Starting phenix.real_space_refine on Sun Dec 29 22:16:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxi_36702/12_2024/8jxi_36702.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxi_36702/12_2024/8jxi_36702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jxi_36702/12_2024/8jxi_36702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxi_36702/12_2024/8jxi_36702.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxi_36702/12_2024/8jxi_36702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxi_36702/12_2024/8jxi_36702.cif" } resolution = 3.4 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 2002 2.21 5 O 2345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11506 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" 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: 9053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1167, 9053 Classifications: {'peptide': 1167} Link IDs: {'PTRANS': 57, 'TRANS': 1109} Chain breaks: 1 Chain: "B" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1124 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 9, 'TRANS': 138} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: "F" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 Chain: "B" 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 Time building chain proxies: 7.02, per 1000 atoms: 0.61 Number of scatterers: 11506 At special positions: 0 Unit cell: (142.511, 129.812, 143.922, 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 2345 8.00 N 2002 7.00 C 7014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=53, symmetry=0 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 208 " distance=2.03 Simple disulfide: pdb=" SG CYS A 202 " - pdb=" SG CYS A 217 " distance=2.03 Simple disulfide: pdb=" SG CYS A 222 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 272 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 285 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 329 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 345 " distance=2.04 Simple disulfide: pdb=" SG CYS A 351 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 357 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 384 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 673 " distance=2.03 Simple disulfide: pdb=" SG CYS A 669 " - pdb=" SG CYS A 688 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 703 " distance=2.03 Simple disulfide: pdb=" SG CYS A 973 " - pdb=" SG CYS A 987 " distance=2.03 Simple disulfide: pdb=" SG CYS A 983 " - pdb=" SG CYS A 997 " distance=2.03 Simple disulfide: pdb=" SG CYS A 999 " - pdb=" SG CYS A1012 " distance=2.03 Simple disulfide: pdb=" SG CYS A1025 " - pdb=" SG CYS A1037 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1050 " distance=2.03 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1059 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1079 " distance=2.03 Simple disulfide: pdb=" SG CYS A1073 " - pdb=" SG CYS A1092 " distance=2.03 Simple disulfide: pdb=" SG CYS A1086 " - pdb=" SG CYS A1101 " distance=2.03 Simple disulfide: pdb=" SG CYS A1110 " - pdb=" SG CYS A1122 " distance=2.03 Simple disulfide: pdb=" SG CYS A1117 " - pdb=" SG CYS A1135 " distance=2.03 Simple disulfide: pdb=" SG CYS A1129 " - pdb=" SG CYS A1144 " distance=2.03 Simple disulfide: pdb=" SG CYS A1150 " - pdb=" SG CYS A1162 " distance=2.03 Simple disulfide: pdb=" SG CYS A1157 " - pdb=" SG CYS A1175 " distance=2.03 Simple disulfide: pdb=" SG CYS A1169 " - pdb=" SG CYS A1184 " distance=2.03 Simple disulfide: pdb=" SG CYS A1188 " - pdb=" SG CYS A1201 " distance=2.03 Simple disulfide: pdb=" SG CYS A1195 " - pdb=" SG CYS A1214 " distance=2.03 Simple disulfide: pdb=" SG CYS A1208 " - pdb=" SG CYS A1223 " distance=2.03 Simple disulfide: pdb=" SG CYS A1231 " - pdb=" SG CYS A1244 " distance=2.03 Simple disulfide: pdb=" SG CYS A1238 " - pdb=" SG CYS A1257 " distance=2.03 Simple disulfide: pdb=" SG CYS A1251 " - pdb=" SG CYS A1267 " distance=2.03 Simple disulfide: pdb=" SG CYS A1272 " - pdb=" SG CYS A1284 " distance=2.03 Simple disulfide: pdb=" SG CYS A1279 " - pdb=" SG CYS A1297 " distance=2.03 Simple disulfide: pdb=" SG CYS A1291 " - pdb=" SG CYS A1306 " distance=2.03 Simple disulfide: pdb=" SG CYS A3165 " - pdb=" SG CYS A3178 " distance=2.03 Simple disulfide: pdb=" SG CYS A3180 " - pdb=" SG CYS A3193 " distance=2.03 Simple disulfide: pdb=" SG CYS B2720 " - pdb=" SG CYS B2737 " distance=2.04 Simple disulfide: pdb=" SG CYS B2742 " - pdb=" SG CYS B2754 " distance=2.03 Simple disulfide: pdb=" SG CYS B2749 " - pdb=" SG CYS B2767 " distance=2.02 Simple disulfide: pdb=" SG CYS B2761 " - pdb=" SG CYS B2776 " distance=2.03 Simple disulfide: pdb=" SG CYS B2781 " - pdb=" SG CYS B2794 " distance=2.03 Simple disulfide: pdb=" SG CYS B2789 " - pdb=" SG CYS B2807 " distance=2.04 Simple disulfide: pdb=" SG CYS B2801 " - pdb=" SG CYS B2818 " distance=2.03 Simple disulfide: pdb=" SG CYS B2823 " - pdb=" SG CYS B2836 " distance=2.03 Simple disulfide: pdb=" SG CYS B2830 " - pdb=" SG CYS B2849 " distance=2.03 Simple disulfide: pdb=" SG CYS B2843 " - pdb=" SG CYS B2860 " 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=6, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA F 3 " - " MAN F 5 " BETA1-3 " NAG F 2 " - " BMA F 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A4701 " - " ASN A 340 " " NAG A4702 " - " ASN A1187 " " NAG B4701 " - " ASN B2782 " " NAG B4702 " - " ASN B2810 " " NAG D 1 " - " ASN A 462 " " NAG E 1 " - " ASN A 657 " " NAG F 1 " - " ASN A 865 " " NAG I 1 " - " ASN A1063 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.6 seconds 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 32 sheets defined 14.4% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'C' and resid 257 through 269 removed outlier: 4.144A pdb=" N SER C 269 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 315 Processing helix chain 'C' and resid 316 through 358 removed outlier: 3.782A pdb=" N LEU C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS C 357 " --> pdb=" O SER C 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 201 Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 309 through 313 removed outlier: 3.517A pdb=" N SER A 312 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 660 through 669 removed outlier: 3.961A pdb=" N SER A 664 " --> pdb=" O PRO A 661 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASN A 665 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASN A 666 " --> pdb=" O GLY A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 983 removed outlier: 4.062A pdb=" N GLY A 981 " --> pdb=" O HIS A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1043 No H-bonds generated for 'chain 'A' and resid 1041 through 1043' Processing helix chain 'A' and resid 1083 through 1085 No H-bonds generated for 'chain 'A' and resid 1083 through 1085' Processing helix chain 'A' and resid 1126 through 1128 No H-bonds generated for 'chain 'A' and resid 1126 through 1128' Processing helix chain 'A' and resid 1138 through 1142 Processing helix chain 'A' and resid 1164 through 1168 Processing helix chain 'A' and resid 1178 through 1182 Processing helix chain 'A' and resid 1205 through 1207 No H-bonds generated for 'chain 'A' and resid 1205 through 1207' Processing helix chain 'A' and resid 1248 through 1250 No H-bonds generated for 'chain 'A' and resid 1248 through 1250' Processing helix chain 'A' and resid 1260 through 1264 removed outlier: 3.824A pdb=" N HIS A1264 " --> pdb=" O SER A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1290 No H-bonds generated for 'chain 'A' and resid 1288 through 1290' Processing helix chain 'A' and resid 1300 through 1305 Processing helix chain 'B' and resid 2733 through 2738 removed outlier: 3.701A pdb=" N CYS B2737 " --> pdb=" O LEU B2733 " (cutoff:3.500A) Processing helix chain 'B' and resid 2758 through 2760 No H-bonds generated for 'chain 'B' and resid 2758 through 2760' Processing helix chain 'B' and resid 2770 through 2774 Processing helix chain 'B' and resid 2812 through 2817 removed outlier: 3.796A pdb=" N ASN B2817 " --> pdb=" O SER B2813 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 189 Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 228 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AA5, first strand: chain 'A' and resid 362 through 364 Processing sheet with id=AA6, first strand: chain 'A' and resid 376 through 379 Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 417 removed outlier: 5.349A pdb=" N ILE A 415 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL A 405 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 398 " --> pdb=" O GLY A 646 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLY A 646 " --> pdb=" O SER A 398 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 428 through 431 removed outlier: 6.431A pdb=" N VAL A 447 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 468 through 474 removed outlier: 3.708A pdb=" N ASN A 470 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 490 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 511 through 516 removed outlier: 3.877A pdb=" N GLY A 513 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG A 539 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ASP A 549 " --> pdb=" O ARG A 539 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 558 through 564 removed outlier: 4.145A pdb=" N GLY A 560 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 580 " --> pdb=" O VAL A 593 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 607 through 609 removed outlier: 6.581A pdb=" N VAL A 623 " --> pdb=" O TYR A 637 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 672 through 675 Processing sheet with id=AB5, first strand: chain 'A' and resid 694 through 696 Processing sheet with id=AB6, first strand: chain 'A' and resid 735 through 736 removed outlier: 3.697A pdb=" N ALA A 717 " --> pdb=" O SER A 714 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS A 958 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 742 through 748 removed outlier: 4.109A pdb=" N GLY A 744 " --> pdb=" O SER A 757 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE A 764 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 785 through 791 removed outlier: 3.923A pdb=" N CYS A 787 " --> pdb=" O THR A 800 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL A 807 " --> pdb=" O