Starting phenix.real_space_refine on Tue Jul 29 01:40:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxc_36696/07_2025/8jxc_36696.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxc_36696/07_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_36696/07_2025/8jxc_36696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxc_36696/07_2025/8jxc_36696.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxc_36696/07_2025/8jxc_36696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxc_36696/07_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-5711/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: 7.17, per 1000 atoms: 0.67 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: 3.14 Conformation dependent library (CDL) restraints added in 1.6 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: 2.03 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: 5.17 Time building geometry restraints manager: 3.74 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 31.970 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.990 ------------------------------------------------------------------------------- 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 : 1.204 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: 0.1872 time to fit residues: 27.7916 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 : 1.213 ------------------------------------------------------------------------------- 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 = 15993.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.107872 restraints weight = 29350.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.108816 restraints weight = 27309.267| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 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 1.81424 ( 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 : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6584 (tp30) REVERT: A 429 ASP cc_start: 0.8247 (t70) cc_final: 0.7951 (t70) REVERT: A 666 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7940 (t0) REVERT: A 851 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7879 (mmm) REVERT: A 905 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7910 (ttt180) REVERT: A 931 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7847 (tpt-90) REVERT: A 986 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8461 (p90) REVERT: A 1156 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7213 (ttt-90) REVERT: A 1300 MET cc_start: 0.7748 (mmm) cc_final: 0.7441 (mmm) outliers start: 56 outliers final: 33 residues processed: 116 average time/residue: 0.3471 time to fit residues: 62.3291 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 : 2.810 ------------------------------------------------------------------------------- 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: 2.9990 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.141564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.109282 restraints weight = 16294.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.106597 restraints weight = 29301.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.107616 restraints weight = 29521.883| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11009 Z= 0.217 Angle : 0.680 6.049 14989 Z= 0.356 Chirality : 0.050 0.204 1609 Planarity : 0.005 0.052 1985 Dihedral : 8.465 59.691 1891 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 5.26 % Allowed : 14.69 % Favored : 80.05 % 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: -2.51 (0.81), residues: 18 sheet: -0.90 (0.29), residues: 290 loop : -0.54 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 528 HIS 0.007 0.001 HIS A 985 PHE 0.018 0.002 PHE A 709 TYR 0.017 0.002 TYR A 798 ARG 0.006 0.001 ARG A 364 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 8) link_NAG-ASN : angle 1.96933 ( 24) link_BETA1-4 : bond 0.00561 ( 4) link_BETA1-4 : angle 2.23515 ( 12) hydrogen bonds : bond 0.04398 ( 219) hydrogen bonds : angle 7.22943 ( 492) SS BOND : bond 0.00312 ( 55) SS BOND : angle 0.94295 ( 110) covalent geometry : bond 0.00514 (10934) covalent geometry : angle 0.67083 (14843) Misc. bond : bond 0.00046 ( 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 123 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 61 time to evaluate : 2.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6762 (tp30) REVERT: A 429 ASP cc_start: 0.8443 (t70) cc_final: 0.8192 (t70) REVERT: A 666 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.8008 (t0) REVERT: A 851 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7930 (mmm) REVERT: A 905 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7897 (ttt180) REVERT: A 931 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7854 (tpt-90) REVERT: A 2739 PHE cc_start: 0.8489 (m-80) cc_final: 0.8224 (m-10) outliers start: 62 outliers final: 49 residues processed: 120 average time/residue: 0.5370 time to fit residues: 98.2298 Evaluate side-chains 112 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 58 time to evaluate : 3.569 ------------------------------------------------------------------------------- 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 377 ILE 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 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 666 ASN 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 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 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 1261 SER 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=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: 2.9990 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 0.1980 chunk 91 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 ** 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 = 0.3704 r_free = 0.3704 target = 0.139639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.107702 restraints weight = 16156.