Starting phenix.real_space_refine on Sun Sep 13 12:01:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nm9_9398/09_2026/6nm9_9398.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nm9_9398/09_2026/6nm9_9398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6nm9_9398/09_2026/6nm9_9398.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nm9_9398/09_2026/6nm9_9398.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nm9_9398/09_2026/6nm9_9398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nm9_9398/09_2026/6nm9_9398.map" model { file = "/net/cci-nas-00/data/ceres_data/6nm9_9398/09_2026/6nm9_9398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nm9_9398/09_2026/6nm9_9398.cif" } resolution = 3.38 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 50 5.49 5 Mg 4 5.21 5 S 70 5.16 5 C 14536 2.51 5 N 3778 2.21 5 O 4478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22916 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 951 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "B" Number of atoms: 9970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1205, 9970 Classifications: {'peptide': 1205} Link IDs: {'PTRANS': 25, 'TRANS': 1179} Chain breaks: 5 Chain: "G" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 535 Classifications: {'RNAv2': 25} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 7} Link IDs: {'rna2p': 9, 'rna3p': 15} Chain: "C" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 951 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "D" Number of atoms: 9970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1205, 9970 Classifications: {'peptide': 1205} Link IDs: {'PTRANS': 25, 'TRANS': 1179} Chain breaks: 5 Chain: "E" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 535 Classifications: {'RNAv2': 25} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 7} Link IDs: {'rna2p': 9, 'rna3p': 15} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.42, per 1000 atoms: 0.19 Number of scatterers: 22916 At special positions: 0 Unit cell: (175.89, 169.494, 110.864, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 70 16.00 P 50 15.00 Mg 4 11.99 O 4478 8.00 N 3778 7.00 C 14536 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.49 Conformation dependent library (CDL) restraints added in 1.0 seconds 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5060 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 24 sheets defined 47.8% alpha, 7.3% beta 8 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'A' and resid 127 through 148 removed outlier: 4.359A pdb=" N ILE A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE A 146 " --> pdb=" O GLN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 removed outlier: 3.791A pdb=" N ARG A 203 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'B' and resid 3 through 7 Processing helix chain 'B' and resid 26 through 34 Processing helix chain 'B' and resid 37 through 46 Processing helix chain 'B' and resid 46 through 67 Processing helix chain 'B' and resid 73 through 82 removed outlier: 3.519A pdb=" N TYR B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 112 removed outlier: 4.120A pdb=" N ALA B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B 109 " --> pdb=" O ILE B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 126 through 131 Processing helix chain 'B' and resid 134 through 142 removed outlier: 4.019A pdb=" N VAL B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 151 through 160 removed outlier: 4.064A pdb=" N ASN B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.510A pdb=" N ARG B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 198 through 208 removed outlier: 3.931A pdb=" N VAL B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLU B 204 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ILE B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 221 removed outlier: 4.284A pdb=" N PHE B 220 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 221' Processing helix chain 'B' and resid 222 through 230 removed outlier: 3.594A pdb=" N PHE B 225 " --> pdb=" O GLY B 222 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 229 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR B 230 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 263 through 266 Processing helix chain 'B' and resid 296 through 308 Processing helix chain 'B' and resid 312 through 326 Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 341 through 352 removed outlier: 4.009A pdb=" N SER B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR B 346 " --> pdb=" O PRO B 342 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 371 removed outlier: 3.556A pdb=" N ASP B 360 " --> pdb=" O ASN B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 392 Processing helix chain 'B' and resid 397 through 404 Processing helix chain 'B' and resid 409 through 437 removed outlier: 5.745A pdb=" N LYS B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEU B 435 " --> pdb=" O SER B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 471 removed outlier: 4.564A pdb=" N MET B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 462 " --> pdb=" O ASP B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 498 removed outlier: 4.221A pdb=" N ASP B 489 " --> pdb=" O SER B 485 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 512 removed outlier: 4.213A pdb=" N HIS B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR B 510 " --> pdb=" O ALA B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 Processing helix chain 'B' and resid 588 through 598 Proline residue: B 594 - end of helix Processing helix chain 'B' and resid 610 through 619 Processing helix chain 'B' and resid 630 through 646 removed outlier: 3.661A pdb=" N LEU B 635 " --> pdb=" O ASP B 631 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 644 " --> pdb=" O LYS B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 676 Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 718 through 727 Processing helix chain 'B' and resid 786 through 790 Processing helix chain 'B' and resid 811 through 823 removed outlier: 3.819A pdb=" N GLU B 815 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 817 " --> pdb=" O ASN B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 884 removed outlier: 3.603A pdb=" N LEU B 876 " --> pdb=" O TYR B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 901 removed outlier: 3.684A pdb=" N LYS B 897 " --> pdb=" O ILE B 893 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA B 901 " --> pdb=" O LYS B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 913 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 927 through 930 removed outlier: 3.548A pdb=" N GLY B 930 " --> pdb=" O LEU B 927 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 927 through 930' Processing helix chain 'B' and resid 939 through 955 removed outlier: 3.761A pdb=" N LYS B 953 " --> pdb=" O MET B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 986 removed outlier: 3.740A pdb=" N MET B 986 " --> pdb=" O PHE B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1020 through 1030 Processing helix chain 'B' and resid 1091 through 1101 Processing helix chain 'B' and resid 1111 through 1116 Processing helix chain 'B' and resid 1120 through 1135 removed outlier: 3.732A pdb=" N TYR B1124 " --> pdb=" O ASP B1120 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER B1125 " --> pdb=" O LYS B1121 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER B1126 " --> pdb=" O ALA B1122 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B1130 " --> pdb=" O SER B1126 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1169 removed outlier: 4.683A pdb=" N ALA B1169 " --> pdb=" O ARG B1165 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1199 Processing helix chain 'B' and resid 1214 through 1225 Processing helix chain 'C' and resid 127 through 148 removed outlier: 4.359A pdb=" N ILE C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE C 146 " --> pdb=" O GLN C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 removed outlier: 3.792A pdb=" N ARG C 203 " --> pdb=" O SER C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 231 Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 37 through 46 Processing helix chain 'D' and resid 46 through 67 Processing helix chain 'D' and resid 73 through 82 removed outlier: 3.520A pdb=" N TYR D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER D 79 " --> pdb=" O ASN D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 112 removed outlier: 4.119A pdb=" N ALA D 108 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE D 109 " --> pdb=" O ILE D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 126 through 131 Processing helix chain 'D' and resid 134 through 142 removed outlier: 4.020A pdb=" N VAL D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 147 through 150 Processing helix chain 'D' and resid 151 through 160 removed outlier: 4.064A pdb=" N ASN D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.510A pdb=" N ARG D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 194 Processing helix chain 'D' and resid 198 through 208 removed outlier: 3.930A pdb=" N VAL D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLU D 204 " --> pdb=" O HIS D 200 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ILE D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 221 removed outlier: 4.284A pdb=" N