Starting phenix.real_space_refine on Fri Jul 3 00:34:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxb_36695/07_2026/8jxb_36695.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxb_36695/07_2026/8jxb_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_2026/8jxb_36695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxb_36695/07_2026/8jxb_36695.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxb_36695/07_2026/8jxb_36695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxb_36695/07_2026/8jxb_36695.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 42 Ad-hoc single atom residues: {' CA': 6} Unusual residues: {'A2G': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 6 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, 140 Ad-hoc single atom residues: {' CA': 12} Unusual residues: {'A2G': 7, 'NAG': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain breaks: 12 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 2.40, per 1000 atoms: 0.22 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: 0.87 Conformation dependent library (CDL) restraints added in 523.9 milliseconds 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: 0.35 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: 2.23 Time building geometry restraints manager: 1.20 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 3.250 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 3.250 nonbonded pdb=" OE2 GLU B1056 " pdb="CA CA B4716 " model vdw 2.191 3.250 ... (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: 1.770 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.910 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 : 8.11 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.000 ARG B 539 TYR 0.021 0.002 TYR B 637 PHE 0.018 0.001 PHE B 993 TRP 0.029 0.002 TRP B1289 HIS 0.004 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.24 (11204) covalent geometry : angle 0.76938 / 0.43 (15208) SS BOND : bond 0.00279 / 0.18 ( 57) SS BOND : angle 1.07613 / 0.71 ( 114) hydrogen bonds : bond 0.24536 / 16.41 ( 220) hydrogen bonds : angle 9.37609 / 6.60 ( 486) Misc. bond : bond 0.03474 / 1.86 ( 7) link_BETA1-4 : bond 0.00401 / 0.20 ( 4) link_BETA1-4 : angle 1.87000 / 1.20 ( 12) link_NAG-ASN : bond 0.00251 / 0.14 ( 6) link_NAG-ASN : angle 2.33831 / 1.26 ( 18) *********************** 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 : 0.451 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: 0.7856 (t0) REVERT: B 308 MET cc_start: 0.5684 (tpp) cc_final: 0.1789 (mtt) 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: 0.0897 time to fit residues: 12.1423 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 : 0.402 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0570 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.0770 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2705 GLN A2847 ASN B 409 HIS B 681 ASN B 895 HIS ** B 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1033 ASN B1057 HIS B1100 ASN B1104 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.140381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.094928 restraints weight = 17792.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.095082 restraints weight = 13478.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.095106 restraints weight = 12117.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.095260 restraints weight = 11715.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.095300 restraints weight = 11227.742| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11278 Z= 0.183 Angle : 0.677 7.502 15352 Z= 0.356 Chirality : 0.048 0.179 1642 Planarity : 0.005 0.043 2039 Dihedral : 9.484 75.593 1957 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.82 % Favored : 92.11 % Rotamer: Outliers : 5.13 % Allowed : 14.64 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.23), residues: 1369 helix: None (None), residues: 0 sheet: -1.04 (0.29), residues: 286 loop : -0.86 (0.20), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 380 TYR 0.013 0.002 TYR B 571 PHE 0.012 0.001 PHE B 712 TRP 0.024 0.002 TRP B1289 HIS 0.004 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (11204) covalent geometry : angle 0.66186 / 0.35 (15208) SS BOND : bond 0.00321 / 0.21 ( 57) SS BOND : angle 1.08119 / 0.73 ( 114) hydrogen bonds : bond 0.04467 / 3.03 ( 220) hydrogen bonds : angle 6.87979 / 4.88 ( 486) Misc. bond : bond 0.00093 / 0.05 ( 7) link_BETA1-4 : bond 0.00485 / 0.24 ( 4) link_BETA1-4 : angle 2.41802 / 1.47 ( 12) link_NAG-ASN : bond 0.00350 / 0.17 ( 6) link_NAG-ASN : angle 3.06157 / 1.72 ( 18) *********************** 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 116 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 54 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 254 ASP cc_start: 0.8323 (t0) cc_final: 0.7910 (t0) REVERT: B 264 ARG cc_start: 0.4693 (OUTLIER) cc_final: 0.4388 (ptt-90) REVERT: B 317 GLU cc_start: 0.4458 (OUTLIER) cc_final: 0.3685 (mp0) REVERT: B 523 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8916 (tp) REVERT: B 728 GLN cc_start: 0.6067 (OUTLIER) cc_final: 0.5724 (mt0) outliers start: 62 outliers final: 40 residues processed: 112 average time/residue: 0.0856 time to fit residues: 14.4187 Evaluate side-chains 95 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 51 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 2854 ASP 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 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 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 1129 CYS Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1261 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 104 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 72 optimal weight: 0.0170 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 82 optimal weight: 0.0070 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2808 HIS B 796 ASN B 971 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.141253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106947 restraints weight = 17922.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.105171 restraints weight = 30415.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.106702 restraints weight = 24742.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.107693 restraints weight = 13840.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.108034 restraints weight = 12339.952| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1331 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= 0.122 Angle : 0.613 10.059 15352 Z= 0.321 Chirality : 0.046 0.174 1642 Planarity : 0.004 0.043 2039 Dihedral : 8.211 56.816 1938 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.72 % Favored : 93.21 % Rotamer: Outliers : 4.80 % Allowed : 16.13 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.22), residues: 1369 helix: -5.06 (0.46), residues: 6 sheet: -0.82 (0.30), residues: 260 loop : -0.96 (0.19), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 489 TYR 0.013 0.001 TYR B 637 PHE 0.011 0.001 PHE B 712 TRP 0.018 0.001 TRP B1289 HIS 0.004 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (11204) covalent geometry : angle 0.59999 / 0.32 (15208) SS BOND : bond 0.00235 / 0.15 ( 57) SS BOND : angle 1.03084 / 0.73 ( 114) hydrogen bonds : bond 0.03459 / 2.33 ( 220) hydrogen bonds : angle 6.32202 / 4.46 ( 486) Misc. bond : bond 0.00032 / 0.02 ( 7) link_BETA1-4 : bond 0.00383 / 0.19 ( 4) link_BETA1-4 : angle 2.12480 / 1.27 ( 12) link_NAG-ASN : bond 0.00155 / 0.08 ( 6) link_NAG-ASN : angle 2.49321 / 1.39 ( 18) *********************** 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 126 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 68 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2882 TYR cc_start: 0.3801 (OUTLIER) cc_final: 0.2084 (t80) REVERT: B 254 ASP cc_start: 0.8104 (t0) cc_final: 0.7839 (t0) REVERT: B 264 ARG cc_start: 0.4900 (OUTLIER) cc_final: 0.4650 (ptt-90) REVERT: B 317 GLU cc_start: 0.4333 (OUTLIER) cc_final: 0.3414 (mp0) REVERT: B 574 ASP cc_start: 0.8594 (t0) cc_final: 0.8195 (t0) REVERT: B 686 TYR cc_start: 0.7927 (p90) cc_final: 0.7657 (p90) REVERT: B 728 GLN cc_start: 0.6089 (OUTLIER) cc_final: 0.5834 (mt0) REVERT: B 861 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7597 (ptp) outliers start: 58 outliers final: 39 residues processed: 117 average time/residue: 0.0845 time to fit residues: 14.6674 Evaluate side-chains 101 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 57 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 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 424 MET 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 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 725 LEU Chi-restraints excluded: chain B residue 728 GLN 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 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 1129 CYS Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1261 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 51 optimal weight: 1.9990 chunk 127 optimal weight: 0.0370 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2710 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.141721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.107493 restraints weight = 17940.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.105889 restraints weight = 32127.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.107602 restraints weight = 23943.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.108291 restraints weight = 13548.