Starting phenix.real_space_refine on Tue Jul 29 08:03:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxb_36695/07_2025/8jxb_36695.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxb_36695/07_2025/8jxb_36695.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/8jxb_36695/07_2025/8jxb_36695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxb_36695/07_2025/8jxb_36695.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxb_36695/07_2025/8jxb_36695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxb_36695/07_2025/8jxb_36695.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 18 9.91 5 S 139 5.16 5 C 6657 2.51 5 N 1917 2.21 5 O 2240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10971 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1851 Classifications: {'peptide': 244} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 231} Chain: "B" Number of atoms: 8767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 8767 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 54, 'TRANS': 1074} Chain: "Q" 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: "R" 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 48 Unusual residues: {' CA': 6, 'A2G': 1, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 152 Unusual residues: {' CA': 12, 'A2G': 7, 'NAG': 3} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 7.00, per 1000 atoms: 0.64 Number of scatterers: 10971 At special positions: 0 Unit cell: (143.922, 122.757, 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 18 19.99 S 139 16.00 O 2240 8.00 N 1917 7.00 C 6657 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 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=2.04 Simple disulfide: pdb=" SG CYS A2843 " - pdb=" SG CYS A2860 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A2908 " - pdb=" SG CYS A2920 " distance=2.03 Simple disulfide: pdb=" SG CYS A2915 " - pdb=" SG CYS A2933 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 208 " distance=2.04 Simple disulfide: pdb=" SG CYS B 202 " - pdb=" SG CYS B 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 222 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 229 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS B 272 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 285 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 311 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 316 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 351 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 357 " - pdb=" SG CYS B 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 372 " - pdb=" SG CYS B 384 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 673 " distance=2.03 Simple disulfide: pdb=" SG CYS B 669 " - pdb=" SG CYS B 688 " distance=2.03 Simple disulfide: pdb=" SG CYS B 690 " - pdb=" SG CYS B 703 " distance=2.03 Simple disulfide: pdb=" SG CYS B 973 " - pdb=" SG CYS B 987 " distance=2.03 Simple disulfide: pdb=" SG CYS B 983 " - pdb=" SG CYS B 997 " distance=2.03 Simple disulfide: pdb=" SG CYS B 999 " - pdb=" SG CYS B1012 " distance=2.03 Simple disulfide: pdb=" SG CYS B1025 " - pdb=" SG CYS B1037 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1050 " distance=2.03 Simple disulfide: pdb=" SG CYS B1044 " - pdb=" SG CYS B1059 " distance=2.03 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1079 " distance=2.03 Simple disulfide: pdb=" SG CYS B1073 " - pdb=" SG CYS B1092 " distance=2.03 Simple disulfide: pdb=" SG CYS B1086 " - pdb=" SG CYS B1101 " distance=2.03 Simple disulfide: pdb=" SG CYS B1110 " - pdb=" SG CYS B1122 " distance=2.03 Simple disulfide: pdb=" SG CYS B1117 " - pdb=" SG CYS B1135 " distance=2.03 Simple disulfide: pdb=" SG CYS B1129 " - pdb=" SG CYS B1144 " distance=2.03 Simple disulfide: pdb=" SG CYS B1157 " - pdb=" SG CYS B1175 " distance=2.03 Simple disulfide: pdb=" SG CYS B1169 " - pdb=" SG CYS B1184 " distance=2.03 Simple disulfide: pdb=" SG CYS B1188 " - pdb=" SG CYS B1201 " distance=2.04 Simple disulfide: pdb=" SG CYS B1195 " - pdb=" SG CYS B1214 " distance=2.03 Simple disulfide: pdb=" SG CYS B1208 " - pdb=" SG CYS B1223 " distance=2.03 Simple disulfide: pdb=" SG CYS B1231 " - pdb=" SG CYS B1244 " distance=2.03 Simple disulfide: pdb=" SG CYS B1238 " - pdb=" SG CYS B1257 " distance=2.03 Simple disulfide: pdb=" SG CYS B1251 " - pdb=" SG CYS B1267 " distance=2.03 Simple disulfide: pdb=" SG CYS B1272 " - pdb=" SG CYS B1284 " distance=2.03 Simple disulfide: pdb=" SG CYS B1279 " - pdb=" SG CYS B1297 " distance=2.03 Simple disulfide: pdb=" SG CYS B1291 " - pdb=" SG CYS B1306 " 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=7, 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 A2782 " " NAG A4702 " - " ASN A2810 " " NAG B4701 " - " ASN B 340 " " NAG B4702 " - " ASN B 462 " " NAG B4703 " - " ASN B1187 " " NAG C 1 " - " ASN B 657 " Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 1.5 seconds 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2536 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 37 sheets defined 10.3% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... 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 2732 Processing helix chain 'A' and resid 2733 through 2738 Processing helix chain 'A' and resid 2756 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 helix chain 'A' and resid 2856 through 2861 removed outlier: 4.083A pdb=" N CYS A2860 " --> pdb=" O ASN A2856 " (cutoff:3.500A) Processing helix chain 'A' and resid 2922 through 2926 removed outlier: 3.751A pdb=" N VAL A2926 " --> pdb=" O GLY A2923 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 201 removed outlier: 3.630A pdb=" N TYR B 200 " --> pdb=" O LEU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'B' and resid 247 through 251 removed outlier: 3.979A pdb=" N GLY B 251 " --> pdb=" O GLN B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 284 No H-bonds generated for 'chain 'B' and resid 282 through 284' Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 388 through 391 removed outlier: 3.927A pdb=" N SER B 391 " --> pdb=" O ASP B 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 388 through 391' Processing helix chain 'B' and resid 660 through 669 removed outlier: 4.524A pdb=" N SER B 664 " --> pdb=" O PRO B 661 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASN B 665 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASN B 666 " --> pdb=" O GLY B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 751 No H-bonds generated for 'chain 'B' and resid 749 through 751' Processing helix chain 'B' and resid 979 through 983 removed outlier: 3.817A pdb=" N CYS B 983 " --> pdb=" O ASN B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1043 Processing helix chain 'B' and resid 1053 through 1057 