PHE D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU D 221 " --> pdb=" O GLU D 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 216 through 221' Processing helix chain 'D' and resid 222 through 230 removed outlier: 3.594A pdb=" N PHE D 225 " --> pdb=" O GLY D 222 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 229 " --> pdb=" O ASN D 226 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR D 230 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 254 through 262 Processing helix chain 'D' and resid 263 through 266 Processing helix chain 'D' and resid 296 through 308 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 341 through 352 removed outlier: 4.009A pdb=" N SER D 345 " --> pdb=" O GLY D 341 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR D 346 " --> pdb=" O PRO D 342 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 371 removed outlier: 3.555A pdb=" N ASP D 360 " --> pdb=" O ASN D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 392 Processing helix chain 'D' and resid 397 through 404 Processing helix chain 'D' and resid 409 through 437 removed outlier: 5.746A pdb=" N LYS D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEU D 435 " --> pdb=" O SER D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 471 removed outlier: 4.563A pdb=" N MET D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 462 " --> pdb=" O ASP D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 498 removed outlier: 4.221A pdb=" N ASP D 489 " --> pdb=" O SER D 485 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 512 removed outlier: 4.213A pdb=" N HIS D 502 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR D 510 " --> pdb=" O ALA D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 543 Processing helix chain 'D' and resid 588 through 598 Proline residue: D 594 - end of helix Processing helix chain 'D' and resid 610 through 619 Processing helix chain 'D' and resid 630 through 646 removed outlier: 3.660A pdb=" N LEU D 635 " --> pdb=" O ASP D 631 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER D 644 " --> pdb=" O LYS D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 676 Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 718 through 727 Processing helix chain 'D' and resid 786 through 790 Processing helix chain 'D' and resid 811 through 823 removed outlier: 3.819A pdb=" N GLU D 815 " --> pdb=" O LYS D 811 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG D 817 " --> pdb=" O ASN D 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 872 through 884 removed outlier: 3.603A pdb=" N LEU D 876 " --> pdb=" O TYR D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 893 through 901 removed outlier: 3.684A pdb=" N LYS D 897 " --> pdb=" O ILE D 893 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA D 901 " --> pdb=" O LYS D 897 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 913 Processing helix chain 'D' and resid 913 through 919 Processing helix chain 'D' and resid 927 through 930 removed outlier: 3.549A pdb=" N GLY D 930 " --> pdb=" O LEU D 927 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 927 through 930' Processing helix chain 'D' and resid 939 through 955 removed outlier: 3.760A pdb=" N LYS D 953 " --> pdb=" O MET D 949 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 986 removed outlier: 3.741A pdb=" N MET D 986 " --> pdb=" O PHE D 983 " (cutoff:3.500A) Processing helix chain 'D' and resid 1020 through 1030 Processing helix chain 'D' and resid 1091 through 1101 Processing helix chain 'D' and resid 1111 through 1116 Processing helix chain 'D' and resid 1120 through 1135 removed outlier: 3.732A pdb=" N TYR D1124 " --> pdb=" O ASP D1120 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER D1125 " --> pdb=" O LYS D1121 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER D1126 " --> pdb=" O ALA D1122 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D1130 " --> pdb=" O SER D1126 " (cutoff:3.500A) Processing helix chain 'D' and resid 1164 through 1169 removed outlier: 4.683A pdb=" N ALA D1169 " --> pdb=" O ARG D1165 " (cutoff:3.500A) Processing helix chain 'D' and resid 1178 through 1199 Processing helix chain 'D' and resid 1214 through 1225 Processing sheet with id=AA1, first strand: chain 'A' and resid 157 through 158 Processing sheet with id=AA2, first strand: chain 'B' and resid 521 through 522 removed outlier: 3.651A pdb=" N ARG B 747 " --> pdb=" O GLN B 793 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN B 793 " --> pdb=" O ARG B 747 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR B 794 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR B 553 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 552 " --> pdb=" O TYR B 549 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR B 554 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AA4, first strand: chain 'B' and resid 736 through 737 removed outlier: 3.932A pdb=" N ARG B 737 " --> pdb=" O ALA B 801 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 757 through 759 removed outlier: 4.696A pdb=" N VAL B 757 " --> pdb=" O LYS B 785 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS B 759 " --> pdb=" O VAL B 783 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 783 " --> pdb=" O HIS B 759 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 765 through 766 Processing sheet with id=AA7, first strand: chain 'B' and resid 850 through 855 removed outlier: 4.510A pdb=" N GLU B 925 " --> pdb=" O ILE B 831 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 922 " --> pdb=" O PHE B 994 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE B 996 " --> pdb=" O ILE B 922 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU B 924 " --> pdb=" O ILE B 996 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 858 through 863 removed outlier: 3.598A pdb=" N ILE B 859 " --> pdb=" O THR B 870 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE B 863 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1033 through 1037 removed outlier: 3.869A pdb=" N ARG B1033 " --> pdb=" O ALA B1046 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET B1035 " --> pdb=" O GLU B1044 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1070 through 1072 Processing sheet with id=AB2, first strand: chain 'B' and resid 1139 through 1140 Processing sheet with id=AB3, first strand: chain 'B' and resid 1151 through 1152 removed outlier: 3.941A pdb=" N TYR B1162 " --> pdb=" O SER B1152 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 157 through 158 Processing sheet with id=AB5, first strand: chain 'D' and resid 521 through 522 removed outlier: 3.651A pdb=" N ARG D 747 " --> pdb=" O GLN D 793 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN D 793 " --> pdb=" O ARG D 747 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR D 794 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR D 553 " --> pdb=" O ILE D 704 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS D 552 " --> pdb=" O TYR D 549 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR D 554 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 337 through 339 Processing sheet with id=AB7, first strand: chain 'D' and resid 736 through 737 removed outlier: 3.931A pdb=" N ARG D 737 " --> pdb=" O ALA D 801 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 757 through 759 removed outlier: 4.685A pdb=" N VAL D 757 " --> pdb=" O LYS D 785 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS D 759 " --> pdb=" O VAL D 783 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 783 " --> pdb=" O HIS D 759 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 765 through 766 Processing sheet with id=AC1, first strand: chain 'D' and resid 850 through 855 removed outlier: 4.508A pdb=" N GLU D 925 " --> pdb=" O ILE D 831 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE D 922 " --> pdb=" O PHE D 994 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE D 996 " --> pdb=" O ILE D 922 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU D 924 " --> pdb=" O ILE D 996 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 858 through 863 removed outlier: 3.598A pdb=" N ILE D 859 " --> pdb=" O THR D 870 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE D 863 " --> pdb=" O ILE D 866 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 1033 through 1037 removed outlier: 3.868A pdb=" N ARG D1033 " --> pdb=" O ALA D1046 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET D1035 " --> pdb=" O GLU D1044 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 1070 through 1072 Processing sheet with id=AC5, first strand: chain 'D' and resid 1139 through 1140 Processing sheet with id=AC6, first strand: chain 'D' and resid 1151 through 1152 removed outlier: 3.941A pdb=" N TYR D1162 " --> pdb=" O SER D1152 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2394 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 4.38 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4818 1.33 - 1.45: 5609 1.45 - 1.57: 12847 1.57 - 1.69: 98 1.69 - 1.81: 116 Bond restraints: 23488 Sorted by residual: bond pdb=" CA ALA D 901 " pdb=" C ALA D 901 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.80e-02 3.09e+03 1.14e+01 bond pdb=" CA ALA B 901 " pdb=" C ALA B 901 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.80e-02 3.09e+03 1.14e+01 bond pdb=" N ASP D 572 " pdb=" CA ASP D 572 