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.108688 restraints weight = 12516.834| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1527 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= 0.135 Angle : 0.604 7.709 15352 Z= 0.314 Chirality : 0.045 0.172 1642 Planarity : 0.004 0.043 2039 Dihedral : 7.683 58.153 1932 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.89 % Favored : 92.04 % Rotamer: Outliers : 5.29 % Allowed : 16.29 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.22), residues: 1369 helix: -4.93 (0.58), residues: 6 sheet: -0.76 (0.30), residues: 271 loop : -0.96 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 380 TYR 0.015 0.001 TYR B 637 PHE 0.019 0.001 PHE A2841 TRP 0.016 0.001 TRP B1289 HIS 0.004 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (11204) covalent geometry : angle 0.59116 / 0.31 (15208) SS BOND : bond 0.00285 / 0.19 ( 57) SS BOND : angle 1.04087 / 0.71 ( 114) hydrogen bonds : bond 0.03150 / 2.12 ( 220) hydrogen bonds : angle 6.15705 / 4.35 ( 486) Misc. bond : bond 0.00029 / 0.01 ( 7) link_BETA1-4 : bond 0.00450 / 0.22 ( 4) link_BETA1-4 : angle 2.12696 / 1.29 ( 12) link_NAG-ASN : bond 0.00230 / 0.12 ( 6) link_NAG-ASN : angle 2.45403 / 1.37 ( 18) *********************** 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 124 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 60 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2882 TYR cc_start: 0.3890 (OUTLIER) cc_final: 0.2119 (t80) REVERT: B 264 ARG cc_start: 0.4905 (OUTLIER) cc_final: 0.4646 (ptt-90) REVERT: B 308 MET cc_start: 0.3669 (tpp) cc_final: 0.3456 (tpp) REVERT: B 317 GLU cc_start: 0.3543 (OUTLIER) cc_final: 0.2703 (mp0) REVERT: B 523 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8910 (tp) REVERT: B 574 ASP cc_start: 0.8576 (t0) cc_final: 0.8221 (t0) REVERT: B 631 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.6299 (tm-30) REVERT: B 686 TYR cc_start: 0.7992 (p90) cc_final: 0.7696 (p90) REVERT: B 728 GLN cc_start: 0.5726 (OUTLIER) cc_final: 0.5482 (mt0) REVERT: B 861 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7633 (ptp) outliers start: 64 outliers final: 42 residues processed: 115 average time/residue: 0.0994 time to fit residues: 17.1030 Evaluate side-chains 103 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 54 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 2882 TYR 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 447 VAL 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 616 THR Chi-restraints excluded: chain B residue 621 MET Chi-restraints excluded: chain B residue 631 GLU 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 968 THR Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1261 SER 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 84 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 924 ASN B1085 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.138551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.103803 restraints weight = 18069.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.101770 restraints weight = 27906.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.103143 restraints weight = 26143.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.103337 restraints weight = 12969.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.105059 restraints weight = 11259.404| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11278 Z= 0.210 Angle : 0.654 7.745 15352 Z= 0.339 Chirality : 0.047 0.171 1642 Planarity : 0.004 0.048 2039 Dihedral : 7.720 58.376 1931 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 5.46 % Allowed : 17.04 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.23), residues: 1369 helix: -4.91 (0.61), residues: 6 sheet: -1.15 (0.29), residues: 288 loop : -0.97 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 380 TYR 0.014 0.002 TYR B 637 PHE 0.015 0.001 PHE B 712 TRP 0.018 0.002 TRP B1289 HIS 0.004 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 (11204) covalent geometry : angle 0.63968 / 0.34 (15208) SS BOND : bond 0.00326 / 0.22 ( 57) SS BOND : angle 1.20156 / 0.82 ( 114) hydrogen bonds : bond 0.03294 / 2.20 ( 220) hydrogen bonds : angle 6.17661 / 4.37 ( 486) Misc. bond : bond 0.00059 / 0.03 ( 7) link_BETA1-4 : bond 0.00436 / 0.21 ( 4) link_BETA1-4 : angle 2.19437 / 1.37 ( 12) link_NAG-ASN : bond 0.00341 / 0.19 ( 6) link_NAG-ASN : angle 2.55311 / 1.45 ( 18) *********************** 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 130 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 64 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2705 GLN cc_start: 0.8292 (mt0) cc_final: 0.7974 (mt0) REVERT: A 2882 TYR cc_start: 0.3740 (OUTLIER) cc_final: 0.2021 (t80) REVERT: B 264 ARG cc_start: 0.5001 (OUTLIER) cc_final: 0.4743 (ptt-90) REVERT: B 317 GLU cc_start: 0.3921 (OUTLIER) cc_final: 0.3215 (mp0) REVERT: B 523 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8953 (tp) REVERT: B 686 