Processing helix chain 'B' and resid 1083 through 1085 No H-bonds generated for 'chain 'B' and resid 1083 through 1085' Processing helix chain 'B' and resid 1095 through 1099 removed outlier: 3.557A pdb=" N GLU B1098 " --> pdb=" O GLY B1095 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN B1099 " --> pdb=" O SER B1096 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1095 through 1099' Processing helix chain 'B' and resid 1126 through 1128 No H-bonds generated for 'chain 'B' and resid 1126 through 1128' Processing helix chain 'B' and resid 1164 through 1168 removed outlier: 3.826A pdb=" N VAL B1168 " --> pdb=" O PRO B1165 " (cutoff:3.500A) Processing helix chain 'B' and resid 1205 through 1207 No H-bonds generated for 'chain 'B' and resid 1205 through 1207' Processing helix chain 'B' and resid 1217 through 1221 removed outlier: 3.591A pdb=" N ALA B1221 " --> pdb=" O SER B1218 " (cutoff:3.500A) Processing helix chain 'B' and resid 1248 through 1250 No H-bonds generated for 'chain 'B' and resid 1248 through 1250' Processing helix chain 'B' and resid 1260 through 1264 Processing helix chain 'B' and resid 1288 through 1290 No H-bonds generated for 'chain 'B' and resid 1288 through 1290' Processing helix chain 'B' and resid 1300 through 1305 Processing sheet with id=AA1, first strand: chain 'A' and resid 2705 through 2707 Processing sheet with id=AA2, first strand: chain 'A' and resid 2747 through 2748 removed outlier: 3.694A pdb=" N VAL A2755 " --> pdb=" O PHE A2747 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2786 through 2788 removed outlier: 3.608A pdb=" N ILE A2795 " --> pdb=" O PHE A2787 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 2828 through 2829 Processing sheet with id=AA5, first strand: chain 'A' and resid 2869 through 2871 Processing sheet with id=AA6, first strand: chain 'A' and resid 2913 through 2914 removed outlier: 3.779A pdb=" N ILE A2921 " --> pdb=" O PHE A2913 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 188 through 189 Processing sheet with id=AA8, first strand: chain 'B' and resid 226 through 228 Processing sheet with id=AA9, first strand: chain 'B' and resid 269 through 271 Processing sheet with id=AB1, first strand: chain 'B' and resid 319 through 323 Processing sheet with id=AB2, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AB3, first strand: chain 'B' and resid 361 through 362 Processing sheet with id=AB4, first strand: chain 'B' and resid 376 through 379 Processing sheet with id=AB5, first strand: chain 'B' and resid 394 through 397 Processing sheet with id=AB6, first strand: chain 'B' and resid 402 through 406 removed outlier: 7.118A pdb=" N LEU B 403 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 428 through 431 removed outlier: 3.531A pdb=" N TRP B 439 " --> pdb=" O PHE B 448 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 468 through 474 removed outlier: 4.316A pdb=" N ASN B 470 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE B 490 " --> pdb=" O LEU B 503 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 511 through 517 removed outlier: 6.596A pdb=" N SER B 526 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE B 514 " --> pdb=" O PHE B 524 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE B 524 " --> pdb=" O ILE B 514 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU B 516 " --> pdb=" O TYR B 522 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TYR B 522 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 537 " --> pdb=" O LEU B 550 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE B 541 " --> pdb=" O ASN B 546 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASN B 546 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 558 through 564 removed outlier: 4.302A pdb=" N GLY B 560 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR B 579 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE B 580 " --> pdb=" O VAL B 593 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 606 through 609 removed outlier: 6.407A pdb=" N LYS B 625 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N VAL B 636 " --> pdb=" O LYS B 625 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 672 through 675 removed outlier: 3.875A pdb=" N VAL B 672 " --> pdb=" O LYS B 689 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 694 through 696 Processing sheet with id=AC5, first strand: chain 'B' and resid 718 through 721 Processing sheet with id=AC6, first strand: chain 'B' and resid 742 through 748 removed outlier: 4.151A pdb=" N GLY B 744 " --> pdb=" O SER B 757 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 763 " --> pdb=" O ASP B 758 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE B 764 " --> pdb=" O ILE B 777 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 785 through 791 removed outlier: 4.188A pdb=" N CYS B 787 " --> pdb=" O THR B 800 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 800 " --> pdb=" O CYS B 787 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 821 " --> pdb=" O VAL B 807 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL B 809 " --> pdb=" O GLN B 819 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLN B 819 " --> pdb=" O VAL B 809 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ARG B 811 " --> pdb=" O ARG B 817 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ARG B 817 " --> pdb=" O ARG B 811 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 827 through 833 removed outlier: 4.966A pdb=" N SER B 829 " --> pdb=" O SER B 842 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 842 " --> pdb=" O SER B 829 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR B 838 " --> pdb=" O HIS B 833 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE B 850 " --> pdb=" O ILE B 863 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 874 through 876 Processing sheet with id=AD1, first strand: chain 'B' and resid 915 through 921 removed outlier: 3.710A pdb=" N GLY B 917 " --> pdb=" O THR B 928 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 934 " --> pdb=" O ASP B 929 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 935 " --> pdb=" O ILE B 949 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 986 through 990 Processing sheet with id=AD3, first strand: chain 'B' and resid 1003 through 1005 Processing sheet with id=AD4, first strand: chain 'B' and resid 1030 through 1031 Processing sheet with id=AD5, first strand: chain 'B' and resid 1070 through 1072 Processing sheet with id=AD6, first strand: chain 'B' and resid 1114 through 1116 Processing sheet with id=AD7, first strand: chain 'B' and resid 1155 through 1156 Processing sheet with id=AD8, first strand: chain 'B' and resid 1192 through 1194 Processing sheet with id=AD9, first strand: chain 'B' and resid 1235 through 1237 Processing sheet with id=AE1, first strand: chain 'B' and resid 1276 through 1277 220 hydrogen bonds defined for protein. 