2G A4707 " ideal model delta sigma weight residual 1.385 1.420 -0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C1 A2G A4708 " pdb=" O5 A2G A4708 " ideal model delta sigma weight residual 1.385 1.420 -0.035 2.00e-02 2.50e+03 2.99e+00 ... (remaining 10929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 14486 2.11 - 4.21: 319 4.21 - 6.32: 32 6.32 - 8.42: 4 8.42 - 10.53: 2 Bond angle restraints: 14843 Sorted by residual: angle pdb=" C PHE A1062 " pdb=" N ASN A1063 " pdb=" CA ASN A1063 " ideal model delta sigma weight residual 121.54 128.38 -6.84 1.91e+00 2.74e-01 1.28e+01 angle pdb=" CB MET A1300 " pdb=" CG MET A1300 " pdb=" SD MET A1300 " ideal model delta sigma weight residual 112.70 123.23 -10.53 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C1 NAG A4703 " pdb=" O5 NAG A4703 " pdb=" C5 NAG A4703 " ideal model delta sigma weight residual 113.21 123.50 -10.29 3.00e+00 1.11e-01 1.18e+01 angle pdb=" N ILE A 953 " pdb=" CA ILE A 953 " pdb=" C ILE A 953 " ideal model delta sigma weight residual 111.91 108.95 2.96 8.90e-01 1.26e+00 1.11e+01 angle pdb=" N GLY A 873 " pdb=" CA GLY A 873 " pdb=" C GLY A 873 " ideal model delta sigma weight residual 110.71 116.43 -5.72 1.78e+00 3.16e-01 1.03e+01 ... (remaining 14838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.34: 6269 21.34 - 42.69: 493 42.69 - 64.03: 93 64.03 - 85.37: 34 85.37 - 106.71: 8 Dihedral angle restraints: 6897 sinusoidal: 3047 harmonic: 3850 Sorted by residual: dihedral pdb=" CB CYS A1272 " pdb=" SG CYS A1272 " pdb=" SG CYS A1284 " pdb=" CB CYS A1284 " ideal model delta sinusoidal sigma weight residual 93.00 -177.85 -89.15 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS A2749 " pdb=" SG CYS A2749 " pdb=" SG CYS A2767 " pdb=" CB CYS A2767 " ideal model delta sinusoidal sigma weight residual 93.00 -179.39 -87.61 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS A1188 " pdb=" SG CYS A1188 " pdb=" SG CYS A1201 " pdb=" CB CYS A1201 " ideal model delta sinusoidal sigma weight residual 93.00 179.25 -86.25 1 1.00e+01 1.00e-02 8.97e+01 ... (remaining 6894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1160 0.047 - 0.093: 344 0.093 - 0.140: 92 0.140 - 0.186: 9 0.186 - 0.233: 4 Chirality restraints: 1609 Sorted by residual: chirality pdb=" C1 NAG A4703 " pdb=" ND2 ASN A1187 " pdb=" C2 NAG A4703 " pdb=" O5 NAG A4703 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A1063 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.48 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1606 not shown) Planarity restraints: 1993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.315 2.00e-02 2.50e+03 2.69e-01 9.01e+02 pdb=" C7 NAG E 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.177 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.470 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.290 2.00e-02 2.50e+03 2.46e-01 7.57e+02 pdb=" C7 NAG D 2 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.423 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A4703 " -0.241 2.00e-02 2.50e+03 2.04e-01 5.21e+02 pdb=" C7 NAG A4703 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG A4703 " -0.160 2.00e-02 2.50e+03 pdb=" N2 NAG A4703 " 0.348 2.00e-02 2.50e+03 pdb=" O7 NAG A4703 " -0.007 2.00e-02 2.50e+03 ... (remaining 1990 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 878 2.73 - 3.28: 11212 3.28 - 3.82: 17073 3.82 - 4.36: 21398 4.36 - 4.90: 35944 Nonbonded interactions: 86505 Sorted by model distance: nonbonded pdb=" OD2 ASP A1140 " pdb="CA CA A4718 " model vdw 2.194 2.510 nonbonded pdb=" OD1 ASP A2721 " pdb="CA CA A4723 " model vdw 2.200 2.510 nonbonded pdb=" OD1 ASP A1130 " pdb="CA CA A4718 " model vdw 2.201 2.510 nonbonded pdb=" O ARG A 846 " pdb=" NH1 ARG A 846 " model vdw 2.204 3.120 nonbonded pdb=" OD2 ASP A2731 " pdb="CA CA A4723 " model vdw 2.221 2.510 ... (remaining 86500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.680 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 27.880 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 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 0.106 11009 Z= 0.251 Angle : 0.750 10.528 14989 Z= 0.405 Chirality : 0.048 0.233 1609 Planarity : 0.011 0.269 1985 Dihedral : 15.809 106.715 4260 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.72 % Allowed : 15.37 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.71 (0.24), residues: 1333 helix: -1.93 (1.09), residues: 12 sheet: -0.80 (0.30), residues: 292 loop : -0.33 (0.21), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 