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.106124 restraints weight = 32037.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.106957 restraints weight = 28488.889| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11009 Z= 0.226 Angle : 0.676 6.366 14989 Z= 0.354 Chirality : 0.050 0.211 1609 Planarity : 0.005 0.051 1985 Dihedral : 8.281 59.611 1888 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 5.69 % Allowed : 14.52 % Favored : 79.80 % 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: -1.12 (0.23), residues: 1333 helix: -2.59 (0.82), residues: 12 sheet: -1.04 (0.29), residues: 289 loop : -0.64 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 528 HIS 0.006 0.001 HIS A 978 PHE 0.018 0.002 PHE A 709 TYR 0.018 0.002 TYR A 798 ARG 0.005 0.000 ARG A 539 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 8) link_NAG-ASN : angle 1.92536 ( 24) link_BETA1-4 : bond 0.00536 ( 4) link_BETA1-4 : angle 2.23424 ( 12) hydrogen bonds : bond 0.04116 ( 219) hydrogen bonds : angle 7.10526 ( 492) SS BOND : bond 0.00309 ( 55) SS BOND : angle 0.95656 ( 110) covalent geometry : bond 0.00539 (10934) covalent geometry : angle 0.66709 (14843) Misc. bond : bond 0.00042 ( 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: 67 poor density : 59 time to evaluate : 1.572 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: 0.7179 (OUTLIER) cc_final: 0.6756 (tp30) REVERT: A 429 ASP cc_start: 0.8415 (t70) cc_final: 0.8166 (t70) REVERT: A 851 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7744 (mmm) REVERT: A 905 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7961 (ttt180) REVERT: A 908 HIS cc_start: 0.7669 (OUTLIER) cc_final: 0.7235 (t70) REVERT: A 931 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7848 (tpt-90) outliers start: 67 outliers final: 55 residues processed: 120 average time/residue: 0.3378 time to fit residues: 63.6862 Evaluate side-chains 116 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 56 time to evaluate : 2.085 ------------------------------------------------------------------------------- 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 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 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 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 912 MET 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 1185 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 2731 ASP 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: 0.2980 chunk 117 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 103 optimal weight: 0.0000 chunk 72 optimal weight: 0.4980 chunk 81 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.142502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.110223 restraints weight = 15961.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.107638 restraints weight = 29067.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.108532 restraints weight = 28979.782| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11009 Z= 0.117 Angle : 0.599 6.258 14989 Z= 0.313 Chirality : 0.047 0.203 1609 Planarity : 0.004 0.050 1985 Dihedral : 7.635 59.701 1888 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 5.43 % Allowed : 14.94 % Favored : 79.63 % 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: -1.04 (0.23), residues: 1333 helix: -2.50 (0.80), residues: 18 sheet: -0.96 (0.29), residues: 287 loop : -0.57 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 844 HIS 0.007 0.001 HIS A 985 PHE 0.013 0.001 PHE A 986 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 0.00425 ( 8) link_NAG-ASN : angle 1.59553 ( 24) link_BETA1-4 : bond 0.00509 ( 4) link_BETA1-4 : angle 2.20320 ( 12) hydrogen bonds : bond 0.03492 ( 219) hydrogen bonds : angle 6.87219 ( 492) SS BOND : bond 0.00227 ( 55) SS BOND : angle 0.83060 ( 110) covalent geometry : bond 0.00263 (10934) covalent geometry : angle 0.59086 (14843) Misc. bond : bond 0.00018 ( 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 134 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 70 time to evaluate : 1.214 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: A 373 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6667 (tp30) REVERT: A 429 ASP cc_start: 0.8266 (t70) cc_final: 0.7936 (t70) REVERT: A 443 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.7974 (mmt) REVERT: A 851 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7658 (mmm) REVERT: A 905 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7746 (ttt180) REVERT: A 931 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7898 (tpt-90) REVERT: A 1300 MET cc_start: 0.7735 (mmm) cc_final: 0.7469 (mmm) outliers start: 64 outliers final: 43 residues processed: 126 average time/residue: 0.2000 time to fit residues: 38.7606 Evaluate side-chains 108 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 60 time to evaluate : 1.340 ------------------------------------------------------------------------------- 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 371 LEU 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 552 THR 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 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 990 VAL Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1032 CYS 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 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 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: 0.9980 chunk 5 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 63 optimal weight: 0.2980 chunk 90 optimal weight: 4.9990 chunk 76 optimal weight: 0.4980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.142772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.109860 restraints weight = 16227.