486 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: 5.20 Time building geometry restraints manager: 3.62 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: 3780 1.34 - 1.46: 2538 1.46 - 1.58: 4728 1.58 - 1.70: 0 1.70 - 1.83: 158 Bond restraints: 11204 Sorted by residual: bond pdb=" N LEU B 966 " pdb=" CA LEU B 966 " ideal model delta sigma weight residual 1.458 1.487 -0.028 1.23e-02 6.61e+03 5.29e+00 bond pdb=" N ASP B 963 " pdb=" CA ASP B 963 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.20e-02 6.94e+03 4.81e+00 bond pdb=" N ASP B 965 " pdb=" CA ASP B 965 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.27e-02 6.20e+03 4.47e+00 bond pdb=" N LYS B 707 " pdb=" CA LYS B 707 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.28e-02 6.10e+03 4.22e+00 bond pdb=" N THR B 968 " pdb=" CA THR B 968 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.23e-02 6.61e+03 4.20e+00 ... (remaining 11199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 14847 2.24 - 4.47: 338 4.47 - 6.71: 21 6.71 - 8.95: 0 8.95 - 11.18: 2 Bond angle restraints: 15208 Sorted by residual: angle pdb=" C SER B 954 " pdb=" CA SER B 954 " pdb=" CB SER B 954 " ideal model delta sigma weight residual 115.89 110.28 5.61 1.32e+00 5.74e-01 1.81e+01 angle pdb=" C VAL B 990 " pdb=" CA VAL B 990 " pdb=" CB VAL B 990 " ideal model delta sigma weight residual 109.33 113.11 -3.78 9.80e-01 1.04e+00 1.49e+01 angle pdb=" CB MET A2936 " pdb=" CG MET A2936 " pdb=" SD MET A2936 " ideal model delta sigma weight residual 112.70 123.88 -11.18 3.00e+00 1.11e-01 1.39e+01 angle pdb=" C ARG B 367 " pdb=" CA ARG B 367 " pdb=" CB ARG B 367 " ideal model delta sigma weight residual 116.34 111.53 4.81 1.40e+00 5.10e-01 1.18e+01 angle pdb=" CA ASP B 254 " pdb=" C ASP B 254 " pdb=" O ASP B 254 " ideal model delta sigma weight residual 122.27 118.34 3.93 1.16e+00 7.43e-01 1.15e+01 ... (remaining 15203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 6445 21.78 - 43.55: 504 43.55 - 65.33: 92 65.33 - 87.10: 17 87.10 - 108.88: 7 Dihedral angle restraints: 7065 sinusoidal: 3115 harmonic: 3950 Sorted by residual: dihedral pdb=" CB CYS B 351 " pdb=" SG CYS B 351 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -161.29 75.29 1 1.00e+01 1.00e-02 7.16e+01 dihedral pdb=" CB CYS B 973 " pdb=" SG CYS B 973 " pdb=" SG CYS B 987 " pdb=" CB CYS B 987 " ideal model delta sinusoidal sigma weight residual 93.00 161.91 -68.91 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CB CYS B1129 " pdb=" SG CYS B1129 " pdb=" SG CYS B1144 " pdb=" CB CYS B1144 " ideal model delta sinusoidal sigma weight residual 93.00 156.11 -63.11 1 1.00e+01 1.00e-02 5.26e+01 ... (remaining 7062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 964 0.036 - 0.073: 467 0.073 - 0.109: 165 0.109 - 0.146: 41 0.146 - 0.182: 5 Chirality restraints: 1642 Sorted by residual: 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 -2.46 0.18 2.00e-01 2.50e+01 8.29e-01 chirality pdb=" C1 NAG A4702 " pdb=" ND2 ASN A2810 " pdb=" C2 NAG A4702 " pdb=" O5 NAG A4702 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CA LEU B 966 " pdb=" N LEU B 966 " pdb=" C LEU B 966 " pdb=" CB LEU B 966 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.36e-01 ... (remaining 1639 not shown) Planarity restraints: 2045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B4702 " -0.254 2.00e-02 2.50e+03 2.14e-01 5.73e+02 pdb=" C7 NAG B4702 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG B4702 " -0.171 2.00e-02 2.50e+03 pdb=" N2 NAG B4702 " 0.362 2.00e-02 2.50e+03 pdb=" O7 NAG B4702 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B4703 " -0.237 2.00e-02 2.50e+03 1.99e-01 4.96e+02 pdb=" C7 NAG B4703 " 0.062 2.00e-02 2.50e+03 pdb=" C8 NAG B4703 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG B4703 " 0.334 2.00e-02 2.50e+03 pdb=" O7 NAG B4703 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.127 2.00e-02 2.50e+03 1.04e-01 1.36e+02 pdb=" C7 NAG E 2 " 0.036 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.095 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.166 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.020 2.00e-02 2.50e+03 ... (remaining 2042 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 394 2.68 - 3.24: 11450 3.24 - 3.79: 16837 3.79 - 4.35: 23163 4.35 - 4.90: 37522 Nonbonded interactions: 89366 Sorted by model distance: nonbonded pdb=" OD2 ASP B1219 " pdb="CA CA B4720 " model vdw 2.126 2.510 nonbonded pdb=" O THR B 976 " pdb=" OG1 THR B 977 " model vdw 2.128 3.040 nonbonded pdb=" NE2 HIS B 914 " pdb=" OD1 ASN R 2 " model vdw 2.169 3.120 nonbonded pdb=" OD2 ASP B1049 " pdb="CA CA B4716 " model vdw 2.183 2.510 nonbonded pdb=" OE2 GLU B1056 " pdb="CA CA B4716 " model vdw 2.191 2.510 ... (remaining 89361 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: 2.320 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.310 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 : 0.005 0.065 11278 Z= 0.253 Angle : 0.777 11.185 15352 Z= 0.431 Chirality : 0.048 0.182 1642 Planarity : 0.009 0.214 2039 Dihedral : 15.623 108.876 4358 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.04 % Favored : 91.89 % Rotamer: Outliers : 2.98 % Allowed : 15.30 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -1.23 (0.23), residues: 1369 helix: -3.94 (1.00), residues: 12 sheet: -1.03 (0.30), residues: 278 loop : -0.74 (0.20), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B1289 HIS 0.004 0.001 HIS B 204 PHE 0.018 0.001 PHE B 993 TYR 0.021 0.002 TYR B 637 ARG 0.003 0.000 ARG B 539 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 6) link_NAG-ASN : angle 2.33831 ( 18) link_BETA1-4 : bond 0.00401 ( 4) link_BETA1-4 : angle 1.87000 ( 12) hydrogen bonds : bond 0.24536 ( 220) hydrogen bonds : angle 9.37609 ( 486) SS BOND : bond 0.00279 ( 57) SS BOND : angle 1.07613 ( 114) covalent geometry : bond 0.00495 (11204) covalent geometry : angle 0.76938 (15208) Misc. bond : bond 0.03474 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 54 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2829 LYS cc_start: 0.3885 (OUTLIER) cc_final: 0.3619 (ptmt) REVERT: B 254 ASP cc_start: 0.8562 (t0) cc_final: 0.7917 (t0) REVERT: B 308 MET cc_start: 0.5684 (tpp) cc_final: 0.1767 (mtp) REVERT: B 861 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8380 (ptp) outliers start: 36 outliers final: 31 residues processed: 88 average time/residue: 0.2108 time to fit residues: 28.3661 Evaluate side-chains 84 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 51 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2704 