844 HIS 0.006 0.001 HIS A 985 PHE 0.018 0.001 PHE A2739 TYR 0.014 0.001 TYR A2763 ARG 0.004 0.000 ARG A 795 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 8) link_NAG-ASN : angle 2.81288 ( 24) link_BETA1-4 : bond 0.00480 ( 4) link_BETA1-4 : angle 1.64585 ( 12) hydrogen bonds : bond 0.25693 ( 219) hydrogen bonds : angle 10.33442 ( 492) SS BOND : bond 0.00186 ( 55) SS BOND : angle 0.83520 ( 110) covalent geometry : bond 0.00384 (10934) covalent geometry : angle 0.73998 (14843) Misc. bond : bond 0.05935 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 62 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 ASP cc_start: 0.8381 (t70) cc_final: 0.8163 (t70) REVERT: A 463 VAL cc_start: 0.8412 (p) cc_final: 0.8163 (t) outliers start: 32 outliers final: 30 residues processed: 92 average time/residue: 0.1772 time to fit residues: 26.1586 Evaluate side-chains 87 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 57 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 971 ASN Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1247 ASN Chi-restraints excluded: chain A residue 2766 ASP Chi-restraints excluded: chain A residue 2781 CYS Chi-restraints excluded: chain A residue 2835 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 HIS ** A 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.142388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.109874 restraints weight = 15993.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.107750 restraints weight = 29355.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.108648 restraints weight = 28509.076| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11009 Z= 0.151 Angle : 0.644 6.469 14989 Z= 0.337 Chirality : 0.048 0.213 1609 Planarity : 0.004 0.052 1985 Dihedral : 8.862 72.043 1904 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 4.75 % Allowed : 13.50 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.78 (0.23), residues: 1333 helix: -2.34 (0.88), residues: 18 sheet: -0.82 (0.30), residues: 294 loop : -0.37 (0.20), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 528 HIS 0.006 0.001 HIS A 985 PHE 0.014 0.001 PHE A 525 TYR 0.013 0.001 TYR A 798 ARG 0.006 0.000 ARG A 846 Details of bonding type rmsd link_NAG-ASN : bond 0.00558 ( 8) link_NAG-ASN : angle 1.81423 ( 24) link_BETA1-4 : bond 0.00481 ( 4) link_BETA1-4 : angle 2.76349 ( 12) hydrogen bonds : bond 0.05210 ( 219) hydrogen bonds : angle 7.62239 ( 492) SS BOND : bond 0.00251 ( 55) SS BOND : angle 0.85346 ( 110) covalent geometry : bond 0.00344 (10934) covalent geometry : angle 0.63408 (14843) Misc. bond : bond 0.00071 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 68 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6585 (tp30) REVERT: A 429 ASP cc_start: 0.8247 (t70) cc_final: 0.7955 (t70) REVERT: A 666 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7939 (t0) REVERT: A 851 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7883 (mmm) REVERT: A 905 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7912 (ttt180) REVERT: A 931 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7845 (tpt-90) REVERT: A 986 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8464 (p90) REVERT: A 1156 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7213 (ttt-90) REVERT: A 1300 MET cc_start: 0.7751 (mmm) cc_final: 0.7440 (mmm) outliers start: 56 outliers final: 33 residues processed: 116 average time/residue: 0.2286 time to fit residues: 39.2878 Evaluate side-chains 99 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 59 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 931 ARG Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 986 PHE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1101 CYS Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1156 ARG Chi-restraints excluded: chain A residue 2766 ASP Chi-restraints excluded: chain A residue 2777 LEU Chi-restraints excluded: chain A residue 2781 CYS Chi-restraints excluded: chain A residue 2835 ILE Chi-restraints excluded: chain A residue 2865 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 83 optimal weight: 0.0270 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 overall best weight: 0.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.144474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.112887 restraints weight = 16228.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.110116 restraints weight = 30167.