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.32e-02 5.74e+03 8.64e+00 bond pdb=" N ASP B 572 " pdb=" CA ASP B 572 " ideal model delta sigma weight residual 1.459 1.497 -0.039 1.32e-02 5.74e+03 8.60e+00 bond pdb=" CA CYS D 912 " pdb=" C CYS D 912 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.80e-02 3.09e+03 7.80e+00 ... (remaining 23483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 30599 1.89 - 3.78: 1043 3.78 - 5.67: 154 5.67 - 7.55: 19 7.55 - 9.44: 3 Bond angle restraints: 31818 Sorted by residual: angle pdb=" N VAL B 216 " pdb=" CA VAL B 216 " pdb=" C VAL B 216 " ideal model delta sigma weight residual 113.71 108.02 5.69 9.50e-01 1.11e+00 3.59e+01 angle pdb=" N VAL D 216 " pdb=" CA VAL D 216 " pdb=" C VAL D 216 " ideal model delta sigma weight residual 113.71 108.02 5.69 9.50e-01 1.11e+00 3.59e+01 angle pdb=" C THR B 85 " pdb=" N ARG B 86 " pdb=" CA ARG B 86 " ideal model delta sigma weight residual 122.68 115.72 6.96 1.47e+00 4.63e-01 2.24e+01 angle pdb=" N ILE C 214 " pdb=" CA ILE C 214 " pdb=" C ILE C 214 " ideal model delta sigma weight residual 112.98 107.27 5.71 1.25e+00 6.40e-01 2.09e+01 angle pdb=" N ILE A 214 " pdb=" CA ILE A 214 " pdb=" C ILE A 214 " ideal model delta sigma weight residual 112.98 107.28 5.70 1.25e+00 6.40e-01 2.08e+01 ... (remaining 31813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 12296 17.99 - 35.99: 1446 35.99 - 53.98: 266 53.98 - 71.98: 94 71.98 - 89.97: 38 Dihedral angle restraints: 14140 sinusoidal: 6296 harmonic: 7844 Sorted by residual: dihedral pdb=" C4' U E 5 " pdb=" C3' U E 5 " pdb=" C2' U E 5 " pdb=" C1' U E 5 " ideal model delta sinusoidal sigma weight residual 36.34 -38.98 75.33 1 3.10e+00 1.04e-01 7.46e+02 dihedral pdb=" C4' U G 5 " pdb=" C3' U G 5 " pdb=" C2' U G 5 " pdb=" C1' U G 5 " ideal model delta sinusoidal sigma weight residual 36.34 -38.95 75.29 1 3.10e+00 1.04e-01 7.45e+02 dihedral pdb=" C4' U E 12 " pdb=" C3' U E 12 " pdb=" C2' U E 12 " pdb=" C1' U E 12 " ideal model delta sinusoidal sigma weight residual 36.34 -38.69 75.04 1 3.10e+00 1.04e-01 7.41e+02 ... (remaining 14137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3116 0.087 - 0.174: 241 0.174 - 0.261: 53 0.261 - 0.347: 24 0.347 - 0.434: 2 Chirality restraints: 3436 Sorted by residual: chirality pdb=" CA ASP D 572 " pdb=" N ASP D 572 " pdb=" C ASP D 572 " pdb=" CB ASP D 572 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CA ASP B 572 " pdb=" N ASP B 572 " pdb=" C ASP B 572 " pdb=" CB ASP B 572 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" C2' U G 5 " pdb=" C3' U G 5 " pdb=" O2' U G 5 " pdb=" C1' U G 5 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 3433 not shown) Planarity restraints: 3876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G G 24 " 0.056 2.00e-02 2.50e+03 2.38e-02 1.71e+01 pdb=" N9 G G 24 " -0.055 2.00e-02 2.50e+03 pdb=" C8 G G 24 " -0.009 2.00e-02 2.50e+03 pdb=" N7 G G 24 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G G 24 " 0.005 2.00e-02 2.50e+03 pdb=" C6 G G 24 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G G 24 " 0.014 2.00e-02 2.50e+03 pdb=" N1 G G 24 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G G 24 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G G 24 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G G 24 " -0.009 2.00e-02 2.50e+03 pdb=" C4 G G 24 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G E 24 " 0.056 2.00e-02 2.50e+03 2.36e-02 1.68e+01 pdb=" N9 G E 24 " -0.055 2.00e-02 2.50e+03 pdb=" C8 G E 24 " -0.008 2.00e-02 2.50e+03 pdb=" N7 G E 24 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G E 24 " 0.005 2.00e-02 2.50e+03 pdb=" C6 G E 24 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G E 24 " 0.014 2.00e-02 2.50e+03 pdb=" N1 G E 24 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G E 24 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G E 24 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G E 24 " -0.009 2.00e-02 2.50e+03 pdb=" C4 G E 24 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A E 25 " 0.039 2.00e-02 2.50e+03 1.78e-02 8.75e+00 pdb=" N9 A E 25 " -0.041 2.00e-02 2.50e+03 pdb=" C8 A E 25 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A E 25 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A E 25 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A E 25 " 0.008 2.00e-02 2.50e+03 pdb=" N6 A E 25 " 0.011 2.00e-02 2.50e+03 pdb=" N1 A E 25 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A E 25 " -0.006 2.00e-02 2.50e+03 pdb=" N3 A E 25 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A E 25 " -0.001 2.00e-02 2.50e+03 ... (remaining 3873 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 249 2.49 - 3.09: 18079 3.09 - 3.69: 35646 3.69 - 4.30: 51424 4.30 - 4.90: 81806 Nonbonded interactions: 187204 Sorted by model distance: nonbonded pdb=" OP2 A G 19 " pdb="MG MG B1301 " model vdw 1.884 2.170 nonbonded pdb=" NZ LYS A 202 " pdb="MG MG A 301 " model vdw 1.991 2.250 nonbonded pdb=" OP2 A E 19 " pdb="MG MG D1301 " model vdw 2.101 2.170 nonbonded pdb=" NZ LYS C 202 " pdb="MG MG C 301 " model vdw 2.122 2.250 nonbonded pdb=" NH1 ARG D 18 " pdb=" O5' G E 24 " model vdw 2.196 3.120 ... (remaining 187199 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.850 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 0.008 0.061 23488 Z= 0.354 Angle : 0.813 9.444 31818 Z= 0.454 Chirality : 0.060 0.434 3436 Planarity : 0.004 0.049 3876 Dihedral : 16.419 89.970 9080 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.60 % Favored : 87.33 % Rotamer: Outliers : 0.29 % Allowed : 8.10 % Favored : 91.60 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.62 (0.13), residues: 2612 helix: -2.53 (0.12), residues: 1142 sheet: -2.86 (0.32), residues: 234 loop : -3.66 (0.15), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 887 TYR 0.032 0.002 TYR A 188 PHE 0.021 0.002 PHE B 61 TRP 0.017 0.002 TRP B 534 HIS 0.005 0.001 HIS D 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00755 / 0.35 (23488) covalent geometry : angle 0.81285 / 0.45 (31818) hydrogen bonds : bond 0.18548 / 12.21 ( 868) hydrogen bonds : angle 8.24906 / 5.69 ( 2434) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 451 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASN cc_start: 0.8892 (m-40) cc_final: 0.8589 (t0) REVERT: A 148 LYS cc_start: 0.8563 (ttpt) cc_final: 0.8281 (ttmm) REVERT: A 174 GLU cc_start: 0.8392 (tt0) cc_final: 0.8092 (tt0) REVERT: A 219 GLU cc_start: 0.8453 (pt0) cc_final: 0.7794 (pm20) REVERT: A 231 ASN cc_start: 0.8264 (t0) cc_final: 0.8045 (t0) REVERT: B 1 MET cc_start: 0.5935 (ttt) cc_final: 0.5199 (ttt) REVERT: B 5 GLU cc_start: 0.8366 (tt0) cc_final: 0.7937 (tt0) REVERT: B 174 ARG cc_start: 0.8350 (tpp80) cc_final: 0.8080 (ttm-80) REVERT: B 179 ASN cc_start: 0.7453 (m110) cc_final: 0.7217 (m110) REVERT: B 219 PHE cc_start: 0.7861 (m-80) cc_final: 0.7587 (m-80) REVERT: B 456 MET cc_start: 0.7715 (mtt) cc_final: 0.7363 (mtp) REVERT: B 496 ILE cc_start: 0.8619 (mm) cc_final: 0.8329 (mm) REVERT: B 514 LYS cc_start: 0.8113 (mmtm) cc_final: 0.7745 (mtmm) REVERT: B 522 LYS cc_start: 0.8833 (tttt) cc_final: 0.8457 (tttm) REVERT: B 525 PHE cc_start: 0.8675 (m-10) cc_final: 0.8441 (m-10) REVERT: B 527 ASN cc_start: 0.8485 (t0) cc_final: 0.8123 (t0) REVERT: B 531 MET cc_start: 0.8048 (ttm) cc_final: 0.7580 (ttm) REVERT: B 701 MET cc_start: 0.7584 (tmm) cc_final: 0.7341 (tmm) REVERT: B 754 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8036 (mp0) REVERT: B 852 GLU cc_start: 0.7383 (tp30) cc_final: 0.7012 (tp30) REVERT: B 882 GLU cc_start: 0.8100 (tp30) cc_final: 0.7597 (tt0) REVERT: B 986 MET cc_start: 0.8461 (mtt) cc_final: 0.8058 (mmm) REVERT: B 1027 PHE cc_start: 0.8532 (t80) cc_final: 0.8112 (t80) REVERT: B 1137 MET cc_start: 0.8963 (mtp) cc_final: 0.8619 (mtp) REVERT: C 148 LYS cc_start: 0.8557 (ttpt) cc_final: 0.8259 (ttmm) REVERT: C 174 GLU cc_start: 0.8420 (tt0) cc_final: 0.8124 (tt0) REVERT: C 219 GLU cc_start: 0.8449 (pt0) cc_final: 0.7524 (pm20) REVERT: C 231 ASN cc_start: 0.8252 (t0) cc_final: 0.8018 (t0) REVERT: D 1 MET cc_start: 0.5927 (ttt) cc_final: 0.5191 (ttt) REVERT: D 5 GLU cc_start: 0.8367 (tt0) cc_final: 0.7937 (tt0) REVERT: D 88 GLU cc_start: 0.4525 (OUTLIER) cc_final: 0.4317 (pp20) REVERT: D 174 ARG cc_start: 0.8353 (tpp80) cc_final: 0.8082 (ttm-80) REVERT: D 179 ASN cc_start: 0.7442 (m110) cc_final: 0.7207 (m110) REVERT: D 456 MET cc_start: 0.7711 (mtt) cc_final: 0.7356 (mtp) REVERT: D 496 ILE cc_start: 0.8621 (mm) cc_final: 0.8338 (mm) REVERT: D 514 LYS cc_start: 0.8088 (mmtm) cc_final: 0.7724 (mtmm) REVERT: D 522 LYS cc_start: 0.8822 (tttt) cc_final: 0.8446 (tttm) REVERT: D 525 PHE cc_start: 0.8675 (m-10) cc_final: 0.8443 (m-10) REVERT: D 527 ASN cc_start: 0.8487 (t0) cc_final: 0.8122 (t0) REVERT: D 531 MET cc_start: 0.8038 (ttm) cc_final: 0.7562 (ttm) REVERT: D 701 MET cc_start: 0.7586 (tmm) cc_final: 0.7343 (tmm) REVERT: D 754 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8164 (mp0) REVERT: D 786 ASP cc_start: 0.8863 (m-30) cc_final: 0.8631 (m-30) REVERT: D 852 GLU cc_start: 0.7370 (tp30) cc_final: 0.6995 (tp30) REVERT: D 882 GLU cc_start: 0.8108 (tp30) cc_final: 0.7602 (tt0) REVERT: D 986 MET cc_start: 0.8464 (mtt) cc_final: 0.8058 (mmm) REVERT: D 1027 PHE cc_start: 0.8534 (t80) cc_final: 0.8112 (t80) REVERT: D 1137 MET cc_start: 0.8996 (mtp) cc_final: 0.8689 (mtp) outliers start: 7 outliers final: 2 residues