Starting phenix.real_space_refine on Tue Aug 26 10:27:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w2l_43751/08_2025/8w2l_43751.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w2l_43751/08_2025/8w2l_43751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w2l_43751/08_2025/8w2l_43751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w2l_43751/08_2025/8w2l_43751.map" model { file = "/net/cci-nas-00/data/ceres_data/8w2l_43751/08_2025/8w2l_43751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w2l_43751/08_2025/8w2l_43751.cif" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.104 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 48 5.49 5 S 196 5.16 5 Cl 4 4.86 5 C 23688 2.51 5 N 5508 2.21 5 O 6352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35797 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 8199 Classifications: {'peptide': 1014} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 972} Chain breaks: 3 Chain: "B" Number of atoms: 8199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 8199 Classifications: {'peptide': 1014} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 972} Chain breaks: 3 Chain: "C" Number of atoms: 8199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 8199 Classifications: {'peptide': 1014} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 972} Chain breaks: 3 Chain: "D" Number of atoms: 8199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 8199 Classifications: {'peptide': 1014} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 972} Chain breaks: 3 Chain: "A" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 710 Unusual residues: {' CA': 1, 'CLR': 1, 'DU0': 1, 'M05': 1, 'POV': 13} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 709 Unusual residues: {'CLR': 1, 'DU0': 1, 'M05': 1, 'POV': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 709 Unusual residues: {'CLR': 1, 'DU0': 1, 'M05': 1, 'POV': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 709 Unusual residues: {'CLR': 1, 'DU0': 1, 'M05': 1, 'POV': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Time building chain proxies: 9.59, per 1000 atoms: 0.27 Number of scatterers: 35797 At special positions: 0 Unit cell: (145, 145, 156, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 Cl 4 17.00 S 196 16.00 P 48 15.00 O 6352 8.00 N 5508 7.00 C 23688 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A1056 " - pdb=" SG CYS A1066 " distance=2.03 Simple disulfide: pdb=" SG CYS B1056 " - pdb=" SG CYS B1066 " distance=2.03 Simple disulfide: pdb=" SG CYS C1056 " - pdb=" SG CYS C1066 " distance=2.03 Simple disulfide: pdb=" SG CYS D1056 " - pdb=" SG CYS D1066 " 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: 3.37 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7664 Finding SS restraints... Secondary structure from input PDB file: 212 helices and 8 sheets defined 68.6% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 116 through 127 Processing helix chain 'A' and resid 149 through 166 removed outlier: 3.636A pdb=" N GLN A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 191 Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.597A pdb=" N ARG A 197 " --> pdb=" O ARG A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.645A pdb=" N ASP A 215 " --> pdb=" O ASN A 212 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 216 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 217 " --> pdb=" O ASN A 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 217' Processing helix chain 'A' and resid 259 through 271 removed outlier: 3.571A pdb=" N ARG A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.666A pdb=" N LEU A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.619A pdb=" N LEU A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN A 331 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.634A pdb=" N PHE A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 372 Processing helix chain 'A' and resid 374 through 378 removed outlier: 3.513A pdb=" N LEU A 377 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 378' Processing helix chain 'A' and resid 390 through 398 removed outlier: 3.862A pdb=" N ALA A 394 " --> pdb=" O ASP A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 418 Processing helix chain 'A' and resid 419 through 427 removed outlier: 3.555A pdb=" N ALA A 423 " --> pdb=" O ARG A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 449 removed outlier: 3.531A pdb=" N VAL A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 470 through 479 removed outlier: 3.644A pdb=" N TYR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 498 removed outlier: 4.256A pdb=" N HIS A 491 " --> pdb=" O PRO A 487 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP A 495 " --> pdb=" O HIS A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 526 through 529 Processing helix chain 'A' and resid 530 through 540 Processing helix chain 'A' and resid 620 through 632 removed outlier: 3.734A pdb=" N GLU A 624 " --> pdb=" O TYR A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 644 removed outlier: 3.677A pdb=" N HIS A 644 " --> pdb=" O PHE A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 668 Processing helix chain 'A' and resid 675 through 701 Processing helix chain 'A' and resid 701 through 709 Processing helix chain 'A' and resid 720 through 728 Processing helix chain 'A' and resid 730 through 735 removed outlier: 3.575A pdb=" N VAL A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 749 Processing helix chain 'A' and resid 757 through 767 Processing helix chain 'A' and resid 768 through 774 removed outlier: 3.503A pdb=" N MET A 773 " --> pdb=" O ALA A 770 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 774 " --> pdb=" O ILE A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 783 removed outlier: 3.681A pdb=" N SER A 783 " --> pdb=" O ALA A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 797 Processing helix chain 'A' and resid 840 through 850 removed outlier: 3.741A pdb=" N PHE A 848 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 876 removed outlier: 3.855A pdb=" N ALA A 862 " --> pdb=" O PHE A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 905 Processing helix chain 'A' and resid 911 through 920 Processing helix chain 'A' and resid 922 through 944 Processing helix chain 'A' and resid 955 through 975 removed outlier: 4.757A pdb=" N ILE A 970 " --> pdb=" O CYS A 966 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP A 972 " --> pdb=" O ASN A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 981 removed outlier: 3.594A pdb=" N PHE A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1000 removed outlier: 4.118A pdb=" N TYR A 989 " --> pdb=" O GLN A 985 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1023 Proline residue: A1017 - end of helix Processing helix chain 'A' and resid 1030 through 1036 removed outlier: 3.661A pdb=" N LYS A1034 " --> pdb=" O TRP A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1044 removed outlier: 3.878A pdb=" N ILE A1044 " --> pdb=" O PRO A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1062 through 1066 removed outlier: 3.543A pdb=" N CYS A1066 " --> pdb=" O PRO A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1071 No H-bonds generated for 'chain 'A' and resid 1069 through 1071' Processing helix chain 'A' and resid 1072 through 1087 Processing helix chain 'A' and resid 1087 through 1125 removed outlier: 5.465A pdb=" N LEU A1101 " --> pdb=" O ASN A1097 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLN A1102 " --> pdb=" O ASN A1098 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR A1116 " --> pdb=" O LYS A1112 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N HIS A1117 " --> pdb=" O TYR A1113 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR A1122 " --> pdb=" O PHE A1118 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A1123 " --> pdb=" O ILE A1119 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU A1124 " --> pdb=" O MET A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1141 removed outlier: 4.076A pdb=" N SER A1136 " --> pdb=" O LEU A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1190 Processing helix chain 'A' and resid 1192 through 1228 removed outlier: 3.842A pdb=" N ARG A1198 " --> pdb=" O GLU A1194 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A1209 " --> pdb=" O GLU A1205 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG A1217 " --> pdb=" O GLU A1213 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A1219 " --> pdb=" O GLY A1215 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS A1222 " --> pdb=" O VAL A1218 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A1223 " --> pdb=" O ASN A1219 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N SER A1224 " --> pdb=" O TYR A1220 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A1225 " --> pdb=" O ILE A1221 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 127 Processing helix chain 'B' and resid 149 through 166 removed outlier: 3.636A pdb=" N GLN B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.597A pdb=" N ARG B 197 " --> pdb=" O ARG B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 217 removed outlier: 3.644A pdb=" N ASP B 215 " --> pdb=" O ASN B 212 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 216 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 217 " --> pdb=" O ASN B 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 212 through 217' Processing helix chain 'B' and resid 259 through 271 removed outlier: 3.572A pdb=" N ARG B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 305 removed outlier: 3.668A pdb=" N LEU B 301 " --> pdb=" O ILE B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 removed outlier: 3.619A pdb=" N LEU B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN B 331 " --> pdb=" O TYR B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.634A pdb=" N PHE B 354 " --> pdb=" O ILE B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 372 Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.512A pdb=" N LEU B 377 " --> pdb=" O LYS B 374 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 374 through 378' Processing helix chain 'B' and resid 390 through 398 removed outlier: 3.862A pdb=" N ALA B 394 " --> pdb=" O ASP B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 418 Processing helix chain 'B' and resid 419 through 427 removed outlier: 3.554A pdb=" N ALA B 423 " --> pdb=" O ARG B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 449 removed outlier: 3.530A pdb=" N VAL B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 464 through 469 Processing helix chain 'B' and resid 470 through 479 removed outlier: 3.644A pdb=" N TYR B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 498 removed outlier: 4.255A pdb=" N HIS B 491 " --> pdb=" O PRO B 487 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP B 495 " --> pdb=" O HIS B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 526 through 529 Processing helix chain 'B' and resid 530 through 540 Processing helix chain 'B' and resid 620 through 632 removed outlier: 3.733A pdb=" N GLU B 624 " --> pdb=" O TYR B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 644 removed outlier: 3.677A pdb=" N HIS B 644 " --> pdb=" O PHE B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 668 Processing helix chain 'B' and resid 675 through 701 Processing helix chain 'B' and resid 701 through 709 Processing helix chain 'B' and resid 720 through 728 Processing helix chain 'B' and resid 730 through 735 