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.111414 restraints weight = 28027.444| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11009 Z= 0.137 Angle : 0.610 6.023 14989 Z= 0.319 Chirality : 0.047 0.198 1609 Planarity : 0.004 0.052 1985 Dihedral : 7.980 59.784 1891 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 4.58 % Allowed : 14.18 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.84 (0.23), residues: 1333 helix: -2.27 (0.88), residues: 18 sheet: -0.79 (0.29), residues: 295 loop : -0.44 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 528 HIS 0.006 0.001 HIS A 908 PHE 0.014 0.001 PHE A 709 TYR 0.013 0.001 TYR A 798 ARG 0.004 0.000 ARG A 364 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 8) link_NAG-ASN : angle 1.74251 ( 24) link_BETA1-4 : bond 0.00565 ( 4) link_BETA1-4 : angle 2.20522 ( 12) hydrogen bonds : bond 0.04038 ( 219) hydrogen bonds : angle 7.06663 ( 492) SS BOND : bond 0.00236 ( 55) SS BOND : angle 0.79696 ( 110) covalent geometry : bond 0.00315 (10934) covalent geometry : angle 0.60161 (14843) Misc. bond : bond 0.00022 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 68 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6466 (tp30) REVERT: A 429 ASP cc_start: 0.8213 (t70) cc_final: 0.7929 (t70) REVERT: A 443 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8194 (mmt) REVERT: A 666 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.7912 (t0) REVERT: A 851 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7607 (mmm) REVERT: A 905 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7886 (ttt180) REVERT: A 931 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7862 (tpt-90) REVERT: A 1156 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7255 (ttt-90) outliers start: 54 outliers final: 37 residues processed: 118 average time/residue: 0.2435 time to fit residues: 42.9727 Evaluate side-chains 103 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 59 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 931 ARG Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1101 CYS Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1156 ARG Chi-restraints excluded: chain A residue 2766 ASP Chi-restraints excluded: chain A residue 2777 LEU Chi-restraints excluded: chain A residue 2781 CYS Chi-restraints excluded: chain A residue 2789 CYS Chi-restraints excluded: chain A residue 2832 THR Chi-restraints excluded: chain A residue 2835 ILE Chi-restraints excluded: chain A residue 2865 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 56 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN A 908 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.140329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.109782 restraints weight = 16129.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.108569 restraints weight = 30362.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.109431 restraints weight = 25776.103| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11009 Z= 0.267 Angle : 0.714 6.499 14989 Z= 0.374 Chirality : 0.052 0.215 1609 Planarity : 0.005 0.050 1985 Dihedral : 8.280 59.282 1886 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 5.94 % Allowed : 14.60 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -1.10 (0.23), residues: 1333 helix: -2.61 (0.78), residues: 18 sheet: -1.06 (0.29), residues: 289 loop : -0.59 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 528 HIS 0.008 0.002 HIS A 978 PHE 0.020 0.002 PHE A 755 TYR 0.019 0.002 TYR A 798 ARG 0.006 0.001 ARG A 539 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 8) link_NAG-ASN : angle 2.00340 ( 24) link_BETA1-4 : bond 0.00506 ( 4) link_BETA1-4 : angle 2.24967 ( 12) hydrogen bonds : bond 0.04256 ( 219) hydrogen bonds : angle 7.14119 ( 492) SS BOND : bond 0.00343 ( 55) SS BOND : angle 1.08283 ( 110) covalent geometry : bond 0.00636 (10934) covalent geometry : angle 0.70385 (14843) Misc. bond : bond 0.00056 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 56 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 ASP cc_start: 0.8465 (t70) cc_final: 0.8215 (t70) REVERT: A 527 ASP cc_start: 0.8169 (t0) cc_final: 0.7825 (t0) REVERT: A 851 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7666 (mmm) REVERT: A 905 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8038 (ttt180) REVERT: A 908 HIS cc_start: 0.7709 (OUTLIER) cc_final: 0.7282 (t70) REVERT: A 931 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7901 (tpt-90) REVERT: A 1156 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.7177 (ttt180) REVERT: A 1194 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7968 (mmmt) REVERT: A 1300 MET cc_start: 0.7741 (mmm) cc_final: 0.7487 (mmm) outliers start: 70 outliers final: 58 residues processed: 122 average time/residue: 0.2019 time to fit residues: 36.8040 Evaluate side-chains 119 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 55 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 908 HIS Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 931 ARG Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 986 PHE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1101 CYS Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1156 ARG Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1194 LYS Chi-restraints excluded: chain A residue 1261 SER Chi-restraints excluded: chain A residue 2713 CYS Chi-restraints excluded: chain A residue 2731 ASP Chi-restraints excluded: chain A residue 2732 GLU Chi-restraints excluded: chain A residue 2755 VAL Chi-restraints excluded: chain A residue 2766 ASP Chi-restraints excluded: chain A residue 2777 LEU Chi-restraints excluded: chain A residue 2781 CYS Chi-restraints excluded: chain A residue 2789 CYS Chi-restraints excluded: chain A residue 2832 THR Chi-restraints excluded: chain A residue 2835 ILE Chi-restraints excluded: chain A residue 2854 ASP Chi-restraints excluded: chain A residue 2865 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 62 optimal weight: 0.4980 chunk 117 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 0.0980 chunk 72 optimal weight: 0.0980 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 HIS ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.143733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.111618 restraints weight = 15873.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.110163 restraints weight = 28323.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.110899 restraints weight = 29580.521| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11009 Z= 0.121 Angle : 0.605 6.130 14989 Z= 0.317 Chirality : 0.047 0.202 1609 Planarity : 0.004 0.050 1985 Dihedral : 7.633 59.379 1886 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 5.35 % Allowed : 14.94 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -1.01 (0.23), residues: 1333 helix: -2.48 (0.80), residues: 18 sheet: -0.93 (0.29), residues: 287 loop : -0.55 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 528 HIS 0.009 0.001 HIS A 908 PHE 0.013 0.001 PHE A 709 TYR 0.014 0.001 TYR A 798 ARG 0.003 0.000 ARG A 539 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 8) link_NAG-ASN : angle 1.61037 ( 24) link_BETA1-4 : bond 0.00509 ( 4) link_BETA1-4 : angle 2.19967 ( 12) hydrogen bonds : bond 0.03522 ( 219) hydrogen bonds : angle 6.87762 ( 492) SS BOND : bond 0.00222 ( 55) SS BOND : angle 0.88235 ( 110) covalent geometry : bond 0.00274 (10934) covalent geometry : angle 0.59597 (14843) Misc. bond : bond 0.00022 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 65 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6667 (tp30) REVERT: A 429 ASP cc_start: 0.8277 (t70) cc_final: 0.7952 (t70) REVERT: A 443 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.7959 (mmt) REVERT: A 851 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7667 (mmm) REVERT: A 905 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7810 (ttt180) REVERT: A 908 HIS cc_start: 0.7569 (OUTLIER) cc_final: 0.6861 (t70) REVERT: A 931 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7883 (tpt-90) REVERT: A 1156 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7171 (ttt180) REVERT: A 1194 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7793 (mmmt) outliers start: 63 outliers final: 48 residues processed: 122 average time/residue: 0.1960 time to fit residues: 36.2580 Evaluate side-chains 114 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 58 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 908 HIS Chi-restraints excluded: chain A residue 931 ARG Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1101 CYS Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1156 ARG Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1194 LYS Chi-restraints excluded: chain A residue 1200 SER Chi-restraints excluded: chain A residue 1261 SER Chi-restraints excluded: chain A residue 2713 CYS Chi-restraints excluded: chain A residue 2732 GLU Chi-restraints excluded: chain A residue 2777 LEU Chi-restraints excluded: chain A residue 2781 CYS Chi-restraints excluded: chain A residue 2789 CYS Chi-restraints excluded: chain A residue 2832 THR Chi-restraints excluded: chain A residue 2835 ILE Chi-restraints excluded: chain A residue 2854 ASP Chi-restraints excluded: chain A residue 2865 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 63 optimal weight: 0.1980 chunk 90 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 HIS A 985 HIS ** A2856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.143011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.110087 restraints weight = 16196.