ILE A 820 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 827 through 833 removed outlier: 6.364A pdb=" N SER A 842 " --> pdb=" O ARG A 828 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 830 " --> pdb=" O PHE A 840 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE A 840 " --> pdb=" O ILE A 830 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL A 832 " --> pdb=" O TYR A 838 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR A 838 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 850 " --> pdb=" O ILE A 863 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 871 through 877 removed outlier: 3.955A pdb=" N GLY A 873 " --> pdb=" O VAL A 886 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 915 through 921 removed outlier: 3.715A pdb=" N GLY A 917 " --> pdb=" O THR A 928 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG A 937 " --> pdb=" O VAL A 948 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N VAL A 948 " --> pdb=" O ARG A 937 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 986 through 990 Processing sheet with id=AC4, first strand: chain 'A' and resid 1003 through 1005 Processing sheet with id=AC5, first strand: chain 'A' and resid 1029 through 1031 Processing sheet with id=AC6, first strand: chain 'A' and resid 1070 through 1072 Processing sheet with id=AC7, first strand: chain 'A' and resid 1114 through 1116 Processing sheet with id=AC8, first strand: chain 'A' and resid 1155 through 1157 removed outlier: 3.707A pdb=" N ARG A1161 " --> pdb=" O CYS A1157 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1192 through 1194 Processing sheet with id=AD1, first strand: chain 'A' and resid 1235 through 1237 Processing sheet with id=AD2, first strand: chain 'A' and resid 1276 through 1278 Processing sheet with id=AD3, first strand: chain 'A' and resid 3184 through 3186 Processing sheet with id=AD4, first strand: chain 'B' and resid 2746 through 2748 Processing sheet with id=AD5, first strand: chain 'B' and resid 2829 through 2830 310 hydrogen bonds defined for protein. 753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.28 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3899 1.34 - 1.46: 2685 1.46 - 1.58: 5018 1.58 - 1.71: 0 1.71 - 1.83: 147 Bond restraints: 11749 Sorted by residual: bond pdb=" N CYS A 372 " pdb=" CA CYS A 372 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.23e-02 6.61e+03 6.41e+00 bond pdb=" N CYS A 384 " pdb=" CA CYS A 384 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.21e-02 6.83e+03 6.11e+00 bond pdb=" C SER A 738 " pdb=" N PRO A 739 " ideal model delta sigma weight residual 1.333 1.352 -0.019 7.80e-03 1.64e+04 5.93e+00 bond pdb=" N GLU A 373 " pdb=" CA GLU A 373 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.32e-02 5.74e+03 5.93e+00 bond pdb=" N GLU A 374 " pdb=" CA GLU A 374 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.25e-02 6.40e+03 5.54e+00 ... (remaining 11744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 15626 2.78 - 5.56: 260 5.56 - 8.34: 31 8.34 - 11.12: 4 11.12 - 13.89: 5 Bond angle restraints: 15926 Sorted by residual: angle pdb=" N PHE B2827 " pdb=" CA PHE B2827 " pdb=" C PHE B2827 " ideal model delta sigma weight residual 111.56 104.71 6.85 1.38e+00 5.25e-01 2.46e+01 angle pdb=" C2 A2G B4703 " pdb=" C1 A2G B4703 " pdb=" O5 A2G B4703 " ideal model delta sigma weight residual 111.38 125.27 -13.89 3.00e+00 1.11e-01 2.15e+01 angle pdb=" C2 A2G A4705 " pdb=" C1 A2G A4705 " pdb=" O5 A2G A4705 " ideal model delta sigma weight residual 111.38 124.48 -13.10 3.00e+00 1.11e-01 1.91e+01 angle pdb=" C GLU A 328 " pdb=" N CYS A 329 " pdb=" CA CYS A 329 " ideal model delta sigma weight residual 122.62 116.03 6.59 1.56e+00 4.11e-01 1.79e+01 angle pdb=" C2 A2G A4703 " pdb=" C1 A2G A4703 " pdb=" O5 A2G A4703 " ideal model delta sigma weight residual 111.38 123.79 -12.41 3.00e+00 1.11e-01 1.71e+01 ... (remaining 15921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.15: 6820 22.15 - 44.31: 542 44.31 - 66.46: 100 66.46 - 88.61: 29 88.61 - 110.76: 10 Dihedral angle restraints: 7501 sinusoidal: 3400 harmonic: 4101 Sorted by residual: dihedral pdb=" CB CYS A1272 " pdb=" SG CYS A1272 " pdb=" SG CYS A1284 " pdb=" CB CYS A1284 " ideal model delta sinusoidal sigma weight residual 93.00 172.70 -79.70 1 1.00e+01 1.00e-02 7.88e+01 dihedral pdb=" CB CYS A 973 " pdb=" SG CYS A 973 " pdb=" SG CYS A 987 " pdb=" CB CYS A 987 " ideal model delta sinusoidal sigma weight residual 93.00 156.31 -63.31 1 1.00e+01 1.00e-02 5.29e+01 dihedral pdb=" CB CYS A 351 " pdb=" SG CYS A 351 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -146.82 60.82 1 1.00e+01 1.00e-02 4.92e+01 ... (remaining 7498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1638 0.104 - 0.207: 98 0.207 - 0.311: 6 0.311 - 0.414: 1 0.414 - 0.518: 1 Chirality restraints: 1744 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O3 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-02 2.50e+03 6.70e+02 chirality pdb=" C2 NAG B4702 " pdb=" C1 NAG B4702 " pdb=" C3 NAG B4702 " pdb=" N2 NAG B4702 " both_signs ideal model delta sigma weight residual False -2.49 -2.13 -0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" C2 