Starting phenix.real_space_refine on Wed May 14 09:08:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxh_36701/05_2025/8jxh_36701.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxh_36701/05_2025/8jxh_36701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jxh_36701/05_2025/8jxh_36701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxh_36701/05_2025/8jxh_36701.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxh_36701/05_2025/8jxh_36701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxh_36701/05_2025/8jxh_36701.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 16 9.91 5 S 129 5.16 5 C 7014 2.51 5 N 2006 2.21 5 O 2338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11503 Number of models: 1 Model: "" Number of chains: 11 Chain: "D" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 895 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain: "A" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1149 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "B" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9047 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 1 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: 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: 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: "F" 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: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 46 Unusual residues: {' CA': 4, 'A2G': 1, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 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, 152 Unusual residues: {' CA': 12, 'A2G': 8, 'NAG': 2} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.56, per 1000 atoms: 0.57 Number of scatterers: 11503 At special positions: 0 Unit cell: (141.1, 129.812, 146.744, 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 16 19.99 S 129 16.00 O 2338 8.00 N 2006 7.00 C 7014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=52, symmetry=0 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=2.04 Simple disulfide: pdb=" SG CYS A2801 " - pdb=" SG CYS A2818 " distance=2.03 Simple disulfide: pdb=" SG CYS A2823 " - pdb=" SG CYS A2836 " distance=2.03 Simple disulfide: pdb=" SG CYS A2830 " - pdb=" SG CYS A2849 " distance=2.03 Simple disulfide: pdb=" SG CYS A2843 " - pdb=" SG CYS A2860 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 208 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 278 " distance=2.02 Simple disulfide: pdb=" SG CYS B 272 " - pdb=" SG CYS B 291 " distance=2.04 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 B1150 " - pdb=" SG CYS B1162 " 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=2.04 Simple disulfide: pdb=" SG CYS B1188 " - pdb=" SG CYS B1201 " distance=2.03 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 B3165 " - pdb=" SG CYS B3178 " distance=2.03 Simple disulfide: pdb=" SG CYS B3180 " - pdb=" SG CYS B3193 " 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=9, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " BETA1-3 " NAG C 1 " - " NAG C 2 " " NAG F 1 " - " NAG F 2 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A4701 " - " ASN A2782 " " NAG A4702 " - " ASN A2810 " " NAG B4701 " - " ASN B 340 " " NAG B4702 " - " ASN B1187 " " NAG C 1 " - " ASN B 462 " " NAG E 1 " - " ASN B 865 " " NAG F 1 " - " ASN B1064 " " NAG G 1 " - " ASN B 657 " Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.4 seconds 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2642 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 34 sheets defined 14.1% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'D' and resid 257 through 269 removed outlier: 3.693A pdb=" N ASP D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER D 269 " --> pdb=" O ASP D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 315 removed outlier: 3.719A pdb=" N GLU D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU D 302 " --> pdb=" O GLN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 356 removed outlier: 3.636A pdb=" N LEU D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR D 339 " --> pdb=" O LYS D 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 2715 through 2719 Processing helix chain 'A' and resid 2733 through 2738 removed outlier: 3.784A pdb=" N CYS A2737 " --> pdb=" O LEU A2733 " (cutoff:3.500A) Processing helix chain 'A' and resid 2758 through 2760 No H-bonds generated for 'chain 'A' and resid 2758 through 2760' Processing helix chain 'A' and resid 2770 through 2774 Processing helix chain 'A' and resid 2782 through 2786 Processing helix chain 'A' and resid 2812 through 2817 removed outlier: 3.740A pdb=" N LYS A2816 " --> pdb=" O THR A2812 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN A2817 " --> pdb=" O SER A2813 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2812 through 2817' Processing helix chain 'A' and resid 2840 through 2842 No H-bonds generated for 'chain 'A' and resid 2840 through 2842' 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 299 through 303 Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 660 through 669 removed outlier: 3.611A pdb=" N SER B 664 " --> pdb=" O PRO B 661 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASN B 665 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN B 666 " --> pdb=" O GLY B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 684 Processing helix chain 'B' and resid 979 through 983 removed outlier: 3.783A pdb=" N CYS B 983 " --> pdb=" O ASN B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1043 No H-bonds generated for 'chain 'B' and resid 1041 through 1043' 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 1126 through 1128 No H-bonds generated for 'chain 'B' and resid 1126 through 1128' Processing helix chain 'B' and resid 1164 through 1168 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 1248 through 1250 No H-bonds generated for 'chain 'B' and resid 1248 through 1250' Processing helix chain 'B' and resid 1260 through 1264 removed outlier: 3.909A pdb=" N HIS B1264 " --> pdb=" O SER B1261 " (cutoff:3.500A) Processing helix chain 'B' and resid 1300 through 1305 Processing sheet with id=AA1, first strand: chain 'A' and resid 2746 through 2748 Processing sheet with id=AA2, first strand: chain 'A' and resid 2827 through 2828 Processing sheet with id=AA3, first strand: chain 'B' and resid 188 through 189 Processing sheet with id=AA4, first strand: chain 'B' and resid 226 through 228 Processing sheet with id=AA5, first strand: chain 'B' and resid 269 through 271 Processing sheet with id=AA6, first strand: chain 'B' and resid 319 through 322 Processing sheet with id=AA7, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AA8, first strand: chain 'B' and resid 360 through 362 removed outlier: 3.743A pdb=" N LYS B 360 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN B 369 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 