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.107464 restraints weight = 28677.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.108733 restraints weight = 27668.889| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11009 Z= 0.223 Angle : 0.665 6.040 14989 Z= 0.349 Chirality : 0.050 0.211 1609 Planarity : 0.004 0.049 1985 Dihedral : 7.742 58.403 1882 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 6.45 % Allowed : 14.43 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -1.14 (0.23), residues: 1333 helix: -2.64 (0.76), residues: 18 sheet: -1.18 (0.28), residues: 297 loop : -0.58 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 528 HIS 0.013 0.001 HIS A 985 PHE 0.018 0.002 PHE A 709 TYR 0.018 0.002 TYR A 798 ARG 0.006 0.000 ARG A 539 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 8) link_NAG-ASN : angle 1.67368 ( 24) link_BETA1-4 : bond 0.00466 ( 4) link_BETA1-4 : angle 2.14119 ( 12) hydrogen bonds : bond 0.03759 ( 219) hydrogen bonds : angle 6.91788 ( 492) SS BOND : bond 0.00290 ( 55) SS BOND : angle 1.02094 ( 110) covalent geometry : bond 0.00534 (10934) covalent geometry : angle 0.65624 (14843) Misc. bond : bond 0.00042 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 61 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6777 (tp30) REVERT: A 429 ASP cc_start: 0.8460 (t70) cc_final: 0.8193 (t70) REVERT: A 851 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7690 (mmm) REVERT: A 905 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7880 (ttt180) REVERT: A 931 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7907 (tpt-90) REVERT: A 1018 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8271 (ttm170) REVERT: A 1156 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.7200 (ttt180) REVERT: A 1194 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7847 (mmmt) outliers start: 76 outliers final: 56 residues processed: 127 average time/residue: 0.1923 time to fit residues: 36.9432 Evaluate side-chains 123 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 60 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 931 ARG Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 986 PHE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1018 ARG Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1101 CYS Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1156 ARG Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1194 LYS Chi-restraints excluded: chain A residue 1200 SER Chi-restraints excluded: chain A residue 1261 SER Chi-restraints excluded: chain A residue 2713 CYS Chi-restraints excluded: chain A residue 2732 GLU Chi-restraints excluded: chain A residue 2755 VAL Chi-restraints excluded: chain A residue 2777 LEU Chi-restraints excluded: chain A residue 2781 CYS Chi-restraints excluded: chain A residue 2789 CYS Chi-restraints excluded: chain A residue 2832 THR Chi-restraints excluded: chain A residue 2835 ILE Chi-restraints excluded: chain A residue 2854 ASP Chi-restraints excluded: chain A residue 2865 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 111 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 101 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 125 optimal weight: 0.0370 chunk 100 optimal weight: 2.9990 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 HIS A1154 GLN ** A2856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.145650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.112382 restraints weight = 16129.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.109199 restraints weight = 26061.