removed outlier: 3.575A pdb=" N VAL B 734 " --> pdb=" O LEU B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 749 Processing helix chain 'B' and resid 757 through 767 Processing helix chain 'B' and resid 768 through 774 removed outlier: 3.503A pdb=" N MET B 773 " --> pdb=" O ALA B 770 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 774 " --> pdb=" O ILE B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 783 removed outlier: 3.682A pdb=" N SER B 783 " --> pdb=" O ALA B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 797 Processing helix chain 'B' and resid 840 through 850 removed outlier: 3.741A pdb=" N PHE B 848 " --> pdb=" O LYS B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 876 removed outlier: 3.856A pdb=" N ALA B 862 " --> pdb=" O PHE B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 905 Processing helix chain 'B' and resid 911 through 920 Processing helix chain 'B' and resid 922 through 944 Processing helix chain 'B' and resid 955 through 975 removed outlier: 4.756A pdb=" N ILE B 970 " --> pdb=" O CYS B 966 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE B 971 " --> pdb=" O LEU B 967 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP B 972 " --> pdb=" O ASN B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 975 through 981 removed outlier: 3.594A pdb=" N PHE B 979 " --> pdb=" O ARG B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1000 removed outlier: 4.119A pdb=" N TYR B 989 " --> pdb=" O GLN B 985 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY B 994 " --> pdb=" O VAL B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1023 Proline residue: B1017 - end of helix Processing helix chain 'B' and resid 1030 through 1036 removed outlier: 3.661A pdb=" N LYS B1034 " --> pdb=" O TRP B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1037 through 1044 removed outlier: 3.878A pdb=" N ILE B1044 " --> pdb=" O PRO B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1049 through 1053 Processing helix chain 'B' and resid 1062 through 1066 removed outlier: 3.544A pdb=" N CYS B1066 " --> pdb=" O PRO B1063 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1071 No H-bonds generated for 'chain 'B' and resid 1069 through 1071' Processing helix chain 'B' and resid 1072 through 1087 Processing helix chain 'B' and resid 1087 through 1125 removed outlier: 5.465A pdb=" N LEU B1101 " --> pdb=" O ASN B1097 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLN B1102 " --> pdb=" O ASN B1098 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR B1116 " --> pdb=" O LYS B1112 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N HIS B1117 " --> pdb=" O TYR B1113 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B1122 " --> pdb=" O PHE B1118 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS B1123 " --> pdb=" O ILE B1119 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU B1124 " --> pdb=" O MET B1120 " (cutoff:3.500A) Processing helix chain 'B' and resid 1132 through 1141 removed outlier: 4.076A pdb=" N SER B1136 " --> pdb=" O LEU B1132 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1190 Processing helix chain 'B' and resid 1192 through 1228 removed outlier: 3.842A pdb=" N ARG B1198 " --> pdb=" O GLU B1194 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B1209 " --> pdb=" O GLU B1205 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG B1217 " --> pdb=" O GLU B1213 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B1219 " --> pdb=" O GLY B1215 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS B1222 " --> pdb=" O VAL B1218 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B1223 " --> pdb=" O ASN B1219 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N SER B1224 " --> pdb=" O TYR B1220 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU B1225 " --> pdb=" O ILE B1221 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 127 Processing helix chain 'C' and resid 149 through 166 removed outlier: 3.636A pdb=" N GLN C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS C 162 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 191 Processing helix chain 'C' and resid 194 through 198 removed outlier: 3.597A pdb=" N ARG C 197 " --> pdb=" O ARG C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 217 removed outlier: 3.645A pdb=" N ASP C 215 " --> pdb=" O ASN C 212 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 216 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL C 217 " --> pdb=" O ASN C 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 212 through 217' Processing helix chain 'C' and resid 259 through 271 removed outlier: 3.571A pdb=" N ARG C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 305 removed outlier: 3.667A pdb=" N LEU C 301 " --> pdb=" O ILE C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 331 removed outlier: 3.619A pdb=" N LEU C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN C 331 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.634A pdb=" N PHE C 354 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 372 Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.512A pdb=" N LEU C 377 " --> pdb=" O LYS C 374 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE C 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 374 through 378' Processing helix chain 'C' and resid 390 through 398 removed outlier: 3.862A pdb=" N ALA C 394 " --> pdb=" O ASP C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 418 Processing helix chain 'C' and resid 419 through 427 removed outlier: 3.555A pdb=" N ALA C 423 " --> pdb=" O ARG C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 449 removed outlier: 3.531A pdb=" N VAL C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 461 Processing helix chain 'C' and resid 464 through 469 Processing helix chain 'C' and resid 470 through 479 removed outlier: 3.644A pdb=" N TYR C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 498 removed outlier: 4.255A pdb=" N HIS C 491 " --> pdb=" O PRO C 487 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP C 495 " --> pdb=" O HIS C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 526 through 529 Processing helix chain 'C' and resid 530 through 540 Processing helix chain 'C' and resid 620 through 632 removed outlier: 3.733A pdb=" N GLU C 624 " --> pdb=" O TYR C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 644 removed outlier: 3.676A pdb=" N HIS C 644 " --> pdb=" O PHE C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 668 Processing helix chain 'C' and resid 675 through 701 Processing helix chain 'C' and resid 701 through 709 Processing helix chain 'C' and resid 720 through 728 Processing helix chain 'C' and resid 730 through 735 removed outlier: 3.575A pdb=" N VAL C 734 " --> pdb=" O LEU C 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 749 Processing helix chain 'C' and resid 757 through 767 Processing helix chain 'C' and resid 768 through 774 removed outlier: 3.503A pdb=" N MET C 773 " --> pdb=" O ALA C 770 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 774 " --> pdb=" O ILE C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 783 removed outlier: 3.681A pdb=" N SER C 783 " --> pdb=" O ALA C 780 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 797 Processing helix chain 'C' and resid 840 through 850 removed outlier: 3.741A pdb=" N PHE C 848 " --> pdb=" O LYS C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 876 removed outlier: 3.856A pdb=" N ALA C 862 " --> pdb=" O PHE C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 905 Processing helix chain 'C' and resid 911 through 920 Processing helix chain 'C' and resid 922 through 944 Processing helix chain 'C' and resid 955 through 975 removed outlier: 4.756A pdb=" N ILE C 970 " --> pdb=" O CYS C 966 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP C 972 " --> pdb=" O ASN C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 975 through 981 removed outlier: 3.593A pdb=" N PHE C 979 " --> pdb=" O ARG C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1000 removed outlier: 4.118A pdb=" N TYR C 989 " --> pdb=" O GLN C 985 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY C 994 " --> pdb=" O VAL C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1023 Proline residue: C1017 - end of helix Processing helix chain 'C' and resid 1030 through 1036 removed outlier: 3.661A pdb=" N LYS C1034 " --> pdb=" O TRP C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1037 through 1044 removed outlier: 3.877A pdb=" N ILE C1044 " --> pdb=" O PRO C1040 " (cutoff:3.500A) Processing helix chain 'C' and resid 1049 through 1053 Processing helix chain 'C' and resid 1062 through 1066 removed outlier: 3.544A pdb=" N CYS C1066 " --> pdb=" O PRO C1063 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1071 No H-bonds generated for 'chain 'C' and resid 1069 through 1071' Processing helix chain 'C' and resid 1072 through 1087 Processing helix chain 'C' and resid 1087 through 1125 removed outlier: 5.464A pdb=" N LEU C1101 " --> pdb=" O ASN C1097 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLN C1102 " --> pdb=" O ASN C1098 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR C1116 " --> pdb=" O LYS C1112 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N HIS C1117 " --> pdb=" O TYR C1113 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR C1122 " --> pdb=" O PHE C1118 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS C1123 " --> pdb=" O ILE C1119 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU C1124 " --> pdb=" O MET C1120 " (cutoff:3.500A) Processing helix chain 'C' and resid 1132 through 1141 removed outlier: 4.076A pdb=" N SER C1136 " --> pdb=" O LEU C1132 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1190 Processing helix chain 'C' and resid 1192 through 1228 removed outlier: 3.842A pdb=" N ARG C1198 " --> pdb=" O GLU C1194 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C1209 " --> pdb=" O GLU C1205 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG C1217 " --> pdb=" O GLU C1213 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN C1219 " --> pdb=" O GLY C1215 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS C1222 " --> pdb=" O VAL C1218 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG C1223 " --> pdb=" O ASN C1219 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N SER C1224 " --> pdb=" O TYR C1220 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU C1225 " --> pdb=" O ILE C1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 127 Processing helix chain 'D' and resid 149 through 166 removed outlier: 3.635A pdb=" N GLN D 154 " --> pdb=" O PRO D 150 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS D 162 " --> pdb=" O LYS D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 191 Processing helix chain 'D' and resid 194 through 198 removed outlier: 3.597A pdb=" N ARG D 197 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 217 removed outlier: 3.645A pdb=" N ASP D 215 " --> pdb=" O ASN D 212 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU D 216 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL D 217 " --> pdb=" O ASN D 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 212 through 217' Processing helix chain 'D' and resid 259 through 271 removed outlier: 3.572A pdb=" N ARG D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 305 removed outlier: 3.667A pdb=" N LEU D 301 " --> pdb=" O ILE D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 331 removed outlier: 3.620A pdb=" N LEU D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN D 331 " --> pdb=" O TYR D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 354 removed outlier: 3.634A pdb=" N PHE D 354 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 372 Processing helix chain 'D' and resid 374 through 378 removed outlier: 3.512A pdb=" N LEU D 377 " --> pdb=" O LYS D 374 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE D 378 " --> pdb=" O LYS D 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 374 through 378' Processing helix chain 'D' and resid 390 through 398 removed outlier: 3.862A pdb=" N ALA D 394 " --> pdb=" O ASP D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 418 Processing helix chain 'D' and resid 419 through 427 removed outlier: 3.555A pdb=" N ALA D 423 " --> pdb=" O ARG D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 449 removed outlier: 3.530A pdb=" N VAL D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 461 Processing helix chain 'D' and resid 464 through 469 Processing helix chain 'D' and resid 470 through 479 removed outlier: 3.644A pdb=" N TYR D 478 " --> pdb=" O LEU D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 498 removed outlier: 4.255A pdb=" N HIS D 491 " --> pdb=" O PRO D 487 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP D 495 " --> pdb=" O HIS D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 526 through 529 Processing helix chain 'D' and resid 530 through 540 Processing helix chain 'D' and resid 620 through 632 removed outlier: 3.733A pdb=" N GLU D 624 " --> pdb=" O TYR D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 644 removed outlier: 3.678A pdb=" N HIS D 644 " --> pdb=" O PHE D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 668 Processing helix chain 'D' and resid 675 through 701 Processing helix chain 'D' and resid 701 through 709 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 730 through 735 removed outlier: 3.575A pdb=" N VAL D 734 " --> pdb=" O LEU D 730 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 749 Processing helix chain 'D' and resid 757 through 767 Processing helix chain 'D' and resid 768 through 774 removed outlier: 3.504A pdb=" N MET D 773 " --> pdb=" O ALA D 770 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU D 774 " --> pdb=" O ILE D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 783 removed outlier: 3.682A pdb=" N SER D 783 " --> pdb=" O ALA D 780 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 797 Processing helix chain 'D' and resid 840 through 850 removed outlier: 3.741A pdb=" N PHE D 848 " --> pdb=" O LYS D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 876 removed outlier: 3.855A pdb=" N ALA D 862 " --> pdb=" O PHE D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 905 Processing helix chain 'D' and resid 911 through 920 Processing helix chain 'D' and resid 922 through 944 Processing helix chain 'D' and resid 955 through 975 removed outlier: 4.756A pdb=" N ILE D 970 " --> pdb=" O CYS D 966 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE D 971 " --> pdb=" O LEU D 967 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP D 972 " --> pdb=" O ASN D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 975 through 981 removed outlier: 3.594A pdb=" N PHE D 979 " --> pdb=" O ARG D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1000 removed outlier: 4.118A pdb=" N TYR D 989 " --> pdb=" O GLN D 985 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY D 994 " --> pdb=" O VAL D 990 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1023 Proline residue: D1017 - end of helix Processing helix chain 'D' and resid 1030 through 1036 removed outlier: 3.662A pdb=" N LYS D1034 " --> pdb=" O TRP D1030 " (cutoff:3.500A) Processing helix chain 'D' and resid 1037 through 1044 removed outlier: 3.878A pdb=" N ILE D1044 " --> pdb=" O PRO D1040 " (cutoff:3.500A) Processing helix chain 'D' and resid 1049 through 1053 Processing helix chain 'D' and resid 1062 through 1066 removed outlier: 3.544A pdb=" N CYS D1066 " --> pdb=" O PRO D1063 " (cutoff:3.500A) Processing helix chain 'D' and resid 1069 through 1071 No H-bonds generated for 'chain 'D' and resid 1069 through 1071' Processing helix chain 'D' and resid 1072 through 1087 Processing helix chain 'D' and resid 1087 through 1125 removed outlier: 5.464A pdb=" N LEU D1101 " --> pdb=" O ASN D1097 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLN D1102 " --> pdb=" O ASN D1098 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR D1116 " --> pdb=" O LYS D1112 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N HIS D1117 " --> pdb=" O TYR D1113 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR D1122 " --> pdb=" O PHE D1118 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS D1123 " --> pdb=" O ILE D1119 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU D1124 " --> pdb=" O MET D1120 " (cutoff:3.500A) Processing helix chain 'D' and resid 1132 through 1141 removed outlier: 4.076A pdb=" N SER D1136 " --> pdb=" O LEU D1132 " (cutoff:3.500A) Processing helix chain 'D' and resid 1163 through 1190 Processing helix chain 'D' and resid 1192 through 1228 removed outlier: 3.842A pdb=" N ARG D1198 " --> pdb=" O GLU D1194 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D1209 " --> pdb=" O GLU D1205 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG D1217 " --> pdb=" O GLU D1213 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN D1219 " --> pdb=" O GLY D1215 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS D1222 " --> pdb=" O VAL D1218 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG D1223 " --> pdb=" O ASN D1219 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N SER D1224 " --> pdb=" O TYR D1220 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU D1225 " --> pdb=" O ILE D1221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 94 removed outlier: 7.521A pdb=" N TYR A 92 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL A 222 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 94 " --> pdb=" O VAL A 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 244 through 248 removed outlier: 6.084A pdb=" N GLY A 203 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL A 248 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA A 205 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE A 202 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE A 171 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE A 204 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR A 173 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL A 136 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU A 288 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N SER A 138 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N VAL A 313 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA A 287 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N CYS A 315 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE A 289 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N PHE A 381 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL A 314 " --> pdb=" O PHE A 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 94 removed outlier: 7.521A pdb=" N TYR B 92 " --> pdb=" O ASP B 220 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL B 222 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B 94 " --> pdb=" O VAL B 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 244 through 248 removed outlier: 6.085A pdb=" N GLY B 203 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL B 248 " --> pdb=" O GLY B 203 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA B 205 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE B 202 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 171 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE B 204 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR B 173 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL B 136 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU B 288 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER B 138 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N VAL B 313 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA B 287 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N CYS B 315 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE B 289 " --> pdb=" O CYS B 315 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N PHE B 381 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL B 314 " --> pdb=" O PHE B 381 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 94 removed outlier: 7.519A pdb=" N TYR C 92 " --> pdb=" O ASP C 220 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL C 222 " --> pdb=" O TYR C 92 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL C 94 " --> pdb=" O VAL C 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 244 through 248 removed outlier: 6.084A pdb=" N GLY C 203 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL C 248 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA C 205 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE C 202 " --> pdb=" O ALA C 169 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE C 171 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE C 204 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR C 173 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL C 136 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU C 288 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER C 138 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N VAL C 313 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA C 287 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N CYS C 315 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE C 289 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N PHE C 381 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL C 314 " --> pdb=" O PHE C 381 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 91 through 94 removed outlier: 7.520A pdb=" N TYR D 92 " --> pdb=" O ASP D 220 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL D 222 " --> pdb=" O TYR D 92 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL D 94 " --> pdb=" O VAL D 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 244 through 248 removed outlier: 6.084A pdb=" N GLY D 203 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL D 248 " --> pdb=" O GLY D 203 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA D 205 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE D 202 " --> pdb=" O ALA D 169 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE D 171 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE D 204 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR D 173 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL D 136 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU D 288 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER D 138 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N VAL D 313 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA D 287 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N CYS D 315 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE D 289 " --> pdb=" O CYS D 315 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N PHE D 381 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL D 314 " --> pdb=" O PHE D 381 " (cutoff:3.500A) 1764 hydrogen bonds defined for protein. 