376 through 379 removed outlier: 3.710A pdb=" N HIS B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 414 through 417 removed outlier: 6.834A pdb=" N LEU B 403 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY B 646 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 427 through 431 removed outlier: 3.928A pdb=" N GLY B 427 " --> pdb=" O THR B 440 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL B 447 " --> pdb=" O ILE B 460 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 468 through 474 removed outlier: 3.636A pdb=" N ASN B 470 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B 490 " --> pdb=" O LEU B 503 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 511 through 516 removed outlier: 3.600A pdb=" N GLY B 513 " --> pdb=" O SER B 526 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG B 539 " --> pdb=" O ASP B 549 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP B 549 " --> pdb=" O ARG B 539 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 558 through 564 removed outlier: 4.270A pdb=" N GLY B 560 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR B 579 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 580 " --> pdb=" O VAL B 593 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 603 through 609 removed outlier: 3.668A pdb=" N GLY B 605 " --> pdb=" O THR B 616 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 622 " --> pdb=" O ASP B 617 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 672 through 675 Processing sheet with id=AB8, first strand: chain 'B' and resid 694 through 696 Processing sheet with id=AB9, first strand: chain 'B' and resid 732 through 736 removed outlier: 6.445A pdb=" N VAL B 733 " --> pdb=" O GLY B 720 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLY B 720 " --> pdb=" O VAL B 733 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 742 through 748 removed outlier: 4.131A pdb=" N GLY B 744 " --> pdb=" O SER B 757 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 763 " --> pdb=" O ASP B 758 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE B 764 " --> pdb=" O ILE B 777 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 785 through 791 removed outlier: 4.215A pdb=" N CYS B 787 " --> pdb=" O THR B 800 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN B 796 " --> pdb=" O ASP B 791 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL B 807 " --> pdb=" O ILE B 820 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 827 through 832 removed outlier: 3.948A pdb=" N SER B 829 " --> pdb=" O SER B 842 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE B 850 " --> pdb=" O ILE B 863 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 873 through 877 removed outlier: 4.050A pdb=" N GLY B 873 " --> pdb=" O VAL B 886 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 915 through 921 removed outlier: 4.050A pdb=" N GLY B 917 " --> pdb=" O THR B 928 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE B 935 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ARG B 939 " --> pdb=" O ASP B 945 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASP B 945 " --> pdb=" O ARG B 939 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 986 through 990 Processing sheet with id=AC7, first strand: chain 'B' and resid 1003 through 1005 Processing sheet with id=AC8, first strand: chain 'B' and resid 1029 through 1031 Processing sheet with id=AC9, first strand: chain 'B' and resid 1070 through 1072 Processing sheet with id=AD1, first strand: chain 'B' and resid 1114 through 1116 Processing sheet with id=AD2, first strand: chain 'B' and resid 1155 through 1157 removed outlier: 3.739A pdb=" N ARG B1161 " --> pdb=" O CYS B1157 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1192 through 1194 Processing sheet with id=AD4, first strand: chain 'B' and resid 1235 through 1237 Processing sheet with id=AD5, first strand: chain 'B' and resid 1276 through 1278 Processing sheet with id=AD6, first strand: chain 'B' and resid 3169 through 3171 Processing sheet with id=AD7, first strand: chain 'B' and resid 3184 through 3186 310 hydrogen bonds defined for protein. 783 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.26 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3815 1.34 - 1.46: 2844 1.46 - 1.59: 4940 1.59 - 1.72: 0 1.72 - 1.85: 147 Bond restraints: 11746 Sorted by residual: bond pdb=" N CYS A2823 " pdb=" CA CYS A2823 " ideal model delta sigma weight residual 1.453 1.487 -0.034 9.20e-03 1.18e+04 1.34e+01 bond pdb=" N VAL B1038 " pdb=" CA VAL B1038 " ideal model delta sigma weight residual 1.461 1.491 -0.031 8.70e-03 1.32e+04 1.23e+01 bond pdb=" N ILE A2835 " pdb=" CA ILE A2835 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.70e+00 bond pdb=" N THR A2828 " pdb=" CA THR A2828 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.22e-02 6.72e+03 8.77e+00 bond pdb=" N GLN B1023 " pdb=" CA GLN B1023 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.22e-02 6.72e+03 8.03e+00 ... (remaining 11741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 15503 2.33 - 4.65: 381 4.65 - 6.98: 30 6.98 - 9.30: 6 9.30 - 11.63: 2 Bond angle restraints: 15922 Sorted by residual: angle pdb=" C2 A2G B4706 " pdb=" C1 A2G B4706 " pdb=" O5 A2G B4706 " ideal model delta sigma weight residual 111.38 123.01 -11.63 3.00e+00 1.11e-01 1.50e+01 angle pdb=" CA ARG B 781 " pdb=" C ARG B 781 " pdb=" O ARG B 781 " ideal model delta sigma weight residual 122.03 117.33 4.70 1.25e+00 6.40e-01 1.42e+01 angle pdb=" N THR A2828 " pdb=" CA THR A2828 " pdb=" C THR A2828 " ideal model delta sigma weight residual 109.96 115.50 -5.54 1.50e+00 4.44e-01 1.36e+01 angle pdb=" CA ASP A2826 " pdb=" C ASP A2826 " pdb=" N PHE A2827 " ideal model delta sigma weight residual 118.87 114.57 4.30 1.18e+00 7.18e-01 1.33e+01 angle pdb=" CA GLN B1024 " pdb=" C GLN B1024 " pdb=" O GLN B1024 " ideal model delta sigma weight residual 120.63 116.72 3.91 1.08e+00 8.57e-01 1.31e+01 ... (remaining 15917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.32: 6767 22.32 - 44.65: 565 44.65 - 66.97: 93 66.97 - 89.29: 38 89.29 - 111.62: 9 Dihedral angle restraints: 7472 sinusoidal: 3365 harmonic: 4107 Sorted by residual: dihedral pdb=" CB CYS B 690 " pdb=" SG CYS B 690 " pdb=" SG CYS B 703 " pdb=" CB CYS B 703 " ideal model delta sinusoidal sigma weight residual 93.00 -178.64 -88.36 1 1.00e+01 1.00e-02 9.32e+01 dihedral pdb=" CB CYS B1251 " pdb=" SG CYS B1251 " pdb=" SG CYS B1267 " pdb=" CB CYS B1267 " ideal model delta sinusoidal sigma weight residual 93.00 179.89 -86.89 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CB CYS B1110 " pdb=" SG CYS B1110 " pdb=" SG CYS B1122 " pdb=" CB CYS B1122 " ideal model delta sinusoidal sigma weight residual 93.00 177.05 -84.05 1 1.00e+01 1.00e-02 8.61e+01 ... (remaining 7469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1663 0.107 - 