Starting phenix.real_space_refine on Wed Jan 22 21:50:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gvq_51639/01_2025/9gvq_51639.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gvq_51639/01_2025/9gvq_51639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gvq_51639/01_2025/9gvq_51639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gvq_51639/01_2025/9gvq_51639.map" model { file = "/net/cci-nas-00/data/ceres_data/9gvq_51639/01_2025/9gvq_51639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gvq_51639/01_2025/9gvq_51639.cif" } resolution = 3.9 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= 0.044 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: 6 Type Number sf(0) Gaussians Ca 24 9.91 5 Cu 8 5.60 5 S 1000 5.16 5 C 43096 2.51 5 N 12016 2.21 5 O 13356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 69500 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8695 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1153, 8633 Classifications: {'peptide': 1153} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 4, 'PTRANS': 63, 'TRANS': 1085} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Conformer: "B" Number of residues, atoms: 1153, 8633 Classifications: {'peptide': 1153} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 4, 'PTRANS': 63, 'TRANS': 1085} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 bond proxies already assigned to first conformer: 8767 Chain: "B" Number of atoms: 8672 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1151, 8616 Classifications: {'peptide': 1151} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 4, 'PTRANS': 63, 'TRANS': 1083} Chain breaks: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Conformer: "B" Number of residues, atoms: 1151, 8616 Classifications: {'peptide': 1151} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 4, 'PTRANS': 63, 'TRANS': 1083} Chain breaks: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 bond proxies already assigned to first conformer: 8756 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 3, ' CU': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 3, ' CU': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: C, E, G, D, F, H Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N AARG A 422 " occ=0.64 ... (20 atoms not shown) pdb=" NH2BARG A 422 " occ=0.36 residue: pdb=" N AARG B 422 " occ=0.71 ... (20 atoms not shown) pdb=" NH2BARG B 422 " occ=0.29 residue: pdb=" N AARG C 422 " occ=0.64 ... (20 atoms not shown) pdb=" NH2BARG C 422 " occ=0.36 residue: pdb=" N AARG D 422 " occ=0.71 ... (20 atoms not shown) pdb=" NH2BARG D 422 " occ=0.29 residue: pdb=" N AARG E 422 " occ=0.64 ... (20 atoms not shown) pdb=" NH2BARG E 422 " occ=0.36 residue: pdb=" N AARG F 422 " occ=0.71 ... (20 atoms not shown) pdb=" NH2BARG F 422 " occ=0.29 residue: pdb=" N AARG G 422 " occ=0.64 ... (20 atoms not shown) pdb=" NH2BARG G 422 " occ=0.36 residue: pdb=" N AARG H 422 " occ=0.71 ... (20 atoms not shown) pdb=" NH2BARG H 422 " occ=0.29 Time building chain proxies: 42.67, per 1000 atoms: 0.61 Number of scatterers: 69500 At special positions: 0 Unit cell: (197.808, 243.963, 451.662, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cu 8 28.99 Ca 24 19.99 S 1000 16.00 O 13356 8.00 N 12016 7.00 C 43096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=106, symmetry=0 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 103 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 208 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 296 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 318 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 334 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 347 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS A 351 " - pdb=" SG CYS A 364 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 374 " - pdb=" SG CYS A 388 " distance=2.03 Simple disulfide: pdb=" SG CYS A 396 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 413 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 425 " distance=2.03 Simple disulfide: pdb=" SG CYS A 434 " - pdb=" SG CYS A 571 " distance=2.03 Simple disulfide: pdb=" SG CYS A 456 " - pdb=" SG CYS A 606 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 662 " distance=2.03 Simple disulfide: pdb=" SG CYS A 631 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 682 " distance=2.03 Simple disulfide: pdb=" SG CYS A 664 " - pdb=" SG CYS A 670 " distance=2.03 Simple disulfide: pdb=" SG CYS A 672 " - pdb=" SG CYS A 697 " distance=2.03 Simple disulfide: pdb=" SG CYS A 704 " - pdb=" SG CYS A 741 " distance=2.03 Simple disulfide: pdb=" SG CYS A 717 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 761 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 755 " distance=2.03 Simple disulfide: pdb=" SG CYS A 763 " - pdb=" SG CYS A 785 " distance=2.03 Simple disulfide: pdb=" SG CYS A 783 " - pdb=" SG CYS A 792 " distance=2.03 Simple disulfide: pdb=" SG CYS A 802 " - pdb=" SG CYS A 843 " distance=2.03 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 839 " distance=2.03 Simple disulfide: pdb=" SG CYS A 823 " - pdb=" SG CYS A 834 " distance=2.03 Simple disulfide: pdb=" SG CYS A 827 " - pdb=" SG CYS A 863 " distance=2.03 Simple disulfide: pdb=" SG CYS A 845 " - pdb=" SG CYS A 857 " distance=2.03 Simple disulfide: pdb=" SG CYS A 865 " - pdb=" SG CYS A 887 " distance=2.03 Simple disulfide: pdb=" SG CYS A 882 " - pdb=" SG CYS A 899 " distance=2.03 Simple disulfide: pdb=" SG CYS A 885 " - pdb=" SG CYS A 894 " distance=2.03 Simple disulfide: pdb=" SG CYS A 903 " - pdb=" SG CYS A1036 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A1071 " distance=2.03 Simple disulfide: pdb=" SG CYS A 934 " - pdb=" SG CYS A1033 " distance=2.03 Simple disulfide: pdb=" SG CYS A 953 " - pdb=" SG CYS A 960 " distance=2.03 Simple disulfide: pdb=" SG CYS A1081 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1095 " - pdb=" SG CYS A1119 " distance=2.04 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1146 " distance=2.03 Simple disulfide: pdb=" SG CYS A1126 " - pdb=" SG CYS A1134 " distance=2.04 Simple disulfide: pdb=" SG CYS A1136 " - pdb=" SG CYS A1161 " distance=2.03 Simple disulfide: pdb=" SG CYS A1152 " - pdb=" SG CYS A1181 " distance=2.03 Simple disulfide: pdb=" SG CYS A1165 " - pdb=" SG CYS A1206 " distance=2.03 Simple disulfide: pdb=" SG CYS A1185 " - pdb=" SG CYS A1196 " distance=2.04 Simple disulfide: pdb=" SG CYS A1189 " - pdb=" SG CYS A1228 " distance=2.03 Simple disulfide: pdb=" SG CYS A1210 " - pdb=" SG CYS A1224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 81 " - pdb=" SG CYS B 211 " distance=2.03 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 111 " - pdb=" SG CYS B 208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 318 " distance=2.03 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 334 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 347 " - pdb=" SG CYS B 368 " distance=2.03 Simple disulfide: pdb=" SG CYS B 351 " - pdb=" SG CYS B 364 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 388 " distance=2.03 Simple disulfide: pdb=" SG CYS B 396 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 413 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 425 " distance=2.03 Simple disulfide: pdb=" SG CYS B 434 " - pdb=" SG CYS B 571 " distance=2.03 Simple disulfide: pdb=" SG CYS B 456 " - pdb=" SG CYS B 606 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 662 " distance=2.03 Simple disulfide: pdb=" SG CYS B 631 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 682 " distance=2.03 Simple disulfide: pdb=" SG CYS B 664 " - pdb=" SG CYS B 670 " distance=2.03 Simple disulfide: pdb=" SG CYS B 672 " - pdb=" SG CYS B 697 " distance=2.03 Simple disulfide: pdb=" SG CYS B 704 " - pdb=" SG CYS B 741 " distance=2.03 Simple disulfide: pdb=" SG CYS B 717 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 761 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 755 " distance=2.03 Simple disulfide: pdb=" SG CYS B 763 " - pdb=" SG CYS B 785 " distance=2.03 Simple disulfide: pdb=" SG CYS B 783 " - pdb=" SG CYS B 792 " distance=2.03 Simple disulfide: pdb=" SG CYS B 802 " - pdb=" SG CYS B 843 " distance=2.03 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 839 " distance=2.03 Simple disulfide: pdb=" SG CYS B 823 " - pdb=" SG CYS B 834 " distance=2.03 Simple disulfide: pdb=" SG CYS B 827 " - pdb=" SG CYS B 863 " distance=2.03 Simple disulfide: pdb=" SG CYS B 845 " - pdb=" SG CYS B 857 " distance=2.03 Simple disulfide: pdb=" SG CYS B 865 " - pdb=" SG CYS B 887 " distance=2.03 Simple disulfide: pdb=" SG CYS B 882 " - pdb=" SG CYS B 899 " distance=2.03 Simple disulfide: pdb=" SG CYS B 885 " - pdb=" SG CYS B 894 " distance=2.03 Simple disulfide: pdb=" SG CYS B 903 " - pdb=" SG CYS B1036 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B1071 " distance=2.03 Simple disulfide: pdb=" SG CYS B 934 " - pdb=" SG CYS B1033 " distance=2.03 Simple disulfide: pdb=" SG CYS B 953 " - pdb=" SG CYS B 960 " distance=2.03 Simple disulfide: pdb=" SG CYS B1081 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B1095 " - pdb=" SG CYS B1119 " distance=2.03 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1146 " distance=2.03 Simple disulfide: pdb=" SG CYS B1126 " - pdb=" SG CYS B1134 " distance=2.04 Simple disulfide: pdb=" SG CYS B1136 " - pdb=" SG CYS B1161 " distance=2.03 Simple disulfide: pdb=" SG CYS B1152 " - pdb=" SG CYS B1181 " distance=2.03 Simple disulfide: pdb=" SG CYS B1165 " - pdb=" SG CYS B1206 " distance=2.03 Simple disulfide: pdb=" SG CYS B1185 " - pdb=" SG CYS B1196 " distance=2.04 Simple disulfide: pdb=" SG CYS B1189 " - pdb=" SG CYS B1228 " distance=2.03 Simple disulfide: pdb=" SG CYS B1210 " - pdb=" SG CYS B1224 " 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=0, symmetry=0 Time building additional restraints: 14.00 Conformation dependent library (CDL) restraints added in 14.3 seconds 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16984 Finding SS restraints... Secondary structure from input PDB file: 248 helices and 160 sheets defined 22.0% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.58 Creating SS restraints... Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 201 through 204 Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 264 through 271 Processing helix chain 'A' and resid 284 through 297 Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.518A pdb=" N CYS A 306 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 321 Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 561 through 564 Processing helix chain 'A' and resid 578 through 583 removed outlier: 4.170A pdb=" N PHE A 582 " --> pdb=" O ALA A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 598 removed outlier: 3.512A pdb=" N PHE A 596 " --> pdb=" O THR A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 601 No H-bonds generated for 'chain 'A' and resid 599 through 601' Processing helix chain 'A' and resid 615 through 619 Processing helix chain 'A' and resid 620 through 632 Processing helix chain 'A' and resid 641 through 645 removed outlier: 3.696A pdb=" N HIS A 645 " --> pdb=" O GLY A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 664 Processing helix chain 'A' and resid 666 through 686 Processing helix chain 'A' and resid 698 through 703 removed outlier: 3.643A pdb=" N THR A 703 " --> pdb=" O PRO A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 727 Processing helix chain 'A' and resid 810 through 814 removed outlier: 4.333A pdb=" N ASN A 813 " --> pdb=" O ASP A 810 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 814 " --> pdb=" O CYS A 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 810 through 814' Processing helix chain 'A' and resid 859 through 863 Processing helix chain 'A' and resid 1026 through 1029 removed outlier: 3.865A pdb=" N LYS A1029 " --> pdb=" O PRO A1026 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1026 through 1029' Processing helix chain 'A' and resid 1043 through 1048 removed outlier: 3.575A pdb=" N ASP A1046 " --> pdb=" O ALA A1043 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE A1047 " --> pdb=" O VAL A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1064 Processing helix chain 'A' and resid 1079 through 1084 Processing helix chain 'A' and resid 1084 through 1096 removed outlier: 3.705A pdb=" N LYS A1088 " --> pdb=" O ASN A1084 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER A1089 " --> pdb=" O PRO A1085 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP A1090 " --> pdb=" O PHE A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1104 removed outlier: 3.586A pdb=" N GLY A1100 " --> pdb=" O ILE A1097 " (cutoff:3.500A) Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1105 through 1109 removed outlier: 3.902A pdb=" N ALA A1108 " --> pdb=" O ALA A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1126 Processing helix chain 'A' and resid 1130 through 1149 removed outlier: 3.733A pdb=" N TYR A1142 " --> pdb=" O ALA A1138 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A1149 " --> pdb=" O ALA A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1169 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 201 through 204 Processing helix chain 'B' and resid 231 through 239 Processing helix chain 'B' and resid 265 through 272 removed outlier: 3.836A pdb=" N LEU B 269 " --> pdb=" O ILE B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 280 removed outlier: 4.066A pdb=" N ALA B 280 " --> pdb=" O SER B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 298 Processing helix chain 'B' and resid 307 through 321 Processing helix chain 'B' and resid 360 through 364 removed outlier: 3.557A pdb=" N CYS B 364 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 561 through 564 Processing helix chain 'B' and resid 578 through 583 removed outlier: 4.089A pdb=" N PHE B 582 " --> pdb=" O ALA B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 599 removed outlier: 3.725A pdb=" N THR B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 619 Processing helix chain 'B' and resid 620 through 632 Processing helix chain 'B' and resid 633 through 635 No H-bonds generated for 'chain 'B' and resid 633 through 635' Processing helix chain 'B' and resid 641 through 645 removed outlier: 3.628A pdb=" N HIS B 645 " --> pdb=" O GLY B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 664 Processing helix chain 'B' and resid 666 through 685 Processing helix chain 'B' and resid 698 through 703 removed outlier: 3.866A pdb=" N THR B 702 " --> pdb=" O THR B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 727 Processing helix chain 'B' and resid 859 through 863 Processing helix chain 'B' and resid 1026 through 1029 Processing helix chain 'B' and resid 1043 through 1047 removed outlier: 3.853A pdb=" N PHE B1047 " --> pdb=" O VAL B1044 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1064 Processing helix chain 'B' and resid 1079 through 1084 Processing helix chain 'B' and resid 1084 through 1095 removed outlier: 3.701A pdb=" N LYS B1088 " --> pdb=" O ASN B1084 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER B1089 " --> pdb=" O PRO B1085 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N TRP B1090 " --> pdb=" O PHE B1086 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1099 Processing helix chain 'B' and resid 1100 through 1107 removed outlier: 3.618A pdb=" N PHE B1103 " --> pdb=" O GLY B1100 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B1104 " --> pdb=" O PRO B1101 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ALA B1105 " --> pdb=" O THR B1102 " (cutoff:3.500A) Processing helix chain 'B' and resid 1112 through 1126 Processing helix chain 'B' and resid 1130 through 1149 removed outlier: 3.704A pdb=" N TYR B1142 " --> pdb=" O ALA B1138 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B1149 " --> pdb=" O ALA B1145 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1169 Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 201 through 204 Processing helix chain 'C' and resid 231 through 238 Processing helix chain 'C' and resid 264 through 271 Processing helix chain 'C' and resid 284 through 297 Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.518A pdb=" N CYS C 306 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 321 Processing helix chain 'C' and resid 392 through 394 No H-bonds generated for 'chain 'C' and resid 392 through 394' Processing helix chain 'C' and resid 561 through 564 Processing helix chain 'C' and resid 578 through 583 removed outlier: 4.170A pdb=" N PHE C 582 " --> pdb=" O ALA C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 598 removed outlier: 3.513A pdb=" N PHE C 596 " --> pdb=" O THR C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 601 No H-bonds generated for 'chain 'C' and resid 599 through 601' Processing helix chain 'C' and resid 615 through 619 Processing helix chain 'C' and resid 620 through 632 Processing helix chain 'C' and resid 641 through 645 removed outlier: 3.695A pdb=" N HIS C 645 " --> pdb=" O GLY C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 664 Processing helix chain 'C' and resid 666 through 686 Processing helix chain 'C' and resid 698 through 703 removed outlier: 3.643A pdb=" N THR C 703 " --> pdb=" O PRO C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 727 Processing helix chain 'C' and resid 810 through 814 removed outlier: 4.334A pdb=" N ASN C 813 " --> pdb=" O ASP C 810 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA C 814 " --> pdb=" O CYS C 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 810 through 814' Processing helix chain 'C' and resid 859 through 863 Processing helix chain 'C' and resid 1026 through 1029 removed outlier: 3.865A pdb=" N LYS C1029 " --> pdb=" O PRO C1026 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1026 through 1029' Processing helix chain 'C' and resid 1043 through 1048 removed outlier: 3.576A pdb=" N ASP C1046 " --> pdb=" O ALA C1043 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE C1047 " --> pdb=" O VAL C1044 " (cutoff:3.500A) Processing helix chain 'C' and resid 1057 through 1064 Processing helix chain 'C' and resid 1079 through 1084 Processing helix chain 'C' and resid 1084 through 1096 removed outlier: 3.705A pdb=" N LYS C1088 " --> pdb=" O ASN C1084 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER C1089 " --> pdb=" O PRO C1085 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP C1090 " --> pdb=" O PHE C1086 " (cutoff:3.500A) Processing helix chain 'C' and resid 1097 through 1104 removed outlier: 3.587A pdb=" N GLY C1100 " --> pdb=" O ILE C1097 " (cutoff:3.500A) Proline residue: C1101 - end of helix Processing helix chain 'C' and resid 1105 through 1109 removed outlier: 3.903A pdb=" N ALA C1108 " --> pdb=" O ALA C1105 " (cutoff:3.500A) Processing helix chain 'C' and resid 1112 through 1126 Processing helix chain 'C' and resid 1130 through 1149 removed outlier: 3.733A pdb=" N TYR C1142 " --> pdb=" O ALA