TYR cc_start: 0.8022 (p90) cc_final: 0.7642 (p90) REVERT: B 728 GLN cc_start: 0.5652 (OUTLIER) cc_final: 0.5343 (mt0) outliers start: 66 outliers final: 48 residues processed: 121 average time/residue: 0.0971 time to fit residues: 17.5247 Evaluate side-chains 110 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 57 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 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 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 447 VAL 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 593 VAL 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 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 1153 THR Chi-restraints excluded: chain B residue 1261 SER 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 12 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 130 optimal weight: 0.2980 chunk 121 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 chunk 17 optimal weight: 9.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 383 HIS B1160 HIS 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 = 0.140246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.105175 restraints weight = 17963.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.103732 restraints weight = 30067.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.105343 restraints weight = 26162.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.105565 restraints weight = 14583.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.106276 restraints weight = 12758.545| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1817 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= 0.134 Angle : 0.589 6.707 15352 Z= 0.307 Chirality : 0.045 0.171 1642 Planarity : 0.004 0.047 2039 Dihedral : 7.310 55.585 1930 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 5.62 % Allowed : 16.96 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.23), residues: 1369 helix: -4.77 (0.74), residues: 6 sheet: -1.02 (0.30), residues: 284 loop : -0.93 (0.19), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 846 TYR 0.015 0.001 TYR B 637 PHE 0.013 0.001 PHE B 712 TRP 0.016 0.001 TRP B1289 HIS 0.006 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (11204) covalent geometry : angle 0.57729 / 0.30 (15208) SS BOND : bond 0.00249 / 0.16 ( 57) SS BOND : angle 1.02816 / 0.71 ( 114) hydrogen bonds : bond 0.02969 / 1.99 ( 220) hydrogen bonds : angle 5.95837 / 4.21 ( 486) Misc. bond : bond 0.00027 / 0.01 ( 7) link_BETA1-4 : bond 0.00413 / 0.20 ( 4) link_BETA1-4 : angle 1.85978 / 1.15 ( 12) link_NAG-ASN : bond 0.00161 / 0.08 ( 6) link_NAG-ASN : angle 2.29462 / 1.29 ( 18) *********************** 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 131 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 63 time to evaluate : 0.423 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: 0.3620 (OUTLIER) cc_final: 0.2195 (t80) REVERT: B 264 ARG cc_start: 0.5078 (OUTLIER) cc_final: 0.4790 (ptt-90) REVERT: B 317 GLU cc_start: 0.4027 (OUTLIER) cc_final: 0.3199 (mp0) REVERT: B 523 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8924 (tp) REVERT: B 574 ASP cc_start: 0.8555 (t0) cc_final: 0.8180 (t0) REVERT: B 686 TYR cc_start: 0.7920 (p90) cc_final: 0.7609 (p90) REVERT: B 728 GLN cc_start: 0.5654 (OUTLIER) cc_final: 0.5318 (mt0) outliers start: 68 outliers final: 50 residues processed: 121 average time/residue: 0.0934 time to fit residues: 17.2435 Evaluate side-chains 113 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 58 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 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 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 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 757 SER 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 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 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 57 optimal weight: 0.9990 chunk 117 optimal weight: 0.0070 chunk 134 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 13 optimal weight: 30.0000 chunk 59 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 108 optimal weight: 0.0030 chunk 42 optimal weight: 0.7980 overall best weight: 0.4808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 383 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.140902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.106548 restraints weight = 18009.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.103331 restraints weight = 23421.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.104694 restraints weight = 23717.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105152 restraints weight = 12252.