0.213: 68 0.213 - 0.320: 2 0.320 - 0.426: 2 0.426 - 0.533: 2 Chirality restraints: 1737 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O3 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-02 2.50e+03 2.55e+02 chirality pdb=" C1 NAG A4701 " pdb=" ND2 ASN A2782 " pdb=" C2 NAG A4701 " pdb=" O5 NAG A4701 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.10e+00 chirality pdb=" C1 NAG B4702 " pdb=" ND2 ASN B1187 " pdb=" C2 NAG B4702 " pdb=" O5 NAG B4702 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.85e+00 ... (remaining 1734 not shown) Planarity restraints: 2120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " 0.302 2.00e-02 2.50e+03 2.56e-01 8.21e+02 pdb=" C7 NAG F 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.184 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " -0.443 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B4702 " 0.274 2.00e-02 2.50e+03 2.33e-01 6.76e+02 pdb=" C7 NAG B4702 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B4702 " 0.176 2.00e-02 2.50e+03 pdb=" N2 NAG B4702 " -0.398 2.00e-02 2.50e+03 pdb=" O7 NAG B4702 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " 0.259 2.00e-02 2.50e+03 2.16e-01 5.84e+02 pdb=" C7 NAG C 2 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " 0.177 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " -0.361 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " -0.005 2.00e-02 2.50e+03 ... (remaining 2117 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 384 2.68 - 3.24: 11870 3.24 - 3.79: 17887 3.79 - 4.35: 24550 4.35 - 4.90: 39595 Nonbonded interactions: 94286 Sorted by model distance: nonbonded pdb=" OD2 ASP B1262 " pdb="CA CA B4721 " model vdw 2.130 2.510 nonbonded pdb=" OD1 ASP B1252 " pdb="CA CA B4721 " model vdw 2.139 2.510 nonbonded pdb=" OD1 ASP B1045 " pdb="CA CA B4716 " model vdw 2.170 2.510 nonbonded pdb=" OD2 ASP B1055 " pdb="CA CA B4716 " model vdw 2.173 2.510 nonbonded pdb=" OD2 ASP A2731 " pdb="CA CA A4704 " model vdw 2.194 2.510 ... (remaining 94281 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 'C' selection = chain 'F' } 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: 1.080 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.890 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 : 0.007 0.403 11823 Z= 0.586 Angle : 0.887 20.179 16074 Z= 0.471 Chirality : 0.055 0.533 1737 Planarity : 0.011 0.256 2112 Dihedral : 16.883 111.618 4674 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.58 % Favored : 93.35 % Rotamer: Outliers : 2.62 % Allowed : 17.62 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.22), residues: 1414 helix: 0.97 (0.49), residues: 115 sheet: -1.01 (0.30), residues: 266 loop : -0.85 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 270 HIS 0.005 0.001 HIS B 638 PHE 0.031 0.001 PHE B1193 TYR 0.016 0.002 TYR B 650 ARG 0.008 0.000 ARG A2779 Details of bonding type rmsd link_NAG-ASN : bond 0.01680 ( 8) link_NAG-ASN : angle 8.46659 ( 24) link_ALPHA1-6 : bond 0.00228 ( 1) link_ALPHA1-6 : angle 0.74739 ( 3) link_BETA1-4 : bond 0.01530 ( 4) link_BETA1-4 : angle 3.93514 ( 12) link_ALPHA1-3 : bond 0.01440 ( 1) link_ALPHA1-3 : angle 1.92581 ( 3) hydrogen bonds : bond 0.23172 ( 310) hydrogen bonds : angle 9.13251 ( 783) SS BOND : bond 0.00327 ( 52) SS BOND : angle 0.94072 ( 104) link_BETA1-3 : bond 0.01122 ( 2) link_BETA1-3 : angle 3.75065 ( 6) covalent geometry : bond 0.00469 (11746) covalent geometry : angle 0.81403 (15922) Misc. bond : bond 0.18862 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 363 ASN cc_start: 0.7267 (OUTLIER) cc_final: 0.6851 (t0) outliers start: 33 outliers final: 26 residues processed: 121 average time/residue: 0.2593 time to fit residues: 45.6884 Evaluate side-chains 112 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain A residue 2741 THR Chi-restraints excluded: chain A residue 2781 CYS Chi-restraints excluded: chain A residue 2812 THR Chi-restraints excluded: chain A residue 2837 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 311 CYS Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 899 ASP Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain B residue 3169 CYS Chi-restraints excluded: chain B residue 3187 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 0.2980 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 0.2980 chunk 82 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 294 HIS A2808 HIS B 315 ASN B 412 ASN B 431 HIS B 507 ASN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 826 ASN B1192 GLN B1283 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.138635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.093235 restraints weight = 18993.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.095223 restraints weight = 11900.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.096465 restraints weight = 9140.425| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11823 Z= 0.153 Angle : 0.728 21.456 16074 Z= 0.354 Chirality : 0.049 0.497 1737 Planarity : 0.005 0.040 2112 Dihedral : 10.695 79.794 2093 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 4.21 % Allowed : 15.71 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.22), residues: 1414 helix: 1.50 (0.48), residues: 112 sheet: -0.96 (0.30), residues: 261 loop : -0.82 (0.20), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 885 HIS 0.006 0.001 HIS B 638 PHE 0.015 0.001 PHE B 986 TYR 0.021 0.002 TYR D 339 ARG 0.003 0.000 ARG A2779 Details of bonding type rmsd link_NAG-ASN : bond 0.01314 ( 8) link_NAG-ASN : angle 7.78649 ( 24) link_ALPHA1-6 : bond 0.00825 ( 1) link_ALPHA1-6 : angle 1.38748 ( 3) link_BETA1-4 : bond 0.01184 ( 4) link_BETA1-4 : angle 4.02947 ( 12) link_ALPHA1-3 : bond 0.01717 ( 1) link_ALPHA1-3 : angle 1.04528 ( 3) hydrogen bonds : bond 0.04758 ( 310) hydrogen bonds : angle 6.48212 ( 783) SS BOND : bond 0.00339 ( 52) SS BOND : angle 0.97605 ( 104) link_BETA1-3 : bond 0.01480 ( 2) link_BETA1-3 : angle 3.78692 ( 6) covalent geometry : bond 0.00335 (11746) covalent geometry : angle 0.64703 (15922) Misc. bond : bond 0.00311 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 103 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: D 290 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7985 (tppt) REVERT: A 2793 ARG cc_start: 0.8361 (mtp-110) cc_final: 0.7789 (mtp-110) REVERT: A 2815 GLU cc_start: 0.6361 (mm-30) cc_final: 0.6155 (mm-30) REVERT: B 187 GLU cc_start: 0.3636 (OUTLIER) cc_final: 0.3042 (mp0) REVERT: B 608 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9081 (pp) REVERT: B 617 ASP cc_start: 0.8149 (t0) cc_final: 0.7764 (t0) REVERT: B 643 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7638 (mmt-90) REVERT: B 657 ASN cc_start: 0.7843 (OUTLIER) cc_final: 0.7579 (m110) REVERT: B 671 GLN cc_start: 0.8567 (mt0) cc_final: 0.8191 (mt0) REVERT: B 918 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8861 (pt) REVERT: B 1028 LEU cc_start: 0.8709 (tt) cc_final: 0.8504 (tt) REVERT: B 1215 ARG cc_start: 0.7585 (mtp180) cc_final: 0.7216 (ttm170) REVERT: B 1285 ILE cc_start: 0.6883 (OUTLIER) cc_final: 0.6587 (tp) REVERT: B 3187 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7446 (mp0) outliers start: 53 outliers final: 30 residues processed: 145 average time/residue: 0.2312 time to fit residues: 48.5242 Evaluate side-chains 130 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 92 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 290 LYS Chi-restraints excluded: chain D residue 344 HIS Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain A residue 2733 LEU Chi-restraints excluded: chain A residue 2777 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 311 CYS Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 899 ASP Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 946 MET Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1285 ILE Chi-restraints excluded: chain B residue 1300 MET Chi-restraints excluded: chain B residue 1312 HIS Chi-restraints excluded: chain B residue 3187 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 84 optimal weight: 0.1980 chunk 32 optimal weight: 4.9990 chunk 108 optimal weight: 0.0570 chunk 131 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 ASN B 433 GLN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.139424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.097639 restraints weight = 19186.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.096348 restraints weight = 11736.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.096899 restraints weight = 10068.278| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11823 Z= 0.130 Angle : 0.682 20.308 16074 Z= 0.333 Chirality : 0.048 0.487 1737 Planarity : 0.004 0.042 2112 Dihedral : 9.282 73.395 2074 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 5.00 % Allowed : 15.48 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.22), residues: 1414 helix: 1.60 (0.48), residues: 112 sheet: -0.90 (0.30), residues: 257 loop : -0.80 (0.20), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 799 HIS 0.005 0.001 HIS B 638 PHE 0.012 0.001 PHE B 525 TYR 0.014 0.001 TYR D 339 ARG 0.005 0.000 ARG B 846 Details of bonding type rmsd link_NAG-ASN : bond 0.01354 ( 8) link_NAG-ASN : angle 7.16345 ( 24) link_ALPHA1-6 : bond 0.00909 ( 1) link_ALPHA1-6 : angle 1.37764 ( 3) link_BETA1-4 : bond 0.01227 ( 4) link_BETA1-4 : angle 3.77982 ( 12) link_ALPHA1-3 : bond 0.01514 ( 1) link_ALPHA1-3 : angle 0.94605 ( 3) hydrogen bonds : bond 0.03912 ( 310) hydrogen bonds : angle 6.04882 ( 783) SS BOND : bond 0.00266 ( 52) SS BOND : angle 1.14656 ( 104) link_BETA1-3 : bond 0.01788 ( 2) link_BETA1-3 : angle 4.02941 ( 6) covalent geometry : bond 0.00282 (11746) covalent geometry : angle 0.60528 (15922) Misc. bond : bond 0.00251 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 101 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 290 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7959 (tppt) REVERT: A 2793 ARG cc_start: 0.8397 (mtp-110) cc_final: 0.7589 (mtp-110) REVERT: B 253 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: B 315 ASN cc_start: 0.7956 (m-40) cc_final: 0.7727 (m-40) REVERT: B 335 HIS cc_start: 0.6740 (OUTLIER) cc_final: 0.6265 (m90) REVERT: B 617 ASP cc_start: 0.8096 (t0) cc_final: 0.7757 (t0) REVERT: B 643 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7622 (mmt-90) REVERT: B 657 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7610 (m-40) REVERT: B 671 GLN cc_start: 0.8485 (mt0) cc_final: 0.8059 (mt0) REVERT: B 736 THR cc_start: 0.8752 (m) cc_final: 0.8544 (m) REVERT: B 918 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8757 (pt) REVERT: B 1028 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8414 (tt) REVERT: B 3187 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7407 (mp0) outliers start: 63 outliers final: 42 residues processed: 151 average time/residue: 0.2550 time to fit residues: 54.2822 Evaluate side-chains 140 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 90 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 290 LYS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 344 HIS Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain A residue 2733 LEU Chi-restraints excluded: chain A residue 2740 HIS Chi-restraints excluded: chain A residue 2777 LEU Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 783 GLU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 899 ASP Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 946 MET Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain B residue 1112 SER Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain B residue 1175 CYS Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1251 CYS Chi-restraints excluded: chain B residue 1300 MET Chi-restraints excluded: chain B residue 3187 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 268 GLN A2740 HIS ** A2821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.138040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.097369 restraints weight = 18976.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.095116 restraints weight = 12367.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.095469 restraints weight = 10170.827| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11823 Z= 0.166 Angle : 0.687 20.456 16074 Z= 0.337 Chirality : 0.049 0.483 1737 Planarity : 0.004 0.041 2112 Dihedral : 8.799 68.905 2072 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.40 % Allowed : 15.63 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.22), residues: 1414 helix: 1.58 (0.47), residues: 112 sheet: -1.03 (0.30), residues: 261 loop : -0.75 (0.20), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 885 HIS 0.006 0.001 HIS B 638 PHE 0.015 0.001 PHE B 986 TYR 0.015 0.001 TYR A2757 ARG 0.005 0.000 ARG B 846 Details of bonding type rmsd link_NAG-ASN : bond 0.01329 ( 8) link_NAG-ASN : angle 7.00424 ( 24) link_ALPHA1-6 : bond 0.00948 ( 1) link_ALPHA1-6 : angle 1.15639 ( 3) link_BETA1-4 : bond 0.01042 ( 4) link_BETA1-4 : angle 3.64944 ( 12) link_ALPHA1-3 : bond 0.01288 ( 1) link_ALPHA1-3 : angle 1.10674 ( 3) hydrogen bonds : bond 0.03758 ( 310) hydrogen bonds : angle 5.93500 ( 783) SS BOND : bond 0.00321 ( 52) SS BOND : angle 1.01102 ( 104) link_BETA1-3 : bond 0.01617 ( 2) link_BETA1-3 : angle 3.69030 ( 6) covalent geometry : bond 0.00376 (11746) covalent geometry : angle 0.61666 (15922) Misc. bond : bond 0.00092 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 98 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: D 290 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7965 (tppt) REVERT: A 2753 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.6984 (mmt90) REVERT: A 2793 ARG cc_start: 0.8365 (mtp-110) cc_final: 0.7567 (mtp-110) REVERT: B 253 