C1138 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C1149 " --> pdb=" O ALA C1145 " (cutoff:3.500A) Processing helix chain 'C' and resid 1164 through 1169 Processing helix chain 'D' and resid 76 through 78 No H-bonds generated for 'chain 'D' and resid 76 through 78' Processing helix chain 'D' and resid 201 through 204 Processing helix chain 'D' and resid 231 through 239 Processing helix chain 'D' and resid 265 through 272 removed outlier: 3.837A pdb=" N LEU D 269 " --> pdb=" O ILE D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 280 removed outlier: 4.067A pdb=" N ALA D 280 " --> pdb=" O SER D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 298 Processing helix chain 'D' and resid 307 through 321 Processing helix chain 'D' and resid 360 through 364 removed outlier: 3.558A pdb=" N CYS D 364 " --> pdb=" O SER D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 394 No H-bonds generated for 'chain 'D' and resid 392 through 394' Processing helix chain 'D' and resid 561 through 564 Processing helix chain 'D' and resid 578 through 583 removed outlier: 4.089A pdb=" N PHE D 582 " --> pdb=" O ALA D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 599 removed outlier: 3.725A pdb=" N THR D 599 " --> pdb=" O ALA D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 619 Processing helix chain 'D' and resid 620 through 632 Processing helix chain 'D' and resid 633 through 635 No H-bonds generated for 'chain 'D' and resid 633 through 635' Processing helix chain 'D' and resid 641 through 645 removed outlier: 3.629A pdb=" N HIS D 645 " --> pdb=" O GLY D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 664 Processing helix chain 'D' and resid 666 through 685 Processing helix chain 'D' and resid 698 through 703 removed outlier: 3.867A pdb=" N THR D 702 " --> pdb=" O THR D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 727 Processing helix chain 'D' and resid 859 through 863 Processing helix chain 'D' and resid 1026 through 1029 Processing helix chain 'D' and resid 1043 through 1047 removed outlier: 3.853A pdb=" N PHE D1047 " --> pdb=" O VAL D1044 " (cutoff:3.500A) Processing helix chain 'D' and resid 1057 through 1064 Processing helix chain 'D' and resid 1079 through 1084 Processing helix chain 'D' and resid 1084 through 1095 removed outlier: 3.700A pdb=" N LYS D1088 " --> pdb=" O ASN D1084 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER D1089 " --> pdb=" O PRO D1085 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N TRP D1090 " --> pdb=" O PHE D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1096 through 1099 Processing helix chain 'D' and resid 1100 through 1107 removed outlier: 3.619A pdb=" N PHE D1103 " --> pdb=" O GLY D1100 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D1104 " --> pdb=" O PRO D1101 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ALA D1105 " --> pdb=" O THR D1102 " (cutoff:3.500A) Processing helix chain 'D' and resid 1112 through 1126 Processing helix chain 'D' and resid 1130 through 1149 removed outlier: 3.704A pdb=" N TYR D1142 " --> pdb=" O ALA D1138 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL D1149 " --> pdb=" O ALA D1145 " (cutoff:3.500A) Processing helix chain 'D' and resid 1164 through 1169 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 201 through 204 Processing helix chain 'E' and resid 231 through 238 Processing helix chain 'E' and resid 264 through 271 Processing helix chain 'E' and resid 284 through 297 Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.518A pdb=" N CYS E 306 " --> pdb=" O LEU E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 321 Processing helix chain 'E' and resid 392 through 394 No H-bonds generated for 'chain 'E' and resid 392 through 394' Processing helix chain 'E' and resid 561 through 564 Processing helix chain 'E' and resid 578 through 583 removed outlier: 4.170A pdb=" N PHE E 582 " --> pdb=" O ALA E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 592 through 598 removed outlier: 3.512A pdb=" N PHE E 596 " --> pdb=" O THR E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 601 No H-bonds generated for 'chain 'E' and resid 599 through 601' Processing helix chain 'E' and resid 615 through 619 Processing helix chain 'E' and resid 620 through 632 Processing helix chain 'E' and resid 641 through 645 removed outlier: 3.695A pdb=" N HIS E 645 " --> pdb=" O GLY E 642 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 664 Processing helix chain 'E' and resid 666 through 686 Processing helix chain 'E' and resid 698 through 703 removed outlier: 3.643A pdb=" N THR E 703 " --> pdb=" O PRO E 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 720 through 727 Processing helix chain 'E' and resid 810 through 814 removed outlier: 4.333A pdb=" N ASN E 813 " --> pdb=" O ASP E 810 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA E 814 " --> pdb=" O CYS E 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 810 through 814' Processing helix chain 'E' and resid 859 through 863 Processing helix chain 'E' and resid 1026 through 1029 removed outlier: 3.865A pdb=" N LYS E1029 " --> pdb=" O PRO E1026 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1026 through 1029' Processing helix chain 'E' and resid 1043 through 1048 removed outlier: 3.575A pdb=" N ASP E1046 " --> pdb=" O ALA E1043 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE E1047 " --> pdb=" O VAL E1044 " (cutoff:3.500A) Processing helix chain 'E' and resid 1057 through 1064 Processing helix chain 'E' and resid 1079 through 1084 Processing helix chain 'E' and resid 1084 through 1096 removed outlier: 3.705A pdb=" N LYS E1088 " --> pdb=" O ASN E1084 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER E1089 " --> pdb=" O PRO E1085 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TRP E1090 " --> pdb=" O PHE E1086 " (cutoff:3.500A) Processing helix chain 'E' and resid 1097 through 1104 removed outlier: 3.586A pdb=" N GLY E1100 " --> pdb=" O ILE E1097 " (cutoff:3.500A) Proline residue: E1101 - end of helix Processing helix chain 'E' and resid 1105 through 1109 removed outlier: 3.903A pdb=" N ALA E1108 " --> pdb=" O ALA E1105 " (cutoff:3.500A) Processing helix chain 'E' and resid 1112 through 1126 Processing helix chain 'E' and resid 1130 through 1149 removed outlier: 3.733A pdb=" N TYR E1142 " --> pdb=" O ALA E1138 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL E1149 " --> pdb=" O ALA E1145 " (cutoff:3.500A) Processing helix chain 'E' and resid 1164 through 1169 Processing helix chain 'F' and resid 76 through 78 No H-bonds generated for 'chain 'F' and resid 76 through 78' Processing helix chain 'F' and resid 201 through 204 Processing helix chain 'F' and resid 231 through 239 Processing helix chain 'F' and resid 265 through 272 removed outlier: 3.837A pdb=" N LEU F 269 " --> pdb=" O ILE F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 280 removed outlier: 4.066A pdb=" N ALA F 280 " --> pdb=" O SER F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 298 Processing helix chain 'F' and resid 307 through 321 Processing helix chain 'F' and resid 360 through 364 removed outlier: 3.557A pdb=" N CYS F 364 " --> pdb=" O SER F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 394 No H-bonds generated for 'chain 'F' and resid 392 through 394' Processing helix chain 'F' and resid 561 through 564 Processing helix chain 'F' and resid 578 through 583 removed outlier: 4.089A pdb=" N PHE F 582 " --> pdb=" O ALA F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 592 through 599 removed outlier: 3.725A pdb=" N THR F 599 " --> pdb=" O ALA F 595 " (cutoff:3.500A) Processing helix chain 'F' and resid 615 through 619 Processing helix chain 'F' and resid 620 through 632 Processing helix chain 'F' and resid 633 through 635 No H-bonds generated for 'chain 'F' and resid 633 through 635' Processing helix chain 'F' and resid 641 through 645 removed outlier: 3.629A pdb=" N HIS F 645 " --> pdb=" O GLY F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 664 Processing helix chain 'F' and resid 666 through 685 Processing helix chain 'F' and resid 698 through 703 removed outlier: 3.867A pdb=" N THR F 702 " --> pdb=" O THR F 698 " (cutoff:3.500A) Processing helix chain 'F' and resid 720 through 727 Processing helix chain 'F' and resid 859 through 863 Processing helix chain 'F' and resid 1026 through 1029 Processing helix chain 'F' and resid 1043 through 1047 removed outlier: 3.853A pdb=" N PHE F1047 " --> pdb=" O VAL F1044 " (cutoff:3.500A) Processing helix chain 'F' and resid 1057 through 1064 Processing helix chain 'F' and resid 1079 through 1084 Processing helix chain 'F' and resid 1084 through 1095 removed outlier: 3.702A pdb=" N LYS F1088 " --> pdb=" O ASN F1084 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER F1089 " --> pdb=" O PRO F1085 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N TRP F1090 " --> pdb=" O PHE F1086 " (cutoff:3.500A) Processing helix chain 'F' and resid 1096 through 1099 Processing helix chain 'F' and resid 1100 through 1107 removed outlier: 3.618A pdb=" N PHE F1103 " --> pdb=" O GLY F1100 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA F1104 " --> pdb=" O PRO F1101 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ALA F1105 " --> pdb=" O THR F1102 " (cutoff:3.500A) Processing helix chain 'F' and resid 1112 through 1126 Processing helix chain 'F' and resid 1130 through 1149 removed outlier: 3.704A pdb=" N TYR F1142 " --> pdb=" O ALA F1138 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL F1149 " --> pdb=" O ALA F1145 " (cutoff:3.500A) Processing helix chain 'F' and resid 1164 through 1169 Processing helix chain 'G' and resid 76 through 78 No H-bonds generated for 'chain 'G' and resid 76 through 78' Processing helix chain 'G' and resid 201 through 204 Processing helix chain 'G' and resid 231 through 238 Processing helix chain 'G' and resid 264 through 271 Processing helix chain 'G' and resid 284 through 297 Processing helix chain 'G' and resid 302 through 306 removed outlier: 3.518A pdb=" N CYS G 306 " --> pdb=" O LEU G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 321 Processing helix chain 'G' and resid 392 through 394 No H-bonds generated for 'chain 'G' and resid 392 through 394' Processing helix chain 'G' and resid 561 through 564 Processing helix chain 'G' and resid 578 through 583 removed outlier: 4.170A pdb=" N PHE G 582 " --> pdb=" O ALA G 579 " (cutoff:3.500A) Processing helix chain 'G' and resid 592 through 598 removed outlier: 3.513A pdb=" N PHE G 596 " --> pdb=" O THR G 592 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 601 No H-bonds generated for 'chain 'G' and resid 599 through 601' Processing helix chain 'G' and resid 615 through 619 Processing helix chain 'G' and resid 620 through 632 Processing helix chain 'G' and resid 641 through 645 removed outlier: 3.696A pdb=" N HIS G 645 " --> pdb=" O GLY G 642 " (cutoff:3.500A) Processing helix chain 'G' and resid 650 through 664 Processing helix chain 'G' and resid 666 through 686 Processing helix chain 'G' and resid 698 through 703 removed outlier: 3.643A pdb=" N THR G 703 " --> pdb=" O PRO G 700 " (cutoff:3.500A) Processing helix chain 'G' and resid 720 through 727 Processing helix chain 'G' and resid 810 through 814 removed outlier: 4.334A pdb=" N ASN G 813 " --> pdb=" O ASP G 810 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA G 814 " --> pdb=" O CYS G 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 810 through 814' Processing helix chain 'G' and resid 859 through 863 Processing helix chain 'G' and resid 1026 through 1029 removed outlier: 3.864A pdb=" N LYS G1029 " --> pdb=" O PRO G1026 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1026 through 1029' Processing helix chain 'G' and resid 1043 through 1048 removed outlier: 3.576A pdb=" N ASP G1046 " --> pdb=" O ALA G1043 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE G1047 " --> pdb=" O VAL G1044 " (cutoff:3.500A) Processing helix chain 'G' and resid 1057 through 1064 Processing helix chain 'G' and resid 1079 through 1084 Processing helix chain 'G' and resid 1084 through 1096 removed outlier: 3.705A pdb=" N LYS G1088 " --> pdb=" O ASN G1084 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER G1089 " --> pdb=" O PRO G1085 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP G1090 " --> pdb=" O PHE G1086 " (cutoff:3.500A) Processing helix chain 'G' and resid 1097 through 1104 removed outlier: 3.587A pdb=" N GLY G1100 " --> pdb=" O ILE G1097 " (cutoff:3.500A) Proline residue: G1101 - end of helix Processing helix chain 'G' and resid 1105 through 1109 removed outlier: 3.903A pdb=" N ALA G1108 " --> pdb=" O ALA G1105 " (cutoff:3.500A) Processing helix chain 'G' and resid 1112 through 1126 Processing helix chain 'G' and resid 1130 through 1149 removed outlier: 3.733A pdb=" N TYR G1142 " --> pdb=" O ALA G1138 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL G1149 " --> pdb=" O ALA G1145 " (cutoff:3.500A) Processing helix chain 'G' and resid 1164 through 1169 Processing helix chain 'H' and resid 76 through 78 No H-bonds generated for 'chain 'H' and resid 76 through 78' Processing helix chain 'H' and resid 201 through 204 Processing helix chain 'H' and resid 231 through 239 Processing helix chain 'H' and resid 265 through 272 removed outlier: 3.837A pdb=" N LEU H 269 " --> pdb=" O ILE H 265 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 280 removed outlier: 4.068A pdb=" N ALA H 280 " --> pdb=" O SER H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 298 Processing helix chain 'H' and resid 307 through 321 Processing helix chain 'H' and resid 360 through 364 removed outlier: 3.558A pdb=" N CYS H 364 " --> pdb=" O SER H 361 " (cutoff:3.500A) Processing helix chain 'H' and resid 392 through 394 No H-bonds generated for 'chain 'H' and resid 392 through 394' Processing helix chain 'H' and resid 561 through 564 Processing helix chain 'H' and resid 578 through 583 removed outlier: 4.089A pdb=" N PHE H 582 " --> pdb=" O ALA H 579 " (cutoff:3.500A) Processing helix chain 'H' and resid 592 through 599 removed outlier: 3.725A pdb=" N THR H 599 " --> pdb=" O ALA H 595 " (cutoff:3.500A) Processing helix chain 'H' and resid 615 through 619 Processing helix chain 'H' and resid 620 through 632 Processing helix chain 'H' and resid 633 through 635 No H-bonds generated for 'chain 'H' and resid 633 through 635' Processing helix chain 'H' and resid 641 through 645 removed outlier: 3.629A pdb=" N HIS H 645 " --> pdb=" O GLY H 642 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 664 Processing helix chain 'H' and resid 666 through 685 Processing helix chain 'H' and resid 698 through 703 removed outlier: 3.866A pdb=" N THR H 702 " --> pdb=" O THR H 698 " (cutoff:3.500A) Processing helix chain 'H' and resid 720 through 727 Processing helix chain 'H' and resid 859 through 863 Processing helix chain 'H' and resid 1026 through 1029 Processing helix chain 'H' and resid 1043 through 1047 removed outlier: 3.853A pdb=" N PHE H1047 " --> pdb=" O VAL H1044 " (cutoff:3.500A) Processing helix chain 'H' and resid 1057 through 1064 Processing helix chain 'H' and resid 1079 through 1084 Processing helix chain 'H' and resid 1084 through 1095 removed outlier: 3.701A pdb=" N LYS H1088 " --> pdb=" O ASN H1084 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER H1089 " --> pdb=" O PRO H1085 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N TRP H1090 " --> pdb=" O PHE H1086 " (cutoff:3.500A) Processing helix chain 'H' and resid 1096 through 1099 Processing helix chain 'H' and resid 1100 through 1107 removed outlier: 3.619A pdb=" N PHE H1103 " --> pdb=" O GLY H1100 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA H1104 " --> pdb=" O PRO H1101 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ALA H1105 " --> pdb=" O THR H1102 " (cutoff:3.500A) Processing helix chain 'H' and resid 1112 through 1126 Processing helix chain 'H' and resid 1130 through 1149 removed outlier: 3.704A pdb=" N TYR H1142 " --> pdb=" O ALA H1138 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL H1149 " --> pdb=" O ALA H1145 " (cutoff:3.500A) Processing helix chain 'H' and resid 1164 through 1169 Processing sheet with id=1, first strand: chain 'A' and resid 68 through 70 removed outlier: 6.704A pdb=" N VAL A 69 " --> pdb=" O VAL B 982 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER B 961 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N VAL B 951 " --> pdb=" O SER B 961 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N PHE B 944 " --> pdb=" O GLN B 931 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLN B 931 " --> pdb=" O PHE B 944 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B 946 " --> pdb=" O LEU B 929 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=3, first strand: chain 'A' and resid 104 through 109 removed outlier: 6.531A pdb=" N ASN A 104 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ARG A 124 " --> pdb=" O ASN A 104 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL A 106 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU A 122 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 135 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N SER A 125 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU A 133 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 343 through 348 removed outlier: 5.348A pdb=" N TYR A 344 " --> pdb=" O PHE A 373 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE A 373 " --> pdb=" O TYR A 344 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLU A 346 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLY A 371 " --> pdb=" O GLU A 346 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 378 through 380 Processing sheet with id=6, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=7, first strand: chain 'A' and resid 408 through 410 Processing sheet with id=8, first strand: chain 'A' and resid 449 through 451 removed outlier: 4.125A pdb=" N LEU A 543 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 525 " --> pdb=" O ALA A 522 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 456 through 461 removed outlier: 6.662A pdb=" N VAL A 471 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER A 489 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG A 476 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU A 487 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL A 509 " --> pdb=" O THR A 516 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'A' and resid 709 through 714 removed outlier: 4.195A pdb=" N HIS A 713 " --> pdb=" O VAL A 738 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 738 " --> pdb=" O HIS A 713 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'A' and resid 748 through 750 removed outlier: 3.721A pdb=" N LYS A 754 " --> pdb=" O ASP A 750 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'A' and resid 763 through 765 Processing sheet with id=13, first strand: chain 'A' and