LEU Chi-restraints excluded: chain A residue 2710 ASN Chi-restraints excluded: chain A residue 2767 CYS Chi-restraints excluded: chain A residue 2772 ASP Chi-restraints excluded: chain A residue 2779 ARG Chi-restraints excluded: chain A residue 2809 ASP Chi-restraints excluded: chain A residue 2829 LYS Chi-restraints excluded: chain A residue 2882 TYR Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 665 ASN Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 800 THR Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 861 MET Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 899 ASP Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1129 CYS Chi-restraints excluded: chain B residue 1168 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 0.2980 chunk 35 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2705 GLN A2847 ASN B 409 HIS B 681 ASN ** B 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1033 ASN B1057 HIS B1100 ASN B1104 HIS B1259 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.138772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.110853 restraints weight = 17845.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.109380 restraints weight = 40786.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.110278 restraints weight = 30355.205| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11278 Z= 0.226 Angle : 0.692 7.439 15352 Z= 0.360 Chirality : 0.048 0.177 1642 Planarity : 0.005 0.042 2039 Dihedral : 9.570 74.742 1957 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.40 % Favored : 91.53 % Rotamer: Outliers : 5.05 % Allowed : 15.38 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -1.30 (0.23), residues: 1369 helix: None (None), residues: 0 sheet: -1.15 (0.29), residues: 288 loop : -0.81 (0.20), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B1289 HIS 0.005 0.001 HIS B 895 PHE 0.013 0.002 PHE B 525 TYR 0.016 0.002 TYR B 571 ARG 0.005 0.001 ARG B 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 6) link_NAG-ASN : angle 3.18124 ( 18) link_BETA1-4 : bond 0.00469 ( 4) link_BETA1-4 : angle 2.54342 ( 12) hydrogen bonds : bond 0.04558 ( 220) hydrogen bonds : angle 6.91575 ( 486) SS BOND : bond 0.00359 ( 57) SS BOND : angle 1.12022 ( 114) covalent geometry : bond 0.00528 (11204) covalent geometry : angle 0.67552 (15208) Misc. bond : bond 0.00078 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 56 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 254 ASP cc_start: 0.8007 (t0) cc_final: 0.7791 (t0) REVERT: B 264 ARG cc_start: 0.4872 (OUTLIER) cc_final: 0.4633 (ptt-90) REVERT: B 317 GLU cc_start: 0.4398 (OUTLIER) cc_final: 0.3133 (mp0) REVERT: B 523 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8850 (tp) REVERT: B 728 GLN cc_start: 0.6143 (OUTLIER) cc_final: 0.5812 (mt0) outliers start: 61 outliers final: 41 residues processed: 113 average time/residue: 0.2569 time to fit residues: 44.2720 Evaluate side-chains 98 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 53 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2710 ASN Chi-restraints excluded: chain A residue 2767 CYS Chi-restraints excluded: chain A residue 2779 ARG Chi-restraints excluded: chain A residue 2786 GLU Chi-restraints excluded: chain A residue 2794 CYS Chi-restraints excluded: chain A residue 2809 ASP Chi-restraints excluded: chain A residue 2831 GLN Chi-restraints excluded: chain A residue 2882 TYR Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 411 ARG Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 621 MET Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 728 GLN Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 794 SER Chi-restraints excluded: chain B residue 800 THR Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 899 ASP Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 968 THR Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1291 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 21 optimal weight: 0.2980 chunk 52 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 132 optimal weight: 8.9990 chunk 85 optimal weight: 0.0020 chunk 80 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 796 ASN B 895 HIS ** B 971 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 = 0.3862 r_free = 0.3862 target = 0.140706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.100720 restraints weight = 18100.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.100177 restraints weight = 20361.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098323 restraints weight = 13675.551| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11278 Z= 0.121 Angle : 0.610 9.887 15352 Z= 0.319 Chirality : 0.045 0.174 1642 Planarity : 0.004 0.042 2039 Dihedral : 8.239 55.716 1938 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.36 % Favored : 93.57 % Rotamer: Outliers : 4.96 % Allowed : 15.72 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -1.25 (0.23), residues: 1369 helix: -5.16 (0.39), residues: 6 sheet: -1.02 (0.30), residues: 272 loop : -0.79 (0.19), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1289 HIS 0.004 0.001 HIS B 204 PHE 0.010 0.001 PHE B 712 TYR 0.012 0.001 TYR B 637 ARG 0.002 0.000 ARG B 489 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 6) link_NAG-ASN : angle 2.49982 ( 18) link_BETA1-4 : bond 0.00425 ( 4) link_BETA1-4 : angle 2.14255 ( 12) hydrogen bonds : bond 0.03597 ( 220) hydrogen bonds : angle 6.40971 ( 486) SS BOND : bond 0.00304 ( 57) SS BOND : angle 1.09171 ( 114) covalent geometry : bond 0.00272 (11204) covalent geometry : angle 0.59683 (15208) Misc. bond : bond 0.00026 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 65 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2882 TYR cc_start: 0.3596 (OUTLIER) cc_final: 0.1686 (p90) REVERT: B 254 ASP cc_start: 0.8205 (t0) cc_final: 0.7993 (t0) REVERT: B 264 ARG cc_start: 0.4939 (OUTLIER) cc_final: 0.4687 (ptt-90) REVERT: B 317 GLU cc_start: 0.4436 (OUTLIER) cc_final: 0.3644 (mp0) REVERT: B 491 ASP cc_start: 0.8235 (m-30) cc_final: 0.8033 (m-30) REVERT: B 686 TYR cc_start: 0.7960 (p90) cc_final: 0.7599 (p90) REVERT: B 728 GLN cc_start: 0.6093 (OUTLIER) cc_final: 0.5781 (mt0) REVERT: B 1296 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.5882 (p0) outliers start: 60 outliers final: 43 residues processed: 117 average time/residue: 0.3162 time to fit residues: 54.6018 Evaluate side-chains 101 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 53 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2704 LEU Chi-restraints excluded: chain A residue 2710 ASN Chi-restraints excluded: chain A residue 2713 CYS Chi-restraints excluded: chain A residue 2767 CYS Chi-restraints excluded: chain A residue 2779 ARG Chi-restraints excluded: chain A residue 2786 GLU Chi-restraints excluded: chain A residue 2794 CYS Chi-restraints excluded: chain A residue 2795 ILE Chi-restraints excluded: chain A residue 2823 CYS Chi-restraints excluded: chain A residue 2831 GLN Chi-restraints excluded: chain A residue 2858 ILE Chi-restraints excluded: chain A residue 2882 TYR Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 411 ARG Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 621 MET Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 665 ASN Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 728 GLN Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 800 THR Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 958 HIS Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1291 CYS Chi-restraints excluded: chain B residue 1296 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 7 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 53 optimal weight: 0.5980 chunk 100 optimal weight: 0.0870 chunk 67 optimal weight: 1.9990 chunk 110 optimal weight: 0.0770 chunk 129 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 128 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2710 ASN B 971 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.141093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.105914 restraints weight = 17888.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.104541 restraints weight = 31579.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.105948 restraints weight = 25134.612| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11278 Z= 0.112 Angle : 0.588 7.901 15352 Z= 0.304 Chirality : 0.045 0.172 1642 Planarity : 0.004 0.044 2039 Dihedral : 7.538 56.944 1932 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.16 % Favored : 92.77 % Rotamer: Outliers : 4.71 % Allowed : 16.63 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -1.18 (0.23), residues: 1369 helix: -5.15 (0.41), residues: 6 sheet: -0.80 (0.30), residues: 278 loop : -0.79 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1289 HIS 0.004 0.001 HIS B 204 PHE 0.032 0.001 PHE A2747 TYR 0.015 0.001 TYR B 637 ARG 0.003 0.000 ARG A2760 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 6) link_NAG-ASN : angle 2.41066 ( 18) link_BETA1-4 : bond 0.00452 ( 4) link_BETA1-4 : angle 2.07713 ( 12) hydrogen bonds : bond 0.03078 ( 220) hydrogen bonds : angle 6.10656 ( 486) SS BOND : bond 0.00217 ( 57) SS BOND : angle 1.04775 ( 114) covalent geometry : bond 0.00257 (11204) covalent geometry : angle 0.57492 (15208) Misc. bond : bond 0.00022 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 61 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2882 TYR cc_start: 0.3608 (OUTLIER) cc_final: 0.1665 (p90) REVERT: B 264 ARG cc_start: 0.4890 (OUTLIER) cc_final: 0.4624 (ptt-90) REVERT: B 308 MET cc_start: 0.3751 (tpp) cc_final: -0.0888 (mtp) REVERT: B 317 GLU cc_start: 0.3787 (OUTLIER) cc_final: 0.2873 (mp0) REVERT: B 523 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8910 (tp) REVERT: B 574 ASP cc_start: 0.8439 (t0) cc_final: 0.8026 (t0) REVERT: B 686 TYR cc_start: 0.7944 (p90) cc_final: 0.7653 (p90) REVERT: B 728 GLN cc_start: 0.6211 (OUTLIER) cc_final: 0.5874 (mt0) REVERT: B 1296 ASP cc_start: 0.6817 (OUTLIER) cc_final: 0.5530 (p0) outliers start: 57 outliers final: 40 residues processed: 113 average time/residue: 0.2779 time to fit residues: 48.8603 Evaluate side-chains 99 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 53 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2704 LEU Chi-restraints excluded: chain A residue 2710 ASN Chi-restraints excluded: chain A residue 2713 CYS Chi-restraints excluded: chain A residue 2767 CYS Chi-restraints excluded: chain A residue 2779 ARG Chi-restraints excluded: chain A residue 2786 GLU Chi-restraints excluded: chain A residue 2794 CYS Chi-restraints excluded: chain A residue 2795 ILE Chi-restraints excluded: chain A residue 2808 HIS Chi-restraints excluded: chain A residue 2823 CYS Chi-restraints excluded: chain A residue 2831 GLN Chi-restraints excluded: chain A residue 2882 TYR Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 728 GLN Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 800 THR Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 958 HIS Chi-restraints excluded: chain B residue 968 THR Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1291 CYS Chi-restraints excluded: chain B residue 1296 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 95 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 111 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 117 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 0.0030 chunk 105 optimal weight: 0.5980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.141199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107200 restraints weight = 17929.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.104943 restraints weight = 32128.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.106773 restraints weight = 24939.486| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11278 Z= 0.111 Angle : 0.566 7.936 15352 Z= 0.294 Chirality : 0.044 0.172 1642 Planarity : 0.004 0.054 2039 Dihedral : 7.150 53.964 1931 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 5.05 % Allowed : 17.04 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -1.13 (0.23), residues: 1369 helix: -5.12 (0.43), residues: 6 sheet: -0.59 (0.30), residues: 270 loop : -0.80 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1289 HIS 0.004 0.001 HIS B 383 PHE 0.014 0.001 PHE A2747 TYR 0.016 0.001 TYR B 637 ARG 0.014 0.000 ARG B 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 6) link_NAG-ASN : angle 2.25235 ( 18) link_BETA1-4 : bond 0.00431 ( 4) link_BETA1-4 : angle 1.90592 ( 12) hydrogen bonds : bond 0.02932 ( 220) hydrogen bonds : angle 5.94825 ( 486) SS BOND : bond 0.00215 ( 57) SS BOND : angle 0.93647 ( 114) covalent geometry : bond 0.00254 (11204) covalent geometry : angle 0.55481 (15208) Misc. bond : bond 0.00020 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 60 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2882 TYR cc_start: 0.3288 (OUTLIER) cc_final: 0.1781 (p90) REVERT: B 264 ARG cc_start: 0.5045 (OUTLIER) cc_final: 0.4753 (ptt-90) REVERT: B 308 MET cc_start: 0.3876 (tpp) cc_final: -0.0796 (mtp) REVERT: B 317 GLU cc_start: 0.3712 (OUTLIER) cc_final: 0.2894 (mp0) REVERT: B 523 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8929 (tp) REVERT: B 574 ASP cc_start: 0.8400 (t0) cc_final: 0.8083 (t0) REVERT: B 686 TYR cc_start: 0.7943 (p90) cc_final: 0.7674 (p90) REVERT: B 728 GLN cc_start: 0.5786 (OUTLIER) cc_final: 0.5529 (mt0) REVERT: B 861 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7966 (ptp) REVERT: B 1296 ASP