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: B 335 HIS cc_start: 0.6881 (OUTLIER) cc_final: 0.6329 (m90) REVERT: B 617 ASP cc_start: 0.8104 (t0) cc_final: 0.7813 (t0) REVERT: B 643 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7676 (mmt-90) REVERT: B 657 ASN cc_start: 0.7735 (OUTLIER) cc_final: 0.7390 (m-40) REVERT: B 736 THR cc_start: 0.8824 (m) cc_final: 0.8617 (m) REVERT: B 918 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8734 (pt) REVERT: B 1028 LEU cc_start: 0.8823 (tt) cc_final: 0.8552 (tt) REVERT: B 1089 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.6871 (mp10) REVERT: B 3187 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7534 (mp0) outliers start: 68 outliers final: 47 residues processed: 152 average time/residue: 0.2431 time to fit residues: 52.5562 Evaluate side-chains 149 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 93 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 290 LYS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 344 HIS Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain A residue 2733 LEU Chi-restraints excluded: chain A residue 2753 ARG Chi-restraints excluded: chain A residue 2777 LEU Chi-restraints excluded: chain A residue 2781 CYS Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 311 CYS Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 899 ASP Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 946 MET Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1074 VAL Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1112 SER Chi-restraints excluded: chain B residue 1121 VAL Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain B residue 1175 CYS Chi-restraints excluded: chain B residue 1185 VAL Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1251 CYS Chi-restraints excluded: chain B residue 1300 MET Chi-restraints excluded: chain B residue 1312 HIS Chi-restraints excluded: chain B residue 3169 CYS Chi-restraints excluded: chain B residue 3187 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 32 optimal weight: 6.9990 chunk 106 optimal weight: 0.0570 chunk 2 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 268 GLN D 271 ASN D 305 HIS ** A2821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.136115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.090805 restraints weight = 18976.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.092718 restraints weight = 12123.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.093876 restraints weight = 9411.572| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11823 Z= 0.230 Angle : 0.727 20.386 16074 Z= 0.360 Chirality : 0.050 0.477 1737 Planarity : 0.005 0.045 2112 Dihedral : 8.726 66.900 2069 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 5.48 % Allowed : 15.71 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.22), residues: 1414 helix: 1.49 (0.47), residues: 112 sheet: -1.11 (0.30), residues: 259 loop : -0.87 (0.20), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 885 HIS 0.008 0.001 HIS B 638 PHE 0.023 0.002 PHE B1193 TYR 0.016 0.002 TYR A2757 ARG 0.006 0.001 ARG B 343 Details of bonding type rmsd link_NAG-ASN : bond 0.01395 ( 8) link_NAG-ASN : angle 6.84872 ( 24) link_ALPHA1-6 : bond 0.01098 ( 1) link_ALPHA1-6 : angle 1.03694 ( 3) link_BETA1-4 : bond 0.01046 ( 4) link_BETA1-4 : angle 3.50674 ( 12) link_ALPHA1-3 : bond 0.01107 ( 1) link_ALPHA1-3 : angle 1.16180 ( 3) hydrogen bonds : bond 0.03922 ( 310) hydrogen bonds : angle 6.00749 ( 783) SS BOND : bond 0.00392 ( 52) SS BOND : angle 1.16183 ( 104) link_BETA1-3 : bond 0.01700 ( 2) link_BETA1-3 : angle 3.84835 ( 6) covalent geometry : bond 0.00534 (11746) covalent geometry : angle 0.66239 (15922) Misc. bond : bond 0.00180 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 93 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: D 290 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.8041 (tppt) REVERT: A 2753 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.6945 (mmt90) REVERT: A 2793 ARG cc_start: 0.8263 (mtp-110) cc_final: 0.7494 (mtp-110) REVERT: B 187 GLU cc_start: 0.3287 (OUTLIER) cc_final: 0.2749 (mp0) REVERT: B 335 HIS cc_start: 0.6858 (OUTLIER) cc_final: 0.6380 (m90) REVERT: B 608 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9180 (pp) REVERT: B 617 ASP cc_start: 0.8244 (t0) cc_final: 0.7915 (t0) REVERT: B 643 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.7667 (mmt-90) REVERT: B 899 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7570 (t0) REVERT: B 918 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8853 (pt) REVERT: B 927 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8727 (mp) REVERT: B 1088 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6769 (mtp-110) REVERT: B 3187 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7535 (mp0) outliers start: 69 outliers final: 51 residues processed: 147 average time/residue: 0.2584 time to fit residues: 53.8299 Evaluate side-chains 151 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 89 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 290 LYS Chi-restraints excluded: chain D residue 305 HIS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 344 HIS Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain A residue 2733 LEU Chi-restraints excluded: chain A residue 2740 HIS Chi-restraints excluded: chain A residue 2753 ARG Chi-restraints excluded: chain A residue 2777 LEU Chi-restraints excluded: chain A residue 2781 CYS Chi-restraints excluded: chain A residue 2835 ILE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 311 CYS Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 899 ASP Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 946 MET Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1074 VAL Chi-restraints excluded: chain B residue 1088 ARG Chi-restraints excluded: chain B residue 1100 ASN Chi-restraints excluded: chain B residue 1112 SER Chi-restraints excluded: chain B residue 1121 VAL Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain B residue 1175 CYS Chi-restraints excluded: chain B residue 1185 VAL Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1234 ASP Chi-restraints excluded: chain B residue 1251 CYS Chi-restraints excluded: chain B residue 1300 MET Chi-restraints excluded: chain B residue 1312 HIS Chi-restraints excluded: chain B residue 3187 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 268 GLN ** A2821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.137450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.092088 restraints weight = 19226.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.094003 restraints weight = 12018.