resid 775 through 778 Processing sheet with id=14, first strand: chain 'A' and resid 807 through 809 Processing sheet with id=15, first strand: chain 'A' and resid 850 through 851 Processing sheet with id=16, first strand: chain 'A' and resid 865 through 867 Processing sheet with id=17, first strand: chain 'A' and resid 877 through 880 Processing sheet with id=18, first strand: chain 'A' and resid 918 through 920 Processing sheet with id=19, first strand: chain 'A' and resid 1032 through 1033 removed outlier: 6.707A pdb=" N VAL A 946 " --> pdb=" O LEU A 929 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLN A 931 " --> pdb=" O PHE A 944 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N PHE A 944 " --> pdb=" O GLN A 931 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 963 " --> pdb=" O GLU A 949 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL A 951 " --> pdb=" O SER A 961 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N SER A 961 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'A' and resid 1176 through 1179 Processing sheet with id=21, first strand: chain 'A' and resid 1216 through 1218 Processing sheet with id=22, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=23, first strand: chain 'B' and resid 104 through 109 removed outlier: 6.587A pdb=" N ASN B 104 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ARG B 124 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL B 106 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU B 122 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N SER B 125 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU B 133 " --> pdb=" O SER B 125 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'B' and resid 343 through 348 removed outlier: 5.391A pdb=" N TYR B 344 " --> pdb=" O PHE B 373 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE B 373 " --> pdb=" O TYR B 344 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLU B 346 " --> pdb=" O GLY B 371 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLY B 371 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'B' and resid 378 through 380 Processing sheet with id=26, first strand: chain 'B' and resid 397 through 398 Processing sheet with id=27, first strand: chain 'B' and resid 408 through 410 Processing sheet with id=28, first strand: chain 'B' and resid 449 through 451 removed outlier: 4.129A pdb=" N LEU B 543 " --> pdb=" O THR B 539 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'B' and resid 456 through 461 removed outlier: 5.085A pdb=" N SER B 457 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU B 475 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL B 459 " --> pdb=" O ALA B 473 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA B 473 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 489 " --> pdb=" O GLU B 474 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG B 476 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LEU B 487 " --> pdb=" O ARG B 476 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'B' and resid 709 through 714 removed outlier: 4.120A pdb=" N HIS B 713 " --> pdb=" O VAL B 738 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL B 738 " --> pdb=" O HIS B 713 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'B' and resid 748 through 749 Processing sheet with id=32, first strand: chain 'B' and resid 763 through 765 Processing sheet with id=33, first strand: chain 'B' and resid 775 through 778 Processing sheet with id=34, first strand: chain 'B' and resid 807 through 809 Processing sheet with id=35, first strand: chain 'B' and resid 850 through 851 Processing sheet with id=36, first strand: chain 'B' and resid 865 through 866 Processing sheet with id=37, first strand: chain 'B' and resid 877 through 880 Processing sheet with id=38, first strand: chain 'B' and resid 918 through 920 Processing sheet with id=39, first strand: chain 'B' and resid 1176 through 1179 Processing sheet with id=40, first strand: chain 'B' and resid 1216 through 1218 Processing sheet with id=41, first strand: chain 'C' and resid 68 through 70 removed outlier: 6.705A pdb=" N VAL C 69 " --> pdb=" O VAL D 982 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER D 961 " --> pdb=" O VAL D 951 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL D 951 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N PHE D 944 " --> pdb=" O GLN D 931 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLN D 931 " --> pdb=" O PHE D 944 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL D 946 " --> pdb=" O LEU D 929 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'C' and resid 96 through 98 Processing sheet with id=43, first strand: chain 'C' and resid 104 through 109 removed outlier: 6.531A pdb=" N ASN C 104 " --> pdb=" O ARG C 124 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ARG C 124 " --> pdb=" O ASN C 104 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL C 106 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU C 122 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG C 135 " --> pdb=" O ARG C 123 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N SER C 125 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LEU C 133 " --> pdb=" O SER C 125 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'C' and resid 343 through 348 removed outlier: 5.348A pdb=" N TYR C 344 " --> pdb=" O PHE C 373 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE C 373 " --> pdb=" O TYR C 344 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLU C 346 " --> pdb=" O GLY C 371 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLY C 371 " --> pdb=" O GLU C 346 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'C' and resid 378 through 380 Processing sheet with id=46, first strand: chain 'C' and resid 397 through 398 Processing sheet with id=47, first strand: chain 'C' and resid 408 through 410 Processing sheet with id=48, first strand: chain 'C' and resid 449 through 451 removed outlier: 4.126A pdb=" N LEU C 543 " --> pdb=" O THR C 539 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 525 " --> pdb=" O ALA C 522 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'C' and resid 456 through 461 removed outlier: 6.662A pdb=" N VAL C 471 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER C 489 " --> pdb=" O GLU C 474 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ARG C 476 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU C 487 " --> pdb=" O ARG C 476 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL C 509 " --> pdb=" O THR C 516 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'C' and resid 709 through 714 removed outlier: 4.195A pdb=" N HIS C 713 " --> pdb=" O VAL C 738 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL C 738 " --> pdb=" O HIS C 713 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'C' and resid 748 through 750 removed outlier: 3.721A pdb=" N LYS C 754 " --> pdb=" O ASP C 750 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'C' and resid 763 through 765 Processing sheet with id=53, first strand: chain 'C' and resid 775 through 778 Processing sheet with id=54, first strand: chain 'C' and resid 807 through 809 Processing sheet with id=55, first strand: chain 'C' and resid 850 through 851 Processing sheet with id=56, first strand: chain 'C' and resid 865 through 867 Processing sheet with id=57, first strand: chain 'C' and resid 877 through 880 Processing sheet with id=58, first strand: chain 'C' and resid 918 through 920 Processing sheet with id=59, first strand: chain 'C' and resid 1032 through 1033 removed outlier: 6.708A pdb=" N VAL C 946 " --> pdb=" O LEU C 929 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLN C 931 " --> pdb=" O PHE C 944 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N PHE C 944 " --> pdb=" O GLN C 931 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 963 " --> pdb=" O GLU C 949 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL C 951 " --> pdb=" O SER C 961 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N SER C 961 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'C' and resid 1176 through 1179 Processing sheet with id=61, first strand: chain 'C' and resid 1216 through 1218 Processing sheet with id=62, first strand: chain 'D' and resid 96 through 98 Processing sheet with id=63, first strand: chain 'D' and resid 104 through 109 removed outlier: 6.586A pdb=" N ASN D 104 " --> pdb=" O ARG D 124 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ARG D 124 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL D 106 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU D 122 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N SER D 125 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU D 133 " --> pdb=" O SER D 125 " (cutoff:3.500A) Processing sheet with id=64, first strand: chain 'D' and resid 343 through 348 removed outlier: 5.390A pdb=" N TYR D 344 " --> pdb=" O PHE D 373 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE D 373 " --> pdb=" O TYR D 344 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLU D 346 " --> pdb=" O GLY D 371 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLY D 371 " --> pdb=" O GLU D 346 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'D' and resid 378 through 380 Processing sheet with id=66, first strand: chain 'D' and resid 397 through 398 Processing sheet with id=67, first strand: chain 'D' and resid 408 through 410 Processing sheet with id=68, first strand: chain 'D' and resid 449 through 451 removed outlier: 4.129A pdb=" N LEU D 543 " --> pdb=" O THR D 539 " (cutoff:3.500A) Processing sheet with id=69, first strand: chain 'D' and resid 456 through 461 removed outlier: 5.085A pdb=" N SER D 457 " --> pdb=" O LEU D 475 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU D 475 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL D 459 " --> pdb=" O ALA D 473 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA D 473 " --> pdb=" O VAL D 459 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER D 489 " --> pdb=" O GLU D 474 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG D 476 " --> pdb=" O LEU D 487 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LEU D 487 " --> pdb=" O ARG D 476 " (cutoff:3.500A) Processing sheet with id=70, first strand: chain 'D' and resid 709 through 714 removed outlier: 4.120A pdb=" N HIS D 713 " --> pdb=" O VAL D 738 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL D 738 " --> pdb=" O HIS D 713 " (cutoff:3.500A) Processing sheet with id=71, first strand: chain 'D' and resid 748 through 749 Processing sheet with id=72, first strand: chain 'D' and resid 763 through 765 Processing sheet with id=73, first strand: chain 'D' and resid 775 through 778 Processing sheet with id=74, first strand: chain 'D' and resid 807 through 809 Processing sheet with id=75, first strand: chain 'D' and resid 850 through 851 Processing sheet with id=76, first strand: chain 'D' and resid 865 through 866 Processing sheet with id=77, first strand: chain 'D' and resid 877 through 880 Processing sheet with id=78, first strand: chain 'D' and resid 918 through 920 Processing sheet with id=79, first strand: chain 'D' and resid 1176 through 1179 Processing sheet with id=80, first strand: chain 'D' and resid 1216 through 1218 Processing sheet with id=81, first strand: chain 'E' and resid 68 through 70 removed outlier: 6.705A pdb=" N VAL E 69 " --> pdb=" O VAL F 982 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER F 961 " --> pdb=" O VAL F 951 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N VAL F 951 " --> pdb=" O SER F 961 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N PHE F 944 " --> pdb=" O GLN F 931 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLN F 931 " --> pdb=" O PHE F 944 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL F 946 " --> pdb=" O LEU F 929 " (cutoff:3.500A) Processing sheet with id=82, first strand: chain 'E' and resid 96 through 98 Processing sheet with id=83, first strand: chain 'E' and resid 104 through 109 removed outlier: 6.531A pdb=" N ASN E 104 " --> pdb=" O ARG E 124 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ARG E 124 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N VAL E 106 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU E 122 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG E 135 " --> pdb=" O ARG E 123 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N SER E 125 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU E 133 " --> pdb=" O SER E 125 " (cutoff:3.500A) Processing sheet with id=84, first strand: chain 'E' and resid 343 through 348 removed outlier: 5.348A pdb=" N TYR E 344 " --> pdb=" O PHE E 373 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE E 373 " --> pdb=" O TYR E 344 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLU E 346 " --> pdb=" O GLY E 371 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLY E 371 " --> pdb=" O GLU E 346 " (cutoff:3.500A) Processing sheet with id=85, first strand: chain 'E' and resid 378 through 380 Processing sheet with id=86, first strand: chain 'E' and resid 397 through 398 Processing sheet with id=87, first strand: chain 'E' and resid 408 through 410 Processing sheet with id=88, first strand: chain 'E' and resid 449 through 451 removed outlier: 4.126A pdb=" N LEU E 543 " --> pdb=" O THR E 539 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL E 525 " --> pdb=" O ALA E 522 " (cutoff:3.500A) Processing sheet with id=89, first strand: chain 'E' and resid 456 through 461 removed outlier: 6.662A pdb=" N VAL E 471 " --> pdb=" O LEU E 460 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER E 489 " --> pdb=" O GLU E 474 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG E 476 " --> pdb=" O LEU E 487 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU E 487 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL E 509 " --> pdb=" O THR E 516 " (cutoff:3.500A) Processing sheet with id=90, first strand: chain 'E' and resid 709 through 714 removed outlier: 4.195A pdb=" N HIS E 713 " --> pdb=" O VAL E 738 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL E 738 " --> pdb=" O HIS E 713 " (cutoff:3.500A) Processing sheet with id=91, first strand: chain 'E' and resid 748 through 750 removed outlier: 3.721A pdb=" N LYS E 754 " --> pdb=" O ASP E 750 " (cutoff:3.500A) Processing sheet with id=92, first strand: chain 'E' and resid 763 through 765 Processing sheet with id=93, first strand: chain 'E' and resid 775 through 778 Processing sheet with id=94, first strand: chain 'E' and resid 807 through 809 Processing sheet with id=95, first strand: chain 'E' and resid 850 through 851 Processing sheet with id=96, first strand: chain 'E' and resid 865 through 867 Processing sheet with id=97, first strand: chain 'E' and resid 877 through 880 Processing sheet with id=98, first strand: chain 'E' and resid 918 through 920 Processing sheet with id=99, first strand: chain 'E' and resid 1032 through 1033 removed outlier: 6.707A pdb=" N VAL E 946 " --> pdb=" O LEU E 929 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLN E 931 " --> pdb=" O PHE E 944 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N PHE E 944 " --> pdb=" O GLN E 931 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA E 963 " --> pdb=" O GLU E 949 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL E 951 " --> pdb=" O SER E 961 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N SER E 961 " --> pdb=" O VAL E 951 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'E' and resid 1176 through 1179 Processing sheet with id=101, first strand: chain 'E' and resid 1216 through 1218 Processing sheet with id=102, first strand: chain 'F' and resid 96 through 98 Processing sheet with id=103, first strand: chain 'F' and resid 104 through 109 removed outlier: 6.586A pdb=" N ASN F 104 " --> pdb=" O ARG F 124 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ARG F 124 " --> pdb=" O ASN F 104 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL F 106 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU F 122 " --> pdb=" O VAL F 106 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N SER F 125 " --> pdb=" O LEU F 133 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU F 133 " --> pdb=" O SER F 125 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'F' and resid 343 through 348 removed outlier: 5.391A pdb=" N TYR F 344 " --> pdb=" O PHE F 373 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE F 373 " --> pdb=" O TYR F 344 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLU F 346 " --> pdb=" O GLY F 371 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLY F 371 " --> pdb=" O GLU F 346 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'F' and resid 378 through 380 Processing sheet with id=106, first strand: chain 'F' and resid 397 through 398 Processing sheet with id=107, first strand: chain 'F' and resid 408 through 410 Processing sheet with id=108, first strand: chain 'F' and resid 449 through 451 removed outlier: 4.129A pdb=" N LEU F 543 " --> pdb=" O THR F 539 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain 'F' and resid 456 through 461 removed outlier: 5.085A pdb=" N SER F 457 " --> pdb=" O LEU F 475 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU F 475 " --> pdb=" O SER F 457 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL F 459 " --> pdb=" O ALA F 473 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA F 473 " --> pdb=" O VAL F 459 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER F 489 " --> pdb=" O GLU F 474 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG F 476 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LEU F 487 " --> pdb=" O ARG F 476 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'F' and resid 709 through 714 removed outlier: 4.120A pdb=" N HIS F 713 " --> pdb=" O VAL F 738 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL F 738 " --> pdb=" O HIS F 713 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain 'F' and resid 748 through 749 Processing sheet with id=112, first strand: chain 'F' and resid 763 through 765 Processing sheet with id=113, first strand: chain 'F' and resid 775 through 778 Processing sheet with id=114, first strand: chain 'F' and resid 807 through 809 Processing sheet with id=115, first strand: chain 'F' and resid 850 through 851 Processing sheet with id=116, first strand: chain 'F' and resid 865 through 866 Processing sheet with id=117, first strand: chain 'F' and resid 877 through 880 Processing sheet with id=118, first strand: chain 'F' and resid 918 through 920 Processing sheet with id=119, first strand: chain 'F' and resid 1176 through 1179 Processing sheet with id=120, first strand: chain 'F' and resid 1216 through 1218 Processing sheet with id=121, first strand: chain 'G' and resid 68 through 70 removed outlier: 6.705A pdb=" N VAL G 69 " --> pdb=" O VAL H 982 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER H 961 " --> pdb=" O VAL H 951 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL H 951 " --> pdb=" O SER H 961 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N PHE H 944 " --> pdb=" O GLN H 931 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLN H 931 " --> pdb=" O PHE H 944 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL H 946 " --> pdb=" O LEU H 929 " (cutoff:3.500A) Processing sheet with id=122, first strand: chain 'G' and resid 96 through 98 Processing sheet with id=123, first strand: chain 'G' and resid 104 through 109 removed outlier: 6.531A pdb=" N ASN G 104 " --> pdb=" O ARG G 124 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ARG G 124 " --> pdb=" O ASN G 104 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N VAL G 106 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU G 122 " --> pdb=" O VAL G 106 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG G 135 " --> pdb=" O ARG G 123 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N SER G 125 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LEU G 133 " --> pdb=" O SER G 125 " (cutoff:3.500A) Processing sheet with id=124, first strand: chain 'G' and resid 343 through 348 removed outlier: 5.348A pdb=" N TYR G 344 " --> pdb=" O PHE G 373 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE G 373 " --> pdb=" O TYR G 344 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLU G 346 " --> pdb=" O GLY G 371 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLY G 371 " --> pdb=" O GLU G 346 " (cutoff:3.500A) Processing sheet with id=125, first strand: chain 'G' and resid 378 through 380 Processing sheet with id=126, first strand: chain 'G' and resid 397 through 398 Processing sheet with id=127, first strand: chain 'G' and resid 408 through 410 Processing sheet with id=128, first strand: chain 'G' and resid 449 through 451 removed outlier: 4.125A pdb=" N LEU G 543 " --> pdb=" O THR G 539 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL G 525 " --> pdb=" O ALA G 522 " (cutoff:3.500A) Processing sheet with id=129, first strand: chain 'G' and resid 456 through 461 removed outlier: 6.662A pdb=" N VAL G 471 " --> pdb=" O LEU G 460 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER G 489 " --> pdb=" O GLU G 474 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG G 476 " --> pdb=" O LEU G 487 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU G 487 " --> pdb=" O ARG G 476 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL G 509 " --> pdb=" O THR G 516 " (cutoff:3.500A) Processing sheet with id=130, first strand: chain 'G' and resid 709 through 714 removed outlier: 4.195A pdb=" N HIS G 713 " --> pdb=" O VAL G 738 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL G 738 " --> pdb=" O HIS G 713 " (cutoff:3.500A) Processing sheet with id=131, first strand: chain 'G' and resid 748 through 750 removed outlier: 3.722A pdb=" N LYS G 754 " --> pdb=" O ASP G 750 " (cutoff:3.500A) Processing sheet with id=132, first strand: chain 'G' and resid 763 through 765 Processing sheet with id=133, first strand: chain 'G' and resid 775 through 778 Processing sheet with id=134, first strand: chain 'G' and resid 807 through 809 Processing sheet with id=135, first strand: chain 'G' and resid 850 through 851 Processing sheet with id=136, first strand: chain 'G' and resid 865 through 867 Processing sheet with id=137, first strand: chain 'G' and resid 877 through 880 Processing sheet with id=138, first strand: chain 'G' and resid 918 through 920 Processing sheet with id=139, first strand: chain 'G' and resid 1032 through 1033 removed outlier: 6.708A pdb=" N VAL G 946 " --> pdb=" O LEU G 929 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLN G 931 " --> pdb=" O PHE G 944 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N PHE G 944 " --> pdb=" O GLN G 931 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA G 963 " --> pdb=" O GLU G 949 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL G 951 " --> pdb=" O SER G 961 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N SER G 961 " --> pdb=" O VAL G 951 " (cutoff:3.500A) Processing sheet with id=140, first strand: chain 'G' and resid 1176 through 1179 Processing sheet with id=141, first strand: chain 'G' and resid 1216 through 1218 Processing sheet with id=142, first strand: chain 'H' and resid 96 through 98 Processing sheet with id=143, first strand: chain 'H' and resid 104 through 109 removed outlier: 6.586A pdb=" N ASN H 104 " --> pdb=" O ARG H 124 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ARG H 124 " --> pdb=" O ASN H 104 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL H 106 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU H 122 " --> pdb=" O VAL H 106 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N SER H 125 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU H 133 " --> pdb=" O SER H 125 " (cutoff:3.500A) Processing sheet with id=144, first strand: chain 'H' and resid 343 through 348 removed outlier: 5.390A pdb=" N TYR H 344 " --> pdb=" O PHE H 373 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE H 373 " --> pdb=" O TYR H 344 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLU H 346 " --> pdb=" O GLY H 371 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLY H 371 " --> pdb=" O GLU H 346 " (cutoff:3.500A) Processing sheet with id=145, first strand: chain 'H' and resid 378 through 380 Processing sheet with id=146, first strand: chain 'H' and resid 397 through 398 Processing sheet with id=147, first strand: chain 'H' and resid 408 through 410 Processing sheet with id=148, first strand: chain 'H' and resid 449 through 451 removed outlier: 4.129A pdb=" N LEU H 543 " --> pdb=" O THR H 539 " (cutoff:3.500A) Processing sheet with id=149, first strand: chain 'H' and resid 456 through 461 removed outlier: 5.085A pdb=" N SER H 457 " --> pdb=" O LEU H 475 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU H 475 " --> pdb=" O SER H 457 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL H 459 " --> pdb=" O ALA H 473 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA H 473 " --> pdb=" O VAL H 459 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER H 489 " --> pdb=" O GLU H 474 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG H 476 " --> pdb=" O LEU H 487 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LEU H 487 " --> pdb=" O ARG H 476 " (cutoff:3.500A) Processing sheet with id=150, first strand: chain 'H' and resid 709 through 714 removed outlier: 4.119A pdb=" N HIS H 713 " --> pdb=" O VAL H 738 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL H 738 " --> pdb=" O HIS H 713 " (cutoff:3.500A) Processing sheet with id=151, first strand: chain 'H' and resid 748 through 749 Processing sheet with id=152, first strand: chain 'H' and resid 763 through 765 Processing sheet with id=153, first strand: chain 'H' and resid 775 through 778 Processing sheet with id=154, first strand: chain 'H' and resid 807 through 809 Processing sheet with id=155, first strand: chain 'H' and resid 850 through 851 Processing sheet with id=156, first strand: chain 'H' and resid 865 through 866 Processing sheet with id=157, first strand: chain 'H' and resid 877 through 880 Processing sheet with id=158, first strand: chain 'H' and resid 918 through 920 Processing sheet with id=159, first strand: chain 'H' and resid 1176 through 1179 Processing sheet with id=160, first strand: chain 'H' and resid 1216 through 1218 2640 hydrogen bonds defined for protein. 6476 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: 51.44 Time building geometry restraints manager: 16.51 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: 23373 1.34 - 1.46: 16371 1.46 - 1.58: 30268 1.58 - 1.71: 8 1.71 - 1.83: 1136 Bond restraints: 71156 Sorted by residual: bond pdb=" C PRO D 762 " pdb=" N CYS D 763 " ideal model delta sigma weight residual 1.329 1.663 -0.334 1.43e-02 4.89e+03 5.46e+02 bond pdb=" C PRO B 762 " pdb=" N CYS B 763 " ideal model delta sigma weight residual 1.329 1.663 -0.334 1.43e-02 4.89e+03 5.46e+02 bond pdb=" C PRO H 762 " pdb=" N CYS H 763 " ideal model delta sigma weight residual 1.329 1.663 -0.334 1.43e-02 4.89e+03 5.45e+02 bond pdb=" C PRO F 762 " pdb=" N CYS F 763 " ideal model delta sigma weight residual 1.329 1.663 -0.334 1.43e-02 4.89e+03 5.45e+02 bond pdb=" C PRO A 762 " pdb=" N CYS A 763 " ideal model delta sigma weight residual 1.328 1.598 -0.269 1.44e-02 4.82e+03 3.50e+02 ... (remaining 71151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 96027 2.35 - 4.70: 797 4.70 - 7.06: 57 7.06 - 9.41: 3 9.41 - 11.76: 8 Bond angle restraints: 96892 Sorted by residual: angle pdb=" O PRO E 762 " pdb=" C PRO E 762 " pdb=" N CYS E 763 " ideal model delta sigma weight residual 122.91 111.15 11.76 1.21e+00 6.83e-01 9.45e+01 angle pdb=" O PRO A 762 " pdb=" C PRO A 762 " pdb=" N CYS A 763 " ideal model delta sigma weight residual 122.91 111.15 11.76 1.21e+00 6.83e-01 9.45e+01 angle pdb=" O PRO C 762 " pdb=" C PRO C 762 " pdb=" N CYS C 763 " ideal model delta sigma weight residual 122.91 111.17 11.74 1.21e+00 6.83e-01 9.41e+01 angle pdb=" O PRO G 762 " pdb=" C PRO G 762 " pdb=" N CYS G 763 " ideal model delta sigma weight residual 122.91 111.20 11.71 1.21e+00 6.83e-01 9.37e+01 angle pdb=" CA PRO B 762 " pdb=" C PRO B 762 " pdb=" N CYS B 763 " ideal model delta sigma weight residual 115.04 124.99 -9.95 1.35e+00 5.49e-01 5.43e+01 ... (remaining 96887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 37612 17.91 - 35.81: 3832 35.81 - 53.72: 1069 53.72 - 71.62: 187 71.62 - 89.53: 82 Dihedral angle restraints: 42782 sinusoidal: 16206 harmonic: 26576 Sorted by residual: dihedral pdb=" CB CYS A 464 " pdb=" SG CYS A 464 " pdb=" SG CYS A 568 " pdb=" CB CYS A 568 " ideal model delta sinusoidal sigma weight residual -86.00 -175.53 89.53 1 1.00e+01 1.00e-02 9.52e+01 dihedral pdb=" CB CYS B 464 " pdb=" SG CYS B 464 " pdb=" SG CYS B 568 " pdb=" CB CYS B 568 " ideal model delta sinusoidal sigma weight residual 93.00 -179.07 -87.93 1 1.00e+01 1.00e-02 9.25e+01 dihedral pdb=" CB CYS B 111 " pdb=" SG CYS B 111 " pdb=" SG CYS B 208 " pdb=" CB CYS B 208 " ideal model delta sinusoidal sigma weight residual -86.00 -166.83 80.83 1 1.00e+01 1.00e-02 8.07e+01 ... (remaining 42779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 7683 0.041 - 0.081: 2029 0.081 - 0.122: 945 0.122 - 0.162: 55 0.162 - 0.203: 4 Chirality restraints: 10716 Sorted by residual: chirality pdb=" CA CYS G1185 " pdb=" N CYS G1185 " pdb=" C CYS G1185 " pdb=" CB CYS G1185 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA CYS C1185 " pdb=" N CYS C1185 " pdb=" C CYS C1185 " pdb=" CB CYS C1185 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA CYS E1185 " pdb=" N CYS E1185 " pdb=" C CYS E1185 " pdb=" CB CYS E1185 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 10713 not shown) Planarity restraints: 12852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 762 " -0.057 2.00e-02 2.50e+03 9.89e-02 9.78e+01 pdb=" C PRO A 762 " 0.171 2.00e-02 2.50e+03 pdb=" O PRO A 762 " -0.064 2.00e-02 2.50e+03 pdb=" N CYS A 763 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 762 " 0.057 2.00e-02 2.50e+03 9.89e-02 9.78e+01 pdb=" C PRO E 762 " -0.171 2.00e-02 2.50e+03 pdb=" O PRO E 762 " 0.064 2.00e-02 2.50e+03 pdb=" N CYS E 763 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO G 762 " -0.057 2.00e-02 2.50e+03 9.88e-02 9.77e+01 pdb=" C PRO G 762 " 0.171 2.00e-02 2.50e+03 pdb=" O PRO G 762 " -0.064 2.00e-02 2.50e+03 pdb=" N CYS G 763 " -0.050 2.00e-02 2.50e+03 ... (remaining 12849 not shown) Histogram of nonbonded interaction distances: 0.94 - 1.73: 17 1.73 - 2.53: 774 2.53 - 3.32: 76189 3.32 - 4.11: 174627 4.11 - 4.90: 320251 Warning: very small nonbonded interaction distances. Nonbonded interactions: 571858 Sorted by model distance: nonbonded pdb=" OD1 ASN C 215 " pdb="CA CA C1501 " model vdw 0.942 2.510 nonbonded pdb=" OD1 ASN G 215 " pdb="CA CA G1501 " model vdw 0.942 2.510 nonbonded pdb=" OD1 ASN A 215 " pdb="CA CA A1501 " model vdw 0.943 2.510 nonbonded pdb=" OD1 ASN E 215 " pdb="CA CA E1501 " model vdw 0.943 2.510 nonbonded pdb=" ND1 HIS A 320 " pdb="CU CU A1503 " model vdw 1.118 2.320 ... (remaining 571853 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: 0.39 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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=0.29 max=1.00 mean=0.99 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: 7.940 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: 0.090 Extract box with map and model: 2.240 Check model and map are aligned: 0.420 Set scattering table: 0.510 Process input model: 175.880 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.240 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:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 190.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1626 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.334 71156 Z= 0.227 Angle : 0.520 11.761 96892 Z= 0.287 Chirality : 0.043 0.203 10716 Planarity : 0.004 0.099 12852 Dihedral : 15.959 88.789 25480 Min Nonbonded Distance : 0.942 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.27 % Allowed : 20.72 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: 0.27 (0.09), residues: 9228 helix: 0.84 (0.14), residues: 1404 sheet: 0.52 (0.12), residues: 1960 loop : -0.03 (0.09), residues: 5864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 84 HIS 0.002 0.000 HIS D 777 PHE 0.011 0.001 PHE E 967 TYR 0.012 0.001 TYR B 176 ARG 0.008 0.000 ARG G 610 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 7740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 804 time to evaluate : 6.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1196 CYS cc_start: 0.1871 (OUTLIER) cc_final: 0.1466 (p) REVERT: B 136 VAL cc_start: 0.5182 (t) cc_final: 0.4977 (t) REVERT: C 1219 GLU cc_start: 0.5187 (OUTLIER) cc_final: 0.4354 (mp0) REVERT: D 553 MET cc_start: 0.0560 (ttt) cc_final: -0.0142 (tpt) REVERT: D 611 ASN cc_start: 0.2227 (m-40) cc_final: 0.2021 (m110) REVERT: D 618 SER cc_start: 0.3649 (p) cc_final: 0.3386 (t) REVERT: D 1222 MET cc_start: 0.5538 (ttt) cc_final: 0.4663 (ttp) REVERT: E 86 SER cc_start: 0.5093 (OUTLIER) cc_final: 0.4450 (t) REVERT: E 233 MET cc_start: -0.4600 (tpp) cc_final: -0.5823 (ppp) REVERT: E 284 VAL cc_start: 0.0102 (OUTLIER) cc_final: -0.0624 (t) REVERT: E 480 LEU cc_start: 0.2938 (OUTLIER) cc_final: 0.2632 (mm) REVERT: E 731 CYS cc_start: 0.0846 (OUTLIER) cc_final: 0.0531 (p) REVERT: E 732 SER cc_start: -0.4549 (OUTLIER) cc_final: -0.4837 (t) REVERT: F 342 MET cc_start: -0.3925 (mtp) cc_final: -0.4243 (mpp) REVERT: F 833 THR cc_start: 0.0342 (m) cc_final: 0.0077 (m) REVERT: G 233 MET cc_start: -0.2717 (tpp) cc_final: -0.3031 (tpt) REVERT: G 302 ASP cc_start: 0.3986 (OUTLIER) cc_final: 0.3527 (t70) REVERT: G 732 SER cc_start: 0.3572 (OUTLIER) cc_final: 0.3303 (m) REVERT: G 806 MET cc_start: -0.0356 (mmm) cc_final: -0.0950 (mtp) REVERT: G 832 MET cc_start: 0.1031 (mmm) cc_final: -0.1719 (tpt) REVERT: G 1222 MET cc_start: -0.2907 (mmm) cc_final: -0.3203 (ttm) outliers start: 160 outliers final: 19 residues processed: 947 average time/residue: 0.6301 time to fit residues: 1042.9531 Evaluate side-chains 418 residues out of total 7740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 390 time to evaluate : 5.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 1196 CYS Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 877 THR Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 704 CYS Chi-restraints excluded: chain E residue 731 CYS Chi-restraints excluded: chain E residue 732 SER Chi-restraints excluded: chain E residue 1196 CYS Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 943 SER Chi-restraints excluded: chain G residue 302 ASP Chi-restraints excluded: chain G residue 424 SER Chi-restraints excluded: chain G residue 731 CYS Chi-restraints excluded: chain G residue 732 SER Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 526 THR Chi-restraints excluded: chain H residue 1157 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 776 optimal weight: 5.9990 chunk 697 optimal weight: 1.9990 chunk 386 optimal weight: 8.9990 chunk 238 optimal weight: 0.9990 chunk 470 optimal weight: 6.9990 chunk 372 optimal weight: 20.0000 chunk 721 optimal weight: 6.9990 chunk 279 optimal weight: 7.9990 chunk 438 optimal weight: 5.9990 chunk 536 optimal weight: 0.9990 chunk 835 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 GLN A 227 ASN A 360 HIS A 554 GLN A 633 GLN A 645 HIS A 757 GLN B ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 HIS A1099 HIS ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN B 110 HIS B 171 GLN B 271 HIS ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN B 498 GLN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 GLN B 629 HIS B 713 HIS C 77 ASN C 88 HIS C 126 GLN C 317 GLN C 546 ASN ** C 645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 GLN C 757 GLN B C 838 GLN ** C 922 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** C1084 ASN C1099 HIS C1147 HIS D 77 ASN D 110 HIS D 309 HIS D 426 GLN D 498 GLN ** D 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 922 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** D 989 GLN D 997 GLN E 126 GLN E 165 GLN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 ASN E 554 GLN E 757 GLN B ** E 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 838 GLN E 922 ASN A E 997 GLN E1099 HIS E1144 GLN E1147 HIS ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS F 426 GLN F 453 HIS ** F 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 824 GLN F 989 GLN F 997 GLN F1038 ASN F1109 HIS G 110 HIS G 247 GLN G 343 GLN G 546 ASN G 554 GLN ** G 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 718 GLN G 757 GLN B G 824 GLN G1147 HIS H 77 ASN H 190 ASN H 426 GLN H 498 GLN H 824 GLN H 922 ASN A H 997 GLN Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.065267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.055036 restraints weight = 2342413.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.057721 restraints weight = 1069941.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.058112 restraints weight = 501329.622| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3953 r_free = 0.3953 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3951 r_free = 0.3951 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 89 | |-----------------------------------------------------------------------------| r_final: 0.3951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3469 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 71156 Z= 0.281 Angle : 0.719 15.642 96892 Z= 0.376 Chirality : 0.047 0.344 10716 Planarity : 0.005 0.067 12852 Dihedral : 4.937 53.568 10005 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.30 % Allowed : 20.77 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.01 (0.09), residues: 9228 helix: 0.32 (0.13), residues: 1476 sheet: 0.54 (0.12), residues: 1788 loop : -0.19 (0.08), residues: 5964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D1155 HIS 0.012 0.001 HIS A 910 PHE 0.027 0.002 PHE E 613 TYR 0.040 0.002 TYR D 993 ARG 0.016 0.001 ARG F 348 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 7740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 244 poor density : 452 time to evaluate : 5.