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.106192 restraints weight = 10851.763| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11278 Z= 0.116 Angle : 0.576 9.757 15352 Z= 0.301 Chirality : 0.045 0.169 1642 Planarity : 0.004 0.076 2039 Dihedral : 7.076 55.164 1929 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 4.96 % Allowed : 18.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.23), residues: 1369 helix: -4.86 (0.66), residues: 6 sheet: -0.82 (0.30), residues: 280 loop : -0.92 (0.20), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 380 TYR 0.015 0.001 TYR B 637 PHE 0.011 0.001 PHE B 712 TRP 0.013 0.001 TRP B 844 HIS 0.009 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (11204) covalent geometry : angle 0.56610 / 0.30 (15208) SS BOND : bond 0.00215 / 0.13 ( 57) SS BOND : angle 0.95821 / 0.66 ( 114) hydrogen bonds : bond 0.02892 / 1.96 ( 220) hydrogen bonds : angle 5.83991 / 4.12 ( 486) Misc. bond : bond 0.00023 / 0.01 ( 7) link_BETA1-4 : bond 0.00417 / 0.20 ( 4) link_BETA1-4 : angle 1.75612 / 1.09 ( 12) link_NAG-ASN : bond 0.00156 / 0.08 ( 6) link_NAG-ASN : angle 2.17774 / 1.22 ( 18) *********************** 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: 60 poor density : 63 time to evaluate : 0.417 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: 0.3656 (OUTLIER) cc_final: 0.2352 (t80) REVERT: B 264 ARG cc_start: 0.4670 (OUTLIER) cc_final: 0.4326 (ptt-90) REVERT: B 308 MET cc_start: 0.4686 (tpp) cc_final: 0.0280 (mtp) REVERT: B 317 GLU cc_start: 0.3766 (OUTLIER) cc_final: 0.3186 (mp0) REVERT: B 523 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8942 (tp) REVERT: B 574 ASP cc_start: 0.8652 (t0) cc_final: 0.8163 (t0) REVERT: B 686 TYR cc_start: 0.7977 (p90) cc_final: 0.7669 (p90) REVERT: B 728 GLN cc_start: 0.5781 (OUTLIER) cc_final: 0.5435 (mt0) outliers start: 60 outliers final: 46 residues processed: 116 average time/residue: 0.0939 time to fit residues: 16.5153 Evaluate side-chains 110 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 59 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 2841 PHE 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 361 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 395 VAL 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 715 LYS Chi-restraints excluded: chain B residue 716 THR 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 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 1139 SER Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1163 ILE 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 99 optimal weight: 2.9990 chunk 131 optimal weight: 0.1980 chunk 88 optimal weight: 0.0870 chunk 115 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 110 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 30 optimal weight: 0.0000 overall best weight: 0.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 383 HIS B 980 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.141802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107394 restraints weight = 17952.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.102981 restraints weight = 24474.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.104046 restraints weight = 27926.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.105121 restraints weight = 14633.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.105579 restraints weight = 11729.145| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11278 Z= 0.106 Angle : 0.561 9.175 15352 Z= 0.294 Chirality : 0.044 0.198 1642 Planarity : 0.004 0.089 2039 Dihedral : 6.688 55.262 1927 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 5.05 % Allowed : 18.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.23), residues: 1369 helix: -3.57 (1.10), residues: 12 sheet: -0.70 (0.30), residues: 281 loop : -0.87 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 380 TYR 0.015 0.001 TYR B 637 PHE 0.011 0.001 PHE B 712 TRP 0.014 0.001 TRP B 844 HIS 0.008 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (11204) covalent geometry : angle 0.55201 / 0.29 (15208) SS BOND : bond 0.00192 / 0.12 ( 57) SS BOND : angle 0.88807 / 0.62 ( 114) hydrogen bonds : bond 0.02754 / 1.85 ( 220) hydrogen bonds : angle 5.77022 / 4.06 ( 486) Misc. bond : bond 0.00022 / 0.01 ( 7) link_BETA1-4 : bond 0.00437 / 0.21 ( 4) link_BETA1-4 : angle 1.62855 / 1.02 ( 12) link_NAG-ASN : bond 0.00129 / 0.06 ( 6) link_NAG-ASN : angle 2.02821 / 1.14 ( 18) *********************** 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 129 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 68 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2882 TYR cc_start: 0.3667 (OUTLIER) cc_final: 0.2315 (t80) REVERT: B 264 ARG cc_start: 0.4619 (OUTLIER) cc_final: 0.4164 (ptt-90) REVERT: B 308 MET cc_start: 0.4799 (tpp) cc_final: 0.0437 (mtp) REVERT: B 317 GLU cc_start: 0.3292 (OUTLIER) cc_final: 0.2633 (mp0) REVERT: B 371 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6578 (tt) REVERT: B 