A2G A4703 " pdb=" C1 A2G A4703 " pdb=" C3 A2G A4703 " pdb=" N2 A2G A4703 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 1741 not shown) Planarity restraints: 2116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.203 2.00e-02 2.50e+03 1.66e-01 3.47e+02 pdb=" C7 NAG F 2 " 0.057 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.268 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " 0.153 2.00e-02 2.50e+03 1.26e-01 1.97e+02 pdb=" C7 NAG I 1 " -0.047 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " 0.114 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " -0.199 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B4702 " 0.152 2.00e-02 2.50e+03 1.24e-01 1.91e+02 pdb=" C7 NAG B4702 " -0.044 2.00e-02 2.50e+03 pdb=" C8 NAG B4702 " 0.114 2.00e-02 2.50e+03 pdb=" N2 NAG B4702 " -0.194 2.00e-02 2.50e+03 pdb=" O7 NAG B4702 " -0.028 2.00e-02 2.50e+03 ... (remaining 2113 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 345 2.68 - 3.24: 11860 3.24 - 3.79: 17921 3.79 - 4.35: 24388 4.35 - 4.90: 39481 Nonbonded interactions: 93995 Sorted by model distance: nonbonded pdb=" OG1 THR A1065 " pdb=" C1 A2G A4705 " model vdw 2.126 3.470 nonbonded pdb=" OD2 ASP B2731 " pdb="CA CA B4704 " model vdw 2.129 2.510 nonbonded pdb=" OD2 ASP A1097 " pdb="CA CA A4717 " model vdw 2.142 2.510 nonbonded pdb=" OD1 ASP B2721 " pdb="CA CA B4704 " model vdw 2.156 2.510 nonbonded pdb=" OD1 ASP A1087 " pdb="CA CA A4717 " model vdw 2.167 2.510 ... (remaining 93990 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' 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 individual isotropic 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 30.260 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11749 Z= 0.333 Angle : 0.889 13.894 15926 Z= 0.464 Chirality : 0.056 0.518 1744 Planarity : 0.008 0.166 2108 Dihedral : 16.694 110.763 4704 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.94 % Favored : 92.99 % Rotamer: Outliers : 2.07 % Allowed : 16.38 % Favored : 81.56 % 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: -0.57 (0.23), residues: 1412 helix: 1.78 (0.47), residues: 112 sheet: -0.66 (0.29), residues: 281 loop : -0.53 (0.21), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 528 HIS 0.005 0.001 HIS A1276 PHE 0.033 0.002 PHE A1062 TYR 0.019 0.002 TYR A 219 ARG 0.011 0.001 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 1.379 Fit side-chains REVERT: C 268 GLN cc_start: 0.6685 (OUTLIER) cc_final: 0.6006 (mp10) REVERT: A 359 GLN cc_start: 0.8293 (mt0) cc_final: 0.8014 (mt0) REVERT: A 496 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8469 (pm20) outliers start: 26 outliers final: 19 residues processed: 120 average time/residue: 0.2559 time to fit residues: 45.2811 Evaluate side-chains 111 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain B residue 2769 ASP Chi-restraints excluded: chain B residue 2786 GLU Chi-restraints excluded: chain B residue 2835 ILE Chi-restraints excluded: chain B residue 2837 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 HIS C 323 ASN A 321 HIS A 382 GLN A 412 ASN A 444 GLN A 456 ASN A 639 GLN A 681 ASN A 895 HIS A 978 HIS A 985 HIS A 992 ASN A1058 GLN A1099 GLN A1254 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11749 Z= 0.228 Angle : 0.681 9.587 15926 Z= 0.350 Chirality : 0.049 0.358 1744 Planarity : 0.004 0.040 2108 Dihedral : 11.281 90.483 2127 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.97 % Allowed : 14.55 % Favored : 81.48 % 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: -0.42 (0.23), residues: 1412 helix: 2.17 (0.46), residues: 106 sheet: -0.47 (0.29), residues: 278 loop : -0.49 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 528 HIS 0.003 0.001 HIS A 985 PHE 0.013 0.002 PHE B2778 TYR 0.017 0.002 TYR C 339 ARG 0.007 0.001 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 96 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: C 259 ARG cc_start: 0.7849 (mpp80) cc_final: 0.7237 (mtt90) REVERT: C 268 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.6010 (mp10) REVERT: C 298 GLN cc_start: 0.8094 (mt0) cc_final: 0.7720 (mm-40) REVERT: C 347 ASP cc_start: 0.7357 (t0) cc_final: 0.7072 (t0) REVERT: A 308 MET cc_start: 0.4361 (OUTLIER) cc_final: 0.3891 (tpt) REVERT: A 359 GLN cc_start: 0.8146 (mt0) cc_final: 0.7674 (mt0) REVERT: A 496 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8541 (pm20) REVERT: A 631 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7000 (tm-30) REVERT: A 3194 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7125 (ttp80) REVERT: A 3198 ASN cc_start: 0.8212 (t0) cc_final: 0.7992 (t0) outliers start: 50 outliers final: 23 residues processed: 139 average time/residue: 0.2603 time to fit residues: 52.5766 Evaluate side-chains 117 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 3194 ARG Chi-restraints excluded: chain B residue 2786 GLU Chi-restraints excluded: chain B residue 2795 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 0.0870 chunk 86 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 0.0470 chunk 137 optimal weight: 0.1980 chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 323 ASN