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 MET cc_start: 0.3998 (tpt) cc_final: 0.3622 (tpt) REVERT: B 217 MET cc_start: 0.8135 (mpp) cc_final: 0.7343 (ttt) REVERT: B 304 LEU cc_start: 0.2377 (tp) cc_final: 0.2148 (tt) REVERT: B 528 PHE cc_start: 0.5096 (p90) cc_final: 0.4848 (p90) REVERT: B 553 MET cc_start: -0.0392 (mmp) cc_final: -0.1245 (mmm) REVERT: B 718 GLN cc_start: 0.1403 (OUTLIER) cc_final: 0.1121 (pt0) REVERT: B 1054 VAL cc_start: 0.6296 (t) cc_final: 0.6081 (p) REVERT: B 1164 PHE cc_start: 0.2483 (OUTLIER) cc_final: 0.1406 (t80) REVERT: C 1222 MET cc_start: 0.5075 (mmt) cc_final: 0.3425 (tmm) REVERT: D 658 MET cc_start: 0.7273 (mmt) cc_final: 0.6917 (mmm) REVERT: D 701 MET cc_start: 0.3675 (mtp) cc_final: 0.3474 (mtm) REVERT: D 708 MET cc_start: 0.2025 (mmm) cc_final: 0.1779 (tpt) REVERT: D 806 MET cc_start: 0.6106 (mmm) cc_final: 0.5882 (mmm) REVERT: D 1222 MET cc_start: 0.5927 (ttt) cc_final: 0.4670 (ttt) REVERT: E 1013 LEU cc_start: 0.6843 (mm) cc_final: 0.6603 (tp) REVERT: F 568 CYS cc_start: 0.4515 (p) cc_final: 0.4163 (t) REVERT: F 736 ILE cc_start: -0.1875 (OUTLIER) cc_final: -0.2081 (mp) REVERT: F 997 GLN cc_start: -0.0468 (OUTLIER) cc_final: -0.1531 (tp-100) REVERT: F 1222 MET cc_start: 0.5525 (mpp) cc_final: 0.5296 (mpp) REVERT: G 492 LEU cc_start: 0.7984 (pp) cc_final: 0.7715 (tp) REVERT: G 513 GLN cc_start: 0.6236 (mt0) cc_final: 0.5406 (mm-40) REVERT: G 708 MET cc_start: 0.1005 (mpp) cc_final: 0.0759 (mmm) REVERT: G 806 MET cc_start: -0.0841 (mmm) cc_final: -0.1234 (mtt) REVERT: G 862 ASP cc_start: 0.6014 (m-30) cc_final: 0.5663 (m-30) REVERT: G 873 ARG cc_start: 0.6592 (tpm170) cc_final: 0.5062 (mmp80) REVERT: G 1222 MET cc_start: -0.4114 (OUTLIER) cc_final: -0.4509 (ttm) REVERT: H 138 MET cc_start: 0.7373 (ttm) cc_final: 0.7150 (tpp) REVERT: H 324 LEU cc_start: 0.6656 (mp) cc_final: 0.6189 (tt) REVERT: H 427 GLU cc_start: 0.6191 (OUTLIER) cc_final: 0.5797 (mt-10) REVERT: H 891 MET cc_start: 0.8996 (ttt) cc_final: 0.8698 (tpp) REVERT: H 1174 CYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6780 (m) outliers start: 244 outliers final: 101 residues processed: 658 average time/residue: 0.6076 time to fit residues: 717.5758 Evaluate side-chains 455 residues out of total 7740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 347 time to evaluate : 6.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 995 ILE Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1196 CYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1164 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 698 THR Chi-restraints excluded: chain C residue 699 LYS Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 877 THR Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 613 PHE Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 789 LYS Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 1022 ILE Chi-restraints excluded: chain D residue 1139 VAL Chi-restraints excluded: chain D residue 1151 LEU Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 165 GLN Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 298 CYS Chi-restraints excluded: chain E residue 786 THR Chi-restraints excluded: chain E residue 968 LEU Chi-restraints excluded: chain E residue 1018 THR Chi-restraints excluded: chain E residue 1135 PHE Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 490 VAL Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 511 LEU Chi-restraints excluded: chain F residue 553 MET Chi-restraints excluded: chain F residue 626 TYR Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain F residue 736 ILE Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 763 CYS Chi-restraints excluded: chain F residue 785 CYS Chi-restraints excluded: chain F residue 884 THR Chi-restraints excluded: chain F residue 912 LEU Chi-restraints excluded: chain F residue 997 GLN Chi-restraints excluded: chain F residue 1012 LEU Chi-restraints excluded: chain F residue 1153 VAL Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 296 CYS Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 849 LEU Chi-restraints excluded: chain G residue 983 ILE Chi-restraints excluded: chain G residue 1018 THR Chi-restraints excluded: chain G residue 1196 CYS Chi-restraints excluded: chain G residue 1222 MET Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 427 GLU Chi-restraints excluded: chain H residue 526 THR Chi-restraints excluded: chain H residue 900 LEU Chi-restraints excluded: chain H residue 1153 VAL Chi-restraints excluded: chain H residue 1174 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 172 optimal weight: 3.9990 chunk 579 optimal weight: 9.9990 chunk 557 optimal weight: 9.9990 chunk 812 optimal weight: 5.9990 chunk 371 optimal weight: 6.9990 chunk 296 optimal weight: 0.7980 chunk 910 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 510 optimal weight: 10.0000 chunk 295 optimal weight: 0.7980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN A 941 GLN ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN B 777 HIS C 119 ASN ** C 645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 GLN C1177 HIS D 258 ASN ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 922 ASN A D 989 GLN D1179 GLN ** E 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN F 77 ASN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 HIS ** F 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 GLN ** F 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 989 GLN F1092 GLN F1094 GLN F1109 HIS G 171 GLN G 247 GLN G 343 GLN G 498 GLN G 680 HIS ** G 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 777 HIS G 828 HIS H 309 HIS ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 680 HIS H 917 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.065025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.054938 restraints weight = 2641492.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.057471 restraints weight = 1225251.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.057882 restraints weight = 593543.602| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3950 r_free = 0.3950 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 89 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3950 r_free = 0.3950 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 102 | |-----------------------------------------------------------------------------| r_final: 0.3950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3880 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 71156 Z= 0.248 Angle : 0.694 18.296 96892 Z= 0.358 Chirality : 0.046 0.279 10716 Planarity : 0.005 0.143 12852 Dihedral : 4.796 48.858 9980 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.89 % Allowed : 21.21 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.14 (0.09), residues: 9228 helix: 0.16 (0.13), residues: 1492 sheet: 0.46 (0.12), residues: 1820 loop : -0.29 (0.08), residues: 5916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1065 HIS 0.011 0.001 HIS B 88 PHE 0.031 0.002 PHE G 214 TYR 0.045 0.002 TYR D 993 ARG 0.014 0.001 ARG G 996 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 7740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 392 time to evaluate : 6.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.4981 (OUTLIER) cc_final: 0.3974 (tmm) REVERT: A 509 VAL cc_start: 0.6428 (t) cc_final: 0.5883 (m) REVERT: A 658 MET cc_start: 0.6031 (mmm) cc_final: 0.5462 (mmt) REVERT: A 741 CYS cc_start: -0.1171 (OUTLIER) cc_final: -0.1609 (m) REVERT: A 769 MET cc_start: 0.0814 (OUTLIER) cc_final: 0.0520 (mmm) REVERT: A 858 ILE cc_start: 0.5455 (OUTLIER) cc_final: 0.5159 (pp) REVERT: B 304 LEU cc_start: 0.2657 (tp) cc_final: 0.2412 (tt) REVERT: B 376 GLU cc_start: 0.6059 (tp30) cc_final: 0.5246 (mm-30) REVERT: B 528 PHE cc_start: 0.6286 (p90) cc_final: 0.6009 (p90) REVERT: B 553 MET cc_start: -0.0001 (mmp) cc_final: -0.1246 (mmm) REVERT: B 658 MET cc_start: 0.4291 (tpp) cc_final: 0.3860 (mmm) REVERT: B 891 MET cc_start: 0.7153 (tpt) cc_final: 0.6776 (tpp) REVERT: B 1079 ASP cc_start: 0.6277 (t0) cc_final: 0.6042 (t0) REVERT: C 658 MET cc_start: 0.2193 (ppp) cc_final: 0.0562 (mtt) REVERT: C 769 MET cc_start: 0.2669 (tpp) cc_final: 0.2458 (tpp) REVERT: C 1007 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7023 (p0) REVERT: C 1222 MET cc_start: 0.5402 (OUTLIER) cc_final: 0.3618 (tmm) REVERT: D 342 MET cc_start: 0.6382 (mmm) cc_final: 0.5965 (mmm) REVERT: D 553 MET cc_start: -0.1816 (tpp) cc_final: -0.2044 (tpp) REVERT: D 613 PHE cc_start: 0.2993 (OUTLIER) cc_final: 0.0483 (m-80) REVERT: D 658 MET cc_start: 0.6834 (mmt) cc_final: 0.5954 (mmm) REVERT: D 708 MET cc_start: 0.2875 (mmm) cc_final: 0.2321 (tpp) REVERT: D 1222 MET cc_start: 0.4876 (ttt) cc_final: 0.3774 (ttt) REVERT: E 873 ARG cc_start: 0.6797 (mmp80) cc_final: 0.6337 (mmp80) REVERT: E 998 MET cc_start: 0.3156 (ptm) cc_final: 0.2884 (ppp) REVERT: F 701 MET cc_start: -0.3228 (tpt) cc_final: -0.3444 (tpt) REVERT: F 726 GLU cc_start: 0.6385 (mp0) cc_final: 0.5615 (tp30) REVERT: F 1222 MET cc_start: 0.6282 (mpp) cc_final: 0.6061 (mpp) REVERT: G 342 MET cc_start: 0.1464 (mpp) cc_final: 0.1138 (mpp) REVERT: G 492 LEU cc_start: 0.7767 (pp) cc_final: 0.7387 (tp) REVERT: G 498 GLN cc_start: 0.6374 (OUTLIER) cc_final: 0.5931 (mt0) REVERT: G 806 MET cc_start: -0.1298 (mmm) cc_final: -0.1663 (mtt) REVERT: G 1222 MET cc_start: -0.4191 (OUTLIER) cc_final: -0.4420 (ttt) REVERT: H 233 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.5777 (mmp) REVERT: H 324 LEU cc_start: 0.6738 (mp) cc_final: 0.6259 (tt) REVERT: H 1153 VAL cc_start: 0.4876 (OUTLIER) cc_final: 0.4620 (p) outliers start: 212 outliers final: 102 residues processed: 568 average time/residue: 0.6118 time to fit residues: 619.5598 Evaluate side-chains 447 residues out of total 7740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 334 time to evaluate : 5.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 610 ARG Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 442 PHE Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 546 ASN Chi-restraints excluded: chain C residue 629 HIS Chi-restraints excluded: chain C residue 698 THR Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 877 THR Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 1007 ASP Chi-restraints excluded: chain C residue 1016 LYS Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1222 MET Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 613 PHE Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 877 THR Chi-restraints excluded: chain D residue 1027 GLU Chi-restraints excluded: chain D residue 1139 VAL Chi-restraints excluded: chain D residue 1201 ARG Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 968 LEU Chi-restraints excluded: chain E residue 983 ILE Chi-restraints excluded: chain E residue 1018 THR Chi-restraints excluded: chain E residue 1099 HIS Chi-restraints excluded: chain E residue 1135 PHE Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 241 MET Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 426 GLN Chi-restraints excluded: chain F residue 490 VAL Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 511 LEU Chi-restraints excluded: chain F residue 553 MET Chi-restraints excluded: chain F residue 626 TYR Chi-restraints excluded: chain F residue 669 ASP Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain F residue 763 CYS Chi-restraints excluded: chain F residue 783 CYS Chi-restraints excluded: chain F residue 785 CYS Chi-restraints excluded: chain F residue 989 GLN Chi-restraints excluded: chain F residue 1012 LEU Chi-restraints excluded: chain F residue 1195 ASP Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 304 LEU Chi-restraints excluded: chain G residue 498 GLN Chi-restraints excluded: chain G residue 859 THR Chi-restraints excluded: chain G residue 891 MET Chi-restraints excluded: chain G residue 983 ILE Chi-restraints excluded: chain G residue 1186 LEU Chi-restraints excluded: chain G residue 1222 MET Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain H residue 526 THR Chi-restraints excluded: chain H residue 900 LEU Chi-restraints excluded: chain H residue 1153 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 645 optimal weight: 9.9990 chunk 325 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 826 optimal weight: 8.9990 chunk 618 optimal weight: 9.9990 chunk 469 optimal weight: 4.9990 chunk 146 optimal weight: 0.0980 chunk 399 optimal weight: 0.7980 chunk 448 optimal weight: 2.9990 chunk 72 optimal weight: 40.0000 chunk 687 optimal weight: 8.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 273 GLN A 336 GLN A 449 GLN A 546 ASN ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 HIS A 688 GLN A 787 HIS ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 977 HIS A 997 GLN A1063 ASN ** A1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 HIS B 578 GLN ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 HIS ** B 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 922 ASN A ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN ** C 645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN ** C 922 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** C1109 HIS D 88 HIS D 320 HIS ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 989 GLN D1099 HIS E 146 GLN E 155 ASN E 320 HIS ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 GLN E 628 GLN E 663 ASN ** E 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1084 ASN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 GLN ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 876 GLN F 910 HIS F 922 ASN A ** F1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1109 HIS F1147 HIS G 121 GLN G 155 ASN ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN H 110 HIS ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 628 GLN H1109 HIS Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.064400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.054962 restraints weight = 2621274.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.057132 restraints weight = 1366489.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.057644 restraints weight = 714876.351| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3957 r_free = 0.3957 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 102 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3957 r_free = 0.3957 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 132 | |-----------------------------------------------------------------------------| r_final: 0.3957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4546 moved from start: 0.6359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.189 71156 Z= 0.353 Angle : 0.820 23.653 96892 Z= 0.431 Chirality : 0.051 0.472 10716 Planarity : 0.006 0.131 12852 Dihedral : 5.306 57.124 9979 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.08 % Favored : 94.90 % Rotamer: Outliers : 3.27 % Allowed : 20.86 % Favored : 75.86 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.09), residues: 9228 helix: -0.21 (0.13), residues: 1480 sheet: 0.27 (0.12), residues: 1744 loop : -0.61 (0.08), residues: 6004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A1065 HIS 0.024 0.002 HIS F 713 PHE 0.069 0.003 PHE C 118 TYR 0.030 0.003 TYR B 409 ARG 0.020 0.001 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 7740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 412 time to evaluate : 6.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 PHE cc_start: 0.6322 (OUTLIER) cc_final: 0.3529 (m-10) REVERT: A 512 ASN cc_start: 0.7599 (m-40) cc_final: 0.7242 (m110) REVERT: A 557 MET cc_start: 0.6480 (pmm) cc_final: 0.5777 (pmm) REVERT: A 769 MET cc_start: 0.2565 (OUTLIER) cc_final: 0.2312 (tpt) REVERT: A 900 LEU cc_start: 0.3412 (pp) cc_final: 0.3204 (pp) REVERT: B 304 LEU cc_start: 0.3592 (tp) cc_final: 0.3089 (tt) REVERT: B 511 LEU cc_start: 0.5455 (OUTLIER) cc_final: 0.4117 (mp) REVERT: B 553 MET cc_start: 0.0428 (mmp) cc_final: -0.0943 (mmm) REVERT: B 718 GLN cc_start: 0.1089 (OUTLIER) cc_final: 0.0417 (pt0) REVERT: B 1079 ASP cc_start: 0.6649 (t0) cc_final: 0.6216 (t70) REVERT: C 658 MET cc_start: 0.3736 (ppp) cc_final: 0.2538 (mtt) REVERT: C 680 HIS cc_start: 0.3476 (t70) cc_final: 0.2792 (t-170) REVERT: C 852 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7480 (m-30) REVERT: C 1013 LEU cc_start: 0.0623 (OUTLIER) cc_final: 0.0096 (mt) REVERT: C 1222 MET cc_start: 0.5515 (mmt) cc_final: 0.3626 (tmm) REVERT: D 187 LEU cc_start: 0.7728 (pp) cc_final: 0.7170 (tp) REVERT: D 342 MET cc_start: 0.7064 (mmm) cc_final: 0.6321 (mmm) REVERT: D 553 MET cc_start: -0.2461 (tpp) cc_final: -0.2928 (tpp) REVERT: D 613 PHE cc_start: 0.3590 (OUTLIER) cc_final: 0.1434 (m-80) REVERT: D 624 GLU cc_start: 0.6380 (tp30) cc_final: 0.6048 (tp30) REVERT: D 701 MET cc_start: 0.3324 (mpp) cc_final: 0.3023 (mpp) REVERT: D 1222 MET cc_start: 0.4755 (ttt) cc_final: 0.3484 (ttp) REVERT: E 427 GLU cc_start: 0.4951 (OUTLIER) cc_final: 0.4520 (mm-30) REVERT: E 979 LYS cc_start: 0.4002 (OUTLIER) cc_final: 0.3744 (mptt) REVERT: E 1007 ASP cc_start: 0.2604 (OUTLIER) cc_final: 0.2321 (p0) REVERT: E 1031 ARG cc_start: 0.5071 (OUTLIER) cc_final: 0.3227 (tpt-90) REVERT: E 1209 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8755 (tmmt) REVERT: F 105 TYR cc_start: 0.3335 (m-80) cc_final: 0.0695 (m-80) REVERT: F 183 LEU cc_start: -0.1545 (OUTLIER) cc_final: -0.2125 (mp) REVERT: F 217 MET cc_start: 0.7543 (ptm) cc_final: 0.7162 (ppp) REVERT: F 726 GLU cc_start: 0.6254 (mp0) cc_final: 0.5244 (tp30) REVERT: F 832 MET cc_start: 0.5887 (mmm) cc_final: 0.5560 (mmt) REVERT: F 834 CYS cc_start: 0.5879 (OUTLIER) cc_final: 0.5032 (p) REVERT: F 998 MET cc_start: 0.0817 (ttt) cc_final: 0.0516 (ttt) REVERT: F 1081 CYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6361 (p) REVERT: G 149 LYS cc_start: 0.1274 (OUTLIER) cc_final: -0.0217 (pttm) REVERT: G 449 GLN cc_start: -0.0250 (OUTLIER) cc_final: -0.1008 (pm20) REVERT: G 492 LEU cc_start: 0.7597 (pp) cc_final: 0.7182 (tp) REVERT: G 553 MET cc_start: -0.3361 (mtt) cc_final: -0.3736 (mtt) REVERT: G 806 MET cc_start: -0.1687 (mmm) cc_final: -0.2073 (mtt) REVERT: G 832 MET cc_start: -0.0792 (tpt) cc_final: -0.1073 (mmm) REVERT: H 241 MET cc_start: 0.5776 (ppp) cc_final: 0.4678 (ptp) REVERT: H 324 LEU cc_start: 0.6681 (mp) cc_final: 0.6251 (tt) REVERT: H 1195 ASP cc_start: 0.5471 (p0) cc_final: 0.4844 (m-30) outliers start: 242 outliers final: 117 residues processed: 611 average time/residue: 0.6164 time to fit residues: 674.6576 Evaluate side-chains 453 residues out of total 7740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 319 time to evaluate : 6.