processed: 458 average time/residue: 0.1768 time to fit residues: 120.3432 Evaluate side-chains 332 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 329 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 297 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN A 208 ASN B 96 ASN B 145 ASN B 157 ASN B 529 GLN B 567 GLN B 676 GLN B 803 ASN ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 ASN B 989 GLN ** B1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1172 ASN C 208 ASN D 96 ASN D 145 ASN D 157 ASN D 529 GLN D 567 GLN D 676 GLN D 803 ASN ** D 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 928 ASN D 989 GLN ** D1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1172 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.158857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.105534 restraints weight = 39856.040| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.86 r_work: 0.3260 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23488 Z= 0.168 Angle : 0.779 12.317 31818 Z= 0.380 Chirality : 0.060 0.768 3436 Planarity : 0.004 0.050 3876 Dihedral : 11.158 150.737 3481 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 1.91 % Allowed : 15.59 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.15), residues: 2612 helix: -1.02 (0.15), residues: 1144 sheet: -2.33 (0.34), residues: 232 loop : -2.87 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 359 TYR 0.018 0.002 TYR B 294 PHE 0.013 0.001 PHE B1149 TRP 0.009 0.001 TRP D 355 HIS 0.003 0.001 HIS B 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (23488) covalent geometry : angle 0.77915 / 0.38 (31818) hydrogen bonds : bond 0.04159 / 2.74 ( 868) hydrogen bonds : angle 5.53656 / 3.76 ( 2434) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 412 time to evaluate : 0.610 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 145 ASN cc_start: 0.9069 (m-40) cc_final: 0.8785 (t0) REVERT: A 148 LYS cc_start: 0.8752 (ttpt) cc_final: 0.8523 (ttmm) REVERT: A 174 GLU cc_start: 0.8472 (tt0) cc_final: 0.8130 (tt0) REVERT: A 176 GLU cc_start: 0.8269 (pm20) cc_final: 0.7740 (pm20) REVERT: A 219 GLU cc_start: 0.8499 (pt0) cc_final: 0.7277 (pm20) REVERT: A 228 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8230 (tm-30) REVERT: A 231 ASN cc_start: 0.8628 (t0) cc_final: 0.8401 (t0) REVERT: B 5 GLU cc_start: 0.8557 (tt0) cc_final: 0.8344 (tt0) REVERT: B 174 ARG cc_start: 0.8402 (tpp80) cc_final: 0.8109 (ttm-80) REVERT: B 179 ASN cc_start: 0.7621 (m-40) cc_final: 0.7363 (m110) REVERT: B 321 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8489 (tt) REVERT: B 398 GLU cc_start: 0.7826 (tp30) cc_final: 0.7521 (tp30) REVERT: B 456 MET cc_start: 0.8246 (mtt) cc_final: 0.8009 (mtp) REVERT: B 501 ASP cc_start: 0.8197 (t0) cc_final: 0.7854 (t0) REVERT: B 514 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7807 (mtmm) REVERT: B 522 LYS cc_start: 0.9019 (tttt) cc_final: 0.8714 (tttm) REVERT: B 524 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.7365 (m-80) REVERT: B 527 ASN cc_start: 0.8665 (t0) cc_final: 0.8084 (t0) REVERT: B 543 ARG cc_start: 0.7710 (mtm-85) cc_final: 0.7377 (mtm-85) REVERT: B 589 PRO cc_start: 0.5730 (Cg_exo) cc_final: 0.5205 (Cg_endo) REVERT: B 674 GLU cc_start: 0.8783 (tp30) cc_final: 0.8403 (tp30) REVERT: B 708 ASP cc_start: 0.8175 (m-30) cc_final: 0.7899 (m-30) REVERT: B 754 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8475 (mp0) REVERT: B 815 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7549 (tt0) REVERT: B 882 GLU cc_start: 0.8208 (tp30) cc_final: 0.7899 (tt0) REVERT: B 939 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7497 (pm20) REVERT: B 1027 PHE cc_start: 0.8574 (t80) cc_final: 0.8135 (t80) REVERT: B 1033 ARG cc_start: 0.8300 (ttm-80) cc_final: 0.7850 (ttm-80) REVERT: B 1137 MET cc_start: 0.8940 (mtp) cc_final: 0.8670 (mtp) REVERT: B 1186 ASN cc_start: 0.9009 (m-40) cc_final: 0.8640 (m-40) REVERT: C 148 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8505 (ttmm) REVERT: C 174 GLU cc_start: 0.8490 (tt0) cc_final: 0.8091 (tt0) REVERT: C 176 GLU cc_start: 0.8327 (pm20) cc_final: 0.7823 (pm20) REVERT: C 219 GLU cc_start: 0.8278 (pt0) cc_final: 0.7449 (pm20) REVERT: C 228 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8265 (tm-30) REVERT: C 231 ASN cc_start: 0.8560 (t0) cc_final: 0.8340 (t0) REVERT: D 5 GLU cc_start: 0.8560 (tt0) cc_final: 0.8350 (tt0) REVERT: D 88 GLU cc_start: 0.4404 (OUTLIER) cc_final: 0.4191 (pp20) REVERT: D 174 ARG cc_start: 0.8403 (tpp80) cc_final: 0.8111 (ttm-80) REVERT: D 179 ASN cc_start: 0.7610 (m-40) cc_final: 0.7352 (m110) REVERT: D 321 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8493 (tt) REVERT: D 330 GLU cc_start: 0.7422 (mp0) cc_final: 0.7062 (pp20) REVERT: D 398 GLU cc_start: 0.7824 (tp30) cc_final: 0.7520 (tp30) REVERT: D 456 MET cc_start: 0.8252 (mtt) cc_final: 0.8017 (mtp) REVERT: D 501 ASP cc_start: 0.8188 (t0) cc_final: 0.7841 (t0) REVERT: D 522 LYS cc_start: 0.9016 (tttt) cc_final: 0.8685 (tttt) REVERT: D 524 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.7349 (m-80) REVERT: D 527 ASN cc_start: 0.8664 (t0) cc_final: 0.8085 (t0) REVERT: D 543 ARG cc_start: 0.7708 (mtm-85) cc_final: 0.7380 (mtm-85) REVERT: D 674 GLU cc_start: 0.8789 (tp30) cc_final: 0.8421 (tp30) REVERT: D 708 ASP cc_start: 0.8155 (m-30) cc_final: 0.7863 (m-30) REVERT: D 754 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8481 (mp0) REVERT: D 815 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7557 (tt0) REVERT: D 882 GLU cc_start: 0.8216 (tp30) cc_final: 0.7905 (tt0) REVERT: D 939 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7569 (pm20) REVERT: D 1033 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.7847 (ttm-80) REVERT: D 1137 MET cc_start: 0.8949 (mtp) cc_final: 0.8675 (mtp) REVERT: D 1186 ASN cc_start: 0.8978 (m-40) cc_final: 0.8604 (m-40) outliers start: 46 outliers final: 22 residues processed: 444 average time/residue: 0.1525 time to fit residues: 104.7902 Evaluate side-chains 361 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 332 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 939 GLU Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 524 TYR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 939 GLU Chi-restraints excluded: chain D residue 958 VAL Chi-restraints excluded: chain D residue 1115 LEU Chi-restraints excluded: chain D residue 1172 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 246 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 204 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 175 optimal weight: 0.5980 chunk 20 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 240 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 258 optimal weight: 10.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 857 ASN B 906 GLN ** D 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 857 ASN D 906 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.158598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.104847 restraints weight = 40017.370| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.90 r_work: 0.3256 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23488 Z= 0.175 Angle : 0.738 13.869 31818 Z= 0.360 Chirality : 0.056 0.510 3436 Planarity : 0.004 0.041 3876 Dihedral : 11.092 150.582 3481 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 2.74 % Allowed : 18.29 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.16), residues: 2612 helix: -0.52 (0.15), residues: 1150 sheet: -2.03 (0.35), residues: 232 loop : -2.61 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 359 TYR 0.018 0.001 TYR B 294 PHE 0.016 0.001 PHE B 530 TRP 0.006 0.001 TRP D 355 HIS 0.003 0.001 HIS D 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (23488) covalent geometry : angle 0.73841 / 0.36 (31818) hydrogen bonds : bond 0.03760 / 2.46 ( 868) hydrogen bonds : angle 5.19598 / 3.53 ( 2434) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 358 time to evaluate : 0.878 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 145 ASN cc_start: 0.9048 (m-40) cc_final: 0.8636 (m-40) REVERT: A 148 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8561 (ttmm) REVERT: A 176 GLU cc_start: 0.8280 (pm20) cc_final: 0.7874 (pm20) REVERT: A 219 GLU cc_start: 0.8214 (pt0) cc_final: 0.7736 (pm20) REVERT: A 228 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8389 (tm-30) REVERT: A 231 ASN cc_start: 0.8603 (t0) cc_final: 0.8252 (t0) REVERT: B 5 GLU cc_start: 0.8577 (tt0) cc_final: 0.8375 (tt0) REVERT: B 82 ARG cc_start: 0.6816 (mtm180) cc_final: 0.6216 (mtm180) REVERT: B 174 ARG cc_start: 0.8342 (tpp80) cc_final: 0.8026 (ttm-80) REVERT: B 179 ASN cc_start: 0.7664 (m-40) cc_final: 0.7425 (m110) REVERT: B 321 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8475 (tt) REVERT: B 354 GLU cc_start: 0.8522 (tp30) cc_final: 0.8303 (tp30) REVERT: B 514 LYS cc_start: 0.8080 (mmtm) cc_final: 0.7775 (mtmm) REVERT: B 522 LYS cc_start: 0.9043 (tttt) cc_final: 0.8665 (tttt) REVERT: B 524 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7043 (m-80) REVERT: B 527 ASN cc_start: 0.8667 (t0) cc_final: 0.8123 (t0) REVERT: B 534 TRP cc_start: 0.7101 (OUTLIER) cc_final: 0.6687 (m-10) REVERT: B 543 ARG cc_start: 0.7890 (mtm-85) cc_final: 0.7636 (mtm-85) REVERT: B 674 GLU cc_start: 0.8770 (tp30) cc_final: 0.8429 (tp30) REVERT: B 754 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8388 (mp0) REVERT: B 815 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7636 (tt0) REVERT: B 882 GLU cc_start: 0.8207 (tp30) cc_final: 0.7967 (tt0) REVERT: B 939 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7603 (pm20) REVERT: B 958 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8741 (t) REVERT: B 1033 ARG cc_start: 0.8328 (ttm-80) cc_final: 0.7864 (ttm-80) REVERT: B 1036 TYR cc_start: 0.6077 (t80) cc_final: 0.5850 (t80) REVERT: B 1137 MET cc_start: 0.8945 (mtp) cc_final: 0.8684 (mtp) REVERT: B 1186 ASN cc_start: 0.9005 (m-40) cc_final: 0.8656 (m110) REVERT: C 145 ASN cc_start: 0.9066 (m-40) cc_final: 0.8716 (t0) REVERT: C 148 LYS cc_start: 0.8772 (ttpt) cc_final: 0.8535 (ttmm) REVERT: C 174 GLU cc_start: 0.8454 (tt0) cc_final: 0.7643 (tt0) REVERT: C 176 GLU cc_start: 0.8320 (pm20) cc_final: 0.7523 (pm20) REVERT: C 219 GLU cc_start: 0.8242 (pt0) cc_final: 0.7716 (pm20) REVERT: C 228 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8393 (tm-30) REVERT: C 231 ASN cc_start: 0.8599 (t0) cc_final: 0.8228 (t0) REVERT: D 5 GLU cc_start: 0.8575 (tt0) cc_final: 0.8372 (tt0) REVERT: D 174 ARG cc_start: 0.8352 (tpp80) cc_final: 0.8034 (ttm-80) REVERT: D 179 ASN cc_start: 0.7656 (m-40) cc_final: 0.7417 (m110) REVERT: D 321 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8476 (tt) REVERT: D 354 GLU cc_start: 0.8525 (tp30) cc_final: 0.8306 (tp30) REVERT: D 398 GLU cc_start: 0.7824 (tp30) cc_final: 0.7499 (tp30) REVERT: D 514 LYS cc_start: 0.8714 (mtmm) cc_final: 0.8464 (ptpt) REVERT: D 522 LYS cc_start: 0.9046 (tttt) cc_final: 0.8629 (tttt) REVERT: D 524 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7080 (m-80) REVERT: D 527 ASN cc_start: 0.8675 (t0) cc_final: 0.8135 (t0) REVERT: D 534 TRP cc_start: 0.7112 (OUTLIER) cc_final: 0.6694 (m-10) REVERT: D 543 ARG cc_start: 0.7894 (mtm-85) cc_final: 0.7646 (mtm-85) REVERT: D 674 GLU cc_start: 0.8773 (tp30) cc_final: 0.8427 (tp30) REVERT: D 754 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8392 (mp0) REVERT: D 815 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7635 (tt0) REVERT: D 882 GLU cc_start: 0.8210 (tp30) cc_final: 0.7972 (tt0) REVERT: D 958 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8794 (t) REVERT: D 1033 ARG cc_start: 0.8332 (ttm-80) cc_final: 0.7866 (ttm-80) REVERT: D 1137 MET cc_start: 0.8959 (mtp) cc_final: 0.8693 (mtp) REVERT: D 1186 ASN cc_start: 0.8982 (m-40) cc_final: 0.8657 (m110) outliers start: 66 outliers final: 33 residues processed: 398 average time/residue: 0.1556 time to fit residues: 96.1432 Evaluate side-chains 359 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 317 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 534 TRP Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 939 GLU Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 1086 TRP Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 524 TYR Chi-restraints excluded: chain D residue 534 TRP Chi-restraints excluded: chain D residue 831 ILE Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 958 VAL Chi-restraints excluded: chain D residue 1086 TRP Chi-restraints excluded: chain D residue 1115 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 37 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 95 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 233 HIS B 797 HIS ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 ASN D 797 HIS ** D 853 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 = 0.4144 r_free = 0.4144 target = 0.162425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.109440 restraints weight = 39670.321| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.92 r_work: 0.3312 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23488 Z= 0.115 Angle : 0.663 11.069 31818 Z= 0.326 Chirality : 0.051 0.496 3436 Planarity : 0.003 0.037 3876 Dihedral : 11.002 151.096 3478 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.66 % Allowed : 19.53 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.16), residues: 2612 helix: -0.02 (0.16), residues: 1140 sheet: -2.00 (0.34), residues: 242 loop : -2.36 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 359 TYR 0.019 0.001 TYR B 294 PHE 0.015 0.001 PHE B1027 TRP 0.006 0.001 TRP B 355 HIS 0.014 0.001 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (23488) covalent geometry : angle 0.66290 / 0.33 (31818) hydrogen bonds : bond 0.03132 / 2.05 ( 868) hydrogen bonds : angle 4.75500 / 3.23 ( 2434) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 385 time to evaluate : 0.661 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: A 145 ASN cc_start: 0.9005 (m-40) cc_final: 0.8709 (t0) REVERT: A 148 LYS cc_start: 0.8755 (ttpt) cc_final: 0.8507 (ttmm) REVERT: A 166 ASP cc_start: 0.7668 (t70) cc_final: 0.7073 (p0) REVERT: A 216 VAL cc_start: 0.7648 (OUTLIER) cc_final: 0.7284 (t) REVERT: A 219 GLU cc_start: 0.8117 (pt0) cc_final: 0.7346 (pm20) REVERT: A 221 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8138 (mm-30) REVERT: A 228 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8375 (tm-30) REVERT: A 231 ASN cc_start: 0.8587 (t0) cc_final: 0.8186 (t0) REVERT: B 5 GLU cc_start: 0.8545 (tt0) cc_final: 0.8280 (tt0) REVERT: B 115 TYR cc_start: 0.7103 (t80) cc_final: 0.6903 (t80) REVERT: B 179 ASN cc_start: 0.7646 (m-40) cc_final: 0.7403 (m110) REVERT: B 321 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8458 (tt) REVERT: B 354 GLU cc_start: 0.8563 (tp30) cc_final: 0.8300 (tp30) REVERT: B 362 TRP cc_start: 0.7407 (t60) cc_final: 0.7197 (t60) REVERT: B 434 LYS cc_start: 0.8984 (ttpt) cc_final: 0.8780 (tmmt) REVERT: B 514 LYS cc_start: 0.8042 (mmtm) cc_final: 0.7757 (mtmm) REVERT: B 522 LYS cc_start: 0.9096 (tttt) cc_final: 0.8716 (tttt) REVERT: B 524 TYR cc_start: 0.8374 (OUTLIER) cc_final: 0.7308 (m-80) REVERT: B 527 ASN cc_start: 0.8634 (t0) cc_final: 0.8093 (t0) REVERT: B 543 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.6514 (ttp-110) REVERT: B 557 ILE cc_start: 0.9101 (mt) cc_final: 0.8844 (mm) REVERT: B 560 LYS cc_start: 0.7753 (tppt) cc_final: 0.7529 (tppt) REVERT: B 592 MET cc_start: 0.7495 (mtm) cc_final: 0.7221 (ppp) REVERT: B 696 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8215 (mt-10) REVERT: B 754 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8454 (mp0) REVERT: B 815 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7628 (tt0) REVERT: B 841 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8230 (tp) REVERT: B 858 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8267 (mt-10) REVERT: B 1033 ARG cc_start: 0.8255 (ttm-80) cc_final: 0.7843 (ttm-80) REVERT: B 1131 MET cc_start: 0.8675 (tpp) cc_final: 0.8376 (mmm) REVERT: B 1132 SER cc_start: 0.8752 (t) cc_final: 0.8314 (m) REVERT: B 1137 MET cc_start: 0.8866 (mtp) cc_final: 0.8610 (mtp) REVERT: B 1156 ASN cc_start: 0.7667 (OUTLIER) cc_final: 0.7411 (p0) REVERT: B 1185 TYR cc_start: 0.9211 (t80) cc_final: 0.8712 (t80) REVERT: B 1186 ASN cc_start: 0.9101 (m-40) cc_final: 0.8742 (m110) REVERT: C 148 LYS cc_start: 0.8758 (ttpt) cc_final: 0.8483 (ttmm) REVERT: C 166 ASP cc_start: 0.7674 (t70) cc_final: 0.7041 (p0) REVERT: C 174 GLU cc_start: 0.8664 (tt0) cc_final: 0.8237 (tt0) REVERT: C 216 VAL cc_start: 0.7688 (OUTLIER) cc_final: 0.7341 (t) REVERT: C 219 GLU cc_start: 0.8120 (pt0) cc_final: 0.7577 (pm20) REVERT: C 228 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8356 (tm-30) REVERT: C 231 ASN cc_start: 0.8543 (t0) cc_final: 0.8196 (t0) REVERT: D 5 GLU cc_start: 0.8532 (tt0) cc_final: 0.8267 (tt0) REVERT: D 82 ARG cc_start: 0.6382 (mtm180) cc_final: 0.5872 (mtm180) REVERT: D 174 ARG cc_start: 0.8301 (tpp80) cc_final: 0.7973 (ttm-80) REVERT: D 179 ASN cc_start: 0.7639 (m-40) cc_final: 0.7400 (m110) REVERT: D 321 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8473 (tt) REVERT: D 330 GLU cc_start: 0.7478 (mp0) cc_final: 0.7170 (pp20) REVERT: D 354 GLU cc_start: 0.8560 (tp30) cc_final: 0.8298 (tp30) REVERT: D 362 TRP cc_start: 0.7415 (t60) cc_final: 0.7201 (t60) REVERT: D 434 LYS cc_start: 0.8986 (ttpt) cc_final: 0.8785 (tmmt) REVERT: D 514 LYS cc_start: 0.8615 (mtmm) cc_final: 0.8400 (ptpt) REVERT: D 522 LYS cc_start: 0.9095 (tttt) cc_final: 0.8711 (tttt) REVERT: D 524 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.7328 (m-80) REVERT: D 527 ASN cc_start: 0.8627 (t0) cc_final: 0.8077 (t0) REVERT: D 543 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.6514 (ttp-110) REVERT: D 557 ILE cc_start: 0.9101 (mt) cc_final: 0.8848 (mm) REVERT: D 560 LYS cc_start: 0.7767 (tppt) cc_final: 0.7536 (tppt) REVERT: D 592 MET cc_start: 0.7512 (mtm) cc_final: 0.7242 (ppp) REVERT: D 696 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8075 (mt-10) REVERT: D 754 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8463 (mp0) REVERT: D 815 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7644 (tt0) REVERT: D 841 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8228 (tp) REVERT: D 858 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8275 (mt-10) REVERT: D 939 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7444 (pm20) REVERT: D 1033 ARG cc_start: 0.8256 (ttm-80) cc_final: 0.7904 (ttm-80) REVERT: D 1073 ARG cc_start: 0.7629 (ttt180) cc_final: 0.7224 (mtp-110) REVERT: D 1131 MET cc_start: 0.8644 (tpp) cc_final: 0.8338 (mmm) REVERT: D 1132 SER cc_start: 0.8758 (t) cc_final: 0.8319 (m) REVERT: D 1137 MET cc_start: 0.8855 (mtp) cc_final: 