A 645 HIS A1160 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11749 Z= 0.156 Angle : 0.595 7.110 15926 Z= 0.307 Chirality : 0.046 0.346 1744 Planarity : 0.004 0.038 2108 Dihedral : 9.863 82.399 2115 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.74 % Allowed : 15.18 % Favored : 81.08 % 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: -0.36 (0.23), residues: 1412 helix: 2.38 (0.47), residues: 106 sheet: -0.46 (0.29), residues: 272 loop : -0.45 (0.21), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 528 HIS 0.004 0.001 HIS A1051 PHE 0.010 0.001 PHE A1071 TYR 0.012 0.001 TYR A 571 ARG 0.006 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 111 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 259 ARG cc_start: 0.7505 (mpp80) cc_final: 0.7163 (mtt90) REVERT: C 268 GLN cc_start: 0.6411 (OUTLIER) cc_final: 0.5727 (mp10) REVERT: C 295 ASN cc_start: 0.8366 (p0) cc_final: 0.8122 (p0) REVERT: C 298 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7748 (mm-40) REVERT: A 321 HIS cc_start: 0.6230 (OUTLIER) cc_final: 0.5091 (m-70) REVERT: A 359 GLN cc_start: 0.8066 (mt0) cc_final: 0.7228 (mt0) REVERT: A 370 CYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7078 (m) REVERT: A 574 ASP cc_start: 0.9019 (t0) cc_final: 0.8770 (t70) REVERT: A 631 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: A 1230 MET cc_start: 0.7977 (tpt) cc_final: 0.7566 (tpp) outliers start: 47 outliers final: 24 residues processed: 151 average time/residue: 0.2592 time to fit residues: 57.0340 Evaluate side-chains 121 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 946 MET Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1066 CYS Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain B residue 2769 ASP Chi-restraints excluded: chain B residue 2786 GLU Chi-restraints excluded: chain B residue 2788 THR Chi-restraints excluded: chain B residue 2797 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 60 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 0.3980 chunk 135 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 323 ASN A1276 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11749 Z= 0.285 Angle : 0.650 6.831 15926 Z= 0.334 Chirality : 0.048 0.325 1744 Planarity : 0.004 0.040 2108 Dihedral : 9.393 80.612 2104 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.21 % Allowed : 16.85 % Favored : 78.93 % 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: -0.48 (0.23), residues: 1412 helix: 2.46 (0.48), residues: 106 sheet: -0.75 (0.29), residues: 276 loop : -0.49 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 528 HIS 0.006 0.001 HIS A 645 PHE 0.013 0.002 PHE A 709 TYR 0.015 0.002 TYR A 579 ARG 0.005 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 95 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 259 ARG cc_start: 0.7546 (mpp80) cc_final: 0.7183 (mtt90) REVERT: C 268 GLN cc_start: 0.6409 (OUTLIER) cc_final: 0.5753 (mp10) REVERT: C 298 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7835 (mm-40) REVERT: A 359 GLN cc_start: 0.8184 (mt0) cc_final: 0.7800 (mt0) REVERT: A 523 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8812 (tp) REVERT: A 631 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7292 (tm-30) REVERT: A 846 ARG cc_start: 0.8245 (tpt170) cc_final: 0.7841 (tpt90) REVERT: A 3194 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7812 (ttp80) REVERT: B 2718 TRP cc_start: 0.7564 (OUTLIER) cc_final: 0.7339 (m-90) REVERT: B 2779 ARG cc_start: 0.7164 (tpp-160) cc_final: 0.6962 (tpp-160) REVERT: B 2799 TYR cc_start: 0.6243 (m-10) cc_final: 0.6031 (m-80) outliers start: 53 outliers final: 40 residues processed: 143 average time/residue: 0.2640 time to fit residues: 53.9340 Evaluate side-chains 133 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 88 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 899 ASP Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1066 CYS Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1200 SER Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1306 CYS Chi-restraints excluded: chain A residue 3194 ARG Chi-restraints excluded: chain B residue 2718 TRP Chi-restraints excluded: chain B residue 2769 ASP Chi-restraints excluded: chain B residue 2786 GLU Chi-restraints excluded: chain B residue 2797 LEU Chi-restraints excluded: chain B residue 2837 VAL Chi-restraints excluded: chain B residue 2858 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 115 optimal weight: 0.2980 chunk 93 optimal weight: 0.0040 chunk 0 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1276 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11749 Z= 0.166 Angle : 0.585 6.711 15926 Z= 0.302 Chirality : 0.046 0.321 1744 Planarity : 0.004 0.036 2108 Dihedral : 8.680 76.979 2104 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.97 % Allowed : 17.49 % Favored : 78.54 % 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: -0.36 (0.23), residues: 1412 helix: 2.62 (0.48), residues: 106 sheet: -0.56 (0.29), residues: 271 loop : -0.44 (0.21), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 528 HIS 0.004 0.001 HIS A 645 PHE 0.011 0.001 PHE A1071 TYR 0.010 0.001 TYR A 571 ARG 0.004 