cc_start: 0.6733 (OUTLIER) cc_final: 0.5497 (p0) outliers start: 61 outliers final: 45 residues processed: 112 average time/residue: 0.2183 time to fit residues: 38.2813 Evaluate side-chains 106 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 54 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2704 LEU Chi-restraints excluded: chain A residue 2710 ASN Chi-restraints excluded: chain A residue 2713 CYS Chi-restraints excluded: chain A residue 2767 CYS Chi-restraints excluded: chain A residue 2779 ARG Chi-restraints excluded: chain A residue 2786 GLU Chi-restraints excluded: chain A residue 2794 CYS Chi-restraints excluded: chain A residue 2795 ILE Chi-restraints excluded: chain A residue 2808 HIS Chi-restraints excluded: chain A residue 2823 CYS Chi-restraints excluded: chain A residue 2831 GLN Chi-restraints excluded: chain A residue 2882 TYR Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 665 ASN Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 728 GLN Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 800 THR Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 861 MET Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 958 HIS Chi-restraints excluded: chain B residue 968 THR Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1291 CYS Chi-restraints excluded: chain B residue 1296 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 125 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 383 HIS B1145 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.140056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.106253 restraints weight = 18001.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.100380 restraints weight = 22607.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.101982 restraints weight = 22936.508| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11278 Z= 0.161 Angle : 0.600 6.860 15352 Z= 0.310 Chirality : 0.046 0.170 1642 Planarity : 0.004 0.047 2039 Dihedral : 7.193 54.618 1929 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 5.46 % Allowed : 17.45 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -1.19 (0.23), residues: 1369 helix: -5.05 (0.49), residues: 6 sheet: -0.80 (0.30), residues: 275 loop : -0.80 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1289 HIS 0.005 0.001 HIS B 383 PHE 0.012 0.001 PHE B 712 TYR 0.015 0.001 TYR B 637 ARG 0.005 0.000 ARG B 364 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 6) link_NAG-ASN : angle 2.31359 ( 18) link_BETA1-4 : bond 0.00394 ( 4) link_BETA1-4 : angle 1.92731 ( 12) hydrogen bonds : bond 0.03013 ( 220) hydrogen bonds : angle 5.94469 ( 486) SS BOND : bond 0.00267 ( 57) SS BOND : angle 0.99026 ( 114) covalent geometry : bond 0.00379 (11204) covalent geometry : angle 0.58841 (15208) Misc. bond : bond 0.00041 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 59 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2882 TYR cc_start: 0.3178 (OUTLIER) cc_final: 0.2007 (p90) REVERT: B 264 ARG cc_start: 0.4822 (OUTLIER) cc_final: 0.4576 (ptt-90) REVERT: B 317 GLU cc_start: 0.3752 (OUTLIER) cc_final: 0.3181 (mp0) REVERT: B 523 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8967 (tp) REVERT: B 686 TYR cc_start: 0.7949 (p90) cc_final: 0.7632 (p90) REVERT: B 728 GLN cc_start: 0.5639 (OUTLIER) cc_final: 0.5263 (mt0) REVERT: B 1296 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.5951 (p0) outliers start: 66 outliers final: 49 residues processed: 118 average time/residue: 0.2101 time to fit residues: 38.7151 Evaluate side-chains 110 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 55 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2704 LEU Chi-restraints excluded: chain A residue 2710 ASN Chi-restraints excluded: chain A residue 2713 CYS Chi-restraints excluded: chain A residue 2767 CYS Chi-restraints excluded: chain A residue 2779 ARG Chi-restraints excluded: chain A residue 2786 GLU Chi-restraints excluded: chain A residue 2794 CYS Chi-restraints excluded: chain A residue 2795 ILE Chi-restraints excluded: chain A residue 2808 HIS Chi-restraints excluded: chain A residue 2809 ASP Chi-restraints excluded: chain A residue 2823 CYS Chi-restraints excluded: chain A residue 2831 GLN Chi-restraints excluded: chain A residue 2882 TYR Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 621 MET Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 665 ASN Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 728 GLN Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 800 THR Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 899 ASP Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 958 HIS Chi-restraints excluded: chain B residue 968 THR Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1296 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 11 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 68 optimal weight: 0.0000 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 383 HIS B1133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.140310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.106401 restraints weight = 18139.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105039 restraints weight = 34013.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.106675 restraints weight = 25730.363| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11278 Z= 0.126 Angle : 0.577 9.332 15352 Z= 0.299 Chirality : 0.045 0.170 1642 Planarity : 0.004 0.048 2039 Dihedral : 7.051 55.879 1929 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 5.13 % Allowed : 18.11 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 1369 helix: -4.91 (0.62), residues: 6 sheet: -0.60 (0.31), residues: 262 loop : -0.80 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1289 HIS 0.010 0.001 HIS B 383 PHE 0.010 0.001 PHE B 712 TYR 0.013 0.001 TYR B 637 ARG 0.005 0.000 ARG B 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00161 ( 6) link_NAG-ASN : angle 2.17302 ( 18) link_BETA1-4 : bond 0.00411 ( 4) link_BETA1-4 : angle 1.77290 ( 12) hydrogen bonds : bond 0.02900 ( 220) hydrogen bonds : angle 5.86745 ( 486) SS BOND : bond 0.00227 ( 57) SS BOND : angle 0.93732 ( 114) covalent geometry : bond 0.00291 (11204) covalent geometry : angle 0.56647 (15208) Misc. bond : bond 0.00026 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 61 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2882 TYR cc_start: 0.4074 (OUTLIER) cc_final: 0.1960 (p90) REVERT: B 264 ARG cc_start: 0.4817 (OUTLIER) cc_final: 0.4350 (ptt-90) REVERT: B 317 GLU cc_start: 0.3522 (OUTLIER) cc_final: 0.2681 (mp0) REVERT: B 523 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8877 (tp) REVERT: B 686 TYR cc_start: 0.7923 (p90) cc_final: 0.7660 (p90) REVERT: B 728 GLN cc_start: 0.5830 (OUTLIER) cc_final: 