523 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8926 (tp) REVERT: B 574 ASP cc_start: 0.8611 (t0) cc_final: 0.8156 (t0) REVERT: B 686 TYR cc_start: 0.7932 (p90) cc_final: 0.7695 (p90) REVERT: B 728 GLN cc_start: 0.5811 (OUTLIER) cc_final: 0.5501 (mt0) REVERT: B 861 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7587 (ptp) REVERT: B 1296 ASP cc_start: 0.5954 (OUTLIER) cc_final: 0.4940 (p0) outliers start: 61 outliers final: 43 residues processed: 122 average time/residue: 0.0997 time to fit residues: 18.1056 Evaluate side-chains 112 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 61 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 2841 PHE 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 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 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 861 MET 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 980 ASN 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 1139 SER Chi-restraints excluded: chain B residue 1153 THR 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 60 optimal weight: 3.9990 chunk 123 optimal weight: 0.0370 chunk 53 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 102 optimal weight: 0.2980 chunk 8 optimal weight: 0.0870 chunk 130 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 111 optimal weight: 0.4980 chunk 32 optimal weight: 7.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 383 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.142331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.107012 restraints weight = 17851.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.105182 restraints weight = 30349.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.106797 restraints weight = 25212.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107720 restraints weight = 14270.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.108106 restraints weight = 12985.320| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11278 Z= 0.106 Angle : 0.564 9.152 15352 Z= 0.293 Chirality : 0.044 0.169 1642 Planarity : 0.004 0.049 2039 Dihedral : 6.476 55.026 1923 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.80 % Allowed : 19.52 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.23), residues: 1369 helix: -3.59 (1.09), residues: 12 sheet: -0.80 (0.30), residues: 288 loop : -0.84 (0.20), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 846 TYR 0.014 0.001 TYR B 765 PHE 0.011 0.001 PHE B 712 TRP 0.013 0.001 TRP B 844 HIS 0.013 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (11204) covalent geometry : angle 0.55550 / 0.29 (15208) SS BOND : bond 0.00195 / 0.12 ( 57) SS BOND : angle 0.88059 / 0.61 ( 114) hydrogen bonds : bond 0.02723 / 1.82 ( 220) hydrogen bonds : angle 5.72232 / 4.03 ( 486) Misc. bond : bond 0.00020 / 0.01 ( 7) link_BETA1-4 : bond 0.00418 / 0.20 ( 4) link_BETA1-4 : angle 1.61044 / 1.01 ( 12) link_NAG-ASN : bond 0.00140 / 0.07 ( 6) link_NAG-ASN : angle 1.97488 / 1.12 ( 18) *********************** 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 121 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 63 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2882 TYR cc_start: 0.3695 (OUTLIER) cc_final: 0.2235 (t80) REVERT: B 264 ARG cc_start: 0.4783 (OUTLIER) cc_final: 0.4286 (ptt-90) REVERT: B 308 MET cc_start: 0.4347 (tpp) cc_final: 0.0140 (mtp) REVERT: B 317 GLU cc_start: 0.3127 (OUTLIER) cc_final: 0.2064 (mp0) REVERT: B 371 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6729 (tt) REVERT: B 523 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8940 (tp) REVERT: B 574 ASP cc_start: 0.8572 (t0) cc_final: 0.8114 (t0) REVERT: B 728 GLN cc_start: 0.5639 (OUTLIER) cc_final: 0.5323 (mt0) REVERT: B 861 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7551 (ptp) REVERT: B 1296 ASP cc_start: 0.5670 (OUTLIER) cc_final: 0.4838 (p0) outliers start: 58 outliers final: 45 residues processed: 112 average time/residue: 0.0975 time to fit residues: 16.3964 Evaluate side-chains 115 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 62 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 2841 PHE 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 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 715 LYS Chi-restraints excluded: chain B residue 716 THR 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 822 SER 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 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 1093 LEU Chi-restraints excluded: chain B residue 1139 SER Chi-restraints excluded: chain B residue 1153 THR 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 32 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.139250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.104912 restraints weight = 17905.