0.8607 (mtp) REVERT: D 1156 ASN cc_start: 0.7610 (OUTLIER) cc_final: 0.7365 (p0) REVERT: D 1185 TYR cc_start: 0.9215 (t80) cc_final: 0.8714 (t80) REVERT: D 1186 ASN cc_start: 0.8980 (m-40) cc_final: 0.8666 (m110) outliers start: 64 outliers final: 30 residues processed: 422 average time/residue: 0.1703 time to fit residues: 109.8507 Evaluate side-chains 369 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 328 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1086 TRP Chi-restraints excluded: chain B residue 1156 ASN Chi-restraints excluded: chain B residue 1174 ILE Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 524 TYR Chi-restraints excluded: chain D residue 545 THR Chi-restraints excluded: chain D residue 831 ILE Chi-restraints excluded: chain D residue 841 ILE Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 939 GLU Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1086 TRP Chi-restraints excluded: chain D residue 1156 ASN Chi-restraints excluded: chain D residue 1174 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 18 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 199 optimal weight: 8.9990 chunk 124 optimal weight: 0.0270 chunk 17 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 209 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 192 optimal weight: 6.9990 overall best weight: 1.1840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.161317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.108061 restraints weight = 39717.664| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.93 r_work: 0.3294 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23488 Z= 0.131 Angle : 0.662 10.905 31818 Z= 0.324 Chirality : 0.051 0.435 3436 Planarity : 0.003 0.041 3876 Dihedral : 11.122 148.073 3478 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.74 % Allowed : 20.78 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.17), residues: 2612 helix: 0.17 (0.16), residues: 1138 sheet: -2.13 (0.33), residues: 252 loop : -2.15 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 174 TYR 0.025 0.001 TYR D 258 PHE 0.016 0.001 PHE D 109 TRP 0.005 0.001 TRP D 602 HIS 0.004 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (23488) covalent geometry : angle 0.66244 / 0.32 (31818) hydrogen bonds : bond 0.03105 / 2.03 ( 868) hydrogen bonds : angle 4.72678 / 3.22 ( 2434) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 343 time to evaluate : 0.884 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 145 ASN cc_start: 0.8989 (m-40) cc_final: 0.8681 (t0) REVERT: A 148 LYS cc_start: 0.8778 (ttpt) cc_final: 0.8546 (ttmm) REVERT: A 219 GLU cc_start: 0.8183 (pt0) cc_final: 0.7929 (pt0) REVERT: A 221 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8180 (mm-30) REVERT: A 231 ASN cc_start: 0.8597 (t0) cc_final: 0.8221 (t0) REVERT: B 179 ASN cc_start: 0.7809 (m-40) cc_final: 0.7509 (m110) REVERT: B 321 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8452 (tt) REVERT: B 354 GLU cc_start: 0.8583 (tp30) cc_final: 0.8348 (tp30) REVERT: B 362 TRP cc_start: 0.7375 (t60) cc_final: 0.6488 (t60) REVERT: B 514 LYS cc_start: 0.7992 (mmtm) cc_final: 0.7772 (mtmm) REVERT: B 522 LYS cc_start: 0.9096 (tttt) cc_final: 0.8681 (tttt) REVERT: B 524 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.7317 (m-80) REVERT: B 527 ASN cc_start: 0.8710 (t0) cc_final: 0.8171 (t0) REVERT: B 543 ARG cc_start: 0.7806 (mtm-85) cc_final: 0.7265 (mtm-85) REVERT: B 592 MET cc_start: 0.7536 (mtm) cc_final: 0.7188 (ppp) REVERT: B 754 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8340 (mp0) REVERT: B 841 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8233 (tp) REVERT: B 858 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8328 (mt-10) REVERT: B 939 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7508 (pm20) REVERT: B 1033 ARG cc_start: 0.8239 (ttm-80) cc_final: 0.7895 (ttm-80) REVERT: B 1073 ARG cc_start: 0.7626 (ttt180) cc_final: 0.7238 (mtp-110) REVERT: B 1131 MET cc_start: 0.8599 (tpp) cc_final: 0.8329 (mmm) REVERT: B 1132 SER cc_start: 0.8769 (t) cc_final: 0.8349 (m) REVERT: B 1137 MET cc_start: 0.8863 (mtp) cc_final: 0.8596 (mtp) REVERT: B 1156 ASN cc_start: 0.7577 (OUTLIER) cc_final: 0.7335 (p0) REVERT: B 1185 TYR cc_start: 0.9184 (t80) cc_final: 0.8728 (t80) REVERT: B 1186 ASN cc_start: 0.9109 (m-40) cc_final: 0.8730 (m110) REVERT: C 148 LYS cc_start: 0.8776 (ttpt) cc_final: 0.8520 (ttmm) REVERT: C 174 GLU cc_start: 0.8716 (tt0) cc_final: 0.8323 (tt0) REVERT: C 200 SER cc_start: 0.9162 (t) cc_final: 0.8506 (m) REVERT: C 231 ASN cc_start: 0.8596 (t0) cc_final: 0.8211 (t0) REVERT: D 179 ASN cc_start: 0.7702 (m-40) cc_final: 0.7420 (m110) REVERT: D 321 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8457 (tt) REVERT: D 354 GLU cc_start: 0.8572 (tp30) cc_final: 0.8337 (tp30) REVERT: D 362 TRP cc_start: 0.7375 (t60) cc_final: 0.6505 (t60) REVERT: D 522 LYS cc_start: 0.9098 (tttt) cc_final: 0.8688 (tttt) REVERT: D 524 TYR cc_start: 0.8401 (OUTLIER) cc_final: 0.7311 (m-80) REVERT: D 527 ASN cc_start: 0.8711 (t0) cc_final: 0.8164 (t0) REVERT: D 543 ARG cc_start: 0.7784 (mtm-85) cc_final: 0.6499 (ttp-110) REVERT: D 557 ILE cc_start: 0.9095 (mt) cc_final: 0.8812 (mm) REVERT: D 592 MET cc_start: 0.7540 (mtm) cc_final: 0.7189 (ppp) REVERT: D 754 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8377 (mp0) REVERT: D 841 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8228 (tp) REVERT: D 858 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8318 (mt-10) REVERT: D 939 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7509 (pm20) REVERT: D 986 MET cc_start: 0.7844 (mtm) cc_final: 0.7640 (mtp) REVERT: D 995 TYR cc_start: 0.8864 (m-10) cc_final: 0.8595 (m-10) REVERT: D 1033 ARG cc_start: 0.8269 (ttm-80) cc_final: 0.7703 (ttm-80) REVERT: D 1035 MET cc_start: 0.6103 (ptm) cc_final: 0.5698 (ppp) REVERT: D 1073 ARG cc_start: 0.7629 (ttt180) cc_final: 0.7241 (mtp-110) REVERT: D 1131 MET cc_start: 0.8609 (tpp) cc_final: 0.8333 (mmm) REVERT: D 1132 SER cc_start: 0.8747 (t) cc_final: 0.8334 (m) REVERT: D 1137 MET cc_start: 0.8882 (mtp) cc_final: 0.8610 (mtp) REVERT: D 1156 ASN cc_start: 0.7567 (OUTLIER) cc_final: 0.7327 (p0) REVERT: D 1185 TYR cc_start: 0.9200 (t80) cc_final: 0.8662 (t80) REVERT: D 1186 ASN cc_start: 0.8994 (m-40) cc_final: 0.8650 (m110) outliers start: 66 outliers final: 44 residues processed: 385 average time/residue: 0.1657 time to fit residues: 99.1561 Evaluate side-chains 369 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 315 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 939 GLU Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1086 TRP Chi-restraints excluded: chain B residue 1090 CYS Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1156 ASN Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 355 TRP Chi-restraints excluded: chain D residue 524 TYR Chi-restraints excluded: chain D residue 545 THR Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 831 ILE Chi-restraints excluded: chain D residue 841 ILE Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 939 GLU Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1086 TRP Chi-restraints excluded: chain D residue 1090 CYS Chi-restraints excluded: chain D residue 1115 LEU Chi-restraints excluded: chain D residue 1156 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 119 optimal weight: 20.0000 chunk 229 optimal weight: 0.1980 chunk 22 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 161 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.157874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.104482 restraints weight = 40192.676| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.90 r_work: 0.3250 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23488 Z= 0.203 Angle : 0.728 11.876 31818 Z= 0.356 Chirality : 0.055 0.470 3436 Planarity : 0.004 0.050 3876 Dihedral : 11.308 148.543 3478 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 3.66 % Allowed : 20.74 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.17), residues: 2612 helix: 0.09 (0.16), residues: 1140 sheet: -2.10 (0.34), residues: 252 loop : -2.12 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1054 TYR 0.022 0.002 TYR D 258 PHE 0.017 0.001 PHE D 315 TRP 0.008 0.001 TRP D1086 HIS 0.005 0.001 HIS B 797 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (23488) covalent geometry : angle 0.72827 / 0.36 (31818) hydrogen bonds : bond 0.03415 / 2.22 ( 868) hydrogen bonds : angle 4.96758 / 3.38 ( 2434) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 340 time to evaluate : 1.005 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 145 ASN cc_start: 0.8997 (m-40) cc_final: 0.8698 (t0) REVERT: A 148 LYS cc_start: 0.8814 (ttpt) cc_final: 0.8569 (ttmm) REVERT: A 174 GLU cc_start: 0.8640 (tt0) cc_final: 0.8397 (tt0) REVERT: A 176 GLU cc_start: 0.8392 (pm20) cc_final: 0.7965 (pm20) REVERT: A 221 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8044 (mp0) REVERT: A 231 ASN cc_start: 0.8599 (t0) cc_final: 0.8255 (t0) REVERT: B 5 GLU cc_start: 0.8591 (tt0) cc_final: 0.8194 (pt0) REVERT: B 179 ASN cc_start: 0.7887 (m-40) cc_final: 0.7571 (m110) REVERT: B 321 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8435 (tt) REVERT: B 362 TRP cc_start: 0.7520 (t60) cc_final: 0.6740 (t60) REVERT: B 527 ASN cc_start: 0.8755 (t0) cc_final: 0.8161 (t0) REVERT: B 534 TRP cc_start: 0.6977 (OUTLIER) cc_final: 