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.107835 restraints weight = 30631.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.108897 restraints weight = 28388.952| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11009 Z= 0.192 Angle : 0.646 6.071 14989 Z= 0.338 Chirality : 0.049 0.218 1609 Planarity : 0.004 0.049 1985 Dihedral : 7.662 58.375 1883 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 6.11 % Allowed : 14.43 % 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: -1.12 (0.23), residues: 1333 helix: -2.62 (0.77), residues: 18 sheet: -1.15 (0.28), residues: 296 loop : -0.57 (0.20), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 528 HIS 0.013 0.001 HIS A 985 PHE 0.016 0.002 PHE A 709 TYR 0.017 0.002 TYR A 798 ARG 0.005 0.000 ARG A 539 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 8) link_NAG-ASN : angle 1.64523 ( 24) link_BETA1-4 : bond 0.00553 ( 4) link_BETA1-4 : angle 2.15367 ( 12) hydrogen bonds : bond 0.03651 ( 219) hydrogen bonds : angle 6.87724 ( 492) SS BOND : bond 0.00262 ( 55) SS BOND : angle 0.99835 ( 110) covalent geometry : bond 0.00459 (10934) covalent geometry : angle 0.63666 (14843) Misc. bond : bond 0.00037 ( 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 138 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 66 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6752 (tp30) REVERT: A 416 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8980 (tt) REVERT: A 429 ASP cc_start: 0.8263 (t70) cc_final: 0.7963 (t70) REVERT: A 443 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8125 (mmt) REVERT: A 851 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7959 (mmm) REVERT: A 905 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7979 (ttt180) REVERT: A 931 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7876 (tpt-90) outliers start: 72 outliers final: 52 residues processed: 129 average time/residue: 0.1855 time to fit residues: 37.4208 Evaluate side-chains 121 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 63 time to evaluate : 1.304 ------------------------------------------------------------------------------- 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 371 LEU Chi-restraints excluded: chain A residue 373 GLU 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 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 552 THR Chi-restraints excluded: chain A residue 555 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 931 ARG Chi-restraints excluded: chain A residue 973 CYS 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 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: 0.0970 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 116 optimal weight: 0.3980 chunk 101 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.145124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.111758 restraints weight = 16189.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.109319 restraints weight = 25703.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.110096 restraints weight = 28644.053| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1685 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= 0.127 Angle : 0.602 6.186 14989 Z= 0.315 Chirality : 0.047 0.212 1609 Planarity : 0.004 0.049 1985 Dihedral : 7.324 57.525 1881 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % 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: -1.04 (0.23), residues: 1333 helix: -2.46 (0.82), residues: 18 sheet: -1.02 (0.29), residues: 283 loop : -0.55 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 844 HIS 0.006 0.001 HIS A 908 PHE 0.013 0.001 PHE A 986 TYR 0.015 0.001 TYR A 798 ARG 0.003 0.000 ARG A 539 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 8) link_NAG-ASN : angle 1.47430 ( 24) link_BETA1-4 : bond 0.00538 ( 4) link_BETA1-4 : angle 2.05888 ( 12) hydrogen bonds : bond 0.03324 ( 219) hydrogen bonds : angle 6.72353 ( 492) SS BOND : bond 0.00204 ( 55) SS BOND : angle 0.86241 ( 110) covalent geometry : bond 0.00295 (10934) covalent geometry : angle 0.59448 (14843) Misc. bond : bond 0.00019 ( 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 128 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 68 time to evaluate : 1.284 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: 0.7092 (OUTLIER) cc_final: 0.6715 (tp30) REVERT: A 429 ASP cc_start: 0.8238 (t70) cc_final: 0.7922 (t70) REVERT: A 443 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8070 (mmt) REVERT: A 726 SER cc_start: 0.6353 (t) cc_final: 0.6091 (p) REVERT: A 851 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7702 (mmm) REVERT: A 905 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7859 (ttt180) REVERT: A 931 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7888 (tpt-90) REVERT: A 1300 MET cc_start: 0.7719 (mmm) cc_final: 0.7306 (mmm) outliers start: 60 outliers final: 46 residues processed: 119 average time/residue: 0.1936 time to fit residues: 35.7322 Evaluate side-chains 115 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 64 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 371 LEU 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 552 THR Chi-restraints excluded: chain A residue 555 VAL 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 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 931 ARG Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1028 LEU 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 2713 CYS Chi-restraints excluded: chain A residue 2716 GLN 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 2865 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 44 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 42 optimal weight: 0.1980 chunk 33 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 91 optimal weight: 9.9990 chunk 96 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 767 GLN A 908 HIS A1154 GLN ** A2856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.145324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.112576 restraints weight = 16044.