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 98 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 259 ARG cc_start: 0.7605 (mpp80) cc_final: 0.7093 (mtt90) REVERT: C 268 GLN cc_start: 0.6449 (tp40) cc_final: 0.5906 (mp10) REVERT: C 298 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7825 (mm-40) REVERT: C 347 ASP cc_start: 0.7284 (t0) cc_final: 0.7076 (t0) REVERT: A 308 MET cc_start: 0.4152 (OUTLIER) cc_final: 0.3409 (tpt) REVERT: A 321 HIS cc_start: 0.6254 (OUTLIER) cc_final: 0.5259 (m-70) REVERT: A 359 GLN cc_start: 0.8184 (mt0) cc_final: 0.7601 (mt0) REVERT: A 621 MET cc_start: 0.8595 (mmm) cc_final: 0.8190 (mmm) REVERT: A 631 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: A 846 ARG cc_start: 0.8152 (tpt170) cc_final: 0.7682 (tpt90) REVERT: A 3194 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7799 (ttp80) REVERT: B 2799 TYR cc_start: 0.6319 (m-10) cc_final: 0.6109 (m-80) outliers start: 50 outliers final: 33 residues processed: 140 average time/residue: 0.2562 time to fit residues: 51.9885 Evaluate side-chains 126 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 899 ASP Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1066 CYS Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1200 SER Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1306 CYS Chi-restraints excluded: chain A residue 3194 ARG Chi-restraints excluded: chain B residue 2769 ASP Chi-restraints excluded: chain B residue 2786 GLU Chi-restraints excluded: chain B residue 2788 THR Chi-restraints excluded: chain B residue 2789 CYS Chi-restraints excluded: chain B residue 2827 PHE Chi-restraints excluded: chain B residue 2837 VAL Chi-restraints excluded: chain B residue 2858 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 135 optimal weight: 0.0770 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 323 ASN A1276 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11749 Z= 0.166 Angle : 0.578 6.728 15926 Z= 0.297 Chirality : 0.045 0.305 1744 Planarity : 0.004 0.038 2108 Dihedral : 8.106 72.562 2101 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.82 % Allowed : 18.28 % Favored : 77.90 % 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: -0.31 (0.23), residues: 1412 helix: 2.69 (0.47), residues: 106 sheet: -0.53 (0.30), residues: 270 loop : -0.41 (0.21), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 528 HIS 0.004 0.001 HIS A 645 PHE 0.012 0.001 PHE A1071 TYR 0.010 0.001 TYR C 297 ARG 0.004 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 96 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 259 ARG cc_start: 0.7623 (mpp80) cc_final: 0.7140 (mtt90) REVERT: C 268 GLN cc_start: 0.6420 (tp40) cc_final: 0.5854 (mp10) REVERT: C 298 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7827 (mm-40) REVERT: C 307 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.7083 (mmmm) REVERT: A 349 ASP cc_start: 0.5954 (t0) cc_final: 0.5663 (t70) REVERT: A 359 GLN cc_start: 0.8055 (mt0) cc_final: 0.7593 (mt0) REVERT: A 500 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8547 (ttt-90) REVERT: A 631 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7533 (tm-30) REVERT: A 846 ARG cc_start: 0.8100 (tpt170) cc_final: 0.7800 (tpt90) REVERT: B 2788 THR cc_start: 0.6336 (OUTLIER) cc_final: 0.5941 (p) REVERT: B 2799 TYR cc_start: 0.6539 (m-10) cc_final: 0.6322 (m-80) outliers start: 48 outliers final: 30 residues processed: 139 average time/residue: 0.2821 time to fit residues: 55.1203 Evaluate side-chains 122 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1066 CYS Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1200 SER Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1306 CYS Chi-restraints excluded: chain B residue 2786 GLU Chi-restraints excluded: chain B residue 2788 THR Chi-restraints excluded: chain B residue 2827 PHE Chi-restraints excluded: chain B residue 2858 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 114 optimal weight: 0.0170 chunk 75 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1276 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11749 Z= 0.193 Angle : 0.588 6.625 15926 Z= 0.305 Chirality : 0.046 0.293 1744 Planarity : 0.004 0.038 2108 Dihedral : 7.935 70.473 2101 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.67 % Favored : 94.26 % Rotamer: Outliers : 3.74 % Allowed : 18.44 % Favored : 77.82 % 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: -0.29 (0.23), residues: 1412 helix: 2.73 (0.47), residues: 106 sheet: -0.51 (0.30), residues: 264 loop : -0.41 (0.21), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 528 HIS 0.004 0.001 HIS A 510 PHE 0.011 0.001 PHE A 615 TYR 0.010 0.001 TYR C 297 ARG 0.004 0.000 ARG B2779 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 93 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 259 ARG cc_start: 0.7625 (mpp80) cc_final: 0.7151 (mtt90) REVERT: C 268 GLN cc_start: 0.6438 (tp40) cc_final: 0.5875 (mp10) REVERT: C 298 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7870 (mm-40) REVERT: A 359 GLN cc_start: 0.8076 (mt0) cc_final: 0.7644 (mt0) REVERT: A 500 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8565 (ttt-90) REVERT: A 631 