0.5492 (mt0) REVERT: B 1296 ASP cc_start: 0.6764 (OUTLIER) cc_final: 0.5667 (p0) outliers start: 62 outliers final: 51 residues processed: 117 average time/residue: 0.1987 time to fit residues: 35.8102 Evaluate side-chains 115 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 58 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2704 LEU Chi-restraints excluded: chain A residue 2710 ASN Chi-restraints excluded: chain A residue 2713 CYS Chi-restraints excluded: chain A residue 2767 CYS Chi-restraints excluded: chain A residue 2779 ARG Chi-restraints excluded: chain A residue 2786 GLU Chi-restraints excluded: chain A residue 2794 CYS Chi-restraints excluded: chain A residue 2795 ILE Chi-restraints excluded: chain A residue 2808 HIS Chi-restraints excluded: chain A residue 2809 ASP Chi-restraints excluded: chain A residue 2823 CYS Chi-restraints excluded: chain A residue 2831 GLN Chi-restraints excluded: chain A residue 2882 TYR Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 728 GLN Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 738 SER Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 800 THR Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 899 ASP Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 958 HIS Chi-restraints excluded: chain B residue 968 THR Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1296 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 26 optimal weight: 0.0470 chunk 71 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 20 optimal weight: 20.0000 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.141107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.106137 restraints weight = 17913.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.102748 restraints weight = 28765.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.104344 restraints weight = 24871.056| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11278 Z= 0.123 Angle : 0.575 9.306 15352 Z= 0.299 Chirality : 0.045 0.170 1642 Planarity : 0.004 0.049 2039 Dihedral : 6.975 55.772 1929 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 5.38 % Allowed : 18.44 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -1.13 (0.23), residues: 1369 helix: -4.96 (0.58), residues: 6 sheet: -0.73 (0.30), residues: 276 loop : -0.77 (0.20), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 439 HIS 0.003 0.001 HIS B 204 PHE 0.010 0.001 PHE B 712 TYR 0.014 0.001 TYR B 637 ARG 0.006 0.000 ARG B 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 6) link_NAG-ASN : angle 2.10808 ( 18) link_BETA1-4 : bond 0.00421 ( 4) link_BETA1-4 : angle 1.73546 ( 12) hydrogen bonds : bond 0.02832 ( 220) hydrogen bonds : angle 5.83500 ( 486) SS BOND : bond 0.00222 ( 57) SS BOND : angle 0.92419 ( 114) covalent geometry : bond 0.00285 (11204) covalent geometry : angle 0.56560 (15208) Misc. bond : bond 0.00024 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 60 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2882 TYR cc_start: 0.3792 (OUTLIER) cc_final: 0.1855 (p90) REVERT: B 264 ARG cc_start: 0.4700 (OUTLIER) cc_final: 0.4226 (ptt-90) REVERT: B 308 MET cc_start: 0.3752 (tpp) cc_final: -0.0593 (mtp) REVERT: B 317 GLU cc_start: 0.3521 (OUTLIER) cc_final: 0.2824 (mp0) REVERT: B 523 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8935 (tp) REVERT: B 621 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7037 (mpp) REVERT: B 686 TYR cc_start: 0.7915 (p90) cc_final: 0.7680 (p90) REVERT: B 728 GLN cc_start: 0.5833 (OUTLIER) cc_final: 0.5497 (mt0) REVERT: B 1296 ASP cc_start: 0.6914 (OUTLIER) cc_final: 0.5903 (p0) outliers start: 65 outliers final: 49 residues processed: 117 average time/residue: 0.2191 time to fit residues: 38.8955 Evaluate side-chains 113 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 57 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2704 LEU Chi-restraints excluded: chain A residue 2710 ASN Chi-restraints excluded: chain A residue 2713 CYS Chi-restraints excluded: chain A residue 2767 CYS Chi-restraints excluded: chain A residue 2779 ARG Chi-restraints excluded: chain A residue 2786 GLU Chi-restraints excluded: chain A residue 2794 CYS Chi-restraints excluded: chain A residue 2795 ILE Chi-restraints excluded: chain A residue 2808 HIS Chi-restraints excluded: chain A residue 2809 ASP Chi-restraints excluded: chain A residue 2823 CYS Chi-restraints excluded: chain A residue 2831 GLN Chi-restraints excluded: chain A residue 2882 TYR Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 621 MET Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 665 ASN Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 728 GLN Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 800 THR Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 958 HIS Chi-restraints excluded: chain B residue 968 THR Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1296 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 5 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 117 optimal weight: 0.0970 chunk 108 optimal weight: 0.0040 chunk 77 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 chunk 102 optimal weight: 4.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.140428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.107285 restraints weight = 18218.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.109416 restraints weight = 34454.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.109867 restraints weight = 18938.500| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11278 Z= 0.127 Angle : 0.574 8.981 15352 Z= 0.297 Chirality : 0.045 0.170 1642 Planarity : 0.004 0.050 2039 Dihedral : 6.746 55.561 1926 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 4.88 % Allowed : 18.69 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 1369 helix: -5.02 (0.53), residues: 6 sheet: -0.71 (0.30), residues: 275 loop : -0.76 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 439 HIS 0.003 0.001 HIS B 204 PHE 0.010 0.001 PHE B 712 TYR 0.011 0.001 TYR B 637 ARG 0.004 0.000 ARG B 846 Details of bonding type rmsd link_NAG-ASN : bond 0.00173 ( 6) link_NAG-ASN : angle 2.05414 ( 18) link_BETA1-4 : bond 0.00412 ( 4) link_BETA1-4 : angle 1.71501 ( 12) hydrogen bonds : bond 0.02825 ( 220) hydrogen bonds : angle 5.82371 ( 486) SS BOND : bond 0.00223 ( 57) SS BOND : angle 0.92664 ( 114) covalent geometry : bond 0.00295 (11204) covalent geometry : angle 0.56488 (15208) Misc. bond : bond 0.00026 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 60 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2882 TYR cc_start: 0.3957 (OUTLIER) cc_final: 0.1730 (p90) REVERT: B 264 ARG cc_start: 0.4854 (OUTLIER) cc_final: 0.4366 (ptt-90) REVERT: B 308 MET cc_start: 0.3434 (tpp) cc_final: -0.0774 (mtp) REVERT: B 317 GLU cc_start: 0.3219 (OUTLIER) cc_final: 0.2055 (mp0) REVERT: B 371 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6820 (tt) REVERT: B 523 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8910 (tp) REVERT: B 686 TYR cc_start: 0.7906 (p90) cc_final: 0.7686 (p90) REVERT: B 728 GLN cc_start: 0.5848 (OUTLIER) cc_final: 0.5511 (mt0) REVERT: B 1296 ASP cc_start: 0.6626 (OUTLIER) cc_final: 0.5718 (p0) outliers start: 59 outliers final: 50 residues processed: 113 average time/residue: 0.2047 time to fit residues: 35.4230 Evaluate side-chains 114 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 57 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2704 LEU Chi-restraints excluded: chain A residue 2710 ASN Chi-restraints excluded: chain A residue 2713 CYS Chi-restraints excluded: chain A residue 2767 CYS Chi-restraints excluded: chain A residue 2779 ARG Chi-restraints excluded: chain A residue 2786 GLU Chi-restraints excluded: chain A residue 2794 CYS Chi-restraints excluded: chain A residue 2795 ILE Chi-restraints excluded: chain A residue 2808 HIS Chi-restraints excluded: chain A residue 2809 ASP Chi-restraints excluded: chain A residue 2823 CYS Chi-restraints excluded: chain A residue 2831 GLN Chi-restraints excluded: chain A residue 2882 TYR Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 621 MET Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 715 LYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 728 GLN Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 800 THR Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 899 ASP Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 958 HIS Chi-restraints excluded: chain B residue 968 THR Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1296 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 88 optimal weight: 0.0980 chunk 67 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.140030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.104762 restraints weight = 17869.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.101797 restraints weight = 27924.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.103270 restraints weight = 28049.744| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11278 Z= 0.133 Angle : 0.573 9.030 15352 Z= 0.297 Chirality : 0.045 0.168 1642 Planarity : 0.004 0.051 2039 Dihedral : 6.651 55.434 1923 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 4.96 % Allowed : 18.94 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 1369 helix: -5.01 (0.54), residues: 6 sheet: -0.74 (0.30), residues: 276 loop : -0.75 (0.20), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 439 HIS 0.003 0.001 HIS B 204 PHE 0.010 0.001 PHE B 712 TYR 0.011 0.001 TYR B 765 ARG 0.007 0.000 ARG B 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 6) link_NAG-ASN : angle 2.01428 ( 18) link_BETA1-4 : bond 0.00434 ( 4) link_BETA1-4 : angle 1.71539 ( 12) hydrogen bonds : bond 0.02814 ( 220) hydrogen bonds : angle 5.81770 ( 486) SS BOND : bond 0.00228 ( 57) SS BOND : angle 0.92747 ( 114) covalent geometry : bond 0.00309 (11204) covalent geometry : angle 0.56412 (15208) Misc. bond : bond 0.00029 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 58 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2882 TYR cc_start: 0.3809 (OUTLIER) cc_final: 0.1775 (p90) REVERT: B 308 MET cc_start: 0.4038 (tpp) cc_final: -0.0345 (mtp) REVERT: B 317 GLU cc_start: 0.3211 (OUTLIER) cc_final: 0.2203 (mp0) REVERT: B 371 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6787 (tt) REVERT: B 523 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8919 (tp) REVERT: B 686 TYR cc_start: 0.7856 (p90) cc_final: 0.7635 (p90) REVERT: B 728 GLN cc_start: 0.5867 (OUTLIER) cc_final: 0.5514 (mt0) REVERT: B 1296 ASP cc_start: 0.6835 (OUTLIER) cc_final: 0.5870 (p0) outliers start: 60 outliers final: 50 residues processed: 112 average time/residue: 0.2065 time to fit residues: 36.0971 Evaluate side-chains 113 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 57 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2704 LEU Chi-restraints excluded: chain A residue 2710 ASN Chi-restraints excluded: chain A residue 2713 CYS Chi-restraints excluded: chain A residue 2767 CYS Chi-restraints excluded: chain A residue 2779 ARG Chi-restraints excluded: chain A residue 2786 GLU Chi-restraints excluded: chain A residue 2794 CYS Chi-restraints excluded: chain A residue 2795 ILE Chi-restraints excluded: chain A residue 2808 HIS Chi-restraints excluded: chain A residue 2809 ASP Chi-restraints excluded: chain A residue 2823 CYS Chi-restraints excluded: chain A residue 2831 GLN Chi-restraints excluded: chain A residue 2882 TYR Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 621 MET Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 715 LYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 728 GLN Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 800 THR Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 899 ASP Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 958 HIS Chi-restraints excluded: chain B residue 968 THR Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1296 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 55 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 924 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.138980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.104875 restraints weight = 17927.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.102574 restraints weight = 32140.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.104172 restraints weight = 25653.230| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11278 Z= 0.174 Angle : 0.603 8.981 15352 Z= 0.312 Chirality : 0.046 0.169 1642 Planarity : 0.004 0.051 2039 Dihedral : 6.841 56.373 1923 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.80 % Allowed : 18.86 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -1.20 (0.23), residues: 1369 helix: -5.00 (0.55), residues: 6 sheet: -0.87 (0.31), residues: 273 loop : -0.78 (0.20), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 439 HIS 0.004 0.001 HIS B 510 PHE 0.011 0.001 PHE B 712 TYR 0.013 0.001 TYR B 765 ARG 0.005 0.000 ARG B 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 6) link_NAG-ASN : angle 2.12265 ( 18) link_BETA1-4 : bond 0.00401 ( 4) link_BETA1-4 : angle 1.83987 ( 12) hydrogen bonds : bond 0.02942 ( 220) hydrogen bonds : angle 5.88989 ( 486) SS BOND : bond 0.00270 ( 57) SS BOND : angle 0.99861 ( 114) covalent geometry : bond 0.00408 (11204) covalent geometry : angle 0.59258 (15208) Misc. bond : bond 0.00042 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3664.51 seconds wall clock time: 67 minutes 36.27 seconds (4056.27 seconds total)