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1164 PHE Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1196 CYS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 442 PHE Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 698 THR Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 840 VAL Chi-restraints excluded: chain C residue 852 ASP Chi-restraints excluded: chain C residue 891 MET Chi-restraints excluded: chain C residue 1013 LEU Chi-restraints excluded: chain C residue 1084 ASN Chi-restraints excluded: chain C residue 1095 CYS Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1209 LYS Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 613 PHE Chi-restraints excluded: chain D residue 696 VAL Chi-restraints excluded: chain D residue 702 THR Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 789 LYS Chi-restraints excluded: chain D residue 854 GLU Chi-restraints excluded: chain D residue 1027 GLU Chi-restraints excluded: chain D residue 1201 ARG Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 427 GLU Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 736 ILE Chi-restraints excluded: chain E residue 786 THR Chi-restraints excluded: chain E residue 968 LEU Chi-restraints excluded: chain E residue 979 LYS Chi-restraints excluded: chain E residue 980 VAL Chi-restraints excluded: chain E residue 983 ILE Chi-restraints excluded: chain E residue 1007 ASP Chi-restraints excluded: chain E residue 1031 ARG Chi-restraints excluded: chain E residue 1099 HIS Chi-restraints excluded: chain E residue 1135 PHE Chi-restraints excluded: chain E residue 1209 LYS Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 426 GLN Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 452 VAL Chi-restraints excluded: chain F residue 490 VAL Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 508 GLU Chi-restraints excluded: chain F residue 553 MET Chi-restraints excluded: chain F residue 626 TYR Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain F residue 698 THR Chi-restraints excluded: chain F residue 713 HIS Chi-restraints excluded: chain F residue 738 VAL Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 785 CYS Chi-restraints excluded: chain F residue 834 CYS Chi-restraints excluded: chain F residue 989 GLN Chi-restraints excluded: chain F residue 1012 LEU Chi-restraints excluded: chain F residue 1081 CYS Chi-restraints excluded: chain F residue 1086 PHE Chi-restraints excluded: chain F residue 1153 VAL Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 428 VAL Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain G residue 549 LEU Chi-restraints excluded: chain G residue 769 MET Chi-restraints excluded: chain G residue 786 THR Chi-restraints excluded: chain G residue 852 ASP Chi-restraints excluded: chain G residue 859 THR Chi-restraints excluded: chain G residue 891 MET Chi-restraints excluded: chain G residue 983 ILE Chi-restraints excluded: chain G residue 1186 LEU Chi-restraints excluded: chain G residue 1196 CYS Chi-restraints excluded: chain H residue 121 GLN Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain H residue 526 THR Chi-restraints excluded: chain H residue 624 GLU Chi-restraints excluded: chain H residue 900 LEU Chi-restraints excluded: chain H residue 1157 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 197 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 619 optimal weight: 3.9990 chunk 441 optimal weight: 8.9990 chunk 741 optimal weight: 5.9990 chunk 311 optimal weight: 1.9990 chunk 562 optimal weight: 6.9990 chunk 272 optimal weight: 5.9990 chunk 744 optimal weight: 8.9990 chunk 208 optimal weight: 9.9990 chunk 229 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 171 GLN ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS A 513 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 GLN ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 GLN ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 HIS ** B 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 GLN B 883 ASN ** B 922 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 ASN ** C 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 HIS C 910 HIS ** C 922 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN D 171 GLN ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS ** D 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 989 GLN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 GLN E 718 GLN E 772 ASN ** E 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 867 HIS E 917 GLN ** E 922 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1177 HIS ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN F 426 GLN ** F 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 623 ASN ** F 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 922 ASN B ** F 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN ** G 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 544 GLN ** G 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 713 HIS G 718 GLN G1099 HIS ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 922 ASN A H 922 ASN B H1099 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.063820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.054469 restraints weight = 2245112.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.056733 restraints weight = 1160515.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.057169 restraints weight = 623634.528| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3943 r_free = 0.3943 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 132 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3943 r_free = 0.3943 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 149 | |-----------------------------------------------------------------------------| r_final: 0.3943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5202 moved from start: 0.9103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 71156 Z= 0.423 Angle : 0.932 16.394 96892 Z= 0.488 Chirality : 0.055 0.380 10716 Planarity : 0.007 0.110 12852 Dihedral : 6.019 49.784 9977 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 25.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.05 % Favored : 93.91 % Rotamer: Outliers : 3.15 % Allowed : 21.27 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.17 (0.08), residues: 9228 helix: -0.87 (0.13), residues: 1444 sheet: -0.20 (0.12), residues: 1780 loop : -0.93 (0.08), residues: 6004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP F1176 HIS 0.040 0.003 HIS F1177 PHE 0.067 0.004 PHE C 235 TYR 0.069 0.004 TYR E 911 ARG 0.020 0.001 ARG B 996 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 7740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 362 time to evaluate : 7.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 VAL cc_start: 0.7757 (m) cc_final: 0.7496 (t) REVERT: A 217 MET cc_start: 0.6129 (ptt) cc_final: 0.5339 (tmm) REVERT: A 424 SER cc_start: 0.8162 (OUTLIER) cc_final: 0.7706 (p) REVERT: A 445 PHE cc_start: 0.5229 (OUTLIER) cc_final: 0.3847 (m-80) REVERT: A 557 MET cc_start: 0.6860 (pmm) cc_final: 0.6568 (ptp) REVERT: A 669 ASP cc_start: 0.7700 (m-30) cc_final: 0.7379 (m-30) REVERT: A 676 SER cc_start: 0.7782 (m) cc_final: 0.6964 (p) REVERT: A 679 VAL cc_start: 0.6977 (OUTLIER) cc_final: 0.6091 (m) REVERT: B 307 VAL cc_start: 0.7486 (m) cc_final: 0.7278 (p) REVERT: B 511 LEU cc_start: 0.4772 (OUTLIER) cc_final: 0.4056 (mp) REVERT: B 701 MET cc_start: 0.3141 (mtt) cc_final: 0.2926 (mpp) REVERT: B 806 MET cc_start: 0.7468 (tpp) cc_final: 0.7151 (tpp) REVERT: B 1164 PHE cc_start: 0.5309 (OUTLIER) cc_final: 0.2370 (m-80) REVERT: C 658 MET cc_start: 0.5684 (ppp) cc_final: 0.4721 (mmt) REVERT: C 998 MET cc_start: 0.3562 (pmm) cc_final: 0.2472 (ppp) REVERT: C 1222 MET cc_start: 0.6122 (mmt) cc_final: 0.5914 (mmm) REVERT: D 161 LEU cc_start: 0.6010 (OUTLIER) cc_final: 0.5800 (tt) REVERT: D 188 MET cc_start: 0.5014 (mpp) cc_final: 0.4267 (mpp) REVERT: D 241 MET cc_start: 0.2526 (ppp) cc_final: 0.1986 (ppp) REVERT: D 342 MET cc_start: 0.6602 (mmm) cc_final: 0.6333 (mmm) REVERT: D 553 MET cc_start: -0.0968 (tpp) cc_final: -0.1341 (tpp) REVERT: D 613 PHE cc_start: 0.3622 (OUTLIER) cc_final: 0.1440 (m-80) REVERT: D 624 GLU cc_start: 0.7018 (tp30) cc_final: 0.6767 (tp30) REVERT: D 701 MET cc_start: 0.3919 (mpp) cc_final: 0.3711 (mpp) REVERT: D 1222 MET cc_start: 0.4422 (ttt) cc_final: 0.3548 (ttp) REVERT: E 108 SER cc_start: 0.3487 (OUTLIER) cc_final: 0.2958 (t) REVERT: E 169 LEU cc_start: 0.4090 (tp) cc_final: 0.3878 (mt) REVERT: E 427 GLU cc_start: 0.5784 (OUTLIER) cc_final: 0.4149 (tp30) REVERT: E 557 MET cc_start: -0.0464 (ptt) cc_final: -0.1072 (ptm) REVERT: E 617 CYS cc_start: 0.6183 (OUTLIER) cc_final: 0.5735 (p) REVERT: E 998 MET cc_start: 0.4093 (ptp) cc_final: 0.3874 (ppp) REVERT: E 1007 ASP cc_start: 0.2163 (OUTLIER) cc_final: 0.1739 (p0) REVERT: F 105 TYR cc_start: 0.3538 (m-80) cc_final: 0.1661 (m-80) REVERT: F 183 LEU cc_start: -0.1201 (OUTLIER) cc_final: -0.1869 (mp) REVERT: F 217 MET cc_start: 0.7625 (ptm) cc_final: 0.7154 (ppp) REVERT: F 508 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7198 (pm20) REVERT: F 832 MET cc_start: 0.6786 (mmm) cc_final: 0.6388 (mmt) REVERT: F 834 CYS cc_start: 0.5868 (OUTLIER) cc_final: 0.4821 (p) REVERT: F 998 MET cc_start: 0.0392 (ttt) cc_final: 0.0159 (ttt) REVERT: F 1081 CYS cc_start: 0.6810 (m) cc_final: 0.6156 (t) REVERT: F 1222 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.6331 (ptp) REVERT: G 149 LYS cc_start: 0.0855 (OUTLIER) cc_final: -0.0444 (pttm) REVERT: G 449 GLN cc_start: 0.0904 (OUTLIER) cc_final: -0.0676 (pm20) REVERT: G 806 MET cc_start: -0.2110 (mmm) cc_final: -0.2622 (mtt) REVERT: H 427 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6561 (mt-10) REVERT: H 891 MET cc_start: 0.9088 (ttt) cc_final: 0.8847 (tpp) outliers start: 230 outliers final: 131 residues processed: 566 average time/residue: 0.6252 time to fit residues: 629.1470 Evaluate side-chains 453 residues out of total 7740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 304 time to evaluate : 6.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain A residue 897 ASP Chi-restraints excluded: chain A residue 914 PHE Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1065 TRP Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1136 CYS Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1196 CYS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 983 ILE Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1160 ILE Chi-restraints excluded: chain B residue 1164 PHE Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 413 CYS Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 840 VAL Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 1097 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 613 PHE Chi-restraints excluded: chain D residue 677 SER Chi-restraints excluded: chain D residue 696 VAL Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 789 LYS Chi-restraints excluded: chain D residue 834 CYS Chi-restraints excluded: chain D residue 854 GLU Chi-restraints excluded: chain D residue 1027 GLU Chi-restraints excluded: chain D residue 1185 CYS Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 110 HIS Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 427 GLU Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 610 ARG Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 736 ILE Chi-restraints excluded: chain E residue 906 TYR Chi-restraints excluded: chain E residue 968 LEU Chi-restraints excluded: chain E residue 979 LYS Chi-restraints excluded: chain E residue 983 ILE Chi-restraints excluded: chain E residue 1007 ASP Chi-restraints excluded: chain E residue 1020 ILE Chi-restraints excluded: chain E residue 1099 HIS Chi-restraints excluded: chain E residue 1135 PHE Chi-restraints excluded: chain F residue 118 PHE Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 355 CYS Chi-restraints excluded: chain F residue 362 ARG Chi-restraints excluded: chain F residue 452 VAL Chi-restraints excluded: chain F residue 490 VAL Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 508 GLU Chi-restraints excluded: chain F residue 553 MET Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain F residue 669 ASP Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 713 HIS Chi-restraints excluded: chain F residue 738 VAL Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 748 PHE Chi-restraints excluded: chain F residue 785 CYS Chi-restraints excluded: chain F residue 834 CYS Chi-restraints excluded: chain F residue 912 LEU Chi-restraints excluded: chain F residue 1012 LEU Chi-restraints excluded: chain F residue 1086 PHE Chi-restraints excluded: chain F residue 1131 ASP Chi-restraints excluded: chain F residue 1153 VAL Chi-restraints excluded: chain F residue 1222 MET Chi-restraints excluded: chain G residue 84 TRP Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain G residue 610 ARG Chi-restraints excluded: chain G residue 769 MET Chi-restraints excluded: chain G residue 801 VAL Chi-restraints excluded: chain G residue 859 THR Chi-restraints excluded: chain G residue 1186 LEU Chi-restraints excluded: chain G residue 1196 CYS Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain H residue 349 SER Chi-restraints excluded: chain H residue 427 GLU Chi-restraints excluded: chain H residue 526 THR Chi-restraints excluded: chain H residue 624 GLU Chi-restraints excluded: chain H residue 655 SER Chi-restraints excluded: chain H residue 834 CYS Chi-restraints excluded: chain H residue 900 LEU Chi-restraints excluded: chain H residue 1157 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 159 optimal weight: 2.9990 chunk 697 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 379 optimal weight: 8.9990 chunk 448 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 484 optimal weight: 7.9990 chunk 172 optimal weight: 6.9990 chunk 745 optimal weight: 0.7980 chunk 641 optimal weight: 20.0000 chunk 194 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 HIS A 554 GLN A 603 GLN A 828 HIS A 917 GLN ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 HIS ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 ASN ** C 645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 HIS ** C 922 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN ** D 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 876 GLN ** D 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 989 GLN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 922 ASN B ** E1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 HIS ** F 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 663 ASN ** F 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 772 ASN F 922 ASN A ** F1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 ASN ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 663 ASN H 317 GLN ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 713 HIS ** H 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.063811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.054216 restraints weight = 2469959.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.056151 restraints weight = 1254345.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.057112 restraints weight = 695196.615| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 149 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 140 | |-----------------------------------------------------------------------------| r_final: 0.3940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5406 moved from start: 1.0146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 71156 Z= 0.298 Angle : 0.761 14.647 96892 Z= 0.396 Chirality : 0.049 0.306 10716 Planarity : 0.006 0.073 12852 Dihedral : 5.553 42.836 9976 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.43 % Favored : 94.55 % Rotamer: Outliers : 2.46 % Allowed : 22.07 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.05 (0.09), residues: 9228 helix: -0.47 (0.13), residues: 1456 sheet: -0.34 (0.12), residues: 1817 loop : -0.87 (0.08), residues: 5955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C1090 HIS 0.022 0.002 HIS C 680 PHE 0.042 0.003 PHE B 107 TYR 0.042 0.003 TYR E1207 ARG 0.021 0.001 ARG B 476 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 7740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 327 time to evaluate : 6.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6505 (ptt) cc_final: 0.5711 (ptm) REVERT: A 233 MET cc_start: 0.6234 (ppp) cc_final: 0.5792 (ppp) REVERT: A 424 SER cc_start: 0.8550 (OUTLIER) cc_final: 0.8139 (p) REVERT: A 543 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7695 (tt) REVERT: A 669 ASP cc_start: 0.7745 (m-30) cc_final: 0.7467 (m-30) REVERT: A 701 MET cc_start: 0.5716 (mpp) cc_final: 0.5315 (ptp) REVERT: B 139 LYS cc_start: 0.6289 (tmtt) cc_final: 0.6087 (tmtt) REVERT: B 397 VAL cc_start: 0.7190 (t) cc_final: 0.6978 (p) REVERT: B 511 LEU cc_start: 0.5155 (OUTLIER) cc_final: 0.4266 (mp) REVERT: B 615 ASP cc_start: 0.6717 (t0) cc_final: 0.6340 (t0) REVERT: B 708 MET cc_start: 0.3132 (ttm) cc_final: 0.2904 (tpp) REVERT: B 713 HIS cc_start: 0.3595 (OUTLIER) cc_final: 0.3393 (p-80) REVERT: B 1164 PHE cc_start: 0.5405 (OUTLIER) cc_final: 0.2527 (m-80) REVERT: C 658 MET cc_start: 0.6329 (ppp) cc_final: 0.6019 (tpp) REVERT: C 1222 MET cc_start: 0.6016 (mmt) cc_final: 0.5815 (mmm) REVERT: D 188 MET cc_start: 0.6023 (mpp) cc_final: 0.5001 (mpp) REVERT: D 233 MET cc_start: 0.7845 (ttt) cc_final: 0.7318 (tpp) REVERT: D 241 MET cc_start: 0.2849 (ppp) cc_final: 0.2099 (ppp) REVERT: D 342 MET cc_start: 0.7086 (mmm) cc_final: 0.6539 (mmm) REVERT: D 410 SER cc_start: 0.4159 (OUTLIER) cc_final: 0.3640 (t) REVERT: D 553 MET cc_start: -0.0844 (tpp) cc_final: -0.1665 (tpp) REVERT: D 613 PHE cc_start: 0.3685 (OUTLIER) cc_final: 0.1867 (m-80) REVERT: D 628 GLN cc_start: 0.8326 (mm-40) cc_final: 0.8060 (mm-40) REVERT: D 701 MET cc_start: 0.3951 (mpp) cc_final: 0.3603 (mpp) REVERT: D 1222 MET cc_start: 0.4567 (ttt) cc_final: 0.4037 (ttp) REVERT: E 427 GLU cc_start: 0.5668 (OUTLIER) cc_final: 0.4328 (tp30) REVERT: E 873 ARG cc_start: 0.7345 (mmp80) cc_final: 0.7032 (mmp80) REVERT: E 1115 TYR cc_start: 0.7201 (m-80) cc_final: 0.6371 (m-80) REVERT: F 183 LEU cc_start: -0.0209 (OUTLIER) cc_final: -0.0716 (mp) REVERT: F 217 MET cc_start: 0.7748 (ptm) cc_final: 0.7307 (ppp) REVERT: F 508 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7184 (pm20) REVERT: F 832 MET cc_start: 0.7093 (mmm) cc_final: 0.6809 (mmt) REVERT: F 989 GLN cc_start: 0.3370 (OUTLIER) cc_final: 0.2918 (pp30) REVERT: F 998 MET cc_start: 0.0814 (ttt) cc_final: 0.0489 (ttt) REVERT: F 1081 CYS cc_start: 0.7052 (m) cc_final: 0.6532 (p) REVERT: F 1222 MET cc_start: 0.6949 (mpp) cc_final: 0.6555 (mpp) REVERT: G 149 LYS cc_start: 0.1225 (OUTLIER) cc_final: -0.0179 (pttm) REVERT: G 449 GLN cc_start: 0.0326 (OUTLIER) cc_final: -0.0926 (pm20) REVERT: G 806 MET cc_start: -0.2133 (mmm) cc_final: -0.2697 (mtp) REVERT: H 427 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6505 (mt-10) REVERT: H 891 MET cc_start: 0.9142 (ttt) cc_final: 0.8834 (tpp) outliers start: 177 outliers final: 112 residues processed: 471 average time/residue: 0.6215 time to fit residues: 522.6393 Evaluate side-chains 419 residues out of total 7740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 293 time to evaluate : 6.