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: A 846 ARG cc_start: 0.8094 (tpt170) cc_final: 0.7787 (tpt90) REVERT: A 887 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8672 (m-30) REVERT: A 3194 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6782 (ptt90) REVERT: B 2788 THR cc_start: 0.6420 (OUTLIER) cc_final: 0.5932 (p) REVERT: B 2860 CYS cc_start: -0.0385 (OUTLIER) cc_final: -0.0676 (p) outliers start: 47 outliers final: 38 residues processed: 135 average time/residue: 0.2748 time to fit residues: 53.2244 Evaluate side-chains 133 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 89 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1066 CYS Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1200 SER Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1306 CYS Chi-restraints excluded: chain A residue 3194 ARG Chi-restraints excluded: chain B residue 2769 ASP Chi-restraints excluded: chain B residue 2786 GLU Chi-restraints excluded: chain B residue 2788 THR Chi-restraints excluded: chain B residue 2797 LEU Chi-restraints excluded: chain B residue 2827 PHE Chi-restraints excluded: chain B residue 2837 VAL Chi-restraints excluded: chain B residue 2858 ILE Chi-restraints excluded: chain B residue 2860 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.1980 chunk 80 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 323 ASN ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1276 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11749 Z= 0.176 Angle : 0.577 6.705 15926 Z= 0.298 Chirality : 0.045 0.285 1744 Planarity : 0.004 0.038 2108 Dihedral : 7.661 66.674 2101 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.95 % Favored : 93.98 % Rotamer: Outliers : 3.82 % Allowed : 18.44 % Favored : 77.74 % 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: -0.26 (0.23), residues: 1412 helix: 2.77 (0.47), residues: 106 sheet: -0.51 (0.30), residues: 264 loop : -0.39 (0.21), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 528 HIS 0.004 0.001 HIS A 645 PHE 0.012 0.001 PHE A 615 TYR 0.010 0.001 TYR A 579 ARG 0.004 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 97 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 259 ARG cc_start: 0.7624 (mpp80) cc_final: 0.7160 (mtt90) REVERT: C 268 GLN cc_start: 0.6430 (tp40) cc_final: 0.5895 (mp10) REVERT: C 298 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7871 (mm-40) REVERT: A 254 ASP cc_start: 0.7639 (t0) cc_final: 0.7111 (t70) REVERT: A 359 GLN cc_start: 0.8079 (mt0) cc_final: 0.7645 (mt0) REVERT: A 500 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8553 (ttt-90) REVERT: A 631 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: A 846 ARG cc_start: 0.7984 (tpt170) cc_final: 0.7304 (tpt90) REVERT: A 887 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8675 (m-30) REVERT: A 957 MET cc_start: 0.8946 (mmt) cc_final: 0.8312 (mmt) REVERT: A 1236 PHE cc_start: 0.8781 (t80) cc_final: 0.8263 (t80) REVERT: A 3194 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6875 (ptt90) REVERT: B 2718 TRP cc_start: 0.7462 (OUTLIER) cc_final: 0.6989 (m-90) REVERT: B 2788 THR cc_start: 0.6408 (OUTLIER) cc_final: 0.5899 (p) REVERT: B 2860 CYS cc_start: -0.0410 (OUTLIER) cc_final: -0.0681 (p) outliers start: 48 outliers final: 33 residues processed: 140 average time/residue: 0.2714 time to fit residues: 54.3159 Evaluate side-chains 132 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 92 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1066 CYS Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1306 CYS Chi-restraints excluded: chain A residue 3194 ARG Chi-restraints excluded: chain B residue 2718 TRP Chi-restraints excluded: chain B residue 2769 ASP Chi-restraints excluded: chain B residue 2786 GLU Chi-restraints excluded: chain B residue 2788 THR Chi-restraints excluded: chain B residue 2797 LEU Chi-restraints excluded: chain B residue 2827 PHE Chi-restraints excluded: chain B residue 2837 VAL Chi-restraints excluded: chain B residue 2858 ILE Chi-restraints excluded: chain B residue 2860 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.3980 chunk 125 optimal weight: 0.0770 chunk 129 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 113 optimal weight: 0.0070 chunk 118 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1033 ASN ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11749 Z= 0.155 Angle : 0.571 6.634 15926 Z= 0.295 Chirality : 0.045 0.278 1744 Planarity : 0.003 0.038 2108 Dihedral : 7.353 62.093 2100 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.88 % Favored : 94.05 % Rotamer: Outliers : 3.26 % Allowed : 19.24 % Favored : 77.50 % 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: -0.22 (0.23), residues: 1412 helix: 2.82 (0.47), residues: 106 sheet: -0.48 (0.30), residues: 269 loop : -0.35 (0.21), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 528 HIS 0.003 0.001 HIS A 645 PHE 0.010 0.001 PHE A 615 TYR 0.010 0.001 TYR A 219 ARG 0.004 0.000 ARG B2779 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 94 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 259 ARG cc_start: 0.7585 (mpp80) cc_final: 0.7138 (mtt90) REVERT: C 268 GLN