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.095201 restraints weight = 9278.747| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11823 Z= 0.156 Angle : 0.677 20.289 16074 Z= 0.334 Chirality : 0.048 0.467 1737 Planarity : 0.004 0.042 2112 Dihedral : 8.443 64.361 2067 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 5.40 % Allowed : 16.03 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.22), residues: 1414 helix: 1.65 (0.47), residues: 113 sheet: -0.95 (0.30), residues: 255 loop : -0.84 (0.20), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 885 HIS 0.010 0.001 HIS D 305 PHE 0.021 0.001 PHE B1193 TYR 0.014 0.002 TYR A2757 ARG 0.003 0.000 ARG B 343 Details of bonding type rmsd link_NAG-ASN : bond 0.01272 ( 8) link_NAG-ASN : angle 6.65996 ( 24) link_ALPHA1-6 : bond 0.00839 ( 1) link_ALPHA1-6 : angle 1.07126 ( 3) link_BETA1-4 : bond 0.01048 ( 4) link_BETA1-4 : angle 3.37696 ( 12) link_ALPHA1-3 : bond 0.01163 ( 1) link_ALPHA1-3 : angle 1.29591 ( 3) hydrogen bonds : bond 0.03611 ( 310) hydrogen bonds : angle 5.86844 ( 783) SS BOND : bond 0.00331 ( 52) SS BOND : angle 0.94314 ( 104) link_BETA1-3 : bond 0.01530 ( 2) link_BETA1-3 : angle 3.75007 ( 6) covalent geometry : bond 0.00350 (11746) covalent geometry : angle 0.61298 (15922) Misc. bond : bond 0.00258 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 92 time to evaluate : 1.305 Fit side-chains revert: symmetry clash REVERT: D 290 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.8018 (tppt) REVERT: A 2753 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.6917 (mmt90) REVERT: B 253 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: B 335 HIS cc_start: 0.6724 (OUTLIER) cc_final: 0.6349 (m90) REVERT: B 608 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9137 (pp) REVERT: B 617 ASP cc_start: 0.8143 (t0) cc_final: 0.7848 (t0) REVERT: B 643 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7614 (mmt-90) REVERT: B 918 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8831 (pt) REVERT: B 927 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8594 (mp) REVERT: B 1088 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6776 (mtp-110) REVERT: B 1089 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.6893 (mp10) REVERT: B 3187 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7495 (mp0) outliers start: 68 outliers final: 48 residues processed: 146 average time/residue: 0.2334 time to fit residues: 49.5147 Evaluate side-chains 148 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 89 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 290 LYS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 344 HIS Chi-restraints excluded: chain A residue 2733 LEU Chi-restraints excluded: chain A residue 2740 HIS Chi-restraints excluded: chain A residue 2753 ARG Chi-restraints excluded: chain A residue 2755 VAL Chi-restraints excluded: chain A residue 2777 LEU Chi-restraints excluded: chain A residue 2781 CYS Chi-restraints excluded: chain A residue 2835 ILE Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 311 CYS Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 946 MET Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1074 VAL Chi-restraints excluded: chain B residue 1088 ARG Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1112 SER Chi-restraints excluded: chain B residue 1121 VAL Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain B residue 1164 SER Chi-restraints excluded: chain B residue 1175 CYS Chi-restraints excluded: chain B residue 1185 VAL Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1251 CYS Chi-restraints excluded: chain B residue 1300 MET Chi-restraints excluded: chain B residue 1312 HIS Chi-restraints excluded: chain B residue 3187 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 22 optimal weight: 0.0370 chunk 83 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 123 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 268 GLN ** A2821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.138509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.097318 restraints weight = 19193.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.096391 restraints weight = 12600.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.096241 restraints weight = 10715.818| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11823 Z= 0.126 Angle : 0.646 19.984 16074 Z= 0.318 Chirality : 0.047 0.456 1737 Planarity : 0.004 0.040 2112 Dihedral : 7.848 59.414 2065 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 4.92 % Allowed : 16.43 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.22), residues: 1414 helix: 1.88 (0.47), residues: 112 sheet: -0.84 (0.30), residues: 256 loop : -0.78 (0.20), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 799 HIS 0.005 0.001 HIS B 638 PHE 0.023 0.001 PHE B1193 TYR 0.012 0.001 TYR B 318 ARG 0.003 0.000 ARG B 343 Details of bonding type rmsd link_NAG-ASN : bond 0.01213 ( 8) link_NAG-ASN : angle 6.46122 ( 24) link_ALPHA1-6 : bond 0.00866 ( 1) link_ALPHA1-6 : angle 1.16008 ( 3) link_BETA1-4 : bond 0.01077 ( 4) link_BETA1-4 : angle 3.21992 ( 12) link_ALPHA1-3 : bond 0.01041 ( 1) link_ALPHA1-3 : angle 1.24182 ( 3) hydrogen bonds : bond 0.03301 ( 310) hydrogen bonds : angle 5.69026 ( 783) SS BOND : bond 0.00257 ( 52) SS BOND : angle 0.85238 ( 104) link_BETA1-3 : bond 0.01510 ( 2) link_BETA1-3 : angle 3.62915 ( 6) covalent geometry : bond 0.00278 (11746) covalent geometry : angle 0.58375 (15922) Misc. bond : bond 0.00183 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 93 time to evaluate : 1.321 Fit side-chains revert: symmetry clash REVERT: B 253 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: B 335 HIS cc_start: 0.6582 (OUTLIER) cc_final: 0.6227 (m90) REVERT: B 617 ASP cc_start: 0.8112 (t0) cc_final: 0.7822 (t0) REVERT: B 643 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7633 (mmt-90) REVERT: B 918 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8786 (pt) REVERT: B 927 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8594 (mp) REVERT: B 1088 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6781 (mtp-110) REVERT: B 1089 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.6826 (mp10) outliers start: 62 outliers final: 45 residues processed: 141 average time/residue: 0.2390 time to fit residues: 49.0428 Evaluate side-chains 140 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 88 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 344 HIS Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain A residue 2733 LEU Chi-restraints excluded: chain A residue 2740 HIS Chi-restraints excluded: chain A residue 2777 LEU Chi-restraints excluded: chain A residue 2781 CYS Chi-restraints excluded: chain A residue 2835 ILE Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 311 CYS Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 946 MET Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1074 VAL Chi-restraints excluded: chain B residue 1088 ARG Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1100 ASN Chi-restraints excluded: chain B residue 1121 VAL Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain B residue 1164 SER Chi-restraints excluded: chain B residue 1175 CYS Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1251 CYS Chi-restraints excluded: chain B residue 1300 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 68 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 129 optimal weight: 0.0670 chunk 102 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 38 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 268 GLN ** A2821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.137949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.096450 restraints weight = 18886.