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1065 TRP Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain B residue 625 LYS Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 713 HIS Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 768 SER Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 876 GLN Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1164 PHE Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1196 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 840 VAL Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 1097 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 613 PHE Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 789 LYS Chi-restraints excluded: chain D residue 834 CYS Chi-restraints excluded: chain D residue 854 GLU Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 110 HIS Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 427 GLU Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 815 THR Chi-restraints excluded: chain E residue 849 LEU Chi-restraints excluded: chain E residue 906 TYR Chi-restraints excluded: chain E residue 968 LEU Chi-restraints excluded: chain E residue 979 LYS Chi-restraints excluded: chain E residue 983 ILE Chi-restraints excluded: chain E residue 1020 ILE Chi-restraints excluded: chain E residue 1135 PHE Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 362 ARG Chi-restraints excluded: chain F residue 452 VAL Chi-restraints excluded: chain F residue 490 VAL Chi-restraints excluded: chain F residue 508 GLU Chi-restraints excluded: chain F residue 553 MET Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain F residue 713 HIS Chi-restraints excluded: chain F residue 748 PHE Chi-restraints excluded: chain F residue 833 THR Chi-restraints excluded: chain F residue 989 GLN Chi-restraints excluded: chain F residue 1067 LEU Chi-restraints excluded: chain F residue 1086 PHE Chi-restraints excluded: chain F residue 1131 ASP Chi-restraints excluded: chain F residue 1153 VAL Chi-restraints excluded: chain F residue 1216 ILE Chi-restraints excluded: chain G residue 84 TRP Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 426 GLN Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain G residue 769 MET Chi-restraints excluded: chain G residue 786 THR Chi-restraints excluded: chain G residue 859 THR Chi-restraints excluded: chain G residue 983 ILE Chi-restraints excluded: chain G residue 1186 LEU Chi-restraints excluded: chain G residue 1196 CYS Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain H residue 427 GLU Chi-restraints excluded: chain H residue 457 SER Chi-restraints excluded: chain H residue 526 THR Chi-restraints excluded: chain H residue 834 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 680 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 708 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 411 optimal weight: 20.0000 chunk 121 optimal weight: 0.9990 chunk 901 optimal weight: 0.0870 chunk 273 optimal weight: 7.9990 chunk 608 optimal weight: 8.9990 chunk 674 optimal weight: 0.0870 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 554 GLN ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN B 326 GLN ** B 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN C 317 GLN C 513 GLN C 548 GLN C 611 ASN ** C 645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 922 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 933 HIS D 989 GLN E 146 GLN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 824 GLN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 GLN ** F 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 680 HIS ** F 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS G 121 GLN ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.064571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.055080 restraints weight = 2480020.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.057195 restraints weight = 1236578.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.057605 restraints weight = 685534.426| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3958 r_free = 0.3958 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 140 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3958 r_free = 0.3958 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 167 | |-----------------------------------------------------------------------------| r_final: 0.3958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5274 moved from start: 1.0059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 71156 Z= 0.182 Angle : 0.664 13.425 96892 Z= 0.337 Chirality : 0.046 0.216 10716 Planarity : 0.005 0.063 12852 Dihedral : 4.942 42.010 9976 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.08 % Favored : 95.90 % Rotamer: Outliers : 1.62 % Allowed : 23.01 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: -0.63 (0.09), residues: 9228 helix: 0.05 (0.13), residues: 1448 sheet: -0.11 (0.12), residues: 1800 loop : -0.61 (0.08), residues: 5980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP B 84 HIS 0.013 0.001 HIS F 345 PHE 0.030 0.002 PHE B 275 TYR 0.030 0.001 TYR B 710 ARG 0.011 0.001 ARG B 693 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 7740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 312 time to evaluate : 6.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.5694 (ptt) cc_final: 0.4971 (ppp) REVERT: A 233 MET cc_start: 0.7105 (ppp) cc_final: 0.6684 (ppp) REVERT: A 424 SER cc_start: 0.8495 (OUTLIER) cc_final: 0.8032 (p) REVERT: A 526 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8570 (p) REVERT: A 669 ASP cc_start: 0.7708 (m-30) cc_final: 0.7446 (m-30) REVERT: A 701 MET cc_start: 0.6182 (mpp) cc_final: 0.5900 (ptp) REVERT: B 326 GLN cc_start: 0.3224 (OUTLIER) cc_final: 0.2900 (pm20) REVERT: B 397 VAL cc_start: 0.6885 (t) cc_final: 0.6669 (p) REVERT: B 511 LEU cc_start: 0.4864 (OUTLIER) cc_final: 0.3867 (mp) REVERT: B 553 MET cc_start: -0.2357 (mmm) cc_final: -0.3885 (ttt) REVERT: B 615 ASP cc_start: 0.6840 (t0) cc_final: 0.6420 (t0) REVERT: B 806 MET cc_start: 0.7789 (tpp) cc_final: 0.7312 (tpp) REVERT: B 1164 PHE cc_start: 0.5134 (OUTLIER) cc_final: 0.2695 (m-80) REVERT: C 658 MET cc_start: 0.6215 (ppp) cc_final: 0.6011 (mmt) REVERT: C 769 MET cc_start: 0.6167 (tpp) cc_final: 0.5924 (tpp) REVERT: D 139 LYS cc_start: 0.2909 (OUTLIER) cc_final: 0.2535 (mttt) REVERT: D 188 MET cc_start: 0.5852 (mpp) cc_final: 0.5154 (mpp) REVERT: D 233 MET cc_start: 0.7880 (ttt) cc_final: 0.7302 (tpp) REVERT: D 241 MET cc_start: 0.2496 (ppp) cc_final: 0.2111 (ppp) REVERT: D 342 MET cc_start: 0.6661 (mmm) cc_final: 0.6315 (mmm) REVERT: D 553 MET cc_start: -0.1313 (tpp) cc_final: -0.1822 (tpp) REVERT: D 658 MET cc_start: 0.7491 (mmm) cc_final: 0.7171 (mmm) REVERT: D 701 MET cc_start: 0.4066 (mpp) cc_final: 0.3703 (mpp) REVERT: D 708 MET cc_start: 0.3230 (mmt) cc_final: 0.2604 (tpp) REVERT: D 1222 MET cc_start: 0.4344 (ttt) cc_final: 0.3648 (ttp) REVERT: E 427 GLU cc_start: 0.5651 (OUTLIER) cc_final: 0.4143 (tp30) REVERT: E 557 MET cc_start: 0.0074 (ptt) cc_final: -0.0207 (ptm) REVERT: E 873 ARG cc_start: 0.7330 (mmp80) cc_final: 0.7027 (mmp80) REVERT: E 919 TYR cc_start: 0.2549 (p90) cc_final: 0.2128 (p90) REVERT: E 998 MET cc_start: 0.3948 (ptp) cc_final: 0.3538 (ppp) REVERT: E 1007 ASP cc_start: 0.2066 (OUTLIER) cc_final: 0.1665 (p0) REVERT: F 183 LEU cc_start: -0.0689 (OUTLIER) cc_final: -0.0969 (tp) REVERT: F 217 MET cc_start: 0.7730 (ptm) cc_final: 0.7358 (ppp) REVERT: F 233 MET cc_start: 0.6047 (tmm) cc_final: 0.5831 (tmm) REVERT: F 553 MET cc_start: 0.0700 (OUTLIER) cc_final: -0.1171 (pmm) REVERT: F 998 MET cc_start: 0.0804 (ttt) cc_final: 0.0526 (ttt) REVERT: F 1081 CYS cc_start: 0.6566 (m) cc_final: 0.6226 (p) REVERT: G 149 LYS cc_start: 0.1233 (OUTLIER) cc_final: 0.0017 (pttm) REVERT: G 304 LEU cc_start: -0.3870 (OUTLIER) cc_final: -0.4100 (pp) REVERT: G 449 GLN cc_start: -0.0180 (OUTLIER) cc_final: -0.1105 (pm20) REVERT: G 498 GLN cc_start: 0.7475 (tm-30) cc_final: 0.7201 (pp30) REVERT: G 513 GLN cc_start: 0.7009 (mt0) cc_final: 0.5701 (mm-40) REVERT: G 701 MET cc_start: 0.0321 (OUTLIER) cc_final: -0.1748 (tpp) REVERT: G 806 MET cc_start: -0.1923 (mmm) cc_final: -0.2501 (mtp) REVERT: G 879 ARG cc_start: 0.4002 (tpt90) cc_final: 0.3619 (tpt90) REVERT: G 891 MET cc_start: 0.4544 (mmp) cc_final: 0.3765 (tpt) REVERT: H 624 GLU cc_start: 0.7428 (tp30) cc_final: 0.6234 (tt0) REVERT: H 891 MET cc_start: 0.8974 (ttt) cc_final: 0.8749 (tpp) outliers start: 112 outliers final: 73 residues processed: 408 average time/residue: 0.6068 time to fit residues: 445.1385 Evaluate side-chains 370 residues out of total 7740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 283 time to evaluate : 5.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 914 PHE Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1196 CYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 863 CYS Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1164 PHE Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1196 CYS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 611 ASN Chi-restraints excluded: chain C residue 840 VAL Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 1097 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 316 ARG Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 789 LYS Chi-restraints excluded: chain D residue 854 GLU Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 427 GLU Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 815 THR Chi-restraints excluded: chain E residue 906 TYR Chi-restraints excluded: chain E residue 983 ILE Chi-restraints excluded: chain E residue 1007 ASP Chi-restraints excluded: chain E residue 1135 PHE Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 362 ARG Chi-restraints excluded: chain F residue 452 VAL Chi-restraints excluded: chain F residue 490 VAL Chi-restraints excluded: chain F residue 553 MET Chi-restraints excluded: chain F residue 626 TYR Chi-restraints excluded: chain F residue 713 HIS Chi-restraints excluded: chain F residue 833 THR Chi-restraints excluded: chain F residue 1086 PHE Chi-restraints excluded: chain F residue 1137 THR Chi-restraints excluded: chain F residue 1153 VAL Chi-restraints excluded: chain G residue 84 TRP Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 304 LEU Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain G residue 701 MET Chi-restraints excluded: chain G residue 769 MET Chi-restraints excluded: chain G residue 859 THR Chi-restraints excluded: chain G residue 983 ILE Chi-restraints excluded: chain G residue 1186 LEU Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain H residue 457 SER Chi-restraints excluded: chain H residue 526 THR Chi-restraints excluded: chain H residue 655 SER Chi-restraints excluded: chain H residue 834 CYS Chi-restraints excluded: chain H residue 1157 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 184 optimal weight: 9.9990 chunk 421 optimal weight: 2.9990 chunk 475 optimal weight: 10.0000 chunk 377 optimal weight: 10.0000 chunk 635 optimal weight: 3.9990 chunk 186 optimal weight: 0.9990 chunk 407 optimal weight: 6.9990 chunk 384 optimal weight: 20.0000 chunk 295 optimal weight: 0.0470 chunk 633 optimal weight: 7.9990 chunk 365 optimal weight: 8.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN A 680 HIS ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 GLN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN B 772 ASN B 883 ASN ** B 922 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 922 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 941 GLN D 989 GLN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN E 336 GLN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 772 ASN ** E1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 336 GLN ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 453 HIS ** H 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.063353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.053440 restraints weight = 2423654.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.055827 restraints weight = 1229891.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.056261 restraints weight = 680530.986| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3916 r_free = 0.3916 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 167 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3916 r_free = 0.3916 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 195 | |-----------------------------------------------------------------------------| r_final: 0.3916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5614 moved from start: 1.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.185 71156 Z= 0.289 Angle : 0.752 13.834 96892 Z= 0.390 Chirality : 0.049 0.499 10716 Planarity : 0.005 0.068 12852 Dihedral : 5.254 41.481 9976 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.05 % Favored : 93.91 % Rotamer: Outliers : 1.83 % Allowed : 22.95 % Favored : 75.22 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.81 (0.09), residues: 9228 helix: -0.19 (0.13), residues: 1458 sheet: -0.29 (0.12), residues: 1854 loop : -0.68 (0.08), residues: 5916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 84 HIS 0.011 0.002 HIS B 309 PHE 0.034 0.003 PHE B 99 TYR 0.039 0.003 TYR E 919 ARG 0.030 0.001 ARG C 610 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 7740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 296 time to evaluate : 6.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.5658 (ptt) cc_final: 0.5248 (ppp) REVERT: A 233 MET cc_start: 0.7504 (ppp) cc_final: 0.7210 (ppp) REVERT: A 424 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8433 (p) REVERT: A 526 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8428 (p) REVERT: A 557 MET cc_start: 0.7247 (mtm) cc_final: 0.6880 (mtm) REVERT: A 676 SER cc_start: 0.8669 (m) cc_final: 0.8184 (p) REVERT: B 138 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.7190 (mmp) REVERT: B 511 LEU cc_start: 0.5896 (OUTLIER) cc_final: 0.5095 (mp) REVERT: B 624 GLU cc_start: 0.6172 (mm-30) cc_final: 0.5927 (mm-30) REVERT: B 625 LYS cc_start: 0.5762 (OUTLIER) cc_final: 0.5240 (tmmt) REVERT: B 658 MET cc_start: 0.6847 (mmm) cc_final: 0.6530 (mmm) REVERT: B 708 MET cc_start: 0.3234 (tpp) cc_final: 0.2833 (tpp) REVERT: B 713 HIS cc_start: 0.4616 (OUTLIER) cc_final: 0.4326 (p-80) REVERT: B 749 LEU cc_start: 0.5976 (OUTLIER) cc_final: 0.5574 (mp) REVERT: B 806 MET cc_start: 0.7753 (tpp) cc_final: 0.7331 (tpp) REVERT: B 883 ASN cc_start: 0.7529 (OUTLIER) cc_final: 0.7211 (m-40) REVERT: B 1164 PHE cc_start: 0.5963 (OUTLIER) cc_final: 0.3586 (m-80) REVERT: C 1222 MET cc_start: 0.5069 (mmm) cc_final: 0.3940 (tmm) REVERT: D 188 MET cc_start: 0.6156 (mpp) cc_final: 0.5505 (mpp) REVERT: D 233 MET cc_start: 0.7897 (ttt) cc_final: 0.7368 (tpp) REVERT: D 241 MET cc_start: 0.3054 (ppp) cc_final: 0.2302 (ppp) REVERT: D 281 LEU cc_start: 0.4166 (OUTLIER) cc_final: 0.3945 (mm) REVERT: D 342 MET cc_start: 0.7053 (mmm) cc_final: 0.6520 (mmm) REVERT: D 666 ARG cc_start: 0.1236 (OUTLIER) cc_final: 0.0670 (mtm-85) REVERT: D 671 LEU cc_start: 0.4921 (tp) cc_final: 0.4421 (tp) REVERT: D 694 ASP cc_start: 0.6400 (m-30) cc_final: 0.6196 (m-30) REVERT: D 701 MET cc_start: 0.4096 (mpp) cc_final: 0.3701 (mpp) REVERT: D 708 MET cc_start: 0.4348 (mmt) cc_final: 0.3820 (mmp) REVERT: D 1222 MET cc_start: 0.4622 (ttt) cc_final: 0.4085 (ttp) REVERT: E 117 ASP cc_start: 0.7595 (m-30) cc_final: 0.6556 (t0) REVERT: E 427 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.4726 (tp30) REVERT: E 553 MET cc_start: 0.0166 (ttm) cc_final: -0.0044 (mtp) REVERT: E 854 GLU cc_start: 0.6775 (mp0) cc_final: 0.6439 (pm20) REVERT: E 873 ARG cc_start: 0.7281 (mmp80) cc_final: 0.6924 (mmp80) REVERT: E 998 MET cc_start: 0.3670 (ptp) cc_final: 0.3094 (ppp) REVERT: E 1115 TYR cc_start: 0.7228 (m-80) cc_final: 0.6587 (m-80) REVERT: F 183 LEU cc_start: -0.0292 (OUTLIER) cc_final: -0.0680 (mp) REVERT: F 217 MET cc_start: 0.7810 (ptm) cc_final: 0.7414 (ppp) REVERT: F 343 GLN cc_start: 0.8079 (mt0) cc_final: 0.7785 (mp10) REVERT: F 508 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7413 (pm20) REVERT: F 998 MET cc_start: 0.1169 (ttt) cc_final: 0.0815 (ttt) REVERT: G 149 LYS cc_start: 0.2414 (OUTLIER) cc_final: 0.0852 (pttm) REVERT: G 449 GLN cc_start: 0.0383 (OUTLIER) cc_final: -0.0653 (pm20) REVERT: G 513 GLN cc_start: 0.6869 (mt0) cc_final: 0.5197 (mm-40) REVERT: G 701 MET cc_start: 0.0560 (mtt) cc_final: -0.2552 (tpt) REVERT: G 806 MET cc_start: -0.2241 (mmm) cc_final: -0.2719 (mtp) REVERT: H 188 MET cc_start: 0.5940 (pmm) cc_final: 0.5731 (pmm) REVERT: H 654 TYR cc_start: 0.5892 (t80) cc_final: 0.5594 (t80) REVERT: H 891 MET cc_start: 0.9112 (ttt) cc_final: 0.8886 (tpp) outliers start: 128 outliers final: 85 residues processed: 403 average time/residue: 0.6304 time to fit residues: 451.8552 Evaluate side-chains 371 residues out of total 7740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 270 time to evaluate : 6.