cc_start: 0.6478 (tp40) cc_final: 0.5939 (mp10) REVERT: C 298 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7886 (mm-40) REVERT: A 254 ASP cc_start: 0.7876 (t0) cc_final: 0.7393 (t70) REVERT: A 359 GLN cc_start: 0.8122 (mt0) cc_final: 0.7641 (mt0) REVERT: A 500 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8531 (ttt-90) REVERT: A 846 ARG cc_start: 0.8048 (tpt170) cc_final: 0.7394 (tpt90) REVERT: A 887 ASP cc_start: 0.8880 (OUTLIER) cc_final: 0.8660 (m-30) REVERT: A 957 MET cc_start: 0.8883 (mmt) cc_final: 0.8366 (mmt) REVERT: A 1177 ASP cc_start: 0.7967 (m-30) cc_final: 0.7724 (m-30) REVERT: A 1236 PHE cc_start: 0.8780 (t80) cc_final: 0.8193 (t80) REVERT: A 3194 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6855 (ptt90) REVERT: B 2718 TRP cc_start: 0.7529 (OUTLIER) cc_final: 0.6981 (m-90) REVERT: B 2781 CYS cc_start: 0.7476 (m) cc_final: 0.7150 (t) REVERT: B 2788 THR cc_start: 0.6410 (OUTLIER) cc_final: 0.5914 (p) REVERT: B 2860 CYS cc_start: -0.0470 (OUTLIER) cc_final: -0.0711 (p) outliers start: 41 outliers final: 29 residues processed: 131 average time/residue: 0.2862 time to fit residues: 53.2674 Evaluate side-chains 128 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1066 CYS Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1306 CYS Chi-restraints excluded: chain A residue 3194 ARG Chi-restraints excluded: chain B residue 2718 TRP Chi-restraints excluded: chain B residue 2786 GLU Chi-restraints excluded: chain B residue 2788 THR Chi-restraints excluded: chain B residue 2797 LEU Chi-restraints excluded: chain B residue 2827 PHE Chi-restraints excluded: chain B residue 2858 ILE Chi-restraints excluded: chain B residue 2860 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 139 optimal weight: 0.0470 chunk 128 optimal weight: 0.5980 chunk 111 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 0.0170 chunk 118 optimal weight: 20.0000 overall best weight: 0.3514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 323 ASN ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11749 Z= 0.152 Angle : 0.575 9.630 15926 Z= 0.297 Chirality : 0.045 0.267 1744 Planarity : 0.003 0.037 2108 Dihedral : 6.984 56.414 2098 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.38 % Favored : 94.55 % Rotamer: Outliers : 2.94 % Allowed : 19.63 % Favored : 77.42 % 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: -0.20 (0.23), residues: 1412 helix: 2.81 (0.47), residues: 106 sheet: -0.47 (0.30), residues: 269 loop : -0.33 (0.21), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 528 HIS 0.003 0.001 HIS A 645 PHE 0.016 0.001 PHE A 615 TYR 0.009 0.001 TYR A 571 ARG 0.004 0.000 ARG B2779 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 259 ARG cc_start: 0.7567 (mpp80) cc_final: 0.7185 (mtt90) REVERT: C 268 GLN cc_start: 0.6304 (tp40) cc_final: 0.5759 (mp10) REVERT: C 298 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7879 (mm-40) REVERT: A 254 ASP cc_start: 0.7865 (t0) cc_final: 0.7361 (t70) REVERT: A 359 GLN cc_start: 0.8116 (mt0) cc_final: 0.7633 (mt0) REVERT: A 500 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8537 (ttt-90) REVERT: A 846 ARG cc_start: 0.7969 (tpt170) cc_final: 0.7552 (tpt90) REVERT: A 957 MET cc_start: 0.8936 (mmt) cc_final: 0.8420 (mmt) REVERT: B 2718 TRP cc_start: 0.7518 (OUTLIER) cc_final: 0.6927 (m-90) REVERT: B 2781 CYS cc_start: 0.7453 (m) cc_final: 0.7199 (t) REVERT: B 2788 THR cc_start: 0.6209 (OUTLIER) cc_final: 0.5694 (p) outliers start: 37 outliers final: 28 residues processed: 131 average time/residue: 0.2857 time to fit residues: 53.3529 Evaluate side-chains 124 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1066 CYS Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1306 CYS Chi-restraints excluded: chain B residue 2718 TRP Chi-restraints excluded: chain B residue 2786 GLU Chi-restraints excluded: chain B residue 2788 THR Chi-restraints excluded: chain B residue 2797 LEU Chi-restraints excluded: chain B residue 2827 PHE Chi-restraints excluded: chain B residue 2858 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS A 958 HIS ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1276 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.142388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.100261 restraints weight = 19197.025| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.27 r_work: 0.3130 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11749 Z= 0.289 Angle : 0.636 10.700 15926 Z= 0.329 Chirality : 0.047 0.280 1744 Planarity : 0.004 0.043 2108 Dihedral : 7.157 55.270 2098 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.16 % Favored : 93.77 % Rotamer: Outliers : 2.78 % Allowed : 20.19 % Favored : 77.03 % 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: -0.37 (0.23), residues: 1412 helix: 2.71 (0.47), residues: 106 sheet: -0.68 (0.30), residues: 273 loop : -0.43 (0.21), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 528 HIS 0.005 0.001 HIS A 895 PHE 0.014 0.002 PHE A 615 TYR 0.018 0.002 TYR A 650 ARG 0.004 0.000 ARG A 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2604.38 seconds wall clock time: 48 minutes 26.53 seconds (2906.53 seconds total)