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.096319 restraints weight = 11882.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.096409 restraints weight = 9707.224| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11823 Z= 0.141 Angle : 0.656 19.829 16074 Z= 0.324 Chirality : 0.048 0.449 1737 Planarity : 0.004 0.041 2112 Dihedral : 7.610 58.731 2062 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 5.16 % Allowed : 15.95 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.22), residues: 1414 helix: 1.89 (0.47), residues: 112 sheet: -0.81 (0.31), residues: 256 loop : -0.79 (0.20), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 799 HIS 0.005 0.001 HIS B 638 PHE 0.024 0.001 PHE B1193 TYR 0.021 0.001 TYR B 318 ARG 0.003 0.000 ARG B 268 Details of bonding type rmsd link_NAG-ASN : bond 0.01221 ( 8) link_NAG-ASN : angle 6.34739 ( 24) link_ALPHA1-6 : bond 0.00887 ( 1) link_ALPHA1-6 : angle 1.15152 ( 3) link_BETA1-4 : bond 0.01056 ( 4) link_BETA1-4 : angle 3.11854 ( 12) link_ALPHA1-3 : bond 0.00962 ( 1) link_ALPHA1-3 : angle 1.20019 ( 3) hydrogen bonds : bond 0.03305 ( 310) hydrogen bonds : angle 5.64149 ( 783) SS BOND : bond 0.00264 ( 52) SS BOND : angle 1.05546 ( 104) link_BETA1-3 : bond 0.01543 ( 2) link_BETA1-3 : angle 3.58095 ( 6) covalent geometry : bond 0.00318 (11746) covalent geometry : angle 0.59469 (15922) Misc. bond : bond 0.00227 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 92 time to evaluate : 1.264 Fit side-chains revert: symmetry clash REVERT: A 2753 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.6889 (mmt90) REVERT: B 253 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: B 335 HIS cc_start: 0.6689 (OUTLIER) cc_final: 0.6383 (m90) REVERT: B 617 ASP cc_start: 0.8036 (t0) cc_final: 0.7774 (t0) REVERT: B 643 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.7674 (mmt-90) REVERT: B 918 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8775 (pt) REVERT: B 927 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8599 (mp) REVERT: B 1088 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6819 (mtp-110) REVERT: B 1089 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.6867 (mp10) outliers start: 65 outliers final: 52 residues processed: 142 average time/residue: 0.2314 time to fit residues: 47.9425 Evaluate side-chains 148 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 88 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 344 HIS Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain A residue 2733 LEU Chi-restraints excluded: chain A residue 2740 HIS Chi-restraints excluded: chain A residue 2753 ARG Chi-restraints excluded: chain A residue 2755 VAL Chi-restraints excluded: chain A residue 2777 LEU Chi-restraints excluded: chain A residue 2781 CYS Chi-restraints excluded: chain A residue 2835 ILE Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 311 CYS Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 783 GLU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 946 MET Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1074 VAL Chi-restraints excluded: chain B residue 1088 ARG Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1100 ASN Chi-restraints excluded: chain B residue 1121 VAL Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain B residue 1164 SER Chi-restraints excluded: chain B residue 1175 CYS Chi-restraints excluded: chain B residue 1185 VAL Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1251 CYS Chi-restraints excluded: chain B residue 1300 MET Chi-restraints excluded: chain B residue 1312 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 25 optimal weight: 0.3980 chunk 122 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 268 GLN ** A2821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.136545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.095325 restraints weight = 18994.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.094571 restraints weight = 12724.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.094679 restraints weight = 10266.995| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11823 Z= 0.186 Angle : 0.681 19.625 16074 Z= 0.337 Chirality : 0.049 0.449 1737 Planarity : 0.004 0.043 2112 Dihedral : 7.824 58.124 2062 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 5.08 % Allowed : 15.95 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.22), residues: 1414 helix: 1.76 (0.46), residues: 115 sheet: -0.97 (0.31), residues: 260 loop : -0.79 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 885 HIS 0.007 0.001 HIS B 638 PHE 0.025 0.001 PHE B1193 TYR 0.019 0.002 TYR B 318 ARG 0.004 0.000 ARG A2779 Details of bonding type rmsd link_NAG-ASN : bond 0.01260 ( 8) link_NAG-ASN : angle 6.30876 ( 24) link_ALPHA1-6 : bond 0.00879 ( 1) link_ALPHA1-6 : angle 1.14028 ( 3) link_BETA1-4 : bond 0.00989 ( 4) link_BETA1-4 : angle 3.06253 ( 12) link_ALPHA1-3 : bond 0.00934 ( 1) link_ALPHA1-3 : angle 1.21857 ( 3) hydrogen bonds : bond 0.03463 ( 310) hydrogen bonds : angle 5.70787 ( 783) SS BOND : bond 0.00302 ( 52) SS BOND : angle 1.09184 ( 104) link_BETA1-3 : bond 0.01544 ( 2) link_BETA1-3 : angle 3.59315 ( 6) covalent geometry : bond 0.00429 (11746) covalent geometry : angle 0.62295 (15922) Misc. bond : bond 0.00209 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 88 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: A 2835 ILE cc_start: 0.2916 (OUTLIER) cc_final: 0.2680 (pp) REVERT: B 253 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: B 335 HIS cc_start: 0.7060 (OUTLIER) cc_final: 0.6645 (m90) REVERT: B 608 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9171 (pp) REVERT: B 617 ASP cc_start: 0.8186 (t0) cc_final: 0.7900 (t0) REVERT: B 643 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.7683 (mmt-90) REVERT: B 918 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8751 (pt) REVERT: B 927 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8628 (mp) REVERT: B 1088 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6864 (mtp-110) REVERT: B 1089 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.6847 (mp10) outliers start: 64 outliers final: 50 residues processed: 138 average time/residue: 0.2324 time to fit residues: 