0.6582 (m-10) REVERT: B 746 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.6796 (tpp) REVERT: B 754 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8488 (mp0) REVERT: B 815 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7753 (tt0) REVERT: B 841 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8236 (tp) REVERT: B 939 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7569 (pm20) REVERT: B 1033 ARG cc_start: 0.8214 (ttm-80) cc_final: 0.7672 (ttm-80) REVERT: B 1035 MET cc_start: 0.5982 (ptm) cc_final: 0.5684 (ppp) REVERT: B 1064 LYS cc_start: 0.8089 (mmtm) cc_final: 0.7884 (ttmm) REVERT: B 1073 ARG cc_start: 0.7692 (ttt180) cc_final: 0.7300 (mtp-110) REVERT: B 1131 MET cc_start: 0.8559 (tpp) cc_final: 0.8256 (mmm) REVERT: B 1132 SER cc_start: 0.8743 (t) cc_final: 0.8329 (m) REVERT: B 1137 MET cc_start: 0.8940 (mtp) cc_final: 0.8603 (mtp) REVERT: B 1185 TYR cc_start: 0.9263 (t80) cc_final: 0.8670 (t80) REVERT: B 1186 ASN cc_start: 0.9098 (m-40) cc_final: 0.8733 (m110) REVERT: C 148 LYS cc_start: 0.8809 (ttpt) cc_final: 0.8543 (ttmm) REVERT: C 174 GLU cc_start: 0.8770 (tt0) cc_final: 0.8336 (tt0) REVERT: C 231 ASN cc_start: 0.8604 (t0) cc_final: 0.8262 (t0) REVERT: D 5 GLU cc_start: 0.8599 (tt0) cc_final: 0.8202 (pt0) REVERT: D 174 ARG cc_start: 0.8459 (ttm-80) cc_final: 0.8252 (ttm-80) REVERT: D 179 ASN cc_start: 0.7806 (m-40) cc_final: 0.7487 (m110) REVERT: D 321 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8449 (tt) REVERT: D 362 TRP cc_start: 0.7510 (t60) cc_final: 0.6738 (t60) REVERT: D 514 LYS cc_start: 0.8480 (ptpt) cc_final: 0.8278 (ptpp) REVERT: D 527 ASN cc_start: 0.8719 (t0) cc_final: 0.7995 (t0) REVERT: D 534 TRP cc_start: 0.7009 (OUTLIER) cc_final: 0.6601 (m-10) REVERT: D 543 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.7386 (mtm-85) REVERT: D 557 ILE cc_start: 0.9097 (mt) cc_final: 0.8863 (mm) REVERT: D 696 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8260 (mt-10) REVERT: D 722 MET cc_start: 0.8296 (ttm) cc_final: 0.8096 (ttm) REVERT: D 746 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.6781 (tpp) REVERT: D 754 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8488 (mp0) REVERT: D 815 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7754 (tt0) REVERT: D 841 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8233 (tp) REVERT: D 939 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7586 (pm20) REVERT: D 995 TYR cc_start: 0.8930 (m-10) cc_final: 0.8628 (m-10) REVERT: D 1033 ARG cc_start: 0.8292 (ttm-80) cc_final: 0.7810 (ttm-80) REVERT: D 1073 ARG cc_start: 0.7687 (ttt180) cc_final: 0.7293 (mtp-110) REVERT: D 1131 MET cc_start: 0.8561 (tpp) cc_final: 0.8253 (mmm) REVERT: D 1132 SER cc_start: 0.8736 (t) cc_final: 0.8318 (m) REVERT: D 1137 MET cc_start: 0.8944 (mtp) cc_final: 0.8604 (mtp) REVERT: D 1185 TYR cc_start: 0.9262 (t80) cc_final: 0.8664 (t80) REVERT: D 1186 ASN cc_start: 0.9018 (m-40) cc_final: 0.8673 (m110) outliers start: 88 outliers final: 66 residues processed: 392 average time/residue: 0.1644 time to fit residues: 100.3681 Evaluate side-chains 393 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 317 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 534 TRP Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 746 MET Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 939 GLU Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1086 TRP Chi-restraints excluded: chain B residue 1090 CYS Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1205 LYS Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 355 TRP Chi-restraints excluded: chain D residue 534 TRP Chi-restraints excluded: chain D residue 545 THR Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 746 MET Chi-restraints excluded: chain D residue 831 ILE Chi-restraints excluded: chain D residue 841 ILE Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 890 TRP Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 939 GLU Chi-restraints excluded: chain D residue 977 THR Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1086 TRP Chi-restraints excluded: chain D residue 1090 CYS Chi-restraints excluded: chain D residue 1115 LEU Chi-restraints excluded: chain D residue 1205 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 195 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 202 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 194 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.159834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.106533 restraints weight = 39976.179| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.89 r_work: 0.3282 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23488 Z= 0.157 Angle : 0.707 12.028 31818 Z= 0.344 Chirality : 0.053 0.449 3436 Planarity : 0.004 0.052 3876 Dihedral : 11.229 150.197 3478 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.20 % Allowed : 22.40 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.17), residues: 2612 helix: 0.18 (0.16), residues: 1138 sheet: -2.17 (0.33), residues: 256 loop : -2.05 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1054 TYR 0.023 0.001 TYR D 258 PHE 0.017 0.001 PHE D1027 TRP 0.005 0.001 TRP D1086 HIS 0.004 0.001 HIS B 797 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (23488) covalent geometry : angle 0.70705 / 0.34 (31818) hydrogen bonds : bond 0.03178 / 2.07 ( 868) hydrogen bonds : angle 4.82198 / 3.28 ( 2434) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 343 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASN cc_start: 0.8986 (m-40) cc_final: 0.8780 (m-40) REVERT: A 148 LYS cc_start: 0.8817 (ttpt) cc_final: 0.8577 (ttmm) REVERT: A 174 GLU cc_start: 0.8641 (tt0) cc_final: 0.8352 (tt0) REVERT: A 176 GLU cc_start: 0.8443 (pm20) cc_final: 0.8048 (pm20) REVERT: A 231 ASN cc_start: 0.8603 (t0) cc_final: 0.8277 (t0) REVERT: B 5 GLU cc_start: 0.8558 (tt0) cc_final: 0.8203 (tt0) REVERT: B 179 ASN cc_start: 0.7896 (m-40) cc_final: 0.7580 (m110) REVERT: B 321 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8445 (tt) REVERT: B 362 TRP cc_start: 0.7492 (t60) cc_final: 0.6707 (t60) REVERT: B 436 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.6622 (m-10) REVERT: B 527 ASN cc_start: 0.8719 (t0) cc_final: 0.8045 (t0) REVERT: B 543 ARG cc_start: 0.7841 (mtm-85) cc_final: 0.6787 (ttp-110) REVERT: B 560 LYS cc_start: 0.8292 (tppt) cc_final: 0.8003 (tppt) REVERT: B 747 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.8098 (ptt90) REVERT: B 754 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8369 (mp0) REVERT: B 815 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7759 (tt0) REVERT: B 841 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8234 (tp) REVERT: B 939 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7491 (pm20) REVERT: B 1033 ARG cc_start: 0.8287 (ttm-80) cc_final: 0.7699 (ttm-80) REVERT: B 1035 MET cc_start: 0.5920 (ptm) cc_final: 0.5694 (ppp) REVERT: B 1073 ARG cc_start: 0.7666 (ttt180) cc_final: 0.7293 (mtp-110) REVERT: B 1132 SER cc_start: 0.8708 (t) cc_final: 0.8329 (m) REVERT: B 1137 MET cc_start: 0.8860 (mtp) cc_final: 0.8588 (mtp) REVERT: B 1156 ASN cc_start: 0.7574 (OUTLIER) cc_final: 0.7355 (p0) REVERT: B 1185 TYR cc_start: 0.9216 (t80) cc_final: 0.8681 (t80) REVERT: B 1186 ASN cc_start: 0.9108 (m-40) cc_final: 0.8725 (m110) REVERT: C 148 LYS cc_start: 0.8791 (ttpt) cc_final: 0.8531 (ttmm) REVERT: C 174 GLU cc_start: 0.8742 (tt0) cc_final: 0.8393 (tt0) REVERT: C 176 GLU cc_start: 0.8228 (pm20) cc_final: 0.7695 (pm20) REVERT: C 231 ASN cc_start: 0.8607 (t0) cc_final: 0.8266 (t0) REVERT: D 5 GLU cc_start: 0.8580 (tt0) cc_final: 0.8239 (tt0) REVERT: D 179 ASN cc_start: 0.7850 (m-40) cc_final: 0.7531 (m110) REVERT: D 321 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8451 (tt) REVERT: D 362 TRP cc_start: 0.7480 (t60) cc_final: 0.6695 (t60) REVERT: D 527 ASN cc_start: 0.8671 (t0) cc_final: 0.8052 (t0) REVERT: D 543 ARG cc_start: 0.7738 (mtm-85) cc_final: 0.7516 (mtm-85) REVERT: D 696 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8242 (mt-10) REVERT: D 722 MET cc_start: 0.8345 (ttm) cc_final: 0.8118 (ttm) REVERT: D 754 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8352 (mp0) REVERT: D 841 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8236 (tp) REVERT: D 939 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7516 (pm20) REVERT: D 995 TYR cc_start: 0.8863 (m-80) cc_final: 0.8588 (m-10) REVERT: D 1073 ARG cc_start: 0.7666 (ttt180) cc_final: 0.7291 (mtp-110) REVERT: D 1132 SER cc_start: 0.8732 (t) cc_final: 0.8353 (m) REVERT: D 1137 MET cc_start: 0.8861 (mtp) cc_final: 0.8592 (mtp) REVERT: D 1185 TYR cc_start: 0.9233 (t80) cc_final: 0.8680 (t80) REVERT: D 1186 ASN cc_start: 0.9007 (m-40) cc_final: 0.8660 (m110) outliers start: 77 outliers final: 59 residues processed: 387 average time/residue: 0.1628 time to fit residues: 98.6780 Evaluate side-chains 384 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 316 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 747 ARG Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 939 GLU Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1086 TRP Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1156 ASN Chi-restraints excluded: chain B residue 1205 LYS Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 81 PHE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 355 TRP Chi-restraints excluded: chain D residue 545 THR Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 831 ILE Chi-restraints excluded: chain D residue 841 ILE Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 939 GLU Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1086 TRP Chi-restraints excluded: chain D residue 1115 LEU Chi-restraints excluded: chain D residue 1205 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 97 optimal weight: 3.9990 chunk 4 optimal weight: 0.0470 chunk 74 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 109 optimal weight: 0.4980 chunk 84 optimal weight: 0.1980 chunk 90 optimal weight: 0.9990 overall best weight: 0.