5184 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: 6.20 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5413 1.32 - 1.44: 9313 1.44 - 1.57: 21245 1.57 - 1.69: 101 1.69 - 1.81: 348 Bond restraints: 36420 Sorted by residual: bond pdb=" C29 POV C1313 " pdb="C210 POV C1313 " ideal model delta sigma weight residual 1.333 1.517 -0.184 2.00e-02 2.50e+03 8.47e+01 bond pdb=" C29 POV B1313 " pdb="C210 POV B1313 " ideal model delta sigma weight residual 1.333 1.516 -0.183 2.00e-02 2.50e+03 8.42e+01 bond pdb=" C29 POV A1311 " pdb="C210 POV A1311 " ideal model delta sigma weight residual 1.333 1.516 -0.183 2.00e-02 2.50e+03 8.37e+01 bond pdb=" C29 POV D1315 " pdb="C210 POV D1315 " ideal model delta sigma weight residual 1.333 1.516 -0.183 2.00e-02 2.50e+03 8.35e+01 bond pdb=" O12 POV D1303 " pdb=" P POV D1303 " ideal model delta sigma weight residual 1.657 1.591 0.066 2.00e-02 2.50e+03 1.10e+01 ... (remaining 36415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 47220 2.86 - 5.72: 1488 5.72 - 8.58: 187 8.58 - 11.44: 29 11.44 - 14.30: 16 Bond angle restraints: 48940 Sorted by residual: angle pdb=" C29 POV D1315 " pdb="C210 POV D1315 " pdb="C211 POV D1315 " ideal model delta sigma weight residual 127.67 113.37 14.30 3.00e+00 1.11e-01 2.27e+01 angle pdb=" C29 POV B1313 " pdb="C210 POV B1313 " pdb="C211 POV B1313 " ideal model delta sigma weight residual 127.67 113.39 14.28 3.00e+00 1.11e-01 2.27e+01 angle pdb=" C29 POV C1313 " pdb="C210 POV C1313 " pdb="C211 POV C1313 " ideal model delta sigma weight residual 127.67 113.42 14.25 3.00e+00 1.11e-01 2.26e+01 angle pdb=" C29 POV A1311 " pdb="C210 POV A1311 " pdb="C211 POV A1311 " ideal model delta sigma weight residual 127.67 113.53 14.14 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C28 POV C1313 " pdb=" C29 POV C1313 " pdb="C210 POV C1313 " ideal model delta sigma weight residual 127.79 114.08 13.71 3.00e+00 1.11e-01 2.09e+01 ... (remaining 48935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 21782 35.79 - 71.58: 682 71.58 - 107.36: 186 107.36 - 143.15: 62 143.15 - 178.94: 32 Dihedral angle restraints: 22744 sinusoidal: 10852 harmonic: 11892 Sorted by residual: dihedral pdb=" CA TYR C 949 " pdb=" C TYR C 949 " pdb=" N ILE C 950 " pdb=" CA ILE C 950 " ideal model delta harmonic sigma weight residual -180.00 -131.84 -48.16 0 5.00e+00 4.00e-02 9.28e+01 dihedral pdb=" CA TYR B 949 " pdb=" C TYR B 949 " pdb=" N ILE B 950 " pdb=" CA ILE B 950 " ideal model delta harmonic sigma weight residual 180.00 -131.85 -48.15 0 5.00e+00 4.00e-02 9.28e+01 dihedral pdb=" CA TYR D 949 " pdb=" C TYR D 949 " pdb=" N ILE D 950 " pdb=" CA ILE D 950 " ideal model delta harmonic sigma weight residual -180.00 -131.86 -48.14 0 5.00e+00 4.00e-02 9.27e+01 ... (remaining 22741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3828 0.053 - 0.105: 1105 0.105 - 0.158: 248 0.158 - 0.211: 43 0.211 - 0.264: 12 Chirality restraints: 5236 Sorted by residual: chirality pdb=" CG LEU B1128 " pdb=" CB LEU B1128 " pdb=" CD1 LEU B1128 " pdb=" CD2 LEU B1128 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CG LEU C1128 " pdb=" CB LEU C1128 " pdb=" CD1 LEU C1128 " pdb=" CD2 LEU C1128 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CG LEU A1128 " pdb=" CB LEU A1128 " pdb=" CD1 LEU A1128 " pdb=" CD2 LEU A1128 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 5233 not shown) Planarity restraints: 5840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV D1315 " 0.156 2.00e-02 2.50e+03 3.16e-01 9.99e+02 pdb=" C29 POV D1315 " -0.425 2.00e-02 2.50e+03 pdb="C210 POV D1315 " 0.416 2.00e-02 2.50e+03 pdb="C211 POV D1315 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C1313 " 0.155 2.00e-02 2.50e+03 3.14e-01 9.84e+02 pdb=" C29 POV C1313 " -0.420 2.00e-02 2.50e+03 pdb="C210 POV C1313 " 0.413 2.00e-02 2.50e+03 pdb="C211 POV C1313 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B1313 " -0.156 2.00e-02 2.50e+03 3.13e-01 9.80e+02 pdb=" C29 POV B1313 " 0.420 2.00e-02 2.50e+03 pdb="C210 POV B1313 " -0.412 2.00e-02 2.50e+03 pdb="C211 POV B1313 " 0.148 2.00e-02 2.50e+03 ... (remaining 5837 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 325 2.56 - 3.14: 28164 3.14 - 3.73: 52619 3.73 - 4.31: 80482 4.31 - 4.90: 129027 Nonbonded interactions: 290617 Sorted by model distance: nonbonded pdb=" OG1 THR B 895 " pdb=" O PRO B1130 " model vdw 1.970 3.040 nonbonded pdb=" OG1 THR D 895 " pdb=" O PRO D1130 " model vdw 1.971 3.040 nonbonded pdb=" OG1 THR A 895 " pdb=" O PRO A1130 " model vdw 1.972 3.040 nonbonded pdb=" OG1 THR C 895 " pdb=" O PRO C1130 " model vdw 1.972 3.040 nonbonded pdb=" OH TYR D 505 " pdb=" OD2 ASP D 511 " model vdw 2.014 3.040 ... (remaining 290612 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 87 through 1301 or resid 1303 or resid 1305 or resid 1307 \ or resid 1309 through 1311 or (resid 1313 and (name C22 or name C23 or name C24 \ or name C25 or name C26 or name C27 or name C28 or name C29 or name C210 or name \ C211 or name C212 or name C213 or name C214 or name C215 or name C216)) or (res \ id 1315 and (name C22 or name C23 or name C24 or name C25 or name C26 or name C2 \ 7 or name C28 or name C29 or name C210 or name C211 or name C212 or name C213 or \ name C214 or name C215 or name C216)))) selection = (chain 'B' and (resid 87 through 1301 or resid 1303 or resid 1305 or resid 1307 \ or (resid 1309 and (name N or name C1 or name C11 or name C12 or name C13 or nam \ e C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C28 or name C29 or name O11 or name O12 \ or name O13 or name O14 or name O21 or name O22 or name P or name C210 or name \ C211 or name C212 or name C213 or name C214 or name C215 or name C216 or name C2 \ 17 or name C218)) or resid 1310 or (resid 1311 and (name C22 or name C23 or name \ C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C210 or \ name C211 or name C212 or name C213 or name C214 or name C215 or name C216)) or \ resid 1313 or (resid 1315 and (name C22 or name C23 or name C24 or name C25 or \ name C26 or name C27 or name C28 or name C29 or name C210 or name C211 or name C \ 212 or name C213 or name C214 or name C215 or name C216)))) selection = (chain 'C' and (resid 87 through 1301 or resid 1303 or resid 1305 or resid 1307 \ or (resid 1309 and (name N or name C1 or name C11 or name C12 or name C13 or nam \ e C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C28 or name C29 or name O11 or name O12 \ or name O13 or name O14 or name O21 or name O22 or name P or name C210 or name \ C211 or name C212 or name C213 or name C214 or name C215 or name C216 or name C2 \ 17 or name C218)) or resid 1310 or (resid 1311 and (name C22 or name C23 or name \ C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C210 or \ name C211 or name C212 or name C213 or name C214 or name C215 or name C216)) or \ resid 1313 or (resid 1315 and (name C22 or name C23 or name C24 or name C25 or \ name C26 or name C27 or name C28 or name C29 or name C210 or name C211 or name C \ 212 or name C213 or name C214 or name C215 or name C216)))) selection = (chain 'D' and (resid 87 through 1301 or resid 1303 or resid 1305 or resid 1307 \ or (resid 1309 and (name N or name C1 or name C11 or name C12 or name C13 or nam \ e C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C28 or name C29 or name O11 or name O12 \ or name O13 or name O14 or name O21 or name O22 or name P or name C210 or name \ C211 or name C212 or name C213 or name C214 or name C215 or name C216 or name C2 \ 17 or name C218)) or resid 1310 or (resid 1311 and (name C22 or name C23 or name \ C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C210 or \ name C211 or name C212 or name C213 or name C214 or name C215 or name C216)) or \ (resid 1313 and (name C22 or name C23 or name C24 or name C25 or name C26 or na \ me C27 or name C28 or name C29 or name C210 or name C211 or name C212 or name C2 \ 13 or name C214 or name C215 or name C216)) or resid 1315)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 32.850 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.080 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:7.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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 : 0.009 0.184 36424 Z= 0.395 Angle : 1.185 14.303 48948 Z= 0.591 Chirality : 0.053 0.264 5236 Planarity : 0.011 0.316 5840 Dihedral : 20.381 178.938 15068 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.18 % Favored : 92.22 % Rotamer: Outliers : 0.11 % Allowed : 2.57 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.72 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.03 (0.11), residues: 4024 helix: -2.48 (0.08), residues: 2492 sheet: -2.56 (0.31), residues: 204 loop : -2.71 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG B 264 TYR 0.055 0.003 TYR C 870 PHE 0.063 0.003 PHE B 858 TRP 0.025 0.003 TRP A1042 HIS 0.012 0.002 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00897 (36420) covalent geometry : angle 1.18481 (48940) SS BOND : bond 0.00188 ( 4) SS BOND : angle 0.91295 ( 8) hydrogen bonds : bond 0.27618 ( 1764) hydrogen bonds : angle 8.14540 ( 5184) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 777 time to evaluate : 1.399 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 616 LYS cc_start: 0.7479 (ptpp) cc_final: 0.7223 (ptpp) REVERT: A 1189 PHE cc_start: 0.8323 (t80) cc_final: 0.8113 (t80) REVERT: B 369 MET cc_start: 0.6968 (tmt) cc_final: 0.6464 (tpt) REVERT: B 465 MET cc_start: 0.8181 (mmt) cc_final: 0.7811 (mmt) REVERT: B 467 LYS cc_start: 0.8293 (mmmm) cc_final: 0.8053 (mmmt) REVERT: B 649 MET cc_start: 0.9020 (ttp) cc_final: 0.8761 (ttp) REVERT: B 1084 GLN cc_start: 0.8169 (mm110) cc_final: 0.7469 (mm-40) REVERT: B 1085 TYR cc_start: 0.7055 (m-10) cc_final: 0.6797 (m-10) REVERT: B 1120 MET cc_start: 0.8400 (mmm) cc_final: 0.8175 (mmp) REVERT: B 1128 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8572 (mt) REVERT: B 1175 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6812 (pt0) REVERT: B 1189 PHE cc_start: 0.8491 (t80) cc_final: 0.8172 (t80) REVERT: B 1207 MET cc_start: 0.8788 (mtp) cc_final: 0.8558 (mtp) REVERT: C 421 ASP cc_start: 0.7356 (p0) cc_final: 0.7147 (p0) REVERT: C 649 MET cc_start: 0.8976 (ttp) cc_final: 0.8631 (ttp) REVERT: C 1084 GLN cc_start: 0.8071 (mm110) cc_final: 0.7268 (mm-40) REVERT: C 1120 MET cc_start: 0.8395 (mmm) cc_final: 0.8182 (mmm) REVERT: C 1128 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8749 (mt) REVERT: D 421 ASP cc_start: 0.7398 (p0) cc_final: 0.7186 (p0) REVERT: D 465 MET cc_start: 0.8096 (mmt) cc_final: 0.7856 (mmt) REVERT: D 649 MET cc_start: 0.8968 (ttp) cc_final: 0.8637 (ttp) REVERT: D 1084 GLN cc_start: 0.8142 (mm110) cc_final: 0.7398 (mm-40) REVERT: D 1085 TYR cc_start: 0.7049 (m-10) cc_final: 0.6773 (m-10) REVERT: D 1128 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8700 (mt) REVERT: D 1189 PHE cc_start: 0.8633 (t80) cc_final: 0.8405 (t80) outliers start: 4 outliers final: 0 residues processed: 781 average time/residue: 0.7433 time to fit residues: 686.2396 Evaluate side-chains 471 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 468 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 1128 LEU Chi-restraints excluded: chain D residue 1128 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 183 HIS A 242 HIS A 276 HIS A 281 GLN A 329 HIS A 668 GLN A 718 ASN A 787 GLN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 GLN B 177 ASN B 183 HIS B 242 HIS B 276 HIS B 329 HIS B 482 GLN B 498 GLN B 635 GLN B 681 GLN B 787 GLN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 ASN C 177 ASN C 183 HIS C 242 HIS C 276 HIS C 329 HIS C 635 GLN C 668 GLN C 681 GLN C 914 GLN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 ASN D 183 HIS D 242 HIS