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.110543 restraints weight = 24541.030| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11009 Z= 0.110 Angle : 0.586 6.275 14989 Z= 0.306 Chirality : 0.046 0.197 1609 Planarity : 0.004 0.049 1985 Dihedral : 7.226 57.638 1882 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 5.18 % Allowed : 15.79 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.99 (0.23), residues: 1333 helix: -2.33 (0.85), residues: 18 sheet: -0.99 (0.29), residues: 284 loop : -0.52 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 844 HIS 0.009 0.001 HIS A 908 PHE 0.011 0.001 PHE A1115 TYR 0.014 0.001 TYR A 798 ARG 0.002 0.000 ARG A 795 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 8) link_NAG-ASN : angle 1.42775 ( 24) link_BETA1-4 : bond 0.00476 ( 4) link_BETA1-4 : angle 2.06569 ( 12) hydrogen bonds : bond 0.03262 ( 219) hydrogen bonds : angle 6.66978 ( 492) SS BOND : bond 0.00200 ( 55) SS BOND : angle 0.84102 ( 110) covalent geometry : bond 0.00247 (10934) covalent geometry : angle 0.57905 (14843) Misc. bond : bond 0.00020 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 72 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6707 (tp30) REVERT: A 429 ASP cc_start: 0.8261 (t70) cc_final: 0.7943 (t70) REVERT: A 443 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.7902 (mmt) REVERT: A 905 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7940 (ttt180) REVERT: A 931 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7783 (tpt-90) REVERT: A 1018 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8298 (ttm170) REVERT: A 1156 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.7075 (ttt180) REVERT: A 1194 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7833 (mmmt) outliers start: 61 outliers final: 44 residues processed: 124 average time/residue: 0.2043 time to fit residues: 37.8969 Evaluate side-chains 111 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 60 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 931 ARG Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1018 ARG Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1101 CYS Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1156 ARG Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1194 LYS Chi-restraints excluded: chain A residue 1200 SER Chi-restraints excluded: chain A residue 1261 SER Chi-restraints excluded: chain A residue 2713 CYS Chi-restraints excluded: chain A residue 2716 GLN Chi-restraints excluded: chain A residue 2732 GLU Chi-restraints excluded: chain A residue 2777 LEU Chi-restraints excluded: chain A residue 2781 CYS Chi-restraints excluded: chain A residue 2789 CYS Chi-restraints excluded: chain A residue 2832 THR Chi-restraints excluded: chain A residue 2835 ILE Chi-restraints excluded: chain A residue 2865 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 44 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 108 optimal weight: 0.2980 chunk 42 optimal weight: 0.1980 chunk 33 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 HIS ** A2856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.144868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.111657 restraints weight = 16044.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.109629 restraints weight = 28139.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.110690 restraints weight = 28928.185| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11009 Z= 0.119 Angle : 0.594 6.669 14989 Z= 0.310 Chirality : 0.047 0.195 1609 Planarity : 0.004 0.048 1985 Dihedral : 7.101 57.097 1881 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 5.26 % Allowed : 15.53 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.95 (0.23), residues: 1333 helix: -2.13 (0.87), residues: 18 sheet: -0.99 (0.29), residues: 284 loop : -0.49 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 844 HIS 0.008 0.001 HIS A 908 PHE 0.011 0.001 PHE A1115 TYR 0.014 0.001 TYR A 798 ARG 0.003 0.000 ARG A 539 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 8) link_NAG-ASN : angle 1.37783 ( 24) link_BETA1-4 : bond 0.00436 ( 4) link_BETA1-4 : angle 1.98845 ( 12) hydrogen bonds : bond 0.03206 ( 219) hydrogen bonds : angle 6.63898 ( 492) SS BOND : bond 0.00196 ( 55) SS BOND : angle 0.78310 ( 110) covalent geometry : bond 0.00275 (10934) covalent geometry : angle 0.58746 (14843) Misc. bond : bond 0.00018 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 62 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6520 (tp30) REVERT: A 416 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8964 (tt) REVERT: A 429 ASP cc_start: 0.8312 (t70) cc_final: 0.7993 (t70) REVERT: A 443 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8001 (mmt) REVERT: A 527 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7326 (m-30) REVERT: A 726 SER cc_start: 0.6157 (t) cc_final: 0.5926 (p) REVERT: A 905 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7935 (ttt180) REVERT: A 908 HIS cc_start: 0.7480 (OUTLIER) cc_final: 