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1196 CYS Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 625 LYS Chi-restraints excluded: chain B residue 713 HIS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 768 SER Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain B residue 883 ASN Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1164 PHE Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1196 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 840 VAL Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 666 ARG Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 807 VAL Chi-restraints excluded: chain D residue 834 CYS Chi-restraints excluded: chain D residue 854 GLU Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 427 GLU Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 815 THR Chi-restraints excluded: chain E residue 906 TYR Chi-restraints excluded: chain E residue 968 LEU Chi-restraints excluded: chain E residue 983 ILE Chi-restraints excluded: chain E residue 1020 ILE Chi-restraints excluded: chain E residue 1135 PHE Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 362 ARG Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 490 VAL Chi-restraints excluded: chain F residue 508 GLU Chi-restraints excluded: chain F residue 553 MET Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain F residue 912 LEU Chi-restraints excluded: chain F residue 1086 PHE Chi-restraints excluded: chain F residue 1131 ASP Chi-restraints excluded: chain F residue 1137 THR Chi-restraints excluded: chain F residue 1153 VAL Chi-restraints excluded: chain G residue 84 TRP Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain G residue 769 MET Chi-restraints excluded: chain G residue 983 ILE Chi-restraints excluded: chain G residue 1186 LEU Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain H residue 457 SER Chi-restraints excluded: chain H residue 526 THR Chi-restraints excluded: chain H residue 655 SER Chi-restraints excluded: chain H residue 834 CYS Chi-restraints excluded: chain H residue 1082 THR Chi-restraints excluded: chain H residue 1157 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 656 optimal weight: 8.9990 chunk 797 optimal weight: 7.9990 chunk 318 optimal weight: 0.9980 chunk 645 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 882 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 674 optimal weight: 5.9990 chunk 751 optimal weight: 9.9990 chunk 893 optimal weight: 10.0000 chunk 253 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 HIS B 883 ASN ** C 645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 922 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** C1094 GLN D 77 ASN ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 989 GLN E 121 GLN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 GLN ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 876 GLN ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.063648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.053614 restraints weight = 2734736.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.055980 restraints weight = 1398501.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.056470 restraints weight = 692733.533| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3920 r_free = 0.3920 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 195 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3920 r_free = 0.3920 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 190 | |-----------------------------------------------------------------------------| r_final: 0.3920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5623 moved from start: 1.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 71156 Z= 0.228 Angle : 0.694 13.145 96892 Z= 0.356 Chirality : 0.047 0.274 10716 Planarity : 0.005 0.060 12852 Dihedral : 5.084 40.311 9976 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.67 % Favored : 95.31 % Rotamer: Outliers : 1.68 % Allowed : 23.01 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.77 (0.09), residues: 9228 helix: -0.15 (0.13), residues: 1482 sheet: -0.32 (0.12), residues: 1850 loop : -0.64 (0.08), residues: 5896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C1090 HIS 0.009 0.001 HIS F 453 PHE 0.037 0.002 PHE B 528 TYR 0.026 0.002 TYR B 710 ARG 0.014 0.001 ARG D 316 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 7740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 294 time to evaluate : 6.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6919 (ptt) cc_final: 0.6411 (tmm) REVERT: A 233 MET cc_start: 0.7471 (ppp) cc_final: 0.7096 (ppp) REVERT: A 424 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8665 (p) REVERT: B 511 LEU cc_start: 0.5579 (OUTLIER) cc_final: 0.4657 (mp) REVERT: B 553 MET cc_start: -0.2565 (mmm) cc_final: -0.3387 (ttt) REVERT: B 701 MET cc_start: 0.4951 (mpp) cc_final: 0.4677 (mpp) REVERT: B 708 MET cc_start: 0.3587 (tpp) cc_final: 0.2863 (tpp) REVERT: B 749 LEU cc_start: 0.6261 (OUTLIER) cc_final: 0.5549 (mp) REVERT: B 806 MET cc_start: 0.8176 (tpp) cc_final: 0.7724 (tpp) REVERT: B 1164 PHE cc_start: 0.6836 (OUTLIER) cc_final: 0.4141 (m-80) REVERT: C 342 MET cc_start: 0.7258 (tpp) cc_final: 0.6860 (tpp) REVERT: C 1222 MET cc_start: 0.5210 (mmm) cc_final: 0.3494 (tmm) REVERT: D 188 MET cc_start: 0.6226 (mpp) cc_final: 0.5410 (mpp) REVERT: D 233 MET cc_start: 0.8094 (ttt) cc_final: 0.7626 (tpp) REVERT: D 241 MET cc_start: 0.3139 (ppp) cc_final: 0.2460 (ppp) REVERT: D 342 MET cc_start: 0.6632 (mmm) cc_final: 0.6324 (mmm) REVERT: D 461 THR cc_start: 0.5606 (OUTLIER) cc_final: 0.5272 (t) REVERT: D 658 MET cc_start: 0.7596 (mmm) cc_final: 0.7136 (mmm) REVERT: D 675 LEU cc_start: 0.6880 (mm) cc_final: 0.6633 (mm) REVERT: D 694 ASP cc_start: 0.6544 (m-30) cc_final: 0.6337 (m-30) REVERT: D 701 MET cc_start: 0.5402 (mpp) cc_final: 0.5007 (mpp) REVERT: D 708 MET cc_start: 0.4311 (mmt) cc_final: 0.3327 (mmt) REVERT: D 806 MET cc_start: 0.5702 (tpp) cc_final: 0.5268 (tpp) REVERT: D 1222 MET cc_start: 0.4620 (ttt) cc_final: 0.4057 (ttp) REVERT: E 117 ASP cc_start: 0.6114 (m-30) cc_final: 0.5563 (t0) REVERT: E 241 MET cc_start: 0.4794 (tpt) cc_final: 0.4085 (mtm) REVERT: E 427 GLU cc_start: 0.5898 (OUTLIER) cc_final: 0.4609 (tp30) REVERT: E 553 MET cc_start: 0.0510 (ttm) cc_final: 0.0109 (mtp) REVERT: E 873 ARG cc_start: 0.7327 (mmp80) cc_final: 0.7005 (mmp80) REVERT: E 919 TYR cc_start: 0.2520 (p90) cc_final: 0.1716 (p90) REVERT: E 998 MET cc_start: 0.3418 (ptp) cc_final: 0.2982 (ppp) REVERT: F 183 LEU cc_start: -0.0259 (OUTLIER) cc_final: -0.0628 (mp) REVERT: F 217 MET cc_start: 0.7759 (ptm) cc_final: 0.7340 (ppp) REVERT: F 241 MET cc_start: 0.6752 (pmm) cc_final: 0.6116 (pmm) REVERT: F 343 GLN cc_start: 0.8200 (mt0) cc_final: 0.7738 (mp10) REVERT: F 508 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7224 (pm20) REVERT: F 553 MET cc_start: 0.1372 (OUTLIER) cc_final: -0.0231 (pmm) REVERT: F 998 MET cc_start: 0.1046 (ttt) cc_final: 0.0511 (ttt) REVERT: G 149 LYS cc_start: 0.2665 (OUTLIER) cc_final: 0.1058 (pttm) REVERT: G 449 GLN cc_start: 0.0054 (OUTLIER) cc_final: -0.0775 (pm20) REVERT: G 498 GLN cc_start: 0.7945 (tm-30) cc_final: 0.7648 (pp30) REVERT: G 701 MET cc_start: 0.2115 (mtt) cc_final: -0.0438 (tpt) REVERT: G 806 MET cc_start: -0.2075 (mmm) cc_final: -0.2672 (mtp) REVERT: H 188 MET cc_start: 0.5877 (pmm) cc_final: 0.5656 (pmm) REVERT: H 891 MET cc_start: 0.9142 (ttt) cc_final: 0.8897 (tpp) outliers start: 115 outliers final: 88 residues processed: 390 average time/residue: 0.6374 time to fit residues: 444.5620 Evaluate side-chains 364 residues out of total 7740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 265 time to evaluate : 6.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1065 TRP Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1196 CYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 768 SER Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain B residue 876 GLN Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 1164 PHE Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1196 CYS Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 840 VAL Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 807 VAL Chi-restraints excluded: chain D residue 834 CYS Chi-restraints excluded: chain D residue 854 GLU Chi-restraints excluded: chain E residue 110 HIS Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 427 GLU Chi-restraints excluded: chain E residue 815 THR Chi-restraints excluded: chain E residue 906 TYR Chi-restraints excluded: chain E residue 983 ILE Chi-restraints excluded: chain E residue 1020 ILE Chi-restraints excluded: chain E residue 1135 PHE Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 362 ARG Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 508 GLU Chi-restraints excluded: chain F residue 553 MET Chi-restraints excluded: chain F residue 626 TYR Chi-restraints excluded: chain F residue 713 HIS Chi-restraints excluded: chain F residue 806 MET Chi-restraints excluded: chain F residue 1086 PHE Chi-restraints excluded: chain F residue 1131 ASP Chi-restraints excluded: chain F residue 1137 THR Chi-restraints excluded: chain F residue 1153 VAL Chi-restraints excluded: chain F residue 1174 CYS Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 84 TRP Chi-restraints excluded: chain G residue 139 LYS Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 426 GLN Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain G residue 492 LEU Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain G residue 769 MET Chi-restraints excluded: chain G residue 876 GLN Chi-restraints excluded: chain G residue 983 ILE Chi-restraints excluded: chain G residue 1186 LEU Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain H residue 457 SER Chi-restraints excluded: chain H residue 526 THR Chi-restraints excluded: chain H residue 834 CYS Chi-restraints excluded: chain H residue 1157 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 566 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 859 optimal weight: 7.9990 chunk 622 optimal weight: 0.8980 chunk 564 optimal weight: 6.9990 chunk 819 optimal weight: 30.0000 chunk 149 optimal weight: 3.9990 chunk 865 optimal weight: 0.5980 chunk 261 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 427 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN ** C 645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 922 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 989 GLN E 121 GLN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 824 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 = 0.4147 r_free = 0.4147 target = 0.063642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.053908 restraints weight = 2450770.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.055980 restraints weight = 1268820.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.056538 restraints weight = 646426.188| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3925 r_free = 0.3925 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 190 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3925 r_free = 0.3925 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 190 | |-----------------------------------------------------------------------------| r_final: 0.3925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5614 moved from start: 1.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.485 71156 Z= 0.366 Angle : 0.770 58.588 96892 Z= 0.405 Chirality : 0.049 1.274 10716 Planarity : 0.005 0.059 12852 Dihedral : 5.083 40.323 9976 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.83 % Favored : 95.14 % Rotamer: Outliers : 1.68 % Allowed : 23.08 % Favored : 75.24 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.77 (0.09), residues: 9228 helix: -0.13 (0.13), residues: 1482 sheet: -0.32 (0.12), residues: 1850 loop : -0.65 (0.08), residues: 5896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.002 TRP B 328 HIS 0.051 0.001 HIS G 110 PHE 0.094 0.002 PHE A 235 TYR 0.108 0.002 TYR G 203 ARG 0.041 0.001 ARG B 329 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 7740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 265 time to evaluate : 6.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6977 (ptt) cc_final: 0.6457 (tmm) REVERT: A 233 MET cc_start: 0.7425 (ppp) cc_final: 0.7066 (ppp) REVERT: A 424 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8646 (p) REVERT: B 206 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.6754 (ttmt) REVERT: B 511 LEU cc_start: 0.5587 (OUTLIER) cc_final: 0.4664 (mp) REVERT: B 553 MET cc_start: -0.2617 (mmm) cc_final: -0.3406 (ttt) REVERT: B 701 MET cc_start: 0.4912 (mpp) cc_final: 0.4653 (mpp) REVERT: B 708 MET cc_start: 0.3642 (tpp) cc_final: 0.2897 (tpp) REVERT: B 749 LEU cc_start: 0.6223 (OUTLIER) cc_final: 0.5511 (mp) REVERT: B 806 MET cc_start: 0.8157 (tpp) cc_final: 0.7714 (tpp) REVERT: B 1164 PHE cc_start: 0.6831 (OUTLIER) cc_final: 0.4130 (m-80) REVERT: C 342 MET cc_start: 0.7200 (tpp) cc_final: 0.6821 (tpp) REVERT: C 1222 MET cc_start: 0.5236 (mmm) cc_final: 0.3519 (tmm) REVERT: D 188 MET cc_start: 0.6202 (mpp) cc_final: 0.5392 (mpp) REVERT: D 233 MET cc_start: 0.8081 (ttt) cc_final: 0.7618 (tpp) REVERT: D 241 MET cc_start: 0.3119 (ppp) cc_final: 0.2455 (ppp) REVERT: D 342 MET cc_start: 0.6596 (mmm) cc_final: 0.6237 (mmm) REVERT: D 461 THR cc_start: 0.5564 (OUTLIER) cc_final: 0.5228 (t) REVERT: D 658 MET cc_start: 0.7608 (mmm) cc_final: 0.7135 (mmm) REVERT: D 675 LEU cc_start: 0.6851 (mm) cc_final: 0.6631 (mm) REVERT: D 694 ASP cc_start: 0.6492 (m-30) cc_final: 0.6275 (m-30) REVERT: D 701 MET cc_start: 0.5365 (mpp) cc_final: 0.4979 (mpp) REVERT: D 708 MET cc_start: 0.4296 (mmt) cc_final: 0.3278 (mmt) REVERT: D 806 MET cc_start: 0.5678 (tpp) cc_final: 0.5235 (tpp) REVERT: D 1222 MET cc_start: 0.4653 (ttt) cc_final: 0.4091 (ttp) REVERT: E 117 ASP cc_start: 0.6135 (m-30) cc_final: 0.5573 (t0) REVERT: E 241 MET cc_start: 0.4800 (tpt) cc_final: 0.4067 (mtm) REVERT: E 427 GLU cc_start: 0.5889 (OUTLIER) cc_final: 0.4608 (tp30) REVERT: E 553 MET cc_start: 0.0480 (ttm) cc_final: 0.0101 (mtp) REVERT: E 873 ARG cc_start: 0.7304 (mmp80) cc_final: 0.6971 (mmp80) REVERT: E 919 TYR cc_start: 0.2377 (p90) cc_final: 0.1507 (p90) REVERT: E 998 MET cc_start: 0.3345 (ptp) cc_final: 0.2927 (ppp) REVERT: F 183 LEU cc_start: -0.0320 (OUTLIER) cc_final: -0.0666 (mp) REVERT: F 217 MET cc_start: 0.7744 (ptm) cc_final: 0.7308 (ppp) REVERT: F 241 MET cc_start: 0.6729 (pmm) cc_final: 0.6071 (pmm) REVERT: F 343 GLN cc_start: 0.8163 (mt0) cc_final: 0.7700 (mp10) REVERT: F 508 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7211 (pm20) REVERT: F 553 MET cc_start: 0.1355 (OUTLIER) cc_final: -0.0241 (pmm) REVERT: F 998 MET cc_start: 0.0959 (ttt) cc_final: 0.0433 (ttt) REVERT: G 105 TYR cc_start: 0.5837 (m-80) cc_final: 0.4884 (m-80) REVERT: G 149 LYS cc_start: 0.2642 (OUTLIER) cc_final: 0.1033 (pttm) REVERT: G 449 GLN cc_start: 0.0042 (OUTLIER) cc_final: -0.0776 (pm20) REVERT: G 498 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7626 (pp30) REVERT: G 701 MET cc_start: 0.2106 (mtt) cc_final: -0.0425 (tpt) REVERT: G 806 MET cc_start: -0.2179 (mmm) cc_final: -0.2777 (mtp) REVERT: H 188 MET cc_start: 0.5880 (pmm) cc_final: 0.5647 (pmm) REVERT: H 891 MET cc_start: 0.9135 (ttt) cc_final: 0.8877 (tpp) outliers start: 115 outliers final: 97 residues processed: 359 average time/residue: 0.6306 time to fit residues: 411.3245 Evaluate side-chains 374 residues out of total 7740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 265 time to evaluate : 6.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1065 TRP Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1196 CYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 768 SER Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain B residue 876 GLN Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 1164 PHE Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1196 CYS Chi-restraints excluded: chain B residue 1222 MET Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 983 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 807 VAL Chi-restraints excluded: chain D residue 834 CYS Chi-restraints excluded: chain D residue 854 GLU Chi-restraints excluded: chain E residue 110 HIS Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 427 GLU Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 815 THR Chi-restraints excluded: chain E residue 854 GLU Chi-restraints excluded: chain E residue 906 TYR Chi-restraints excluded: chain E residue 983 ILE Chi-restraints excluded: chain E residue 1020 ILE Chi-restraints excluded: chain E residue 1135 PHE Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 362 ARG Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 508 GLU Chi-restraints excluded: chain F residue 553 MET Chi-restraints excluded: chain F residue 557 MET Chi-restraints excluded: chain F residue 626 TYR Chi-restraints excluded: chain F residue 713 HIS Chi-restraints excluded: chain F residue 806 MET Chi-restraints excluded: chain F residue 1086 PHE Chi-restraints excluded: chain F residue 1131 ASP Chi-restraints excluded: chain F residue 1137 THR Chi-restraints excluded: chain F residue 1153 VAL Chi-restraints excluded: chain F residue 1174 CYS Chi-restraints excluded: chain F residue 1222 MET Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 84 TRP Chi-restraints excluded: chain G residue 139 LYS Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 426 GLN Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain G residue 492 LEU Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain G residue 557 MET Chi-restraints excluded: chain G residue 769 MET Chi-restraints excluded: chain G residue 859 THR Chi-restraints excluded: chain G residue 876 GLN Chi-restraints excluded: chain G residue 983 ILE Chi-restraints excluded: chain G residue 1186 LEU Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain H residue 457 SER Chi-restraints excluded: chain H residue 526 THR Chi-restraints excluded: chain H residue 834 CYS Chi-restraints excluded: chain H residue 1157 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 257 optimal weight: 7.9990 chunk 842 optimal weight: 5.9990 chunk 475 optimal weight: 0.8980 chunk 906 optimal weight: 1.9990 chunk 195 optimal weight: 7.9990 chunk 402 optimal weight: 1.9990 chunk 661 optimal weight: 0.0030 chunk 848 optimal weight: 0.1980 chunk 738 optimal weight: 3.9990 chunk 264 optimal weight: 10.0000 chunk 144 optimal weight: 0.7980 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 GLN ** A 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN ** B 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN ** C 645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 922 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 989 GLN E 121 GLN E 146 GLN ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 247 GLN ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.064071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.053794 restraints weight = 2620773.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.056394 restraints weight = 1303165.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.057319 restraints weight = 644846.075| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3955 r_free = 0.3955 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 190 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3955 r_free = 0.3955 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 204 | |-----------------------------------------------------------------------------| r_final: 0.3955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5566 moved from start: 1.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 71156 Z= 0.184 Angle : 0.664 17.180 96892 Z= 0.335 Chirality : 0.045 0.236 10716 Planarity : 0.005 0.065 12852 Dihedral : 4.833 39.496 9976 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.69 % Favored : 95.29 % Rotamer: Outliers : 1.34 % Allowed : 23.35 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.58 (0.09), residues: 9228 helix: 0.22 (0.14), residues: 1434 sheet: -0.27 (0.12), residues: 1904 loop : -0.54 (0.08), residues: 5890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP B 328 HIS 0.006 0.001 HIS E 88 PHE 0.030 0.002 PHE F 582 TYR 0.022 0.002 TYR G 105 ARG 0.012 0.001 ARG G 879 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24753.15 seconds wall clock time: 430 minutes 55.16 seconds (25855.16 seconds total)