D 276 HIS D 329 HIS D 482 GLN D 681 GLN D 700 GLN D 914 GLN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.204281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.133230 restraints weight = 37692.789| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.89 r_work: 0.3337 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 36424 Z= 0.189 Angle : 0.768 8.226 48948 Z= 0.388 Chirality : 0.047 0.198 5236 Planarity : 0.006 0.064 5840 Dihedral : 22.644 174.190 7126 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.91 % Favored : 93.69 % Rotamer: Outliers : 1.96 % Allowed : 10.31 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.12), residues: 4024 helix: 0.00 (0.09), residues: 2536 sheet: -1.48 (0.34), residues: 192 loop : -2.00 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1115 TYR 0.046 0.003 TYR C 953 PHE 0.026 0.003 PHE D 935 TRP 0.015 0.002 TRP D1111 HIS 0.011 0.002 HIS C1137 Details of bonding type rmsd covalent geometry : bond 0.00434 (36420) covalent geometry : angle 0.76778 (48940) SS BOND : bond 0.00117 ( 4) SS BOND : angle 1.02523 ( 8) hydrogen bonds : bond 0.06089 ( 1764) hydrogen bonds : angle 4.53579 ( 5184) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 550 time to evaluate : 1.041 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 531 LYS cc_start: 0.7733 (mppt) cc_final: 0.7312 (mptt) REVERT: A 616 LYS cc_start: 0.7702 (ptpp) cc_final: 0.7486 (mtmm) REVERT: A 759 TYR cc_start: 0.7430 (m-10) cc_final: 0.7194 (m-10) REVERT: A 789 GLN cc_start: 0.7405 (tp40) cc_final: 0.7197 (tp-100) REVERT: A 906 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7379 (mtm) REVERT: A 918 VAL cc_start: 0.8915 (t) cc_final: 0.8713 (p) REVERT: A 946 LYS cc_start: 0.8304 (tppt) cc_final: 0.7652 (ttpp) REVERT: A 975 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8478 (ttt-90) REVERT: A 1189 PHE cc_start: 0.8125 (t80) cc_final: 0.7702 (t80) REVERT: A 1213 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7633 (tp30) REVERT: B 369 MET cc_start: 0.7282 (tmt) cc_final: 0.6714 (tpt) REVERT: B 418 ASP cc_start: 0.8092 (t0) cc_final: 0.7833 (t0) REVERT: B 467 LYS cc_start: 0.8533 (mmmm) cc_final: 0.7993 (mmmt) REVERT: B 488 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7914 (ptm) REVERT: B 520 MET cc_start: 0.9071 (mmm) cc_final: 0.8861 (mmm) REVERT: B 763 LEU cc_start: 0.8643 (tt) cc_final: 0.8390 (tm) REVERT: B 906 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7105 (mtm) REVERT: B 917 LYS cc_start: 0.7372 (mmmt) cc_final: 0.6923 (tptt) REVERT: B 946 LYS cc_start: 0.8358 (tppt) cc_final: 0.7750 (ttpp) REVERT: B 1043 MET cc_start: 0.9197 (mtt) cc_final: 0.8917 (mtt) REVERT: B 1168 LYS cc_start: 0.7632 (mmtm) cc_final: 0.7423 (mmtm) REVERT: B 1175 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7370 (pt0) REVERT: B 1189 PHE cc_start: 0.8591 (t80) cc_final: 0.8183 (t80) REVERT: C 418 ASP cc_start: 0.8122 (t0) cc_final: 0.7875 (t0) REVERT: C 421 ASP cc_start: 0.8285 (p0) cc_final: 0.8064 (p0) REVERT: C 488 MET cc_start: 0.8229 (ptm) cc_final: 0.7969 (ptm) REVERT: C 520 MET cc_start: 0.9045 (mmm) cc_final: 0.8827 (mmm) REVERT: C 763 LEU cc_start: 0.8649 (tt) cc_final: 0.8391 (tm) REVERT: C 906 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7071 (mtm) REVERT: C 917 LYS cc_start: 0.7455 (mmmt) cc_final: 0.6983 (tptp) REVERT: C 946 LYS cc_start: 0.8388 (tppt) cc_final: 0.8150 (tppp) REVERT: C 1185 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8166 (ttmm) REVERT: C 1189 PHE cc_start: 0.8546 (t80) cc_final: 0.8151 (t80) REVERT: C 1212 LYS cc_start: 0.8700 (mmtm) cc_final: 0.8418 (mmmt) REVERT: D 418 ASP cc_start: 0.8125 (t0) cc_final: 0.7856 (t0) REVERT: D 421 ASP cc_start: 0.8291 (p0) cc_final: 0.8074 (p0) REVERT: D 488 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7919 (ptm) REVERT: D 506 LYS cc_start: 0.8087 (mmpt) cc_final: 0.7766 (mmtt) REVERT: D 763 LEU cc_start: 0.8670 (tt) cc_final: 0.8409 (tm) REVERT: D 906 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7114 (mtm) REVERT: D 917 LYS cc_start: 0.7404 (mmmt) cc_final: 0.6916 (tptt) REVERT: D 946 LYS cc_start: 0.8346 (tppt) cc_final: 0.7695 (ttpp) REVERT: D 1189 PHE cc_start: 0.8610 (t80) cc_final: 0.8218 (t80) REVERT: D 1212 LYS cc_start: 0.8664 (mmtm) cc_final: 0.8435 (mmtt) outliers start: 70 outliers final: 15 residues processed: 595 average time/residue: 0.7050 time to fit residues: 497.4231 Evaluate side-chains 485 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 462 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 975 ARG Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 646 GLU Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 646 GLU Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1185 LYS Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 646 GLU Chi-restraints excluded: chain D residue 790 ASP Chi-restraints excluded: chain D residue 906 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 33 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 346 optimal weight: 3.9990 chunk 176 optimal weight: 8.9990 chunk 190 optimal weight: 0.9990 chunk 199 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 318 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 183 HIS A 281 GLN A 681 GLN A 914 GLN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 ASN A1210 GLN B 102 HIS B 183 HIS B 668 GLN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 ASN B1137 HIS B1210 GLN C 102 HIS ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 968 ASN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1098 ASN C1210 GLN D 102 HIS D 183 HIS D 668 GLN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1098 ASN ** D1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.200724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.127962 restraints weight = 37448.510| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.83 r_work: 0.3259 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 36424 Z= 0.220 Angle : 0.733 11.046 48948 Z= 0.377 Chirality : 0.048 0.239 5236 Planarity : 0.006 0.054 5840 Dihedral : 22.136 160.658 7120 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.82 % Favored : 93.76 % Rotamer: Outliers : 2.93 % Allowed : 11.76 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.13), residues: 4024 helix: 0.70 (0.10), residues: 2536 sheet: -1.02 (0.35), residues: 204 loop : -1.82 (0.18), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 617 TYR 0.050 0.003 TYR C 953 PHE 0.026 0.003 PHE D 935 TRP 0.013 0.002 TRP A 857 HIS 0.009 0.002 HIS C1137 Details of bonding type rmsd covalent geometry : bond 0.00530 (36420) covalent geometry : angle 0.73324 (48940) SS BOND : bond 0.00129 ( 4) SS BOND : angle 1.38082 ( 8) hydrogen bonds : bond 0.06693 ( 1764) hydrogen bonds : angle 4.33363 ( 5184) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 468 time to evaluate : 1.378 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: A 302 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7318 (pt0) REVERT: A 368 MET cc_start: 0.5665 (mtt) cc_final: 0.5189 (tmm) REVERT: A 372 MET cc_start: 0.7684 (tpp) cc_final: 0.7355 (tpp) REVERT: A 488 MET cc_start: 0.8125 (ptm) cc_final: 0.7923 (ptm) REVERT: A 906 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7216 (mtm) REVERT: A 1189 PHE cc_start: 0.8516 (t80) cc_final: 0.8176 (t80) REVERT: A 1213 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7702 (tp30) REVERT: B 369 MET cc_start: 0.7060 (tmt) cc_final: 0.6596 (tpt) REVERT: B 467 LYS cc_start: 0.8592 (mmmm) cc_final: 0.8334 (ttmm) REVERT: B 469 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8534 (tm) REVERT: B 506 LYS cc_start: 0.8238 (mmpt) cc_final: 0.7926 (mmtt) REVERT: B 906 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7061 (mtm) REVERT: B 917 LYS cc_start: 0.7537 (mmmt) cc_final: 0.7036 (tptp) REVERT: B 946 LYS cc_start: 0.8455 (tppt) cc_final: 0.7822 (ttpp) REVERT: B 1174 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: B 1175 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7642 (pt0) REVERT: B 1184 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: B 1189 PHE cc_start: 0.8602 (t80) cc_final: 0.8196 (t80) REVERT: C 421 ASP cc_start: 0.8330 (p0) cc_final: 0.8128 (p0) REVERT: C 488 MET cc_start: 0.8273 (ptm) cc_final: 0.8001 (ptm) REVERT: C 906 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7119 (mtm) REVERT: C 917 LYS cc_start: 0.7499 (mmmt) cc_final: 0.7017 (tptp) REVERT: C 1185 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8271 (tttm) REVERT: C 1189 PHE cc_start: 0.8606 (t80) cc_final: 0.8195 (t80) REVERT: D 418 ASP cc_start: 0.8348 (t0) cc_final: 0.8114 (t0) REVERT: D 421 ASP cc_start: 0.8319 (p0) cc_final: 0.8117 (p0) REVERT: D 469 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8547 (tm) REVERT: D 488 MET cc_start: 0.8131 (ptm) cc_final: 0.7898 (ptm) REVERT: D 506 LYS cc_start: 0.8208 (mmpt) cc_final: 0.7922 (mmtt) REVERT: D 906 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.7070 (mtm) REVERT: D 917 LYS cc_start: 0.7557 (mmmt) cc_final: 0.7068 (tptp) REVERT: D 946 LYS cc_start: 0.8446 (tppt) cc_final: 0.7801 (ttpp) REVERT: D 1189 PHE cc_start: 0.8624 (t80) cc_final: 0.8226 (t80) outliers start: 105 outliers final: 45 residues processed: 548 average time/residue: 0.7431 time to fit residues: 486.0868 Evaluate side-chains 505 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 451 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 643 GLN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 646 GLU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 754 ARG Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1174 GLU Chi-restraints excluded: chain B residue 1184 GLU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 646 GLU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 754 ARG Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1185 LYS Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 646 GLU Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 754 ARG Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 1037 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 392 optimal weight: 0.7980 chunk 262 optimal weight: 0.9980 chunk 206 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 227 optimal weight: 30.0000 chunk 324 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 371 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 HIS ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1137 HIS D 787 GLN D 914 GLN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1137 HIS D1210 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.202830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.131801 restraints weight = 37574.644| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.89 r_work: 0.3321 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36424 Z= 0.137 Angle : 0.615 9.511 48948 Z= 0.315 Chirality : 0.042 0.181 5236 Planarity : 0.005 0.046 5840 Dihedral : 21.022 160.126 7120 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.82 % Favored : 94.01 % Rotamer: Outliers : 2.32 % Allowed : 12.71 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.13), residues: 4024 helix: 1.29 (0.10), residues: 2548 sheet: -0.52 (0.38), residues: 192 loop : -1.76 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1217 TYR 0.027 0.002 TYR C 953 PHE 0.020 0.002 PHE C 935 TRP 0.011 0.002 TRP C 747 HIS 0.006 0.001 HIS A1137 Details of bonding type rmsd covalent geometry : bond 0.00310 (36420) covalent geometry : angle 0.61547 (48940) SS BOND : bond 0.00048 ( 4) SS BOND : angle 