46.9838 Evaluate side-chains 146 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 87 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 344 HIS Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain A residue 2733 LEU Chi-restraints excluded: chain A residue 2740 HIS Chi-restraints excluded: chain A residue 2755 VAL Chi-restraints excluded: chain A residue 2777 LEU Chi-restraints excluded: chain A residue 2781 CYS Chi-restraints excluded: chain A residue 2835 ILE Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 311 CYS Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 946 MET Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1074 VAL Chi-restraints excluded: chain B residue 1088 ARG Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1100 ASN Chi-restraints excluded: chain B residue 1121 VAL Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain B residue 1164 SER Chi-restraints excluded: chain B residue 1185 VAL Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1234 ASP Chi-restraints excluded: chain B residue 1251 CYS Chi-restraints excluded: chain B residue 1300 MET Chi-restraints excluded: chain B residue 1312 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 40 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 48 optimal weight: 0.1980 chunk 98 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 chunk 108 optimal weight: 0.0170 chunk 44 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.138451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.093282 restraints weight = 18983.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.095269 restraints weight = 11922.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.096506 restraints weight = 9187.915| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11823 Z= 0.131 Angle : 0.650 19.602 16074 Z= 0.321 Chirality : 0.047 0.441 1737 Planarity : 0.004 0.041 2112 Dihedral : 7.618 59.608 2062 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 4.76 % Allowed : 16.27 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.22), residues: 1414 helix: 1.91 (0.47), residues: 112 sheet: -0.84 (0.31), residues: 258 loop : -0.77 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 799 HIS 0.005 0.001 HIS B 638 PHE 0.025 0.001 PHE B1193 TYR 0.020 0.001 TYR B 318 ARG 0.003 0.000 ARG B 268 Details of bonding type rmsd link_NAG-ASN : bond 0.01205 ( 8) link_NAG-ASN : angle 6.19569 ( 24) link_ALPHA1-6 : bond 0.00863 ( 1) link_ALPHA1-6 : angle 1.17306 ( 3) link_BETA1-4 : bond 0.01040 ( 4) link_BETA1-4 : angle 2.99840 ( 12) link_ALPHA1-3 : bond 0.00979 ( 1) link_ALPHA1-3 : angle 1.27229 ( 3) hydrogen bonds : bond 0.03215 ( 310) hydrogen bonds : angle 5.60339 ( 783) SS BOND : bond 0.00249 ( 52) SS BOND : angle 0.89542 ( 104) link_BETA1-3 : bond 0.01446 ( 2) link_BETA1-3 : angle 3.48283 ( 6) covalent geometry : bond 0.00295 (11746) covalent geometry : angle 0.59272 (15922) Misc. bond : bond 0.00162 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 88 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: A 2835 ILE cc_start: 0.3001 (OUTLIER) cc_final: 0.2782 (pp) REVERT: B 253 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: B 335 HIS cc_start: 0.6749 (OUTLIER) cc_final: 0.6438 (m90) REVERT: B 617 ASP cc_start: 0.8048 (t0) cc_final: 0.7759 (t0) REVERT: B 643 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7605 (mmt-90) REVERT: B 918 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8836 (pt) REVERT: B 927 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8572 (mp) REVERT: B 1088 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6790 (mtp-110) REVERT: B 1089 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.6885 (mp10) REVERT: B 1201 CYS cc_start: 0.6080 (OUTLIER) cc_final: 0.5760 (m) outliers start: 60 outliers final: 45 residues processed: 133 average time/residue: 0.2312 time to fit residues: 45.4734 Evaluate side-chains 142 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 88 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 344 HIS Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain A residue 2733 LEU Chi-restraints excluded: chain A residue 2740 HIS Chi-restraints excluded: chain A residue 2755 VAL Chi-restraints excluded: chain A residue 2777 LEU Chi-restraints excluded: chain A residue 2781 CYS Chi-restraints excluded: chain A residue 2835 ILE Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 311 CYS Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 946 MET Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1074 VAL Chi-restraints excluded: chain B residue 1088 ARG Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1100 ASN Chi-restraints excluded: chain B residue 1121 VAL Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain B residue 1164 SER Chi-restraints excluded: chain B residue 1185 VAL Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1251 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 58 optimal weight: 0.0070 chunk 38 optimal weight: 0.0670 chunk 133 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 80 optimal weight: 0.0970 chunk 140 optimal weight: 4.9990 chunk 96 optimal weight: 0.0170 chunk 83 optimal weight: 0.5980 overall best weight: 0.1572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.141242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.095982 restraints weight = 18875.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.098107 restraints weight = 11202.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.099417 restraints weight = 8444.312| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11823 Z= 0.107 Angle : 0.616 19.542 16074 Z= 0.303 Chirality : 0.046 0.429 1737 Planarity : 0.004 0.036 2112 Dihedral : 7.016 58.851 2062 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.17 % Allowed : 17.62 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.23), residues: 1414 helix: 1.98 (0.48), residues: 114 sheet: -0.84 (0.31), residues: 263 loop : -0.65 (0.20), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 885 HIS 0.003 0.001 HIS B 638 PHE 0.025 0.001 PHE B1193 TYR 0.016 0.001 TYR B 318 ARG 0.003 0.000 ARG B 367 Details of bonding type rmsd link_NAG-ASN : bond 0.01165 ( 8) link_NAG-ASN : angle 5.97565 ( 24) link_ALPHA1-6 : bond 0.00799 ( 1) link_ALPHA1-6 : angle 1.22359 ( 3) link_BETA1-4 : bond 0.01092 ( 4) link_BETA1-4 : angle 2.91809 ( 12) link_ALPHA1-3 : bond 0.00932 ( 1) link_ALPHA1-3 : angle 1.24610 ( 3) hydrogen bonds : bond 0.02909 ( 310) hydrogen bonds : angle 5.38842 ( 783) SS BOND : bond 0.00217 ( 52) SS BOND : angle 0.71569 ( 104) link_BETA1-3 : bond 0.01319 ( 2) link_BETA1-3 : angle 3.31117 ( 6) covalent geometry : bond 0.00227 (11746) covalent geometry : angle 0.56051 (15922) Misc. bond : bond 0.00172 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3861.16 seconds wall clock time: 68 minutes 12.05 seconds (4092.05 seconds total)