0.7066 (t70) REVERT: A 1018 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8306 (ttm170) REVERT: A 1194 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7927 (mmmt) REVERT: A 1300 MET cc_start: 0.7701 (mmm) cc_final: 0.7349 (mmm) REVERT: A 2854 ASP cc_start: 0.3962 (OUTLIER) cc_final: 0.3332 (p0) outliers start: 62 outliers final: 47 residues processed: 116 average time/residue: 0.2159 time to fit residues: 37.0651 Evaluate side-chains 116 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 60 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 908 HIS Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1018 ARG Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1101 CYS Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1194 LYS Chi-restraints excluded: chain A residue 1261 SER Chi-restraints excluded: chain A residue 2713 CYS Chi-restraints excluded: chain A residue 2732 GLU Chi-restraints excluded: chain A residue 2777 LEU Chi-restraints excluded: chain A residue 2781 CYS Chi-restraints excluded: chain A residue 2789 CYS Chi-restraints excluded: chain A residue 2832 THR Chi-restraints excluded: chain A residue 2835 ILE Chi-restraints excluded: chain A residue 2854 ASP Chi-restraints excluded: chain A residue 2865 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 27 optimal weight: 3.9990 chunk 96 optimal weight: 0.3980 chunk 4 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 82 optimal weight: 0.0470 chunk 1 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 HIS ** A2856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.144202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.111379 restraints weight = 16187.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.109284 restraints weight = 29535.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.110232 restraints weight = 26722.872| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11009 Z= 0.139 Angle : 0.598 6.436 14989 Z= 0.312 Chirality : 0.047 0.197 1609 Planarity : 0.004 0.048 1985 Dihedral : 7.102 58.592 1881 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 5.09 % Allowed : 15.53 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.95 (0.23), residues: 1333 helix: -2.06 (0.92), residues: 18 sheet: -1.02 (0.29), residues: 284 loop : -0.47 (0.21), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 528 HIS 0.015 0.001 HIS A 908 PHE 0.012 0.001 PHE A 709 TYR 0.014 0.001 TYR A 798 ARG 0.004 0.000 ARG A 931 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 8) link_NAG-ASN : angle 1.37774 ( 24) link_BETA1-4 : bond 0.00410 ( 4) link_BETA1-4 : angle 1.97328 ( 12) hydrogen bonds : bond 0.03232 ( 219) hydrogen bonds : angle 6.61797 ( 492) SS BOND : bond 0.00213 ( 55) SS BOND : angle 0.79585 ( 110) covalent geometry : bond 0.00326 (10934) covalent geometry : angle 0.59196 (14843) Misc. bond : bond 0.00021 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 60 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6493 (tp30) REVERT: A 416 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8997 (tt) REVERT: A 443 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8061 (mmt) REVERT: A 851 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7681 (mmm) REVERT: A 905 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7887 (ttt180) REVERT: A 1018 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8304 (ttm170) REVERT: A 2854 ASP cc_start: 0.4078 (OUTLIER) cc_final: 0.3424 (p0) outliers start: 60 outliers final: 49 residues processed: 113 average time/residue: 0.1926 time to fit residues: 33.6043 Evaluate side-chains 114 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 58 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1018 ARG Chi-restraints excluded: chain A residue 1101 CYS Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1261 SER Chi-restraints excluded: chain A residue 2713 CYS Chi-restraints excluded: chain A residue 2732 GLU Chi-restraints excluded: chain A residue 2777 LEU Chi-restraints excluded: chain A residue 2781 CYS Chi-restraints excluded: chain A residue 2789 CYS Chi-restraints excluded: chain A residue 2832 THR Chi-restraints excluded: chain A residue 2835 ILE Chi-restraints excluded: chain A residue 2854 ASP Chi-restraints excluded: chain A residue 2865 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 89 optimal weight: 0.0970 chunk 15 optimal weight: 0.5980 chunk 126 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 HIS ** A2856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.146368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112406 restraints weight = 15945.