0.57468 ( 8) hydrogen bonds : bond 0.05086 ( 1764) hydrogen bonds : angle 4.01245 ( 5184) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 484 time to evaluate : 1.411 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: A 368 MET cc_start: 0.5731 (mtt) cc_final: 0.5070 (tmm) REVERT: A 488 MET cc_start: 0.7999 (ptm) cc_final: 0.7776 (ptm) REVERT: A 616 LYS cc_start: 0.8006 (mtmm) cc_final: 0.7150 (mmtt) REVERT: A 906 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.7074 (mtm) REVERT: A 946 LYS cc_start: 0.8352 (tppp) cc_final: 0.7779 (ttpp) REVERT: A 975 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8323 (ttt-90) REVERT: A 1189 PHE cc_start: 0.8322 (t80) cc_final: 0.7995 (t80) REVERT: B 369 MET cc_start: 0.6928 (tmt) cc_final: 0.6457 (tpt) REVERT: B 467 LYS cc_start: 0.8506 (mmmm) cc_final: 0.8244 (ttmm) REVERT: B 506 LYS cc_start: 0.8169 (mmpt) cc_final: 0.7905 (mmtt) REVERT: B 763 LEU cc_start: 0.8506 (tt) cc_final: 0.8278 (tm) REVERT: B 906 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6844 (mtm) REVERT: B 917 LYS cc_start: 0.7435 (mmmt) cc_final: 0.6926 (tptp) REVERT: B 946 LYS cc_start: 0.8410 (tppt) cc_final: 0.7842 (ttpp) REVERT: B 1043 MET cc_start: 0.9138 (mtt) cc_final: 0.8834 (mtt) REVERT: B 1175 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7431 (pt0) REVERT: B 1189 PHE cc_start: 0.8560 (t80) cc_final: 0.8152 (t80) REVERT: C 420 VAL cc_start: 0.8587 (t) cc_final: 0.8260 (p) REVERT: C 488 MET cc_start: 0.8140 (ptm) cc_final: 0.7870 (ptm) REVERT: C 494 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7982 (mtp180) REVERT: C 763 LEU cc_start: 0.8519 (tt) cc_final: 0.8296 (tm) REVERT: C 906 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6907 (mtm) REVERT: C 917 LYS cc_start: 0.7354 (mmmt) cc_final: 0.6921 (tptp) REVERT: C 946 LYS cc_start: 0.8362 (tppp) cc_final: 0.7812 (ttpp) REVERT: C 1184 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7976 (mt-10) REVERT: C 1185 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8207 (tttm) REVERT: C 1189 PHE cc_start: 0.8522 (t80) cc_final: 0.8107 (t80) REVERT: D 506 LYS cc_start: 0.8189 (mmpt) cc_final: 0.7952 (mmmt) REVERT: D 763 LEU cc_start: 0.8565 (tt) cc_final: 0.8319 (tm) REVERT: D 906 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6905 (mtm) REVERT: D 917 LYS cc_start: 0.7453 (mmmt) cc_final: 0.6962 (tptp) REVERT: D 946 LYS cc_start: 0.8395 (tppt) cc_final: 0.7820 (ttpp) REVERT: D 1189 PHE cc_start: 0.8573 (t80) cc_final: 0.8162 (t80) REVERT: D 1206 GLN cc_start: 0.8189 (mt0) cc_final: 0.7906 (mm110) outliers start: 83 outliers final: 38 residues processed: 544 average time/residue: 0.7916 time to fit residues: 513.6651 Evaluate side-chains 504 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 458 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 975 ARG Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 754 ARG Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1226 GLN Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 494 ARG Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 841 ILE Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1053 ILE Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1185 LYS Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 754 ARG Chi-restraints excluded: chain D residue 767 VAL Chi-restraints excluded: chain D residue 841 ILE Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1053 ILE Chi-restraints excluded: chain D residue 1194 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 78 optimal weight: 0.1980 chunk 234 optimal weight: 0.9980 chunk 224 optimal weight: 0.5980 chunk 26 optimal weight: 9.9990 chunk 347 optimal weight: 7.9990 chunk 226 optimal weight: 4.9990 chunk 365 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 400 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 294 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 GLN B 331 GLN B 461 ASN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN C 461 ASN C 914 GLN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 461 ASN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.204437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.134513 restraints weight = 37369.223| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.87 r_work: 0.3344 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36424 Z= 0.120 Angle : 0.589 10.368 48948 Z= 0.300 Chirality : 0.041 0.161 5236 Planarity : 0.004 0.045 5840 Dihedral : 20.048 156.492 7120 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.69 % Favored : 94.21 % Rotamer: Outliers : 2.09 % Allowed : 13.94 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.14), residues: 4024 helix: 1.67 (0.10), residues: 2552 sheet: -0.41 (0.39), residues: 192 loop : -1.76 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 843 TYR 0.022 0.001 TYR C 953 PHE 0.017 0.001 PHE C 935 TRP 0.010 0.001 TRP D 747 HIS 0.005 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00259 (36420) covalent geometry : angle 0.58927 (48940) SS BOND : bond 0.00032 ( 4) SS BOND : angle 0.45119 ( 8) hydrogen bonds : bond 0.04577 ( 1764) hydrogen bonds : angle 3.85513 ( 5184) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 469 time to evaluate : 1.421 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: A 368 MET cc_start: 0.5753 (mtt) cc_final: 0.5224 (tmm) REVERT: A 488 MET cc_start: 0.8084 (ptm) cc_final: 0.7873 (ptm) REVERT: A 903 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7587 (mt-10) REVERT: A 906 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6959 (mtm) REVERT: A 946 LYS cc_start: 0.8258 (tppp) cc_final: 0.7771 (ttpp) REVERT: A 975 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8261 (ttt-90) REVERT: A 1189 PHE cc_start: 0.8229 (t80) cc_final: 0.7943 (t80) REVERT: A 1206 GLN cc_start: 0.8112 (mt0) cc_final: 0.7817 (mm110) REVERT: B 278 ARG cc_start: 0.8077 (ttm-80) cc_final: 0.7861 (ttt90) REVERT: B 331 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.6658 (pm20) REVERT: B 369 MET cc_start: 0.6927 (tmt) cc_final: 0.6625 (tpt) REVERT: B 421 ASP cc_start: 0.8406 (p0) cc_final: 0.7920 (p0) REVERT: B 467 LYS cc_start: 0.8551 (mmmm) cc_final: 0.8277 (ttmm) REVERT: B 506 LYS cc_start: 0.8202 (mmpt) cc_final: 0.7930 (mmtt) REVERT: B 763 LEU cc_start: 0.8510 (tt) cc_final: 0.8196 (tm) REVERT: B 906 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6782 (mtm) REVERT: B 917 LYS cc_start: 0.7427 (mmmt) cc_final: 0.6961 (tptp) REVERT: B 946 LYS cc_start: 0.8371 (tppt) cc_final: 0.7817 (ttpp) REVERT: B 1043 MET cc_start: 0.9127 (mtt) cc_final: 0.8863 (mtt) REVERT: B 1175 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7414 (pt0) REVERT: B 1184 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: B 1189 PHE cc_start: 0.8468 (t80) cc_final: 0.8181 (t80) REVERT: B 1206 GLN cc_start: 0.8240 (mt0) cc_final: 0.7875 (mm110) REVERT: C 264 ARG cc_start: 0.6945 (tpt90) cc_final: 0.6662 (mmm-85) REVERT: C 331 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.6993 (pp30) REVERT: C 421 ASP cc_start: 0.8470 (p0) cc_final: 0.7973 (p0) REVERT: C 763 LEU cc_start: 0.8531 (tt) cc_final: 0.8210 (tm) REVERT: C 906 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6909 (mtm) REVERT: C 917 LYS cc_start: 0.7402 (mmmt) cc_final: 0.6913 (tptp) REVERT: C 946 LYS cc_start: 0.8261 (tppp) cc_final: 0.7763 (ttpp) REVERT: C 1189 PHE cc_start: 0.8542 (t80) cc_final: 0.8144 (t80) REVERT: C 1206 GLN cc_start: 0.8167 (mt0) cc_final: 0.7774 (mm110) REVERT: D 278 ARG cc_start: 0.8056 (ttm-80) cc_final: 0.7840 (ttt90) REVERT: D 420 VAL cc_start: 0.8595 (t) cc_final: 0.8272 (p) REVERT: D 506 LYS cc_start: 0.8222 (mmpt) cc_final: 0.8008 (mmmt) REVERT: D 763 LEU cc_start: 0.8522 (tt) cc_final: 0.8210 (tm) REVERT: D 906 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6919 (mtm) REVERT: D 917 LYS cc_start: 0.7449 (mmmt) cc_final: 0.6985 (tptp) REVERT: D 946 LYS cc_start: 0.8375 (tppt) cc_final: 0.7822 (ttpp) REVERT: D 992 MET cc_start: 0.9283 (mtp) cc_final: 0.9033 (ttt) REVERT: D 1184 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7804 (mp0) REVERT: D 1189 PHE cc_start: 0.8475 (t80) cc_final: 0.8173 (t80) REVERT: D 1206 GLN cc_start: 0.8240 (mt0) cc_final: 0.7827 (mm110) outliers start: 75 outliers final: 38 residues processed: 528 average time/residue: 0.7560 time to fit residues: 479.1379 Evaluate side-chains 491 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 445 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 975 ARG Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1053 ILE Chi-restraints excluded: chain B residue 1184 GLU Chi-restraints excluded: chain B residue 1226 GLN Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 841 ILE Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 841 ILE Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1194 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 259 optimal weight: 4.9990 chunk 274 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 368 optimal weight: 4.9990 chunk 234 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 213 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 339 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 696 GLN C 914 GLN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.200736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.129306 restraints weight = 37188.405| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.85 r_work: 0.3277 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 36424 Z= 0.199 Angle : 0.690 10.667 48948 Z= 0.350 Chirality : 0.046 0.214 5236 Planarity : 0.005 0.052 5840 Dihedral : 20.657 155.480 7120 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.96 % Favored : 93.89 % Rotamer: Outliers : 2.82 % Allowed : 13.21 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.13), residues: 4024 helix: 1.47 (0.10), residues: 2568 sheet: -0.45 (0.38), residues: 192 loop : -1.67 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 105 TYR 0.031 0.002 TYR C 953 PHE 0.024 0.002 PHE D 935 TRP 0.014 0.002 TRP D 947 HIS 0.006 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00477 (36420) covalent geometry : angle 0.68966 (48940) SS BOND : bond 0.00151 ( 4) SS BOND : angle 1.13654 ( 8) hydrogen bonds : bond 0.06086 ( 1764) hydrogen bonds : angle 4.06664 ( 5184) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 463 time to evaluate : 1.676 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: A 302 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7323 (pt0) REVERT: A 510 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8314 (mm) REVERT: A 906 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.7109 (mtm) REVERT: A 946 LYS cc_start: 0.8326 (tppp) cc_final: 0.7783 (ttpp) REVERT: A 1189 PHE cc_start: 0.8505 (t80) cc_final: 0.8124 (t80) REVERT: A 1206 GLN cc_start: 0.8159 (mt0) cc_final: 0.7867 (mm110) REVERT: B 278 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7887 (ttt90) REVERT: B 331 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6766 (pm20) REVERT: B 369 MET cc_start: 0.6918 (tmt) cc_final: 0.6601 (tpt) REVERT: B 421 ASP cc_start: 0.8421 (p0) cc_final: 0.7914 (p0) REVERT: B 467 LYS cc_start: 0.8556 (mmmm) cc_final: 0.8270 (ttmm) REVERT: B 506 LYS cc_start: 0.8061 (mmpt) cc_final: 0.7846 (mmtt) REVERT: B 906 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7060 (mtm) REVERT: B 917 LYS cc_start: 0.7480 (mmmt) cc_final: 0.6976 (tptp) REVERT: B 946 LYS cc_start: 0.8415 (tppt) cc_final: 0.7792 (ttpp) REVERT: B 1175 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7538 (pt0) REVERT: B 1189 PHE cc_start: 0.8539 (t80) cc_final: 0.8126 (t80) REVERT: B 1206 GLN cc_start: 0.8223 (mt0) cc_final: 0.7890 (mm110) REVERT: C 494 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7975 (mtp180) REVERT: C 906 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.7130 (mtm) REVERT: C 917 LYS cc_start: 0.7437 (mmmt) cc_final: 0.6935 (tptp) REVERT: C 946 LYS cc_start: 0.8335 (tppp) cc_final: 0.7779 (ttpp) REVERT: C 1185 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8212 (tttm) REVERT: C 1189 PHE cc_start: 0.8577 (t80) cc_final: 0.8167 (t80) REVERT: C 1206 GLN cc_start: 0.8219 (mt0) cc_final: 0.7893 (mm110) REVERT: D 278 ARG cc_start: 0.8166 (ttm-80) cc_final: 0.7887 (ttt90) REVERT: D 420 VAL cc_start: 0.8583 (t) cc_final: 0.8307 (p) REVERT: D 421 ASP cc_start: 0.8420 (p0) cc_final: 0.7944 (p0) REVERT: D 506 LYS cc_start: 0.8106 (mmpt) cc_final: 0.7897 (mmmt) REVERT: D 906 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7163 (mtm) REVERT: D 917 LYS cc_start: 0.7482 (mmmt) cc_final: 0.6981 (tptp) REVERT: D 946 LYS cc_start: 0.8408 (tppt) cc_final: 0.7784 (ttpp) REVERT: D 1189 PHE cc_start: 0.8544 (t80) cc_final: 0.8127 (t80) REVERT: D 1206 GLN cc_start: 0.8140 (mt0) cc_final: 0.7866 (mm110) outliers start: 101 outliers final: 47 residues processed: 539 average time/residue: 0.7309 time to fit residues: 475.8474 Evaluate side-chains 506 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 451 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1053 ILE Chi-restraints excluded: chain B residue 1226 GLN Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 494 ARG Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 754 ARG Chi-restraints excluded: chain C residue 841 ILE Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1053 ILE Chi-restraints excluded: chain C residue 1185 LYS Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 646 GLU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 841 ILE Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 1037 VAL Chi-restraints excluded: chain D residue 1053 ILE Chi-restraints excluded: chain D residue 1194 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 312 optimal weight: 9.9990 chunk 330 optimal weight: 10.0000 chunk 324 optimal weight: 0.6980 chunk 156 optimal weight: 0.9990 chunk 352 optimal weight: 0.9980 chunk 265 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 chunk 220 optimal weight: 9.9990 chunk 253 optimal weight: 6.9990 chunk 349 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 461 ASN C 696 GLN C 914 GLN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1210 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 = 0.4308 r_free = 0.4308 target = 0.204002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.134835 restraints weight = 37355.036| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.94 r_work: 0.3323 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36424 Z= 0.120 Angle : 0.586 9.810 48948 Z= 0.299 Chirality : 0.041 0.164 5236 Planarity : 0.004 0.045 5840 Dihedral : 19.554 156.654 7120 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.72 % Favored : 94.18 % Rotamer: Outliers : 2.04 % Allowed : 14.75 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.14), residues: 4024 helix: 1.82 (0.10), residues: 2552 sheet: -0.41 (0.38), residues: 192 loop : -1.70 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 105 TYR 0.017 0.001 TYR C 953 PHE 0.016 0.001 PHE C 935 TRP 0.011 0.001 TRP A 417 HIS 0.006 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00258 (36420) covalent geometry : angle 0.58634 (48940) SS BOND : bond 0.00021 ( 4) SS BOND : angle 0.36725 ( 8) hydrogen bonds : bond 0.04546 ( 1764) hydrogen bonds : angle 3.84167 ( 5184) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 465 time to evaluate : 1.451 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: A 302 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7360 (pt0) REVERT: A 616 LYS cc_start: 0.8061 (mtmm) cc_final: 0.7319 (mttm) REVERT: A 903 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7660 (mt-10) REVERT: A 906 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.7008 (mtm) REVERT: A 946 LYS cc_start: 0.8290 (tppp) cc_final: 0.7777 (ttpp) REVERT: A 975 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8339 (ttt-90) REVERT: A 1168 LYS cc_start: 0.7885 (pptt) cc_final: 0.7626 (pptt) REVERT: A 1189 PHE cc_start: 0.8349 (t80) cc_final: 0.8036 (t80) REVERT: A 1206 GLN cc_start: 0.8264 (mt0) cc_final: 0.7885 (mm110) REVERT: B 143 MET cc_start: 0.6135 (OUTLIER) cc_final: 0.5718 (mmm) REVERT: B 278 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7788 (ttt90) REVERT: B 369 MET cc_start: 0.6864 (tmt) cc_final: 0.6577 (tpt) REVERT: B 421 ASP cc_start: 0.8427 (p0) cc_final: 0.7936 (p0) REVERT: B 467 LYS cc_start: 0.8547 (mmmm) cc_final: 0.7967 (mmmt) REVERT: B 906 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6888 (mtm) REVERT: B 917 LYS cc_start: 0.7476 (mmmt) cc_final: 0.6989 (tptp) REVERT: B 946 LYS cc_start: 0.8387 (tppt) cc_final: 0.7858 (ttpt) REVERT: B 1175 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7525 (pt0) REVERT: B 1189 PHE cc_start: 0.8428 (t80) cc_final: 0.8034 (t80) REVERT: B 1206 GLN cc_start: 0.8263 (mt0) cc_final: 0.7887 (mm110) REVERT: C 264 ARG cc_start: 0.7094 (tpt90) cc_final: 0.6771 (mmm-85) REVERT: C 331 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6774 (pp30) REVERT: C 421 ASP cc_start: 0.8456 (p0) cc_final: 0.7988 (p0) REVERT: C 906 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.7048 (mtm) REVERT: C 917 LYS cc_start: 0.7460 (mmmt) cc_final: 0.6965 (tptp) REVERT: C 946 LYS cc_start: 0.8318 (tppp) cc_final: 0.7788 (ttpp) REVERT: C 1185 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8249 (tttm) REVERT: C 1189 PHE cc_start: 0.8467 (t80) cc_final: 0.8078 (t80) REVERT: C 1206 GLN cc_start: 0.8197 (mt0) cc_final: 0.7909 (mm110) REVERT: D 278 ARG cc_start: 0.8087 (ttm-80) cc_final: 0.7820 (ttt90) REVERT: D 420 VAL cc_start: 0.8555 (t) cc_final: 0.8316 (p) REVERT: D 421 ASP cc_start: 0.8413 (p0) cc_final: 0.7978 (p0) REVERT: D 906 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.7085 (mtm) REVERT: D 917 LYS cc_start: 0.7488 (mmmt) cc_final: 0.7017 (tptp) REVERT: D 946 LYS cc_start: 0.8350 (tppt) cc_final: 0.7752 (ttpp) REVERT: D 1189 PHE cc_start: 0.8427 (t80) cc_final: 0.8059 (t80) REVERT: D 1206 GLN cc_start: 0.8235 (mt0) cc_final: 0.7804 (mm110) outliers start: 73 outliers final: 38 residues processed: 522 average time/residue: 0.7319 time to fit residues: 460.2925 Evaluate side-chains 496 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 450 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 975 ARG Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1053 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 841 ILE Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1053 ILE Chi-restraints excluded: chain C residue 1185 LYS Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1053 ILE Chi-restraints excluded: chain D residue 1194 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 28 optimal weight: 20.0000 chunk 136 optimal weight: 9.9990 chunk 353 optimal weight: 4.9990 chunk 376 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 395 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 GLN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1210 GLN B 281 GLN B 696 GLN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 696 GLN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.200424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.133025 restraints weight = 37156.038| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.93 r_work: 0.3247 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 36424 Z= 0.213 Angle : 0.702 10.119 48948 Z= 0.355 Chirality : 0.047 0.230 5236 Planarity : 0.005 0.053 5840 Dihedral : 20.236 153.886 7120 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.29 % Favored : 93.56 % Rotamer: Outliers : 2.26 % Allowed : 14.64 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.13), residues: 4024 helix: 1.52 (0.10), residues: 2568 sheet: -0.40 (0.37), residues: 192 loop : -1.62 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 105 TYR 0.029 0.002 TYR C 953 PHE 0.024 0.002 PHE C 935 TRP 0.016 0.002 TRP D 947 HIS 0.005 0.001 HIS B 850 Details of bonding type rmsd covalent geometry : bond 0.00516 (36420) covalent geometry : angle 0.70169 (48940) SS BOND : bond 0.00119 ( 4) SS BOND : angle 1.20864 ( 8) hydrogen bonds : bond 0.06232 ( 1764) hydrogen bonds : angle 4.09405 ( 5184) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 451 time to evaluate : 1.394 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: A 510 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8392 (mm) REVERT: A 616 LYS cc_start: 0.8086 (mtmm) cc_final: 0.7375 (mttm) REVERT: A 906 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7208 (mtm) REVERT: A 946 LYS cc_start: 0.8468 (tppp) cc_final: 0.7934 (ttpp) REVERT: A 1189 PHE cc_start: 0.8579 (t80) cc_final: 0.8197 (t80) REVERT: A 1206 GLN cc_start: 0.8238 (mt0) cc_final: 0.7932 (mm110) REVERT: B 143 MET cc_start: 0.5940 (OUTLIER) cc_final: 0.5565 (mmt) REVERT: B 278 ARG cc_start: 0.8233 (ttm-80) cc_final: 0.7933 (ttt90) REVERT: B 320 ARG cc_start: 0.6294 (mtt180) cc_final: 0.6010 (mtt180) REVERT: B 369 MET cc_start: 0.6888 (tmt) cc_final: 0.6598 (tpt) REVERT: B 421 ASP cc_start: 0.8446 (p0) cc_final: 0.7943 (p0) REVERT: B 467 LYS cc_start: 0.8576 (mmmm) cc_final: 0.8019 (mmmt) REVERT: B 906 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7216 (mtm) REVERT: B 917 LYS cc_start: 0.7587 (mmmt) cc_final: 0.7099 (tptp) REVERT: B 946 LYS cc_start: 0.8478 (tppt) cc_final: 0.7859 (ttpp) REVERT: B 1175 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7718 (pt0) REVERT: B 1189 PHE cc_start: 0.8585 (t80) cc_final: 0.8159 (t80) REVERT: B 1206 GLN cc_start: 0.8274 (mt0) cc_final: 0.8030 (mm110) REVERT: C 264 ARG cc_start: 0.7382 (tpt90) cc_final: 0.7159 (mmm-85) REVERT: C 331 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.6975 (pp30) REVERT: C 421 ASP cc_start: 0.8464 (p0) cc_final: 0.8025 (p0) REVERT: C 467 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8217 (mmmt) REVERT: C 906 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7270 (mtm) REVERT: C 917 LYS cc_start: 0.7521 (mmmt) cc_final: 0.7071 (tptp) REVERT: C 946 LYS cc_start: 0.8414 (tppp) cc_final: 0.7876 (tttm) REVERT: C 1185 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8302 (tttm) REVERT: C 1189 PHE cc_start: 0.8641 (t80) cc_final: 0.8228 (t80) REVERT: D 278 ARG cc_start: 0.8208 (ttm-80) cc_final: 0.7914 (ttt90) REVERT: D 420 VAL cc_start: 0.8569 (t) cc_final: 0.8350 (p) REVERT: D 421 ASP cc_start: 0.8409 (p0) cc_final: 0.7939 (p0) REVERT: D 496 VAL cc_start: 0.8216 (OUTLIER) cc_final: 0.7937 (t) REVERT: D 906 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.7266 (mtm) REVERT: D 917 LYS cc_start: 0.7590 (mmmt) cc_final: 0.7107 (tptp) REVERT: D 946 LYS cc_start: 0.8442 (tppt) cc_final: 0.7827 (ttpp) REVERT: D 1189 PHE cc_start: 0.8615 (t80) cc_final: 0.8197 (t80) REVERT: D 1206 GLN cc_start: 0.8191 (mt0) cc_final: 0.7956 (mm110) outliers start: 81 outliers final: 51 residues processed: 507 average time/residue: 0.7062 time to fit residues: 432.1501 Evaluate side-chains 504 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 443 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 992 MET Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1053 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 467 LYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 754 ARG Chi-restraints excluded: chain C residue 796 MET Chi-restraints excluded: chain C residue 841 ILE Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1053 ILE Chi-restraints excluded: chain C residue 1185 LYS Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 646 GLU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 796 MET Chi-restraints excluded: chain D residue 841 ILE Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 1037 VAL Chi-restraints excluded: chain D residue 1053 ILE Chi-restraints excluded: chain D residue 1194 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 51 optimal weight: 5.9990 chunk 195 optimal weight: 7.9990 chunk 175 optimal weight: 8.9990 chunk 259 optimal weight: 1.9990 chunk 117 optimal weight: 0.0570 chunk 325 optimal weight: 8.9990 chunk 361 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 345 optimal weight: 4.9990 chunk 265 optimal weight: 1.