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.109646 restraints weight = 28459.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.111008 restraints weight = 26327.082| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1800 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 : 0.582 6.008 14989 Z= 0.305 Chirality : 0.047 0.205 1609 Planarity : 0.004 0.048 1985 Dihedral : 7.081 59.317 1881 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 5.18 % Allowed : 15.45 % 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: -0.97 (0.23), residues: 1333 helix: -2.13 (0.89), residues: 18 sheet: -0.99 (0.29), residues: 284 loop : -0.51 (0.21), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 844 HIS 0.007 0.001 HIS A 908 PHE 0.012 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 0.00372 ( 8) link_NAG-ASN : angle 1.37547 ( 24) link_BETA1-4 : bond 0.00430 ( 4) link_BETA1-4 : angle 1.95051 ( 12) hydrogen bonds : bond 0.03181 ( 219) hydrogen bonds : angle 6.57932 ( 492) SS BOND : bond 0.00225 ( 55) SS BOND : angle 0.80634 ( 110) covalent geometry : bond 0.00276 (10934) covalent geometry : angle 0.57539 (14843) Misc. bond : bond 0.00020 ( 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 129 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 68 time to evaluate : 1.437 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: 0.6966 (OUTLIER) cc_final: 0.6561 (tp30) REVERT: A 416 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8967 (tt) REVERT: A 443 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8063 (mmt) REVERT: A 726 SER cc_start: 0.6001 (t) cc_final: 0.5794 (p) REVERT: A 851 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7657 (mmm) REVERT: A 905 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7894 (ttt180) REVERT: A 931 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7758 (tpt-90) REVERT: A 1312 HIS cc_start: 0.0459 (OUTLIER) cc_final: -0.0371 (p90) outliers start: 61 outliers final: 46 residues processed: 119 average time/residue: 0.2009 time to fit residues: 37.1599 Evaluate side-chains 115 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 62 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 371 LEU 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 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 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 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 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 1113 THR Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1312 HIS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 27 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 GLN A 908 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 = 0.3765 r_free = 0.3765 target = 0.144779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.111132 restraints weight = 16124.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.108166 restraints weight = 29466.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.109664 restraints weight = 25992.062| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11009 Z= 0.159 Angle : 0.613 6.659 14989 Z= 0.320 Chirality : 0.048 0.209 1609 Planarity : 0.004 0.048 1985 Dihedral : 7.204 58.050 1880 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 5.60 % Allowed : 15.37 % 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: -1.03 (0.23), residues: 1333 helix: -1.97 (0.96), residues: 18 sheet: -1.07 (0.29), residues: 284 loop : -0.54 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 528 HIS 0.007 0.001 HIS A 908 PHE 0.014 0.001 PHE A1115 TYR 0.016 0.001 TYR A 798 ARG 0.004 0.000 ARG A 539 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 8) link_NAG-ASN : angle 1.42960 ( 24) link_BETA1-4 : bond 0.00475 ( 4) link_BETA1-4 : angle 1.94575 ( 12) hydrogen bonds : bond 0.03314 ( 219) hydrogen bonds : angle 6.64648 ( 492) SS BOND : bond 0.00219 ( 55) SS BOND : angle 0.85940 ( 110) covalent geometry : bond 0.00377 (10934) covalent geometry : angle 0.60625 (14843) Misc. bond : bond 0.00026 ( 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 129 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 63 time to evaluate : 1.297 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: A 373 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6593 (tp30) REVERT: A 416 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8966 (tt) REVERT: A 429 ASP cc_start: 0.8447 (t70) cc_final: 0.8147 (t70) REVERT: A 443 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8155 (mmt) REVERT: A 726 SER cc_start: 0.6008 (t) cc_final: 0.5799 (p) REVERT: A 851 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7913 (mmm) REVERT: A 905 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7894 (ttt180) REVERT: A 931 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7736 (tpt-90) REVERT: A 1300 MET cc_start: 0.7715 (mmm) cc_final: 0.7259 (mmm) REVERT: A 1312 HIS cc_start: 0.0614 (OUTLIER) cc_final: -0.0109 (p90) outliers start: 66 outliers