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.101392 restraints weight = 27647.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.103335 restraints weight = 27087.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.103624 restraints weight = 14059.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105082 restraints weight = 12503.344| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11278 Z= 0.207 Angle : 0.641 9.029 15352 Z= 0.333 Chirality : 0.047 0.174 1642 Planarity : 0.004 0.052 2039 Dihedral : 6.937 54.481 1923 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 4.55 % Allowed : 19.93 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.23), residues: 1369 helix: -3.56 (1.13), residues: 12 sheet: -1.13 (0.29), residues: 293 loop : -0.91 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 846 TYR 0.023 0.002 TYR B 765 PHE 0.013 0.001 PHE B 712 TRP 0.015 0.002 TRP B1289 HIS 0.004 0.001 HIS B 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (11204) covalent geometry : angle 0.63020 / 0.33 (15208) SS BOND : bond 0.00333 / 0.21 ( 57) SS BOND : angle 1.09929 / 0.73 ( 114) hydrogen bonds : bond 0.03060 / 2.04 ( 220) hydrogen bonds : angle 5.93243 / 4.20 ( 486) Misc. bond : bond 0.00052 / 0.03 ( 7) link_BETA1-4 : bond 0.00387 / 0.19 ( 4) link_BETA1-4 : angle 1.94106 / 1.25 ( 12) link_NAG-ASN : bond 0.00343 / 0.19 ( 6) link_NAG-ASN : angle 2.20394 / 1.29 ( 18) ********************** 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 117 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 62 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 ARG cc_start: 0.4756 (OUTLIER) cc_final: 0.4275 (ptt-90) REVERT: B 317 GLU cc_start: 0.3366 (OUTLIER) cc_final: 0.2346 (mp0) REVERT: B 371 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6819 (tt) REVERT: B 484 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7433 (tm-30) REVERT: B 523 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8906 (tp) REVERT: B 728 GLN cc_start: 0.5826 (OUTLIER) cc_final: 0.5549 (mt0) REVERT: B 861 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7826 (ptp) REVERT: B 1296 ASP cc_start: 0.6061 (OUTLIER) cc_final: 0.4954 (p0) outliers start: 55 outliers final: 43 residues processed: 110 average time/residue: 0.1002 time to fit residues: 16.3374 Evaluate side-chains 111 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 60 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 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 2841 PHE 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 371 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 484 GLU 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 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 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 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 1139 SER Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1296 ASP Chi-restraints excluded: chain B residue 1300 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 28 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 79 optimal weight: 0.9980 chunk 121 optimal weight: 0.3980 chunk 63 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.141162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.106352 restraints weight = 17981.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.103089 restraints weight = 30333.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.105023 restraints weight = 23718.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105517 restraints weight = 13617.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.106219 restraints weight = 12329.536| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2239 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= 0.128 Angle : 0.588 9.042 15352 Z= 0.305 Chirality : 0.045 0.187 1642 Planarity : 0.004 0.051 2039 Dihedral : 6.630 55.660 1922 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 4.38 % Allowed : 19.93 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.23), residues: 1369 helix: -3.56 (1.14), residues: 12 sheet: -0.95 (0.30), residues: 281 loop : -0.88 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 846 TYR 0.017 0.001 TYR B 765 PHE 0.010 0.001 PHE B 712 TRP 0.014 0.001 TRP B 439 HIS 0.003 0.000 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (11204) covalent geometry : angle 0.57875 / 0.30 (15208) SS BOND : bond 0.00220 / 0.14 ( 57) SS BOND : angle 0.94061 / 0.64 ( 114) hydrogen bonds : bond 0.02813 / 1.91 ( 220) hydrogen bonds : angle 5.79316 / 4.09 ( 486) Misc. bond : bond 0.00027 / 0.01 ( 7) link_BETA1-4 : bond 0.00406 / 0.20 ( 4) link_BETA1-4 : angle 1.67484 / 1.06 ( 12) link_NAG-ASN : bond 0.00163 / 0.08 ( 6) link_NAG-ASN : angle 2.04952 / 1.17 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1848.78 seconds wall clock time: 32 minutes 43.63 seconds (1963.63 seconds total)