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 GLN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.202731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.132798 restraints weight = 37334.548| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.87 r_work: 0.3292 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36424 Z= 0.138 Angle : 0.619 11.975 48948 Z= 0.314 Chirality : 0.042 0.170 5236 Planarity : 0.005 0.053 5840 Dihedral : 19.398 154.432 7120 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.69 % Favored : 94.21 % Rotamer: Outliers : 2.01 % Allowed : 15.20 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.13), residues: 4024 helix: 1.71 (0.10), residues: 2580 sheet: -0.22 (0.38), residues: 188 loop : -1.68 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 105 TYR 0.021 0.002 TYR C 953 PHE 0.018 0.002 PHE C 935 TRP 0.012 0.002 TRP A 417 HIS 0.005 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00314 (36420) covalent geometry : angle 0.61918 (48940) SS BOND : bond 0.00047 ( 4) SS BOND : angle 0.61440 ( 8) hydrogen bonds : bond 0.04977 ( 1764) hydrogen bonds : angle 3.91762 ( 5184) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 458 time to evaluate : 1.520 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: A 421 ASP cc_start: 0.8399 (p0) cc_final: 0.7989 (p0) REVERT: A 616 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7417 (mttm) REVERT: A 906 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.7174 (mtm) REVERT: A 946 LYS cc_start: 0.8433 (tppp) cc_final: 0.7910 (ttpp) REVERT: A 1168 LYS cc_start: 0.7884 (pptt) cc_final: 0.7662 (pptt) REVERT: A 1189 PHE cc_start: 0.8450 (t80) cc_final: 0.8038 (t80) REVERT: A 1206 GLN cc_start: 0.8343 (mt0) cc_final: 0.8006 (mm110) REVERT: B 143 MET cc_start: 0.5992 (OUTLIER) cc_final: 0.5561 (mmt) REVERT: B 278 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7797 (ttt90) REVERT: B 369 MET cc_start: 0.7033 (tmt) cc_final: 0.6683 (tpt) REVERT: B 421 ASP cc_start: 0.8459 (p0) cc_final: 0.7966 (p0) REVERT: B 467 LYS cc_start: 0.8552 (mmmm) cc_final: 0.7989 (mmmt) REVERT: B 906 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7095 (mtm) REVERT: B 917 LYS cc_start: 0.7560 (mmmt) cc_final: 0.7109 (tptp) REVERT: B 946 LYS cc_start: 0.8414 (tppt) cc_final: 0.7897 (ttpm) REVERT: B 1175 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7649 (pt0) REVERT: B 1189 PHE cc_start: 0.8509 (t80) cc_final: 0.8120 (t80) REVERT: B 1206 GLN cc_start: 0.8184 (mt0) cc_final: 0.7977 (mm110) REVERT: C 331 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.6943 (pp30) REVERT: C 421 ASP cc_start: 0.8469 (p0) cc_final: 0.8009 (p0) REVERT: C 906 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7252 (mtm) REVERT: C 917 LYS cc_start: 0.7484 (mmmt) cc_final: 0.7058 (tptp) REVERT: C 946 LYS cc_start: 0.8365 (tppp) cc_final: 0.7865 (ttpm) REVERT: C 1185 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8311 (tttm) REVERT: C 1189 PHE cc_start: 0.8534 (t80) cc_final: 0.8146 (t80) REVERT: C 1206 GLN cc_start: 0.8254 (mt0) cc_final: 0.7991 (mm110) REVERT: D 278 ARG cc_start: 0.8075 (ttm-80) cc_final: 0.7792 (ttt90) REVERT: D 421 ASP cc_start: 0.8400 (p0) cc_final: 0.7948 (p0) REVERT: D 906 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7261 (mtm) REVERT: D 917 LYS cc_start: 0.7578 (mmmt) cc_final: 0.7123 (tptp) REVERT: D 946 LYS cc_start: 0.8383 (tppt) cc_final: 0.7786 (ttpp) REVERT: D 1189 PHE cc_start: 0.8521 (t80) cc_final: 0.8144 (t80) REVERT: D 1206 GLN cc_start: 0.8272 (mt0) cc_final: 0.7884 (mm110) outliers start: 72 outliers final: 44 residues processed: 511 average time/residue: 0.7247 time to fit residues: 446.0452 Evaluate side-chains 499 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 448 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1053 ILE Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1053 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1185 LYS Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1053 ILE Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1194 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 380 optimal weight: 0.7980 chunk 387 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 208 optimal weight: 4.9990 chunk 341 optimal weight: 0.0770 chunk 223 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 362 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 GLN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 GLN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.201564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.130088 restraints weight = 37061.549| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.01 r_work: 0.3234 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 36424 Z= 0.117 Angle : 0.593 12.173 48948 Z= 0.300 Chirality : 0.041 0.170 5236 Planarity : 0.005 0.094 5840 Dihedral : 18.376 151.817 7120 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.74 % Favored : 94.16 % Rotamer: Outliers : 1.51 % Allowed : 15.75 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.14), residues: 4024 helix: 1.89 (0.10), residues: 2580 sheet: -0.07 (0.38), residues: 188 loop : -1.60 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D1217 TYR 0.018 0.001 TYR C 953 PHE 0.016 0.001 PHE C 935 TRP 0.016 0.001 TRP A 417 HIS 0.006 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00252 (36420) covalent geometry : angle 0.59336 (48940) SS BOND : bond 0.00014 ( 4) SS BOND : angle 0.37912 ( 8) hydrogen bonds : bond 0.04320 ( 1764) hydrogen bonds : angle 3.78838 ( 5184) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 461 time to evaluate : 1.387 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: A 421 ASP cc_start: 0.8415 (p0) cc_final: 0.7996 (p0) REVERT: A 616 LYS cc_start: 0.8030 (mtmm) cc_final: 0.7309 (mttm) REVERT: A 906 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.7001 (mtm) REVERT: A 946 LYS cc_start: 0.8379 (tppp) cc_final: 0.7812 (ttpp) REVERT: A 975 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8341 (ttt-90) REVERT: A 1168 LYS cc_start: 0.7786 (pptt) cc_final: 0.7576 (pptt) REVERT: A 1189 PHE cc_start: 0.8265 (t80) cc_final: 0.7997 (t80) REVERT: A 1206 GLN cc_start: 0.8263 (mt0) cc_final: 0.7969 (mm110) REVERT: B 143 MET cc_start: 0.5974 (OUTLIER) cc_final: 0.5413 (mmt) REVERT: B 278 ARG cc_start: 0.8050 (ttm-80) cc_final: 0.7742 (ttt90) REVERT: B 331 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6762 (pp30) REVERT: B 369 MET cc_start: 0.7102 (tmt) cc_final: 0.6812 (tpt) REVERT: B 421 ASP cc_start: 0.8476 (p0) cc_final: 0.8006 (p0) REVERT: B 906 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6942 (mtm) REVERT: B 917 LYS cc_start: 0.7475 (mmmt) cc_final: 0.6979 (tptp) REVERT: B 946 LYS cc_start: 0.8300 (tppt) cc_final: 0.7693 (ttpp) REVERT: B 1175 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7541 (pt0) REVERT: B 1189 PHE cc_start: 0.8299 (t80) cc_final: 0.8013 (t80) REVERT: B 1206 GLN cc_start: 0.8136 (mt0) cc_final: 0.7864 (mm110) REVERT: C 331 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.7056 (pp30) REVERT: C 421 ASP cc_start: 0.8443 (p0) cc_final: 0.7987 (p0) REVERT: C 906 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6983 (mtm) REVERT: C 917 LYS cc_start: 0.7476 (mmmt) cc_final: 0.6953 (tptp) REVERT: C 946 LYS cc_start: 0.8372 (tppp) cc_final: 0.7785 (ttpp) REVERT: C 1185 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8212 (tttm) REVERT: C 1189 PHE cc_start: 0.8370 (t80) cc_final: 0.8071 (t80) REVERT: C 1206 GLN cc_start: 0.8265 (mt0) cc_final: 0.7919 (mm110) REVERT: D 278 ARG cc_start: 0.8026 (ttm-80) cc_final: 0.7720 (ttt90) REVERT: D 331 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6824 (pp30) REVERT: D 421 ASP cc_start: 0.8496 (p0) cc_final: 0.8062 (p0) REVERT: D 531 LYS cc_start: 0.8019 (mptm) cc_final: 0.7507 (mppt) REVERT: D 903 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7579 (mt-10) REVERT: D 906 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6991 (mtm) REVERT: D 917 LYS cc_start: 0.7461 (mmmt) cc_final: 0.6963 (tptp) REVERT: D 946 LYS cc_start: 0.8299 (tppt) cc_final: 0.7688 (ttpp) REVERT: D 1189 PHE cc_start: 0.8298 (t80) cc_final: 0.8010 (t80) REVERT: D 1206 GLN cc_start: 0.8147 (mt0) cc_final: 0.7741 (mm110) REVERT: D 1207 MET cc_start: 0.8438 (mtp) cc_final: 0.8196 (mtp) outliers start: 54 outliers final: 28 residues processed: 496 average time/residue: 0.7532 time to fit residues: 448.6302 Evaluate side-chains 482 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 444 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 975 ARG Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1053 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 1053 ILE Chi-restraints excluded: chain C residue 1185 LYS Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 1053 ILE Chi-restraints excluded: chain D residue 1194 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 88 optimal weight: 4.9990 chunk 365 optimal weight: 0.8980 chunk 382 optimal weight: 0.9980 chunk 284 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 245 optimal weight: 4.9990 chunk 51 optimal weight: 0.0020 chunk 283 optimal weight: 0.5980 chunk 359 optimal weight: 0.0970 chunk 298 optimal weight: 5.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 GLN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.201566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.130512 restraints weight = 36836.283| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.88 r_work: 0.3242 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.253 36424 Z= 0.171 Angle : 0.806 59.174 48948 Z= 0.441 Chirality : 0.046 1.105 5236 Planarity : 0.005 0.152 5840 Dihedral : 18.373 151.799 7120 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.72 % Favored : 94.18 % Rotamer: Outliers : 1.54 % Allowed : 16.23 % Favored : 82.23 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.14), residues: 4024 helix: 1.90 (0.10), residues: 2580 sheet: -0.06 (0.38), residues: 188 loop : -1.60 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D1217 TYR 0.017 0.001 TYR C 953 PHE 0.016 0.001 PHE C 935 TRP 0.015 0.001 TRP A 417 HIS 0.004 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00402 (36420) covalent geometry : angle 0.80612 (48940) SS BOND : bond 0.00026 ( 4) SS BOND : angle 0.35497 ( 8) hydrogen bonds : bond 0.04296 ( 1764) hydrogen bonds : angle 3.79228 ( 5184) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19594.34 seconds wall clock time: 333 minutes 10.31 seconds (19990.31 seconds total)