final: 54 residues processed: 118 average time/residue: 0.1924 time to fit residues: 35.2728 Evaluate side-chains 122 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 61 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 371 LEU 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 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 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 931 ARG Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1028 LEU 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 1163 ILE Chi-restraints excluded: chain A residue 1200 SER Chi-restraints excluded: chain A residue 1261 SER Chi-restraints excluded: chain A residue 1312 HIS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 39 optimal weight: 0.4980 chunk 6 optimal weight: 7.9990 chunk 65 optimal weight: 0.0870 chunk 89 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 4 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 125 optimal weight: 8.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN A 767 GLN A 908 HIS A1283 ASN ** A2856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.145264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.112076 restraints weight = 16081.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.109247 restraints weight = 26336.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.110503 restraints weight = 25587.386| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11009 Z= 0.116 Angle : 0.580 6.747 14989 Z= 0.303 Chirality : 0.046 0.201 1609 Planarity : 0.004 0.048 1985 Dihedral : 6.919 54.985 1880 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.75 % Allowed : 16.21 % 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: -0.95 (0.23), residues: 1333 helix: -1.55 (1.07), residues: 18 sheet: -1.00 (0.29), residues: 284 loop : -0.49 (0.21), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 844 HIS 0.007 0.001 HIS A 908 PHE 0.012 0.001 PHE A1115 TYR 0.014 0.001 TYR A 798 ARG 0.003 0.000 ARG A 411 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 8) link_NAG-ASN : angle 1.25315 ( 24) link_BETA1-4 : bond 0.00466 ( 4) link_BETA1-4 : angle 1.91959 ( 12) hydrogen bonds : bond 0.03068 ( 219) hydrogen bonds : angle 6.51558 ( 492) SS BOND : bond 0.00186 ( 55) SS BOND : angle 0.79473 ( 110) covalent geometry : bond 0.00266 (10934) covalent geometry : angle 0.57365 (14843) Misc. bond : bond 0.00019 ( 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 126 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 70 time to evaluate : 1.211 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: 0.6948 (OUTLIER) cc_final: 0.6546 (tp30) REVERT: A 416 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8961 (tt) REVERT: A 443 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.7998 (mmt) REVERT: A 846 ARG cc_start: 0.8047 (tpt90) cc_final: 0.7466 (tpt90) REVERT: A 851 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7665 (mmm) REVERT: A 905 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7960 (ttt180) REVERT: A 1300 MET cc_start: 0.7674 (mmm) cc_final: 0.7331 (mmm) REVERT: A 1312 HIS cc_start: 0.0622 (OUTLIER) cc_final: -0.0180 (p90) outliers start: 56 outliers final: 45 residues processed: 115 average time/residue: 0.2638 time to fit residues: 46.0683 Evaluate side-chains 115 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 64 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 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 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 532 SER Chi-restraints excluded: chain A residue 555 VAL 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 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 973 CYS Chi-restraints excluded: chain A residue 1028 LEU 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 1163 ILE Chi-restraints excluded: chain A residue 1261 SER Chi-restraints excluded: chain A residue 1312 HIS 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 2755 VAL 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: 0.9980 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 HIS ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 GLN A 908 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 = 0.3760 r_free = 0.3760 target = 0.144420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.111721 restraints weight = 15992.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.109649 restraints weight = 28384.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.110787 restraints weight = 28214.756| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11009 Z= 0.183 Angle : 0.633 6.636 14989 Z= 0.331 Chirality : 0.048 0.209 1609 Planarity : 0.004 0.051 1985 Dihedral : 7.120 57.767 1877 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 4.92 % Allowed : 16.04 % 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: -1.03 (0.23), residues: 1333 helix: -1.53 (1.07), residues: 18 sheet: -1.13 (0.29), residues: 286 loop : -0.52 (0.21), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 528 HIS 0.006 0.001 HIS A 978 PHE 0.015 0.002 PHE A1062 TYR 0.017 0.002 TYR A 798 ARG 0.004 0.000 ARG A 931 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 8) link_NAG-ASN : angle 1.40369 ( 24) link_BETA1-4 : bond 0.00511 ( 4) link_BETA1-4 : angle 1.90590 ( 12) hydrogen bonds : bond 0.03361 ( 219) hydrogen bonds : angle 6.62339 ( 492) SS BOND : bond 0.00238 ( 55) SS BOND : angle 0.92197 ( 110) covalent geometry : bond 0.00433 (10934) covalent geometry : angle 0.62611 (14843) Misc. bond : bond 0.00034 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3988.40 seconds wall clock time: 74 minutes 16.60 seconds (4456.60 seconds total)