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.109038 restraints weight = 26169.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.110128 restraints weight = 25892.505| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11009 Z= 0.120 Angle : 0.584 7.047 14989 Z= 0.304 Chirality : 0.047 0.206 1609 Planarity : 0.004 0.048 1985 Dihedral : 6.925 55.668 1881 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.84 % Allowed : 15.87 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.89 (0.23), residues: 1333 helix: -1.69 (0.99), residues: 18 sheet: -0.99 (0.29), residues: 284 loop : -0.43 (0.21), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 844 HIS 0.007 0.001 HIS A 908 PHE 0.011 0.001 PHE A1115 TYR 0.014 0.001 TYR A 798 ARG 0.005 0.000 ARG A 411 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 8) link_NAG-ASN : angle 1.36188 ( 24) link_BETA1-4 : bond 0.00449 ( 4) link_BETA1-4 : angle 1.90788 ( 12) hydrogen bonds : bond 0.03138 ( 219) hydrogen bonds : angle 6.53232 ( 492) SS BOND : bond 0.00204 ( 55) SS BOND : angle 0.79166 ( 110) covalent geometry : bond 0.00279 (10934) covalent geometry : angle 0.57772 (14843) Misc. bond : bond 0.00018 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 65 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6542 (tp30) REVERT: A 416 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8976 (tt) REVERT: A 443 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8059 (mmt) REVERT: A 527 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7478 (m-30) REVERT: A 846 ARG cc_start: 0.8067 (tpt90) cc_final: 0.7469 (tpt90) REVERT: A 905 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7890 (ttt180) REVERT: A 1018 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8295 (ttm170) REVERT: A 1300 MET cc_start: 0.7625 (mmm) cc_final: 0.7340 (mmm) REVERT: A 2854 ASP cc_start: 0.3421 (OUTLIER) cc_final: 0.2746 (p0) outliers start: 57 outliers final: 45 residues processed: 115 average time/residue: 0.2019 time to fit residues: 34.6368 Evaluate side-chains 111 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 59 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1018 ARG Chi-restraints excluded: chain A residue 1101 CYS Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1200 SER Chi-restraints excluded: chain A residue 1261 SER Chi-restraints excluded: chain A residue 2713 CYS Chi-restraints excluded: chain A residue 2716 GLN Chi-restraints excluded: chain A residue 2732 GLU Chi-restraints excluded: chain A residue 2777 LEU Chi-restraints excluded: chain A residue 2781 CYS Chi-restraints excluded: chain A residue 2789 CYS Chi-restraints excluded: chain A residue 2832 THR Chi-restraints excluded: chain A residue 2835 ILE Chi-restraints excluded: chain A residue 2854 ASP Chi-restraints excluded: chain A residue 2865 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 59 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 HIS ** A2856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.145814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.112776 restraints weight = 15875.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.109967 restraints weight = 26955.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.110916 restraints weight = 26838.074| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11009 Z= 0.139 Angle : 0.600 6.408 14989 Z= 0.313 Chirality : 0.047 0.219 1609 Planarity : 0.004 0.049 1985 Dihedral : 6.844 54.858 1879 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 4.67 % Allowed : 16.13 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.91 (0.23), residues: 1333 helix: -1.48 (1.08), residues: 18 sheet: -1.03 (0.29), residues: 284 loop : -0.44 (0.21), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 528 HIS 0.008 0.001 HIS A 908 PHE 0.012 0.001 PHE A 709 TYR 0.014 0.001 TYR A 798 ARG 0.004 0.000 ARG A 931 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 8) link_NAG-ASN : angle 1.31382 ( 24) link_BETA1-4 : bond 0.00457 ( 4) link_BETA1-4 : angle 1.90769 ( 12) hydrogen bonds : bond 0.03166 ( 219) hydrogen bonds : angle 6.54695 ( 492) SS BOND : bond 0.00211 ( 55) SS BOND : angle 0.80009 ( 110) covalent geometry : bond 0.00325 (10934) covalent geometry : angle 0.59419 (14843) Misc. bond : bond 0.00021 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3224.50 seconds wall clock time: 57 minutes 35.83 seconds (3455.83 seconds total)