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 803 ASN ** D 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 975 GLN ** D1107 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 = 0.4163 r_free = 0.4163 target = 0.164145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.111127 restraints weight = 39482.256| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.95 r_work: 0.3334 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23488 Z= 0.113 Angle : 0.670 10.793 31818 Z= 0.325 Chirality : 0.049 0.425 3436 Planarity : 0.003 0.048 3876 Dihedral : 11.095 149.469 3478 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.78 % Allowed : 23.44 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.17), residues: 2612 helix: 0.35 (0.16), residues: 1136 sheet: -2.13 (0.32), residues: 266 loop : -1.97 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1054 TYR 0.043 0.001 TYR D 115 PHE 0.016 0.001 PHE B1027 TRP 0.007 0.001 TRP A 178 HIS 0.003 0.001 HIS B 797 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (23488) covalent geometry : angle 0.66953 / 0.33 (31818) hydrogen bonds : bond 0.02898 / 1.89 ( 868) hydrogen bonds : angle 4.61199 / 3.14 ( 2434) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 364 time to evaluate : 0.896 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 148 LYS cc_start: 0.8770 (ttpt) cc_final: 0.8523 (ttmm) REVERT: A 166 ASP cc_start: 0.7533 (t70) cc_final: 0.7068 (p0) REVERT: A 174 GLU cc_start: 0.8583 (tt0) cc_final: 0.8265 (tt0) REVERT: A 176 GLU cc_start: 0.8356 (pm20) cc_final: 0.7905 (pm20) REVERT: A 200 SER cc_start: 0.9156 (t) cc_final: 0.8686 (m) REVERT: A 231 ASN cc_start: 0.8598 (t0) cc_final: 0.8265 (t0) REVERT: B 5 GLU cc_start: 0.8487 (tt0) cc_final: 0.8153 (tt0) REVERT: B 179 ASN cc_start: 0.7934 (m-40) cc_final: 0.7618 (m110) REVERT: B 257 GLU cc_start: 0.7890 (tp30) cc_final: 0.7676 (tp30) REVERT: B 321 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8354 (tt) REVERT: B 362 TRP cc_start: 0.7427 (t60) cc_final: 0.6597 (t60) REVERT: B 436 PHE cc_start: 0.6963 (OUTLIER) cc_final: 0.6396 (m-10) REVERT: B 514 LYS cc_start: 0.8204 (ptpp) cc_final: 0.7994 (ptpt) REVERT: B 527 ASN cc_start: 0.8571 (t0) cc_final: 0.7870 (t0) REVERT: B 543 ARG cc_start: 0.7749 (mtm-85) cc_final: 0.6705 (ttp-110) REVERT: B 560 LYS cc_start: 0.7935 (tppt) cc_final: 0.7591 (tppt) REVERT: B 581 ILE cc_start: 0.7936 (mm) cc_final: 0.7713 (mm) REVERT: B 754 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8346 (mp0) REVERT: B 778 THR cc_start: 0.8957 (p) cc_final: 0.8728 (p) REVERT: B 841 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8185 (tp) REVERT: B 858 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8327 (mt-10) REVERT: B 1033 ARG cc_start: 0.8168 (ttm-80) cc_final: 0.7700 (ttm-80) REVERT: B 1035 MET cc_start: 0.5867 (ptm) cc_final: 0.5536 (ppp) REVERT: B 1064 LYS cc_start: 0.7374 (ttmm) cc_final: 0.7174 (ttmm) REVERT: B 1073 ARG cc_start: 0.7446 (ttt180) cc_final: 0.7196 (mtp-110) REVERT: B 1112 ARG cc_start: 0.7493 (mtm110) cc_final: 0.7273 (mtm-85) REVERT: B 1115 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7506 (mm) REVERT: B 1132 SER cc_start: 0.8750 (t) cc_final: 0.8417 (m) REVERT: B 1156 ASN cc_start: 0.7582 (OUTLIER) cc_final: 0.7337 (p0) REVERT: B 1185 TYR cc_start: 0.9144 (t80) cc_final: 0.8721 (t80) REVERT: B 1186 ASN cc_start: 0.9109 (m-40) cc_final: 0.8717 (m110) REVERT: C 148 LYS cc_start: 0.8768 (ttpt) cc_final: 0.8521 (ttmm) REVERT: C 166 ASP cc_start: 0.7500 (t70) cc_final: 0.7034 (p0) REVERT: C 174 GLU cc_start: 0.8646 (tt0) cc_final: 0.8207 (tt0) REVERT: C 200 SER cc_start: 0.9172 (t) cc_final: 0.8717 (m) REVERT: C 231 ASN cc_start: 0.8615 (t0) cc_final: 0.8277 (t0) REVERT: D 5 GLU cc_start: 0.8502 (tt0) cc_final: 0.8161 (tt0) REVERT: D 179 ASN cc_start: 0.7916 (m-40) cc_final: 0.7596 (m110) REVERT: D 257 GLU cc_start: 0.7890 (tp30) cc_final: 0.7674 (tp30) REVERT: D 321 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8360 (tt) REVERT: D 362 TRP cc_start: 0.7430 (t60) cc_final: 0.6597 (t60) REVERT: D 436 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.6472 (m-10) REVERT: D 527 ASN cc_start: 0.8576 (t0) cc_final: 0.8016 (t0) REVERT: D 696 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8237 (mt-10) REVERT: D 754 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8363 (mp0) REVERT: D 778 THR cc_start: 0.8936 (p) cc_final: 0.8706 (p) REVERT: D 841 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8169 (tp) REVERT: D 858 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8296 (mt-10) REVERT: D 939 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7386 (pm20) REVERT: D 978 ASN cc_start: 0.8791 (m-40) cc_final: 0.8333 (m-40) REVERT: D 995 TYR cc_start: 0.8785 (m-80) cc_final: 0.8566 (m-10) REVERT: D 1073 ARG cc_start: 0.7449 (ttt180) cc_final: 0.7198 (mtp-110) REVERT: D 1115 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7456 (mm) REVERT: D 1132 SER cc_start: 0.8755 (t) cc_final: 0.8421 (m) REVERT: D 1156 ASN cc_start: 0.7572 (OUTLIER) cc_final: 0.7349 (p0) REVERT: D 1185 TYR cc_start: 0.9151 (t80) cc_final: 0.8673 (t80) REVERT: D 1186 ASN cc_start: 0.9068 (m-40) cc_final: 0.8691 (m110) outliers start: 67 outliers final: 45 residues processed: 403 average time/residue: 0.1515 time to fit residues: 94.3847 Evaluate side-chains 394 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 338 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 939 GLU Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1156 ASN Chi-restraints excluded: chain B residue 1205 LYS Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 81 PHE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 436 PHE Chi-restraints excluded: chain D residue 545 THR Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 831 ILE Chi-restraints excluded: chain D residue 841 ILE Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 890 TRP Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 939 GLU Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1115 LEU Chi-restraints excluded: chain D residue 1156 ASN Chi-restraints excluded: chain D residue 1205 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 59 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 231 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 803 ASN ** D 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 975 GLN ** D1107 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 = 0.4128 r_free = 0.4128 target = 0.161156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.107847 restraints weight = 39723.812| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.90 r_work: 0.3299 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23488 Z= 0.162 Angle : 0.723 11.218 31818 Z= 0.350 Chirality : 0.053 0.468 3436 Planarity : 0.004 0.047 3876 Dihedral : 11.099 146.381 3478 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 3.12 % Allowed : 23.69 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.17), residues: 2612 helix: 0.30 (0.16), residues: 1136 sheet: -2.09 (0.33), residues: 256 loop : -1.93 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 935 TYR 0.041 0.002 TYR D 258 PHE 0.018 0.001 PHE D1027 TRP 0.010 0.001 TRP D 999 HIS 0.004 0.001 HIS D 797 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (23488) covalent geometry : angle 0.72339 / 0.35 (31818) hydrogen bonds : bond 0.03180 / 2.05 ( 868) hydrogen bonds : angle 4.73955 / 3.23 ( 2434) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 328 time to evaluate : 0.832 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 148 LYS cc_start: 0.8801 (ttpt) cc_final: 0.8561 (ttmm) REVERT: A 174 GLU cc_start: 0.8644 (tt0) cc_final: 0.8295 (tt0) REVERT: A 176 GLU cc_start: 0.8407 (pm20) cc_final: 0.7952 (pm20) REVERT: A 200 SER cc_start: 0.9297 (t) cc_final: 0.8771 (m) REVERT: A 231 ASN cc_start: 0.8598 (t0) cc_final: 0.8273 (t0) REVERT: B 5 GLU cc_start: 0.8538 (tt0) cc_final: 0.8182 (tt0) REVERT: B 321 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8370 (tt) REVERT: B 436 PHE cc_start: 0.7205 (OUTLIER) cc_final: 0.6589 (m-10) REVERT: B 514 LYS cc_start: 0.8264 (ptpp) cc_final: 0.8063 (ptpt) REVERT: B 527 ASN cc_start: 0.8604 (t0) cc_final: 0.8014 (t0) REVERT: B 747 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8119 (ptt-90) REVERT: B 754 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8396 (mp0) REVERT: B 778 THR cc_start: 0.8990 (p) cc_final: 0.8767 (p) REVERT: B 815 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7663 (tt0) REVERT: B 841 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8260 (tp) REVERT: B 935 ARG cc_start: 0.8141 (ptp90) cc_final: 0.7795 (ttp-110) REVERT: B 939 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7561 (pm20) REVERT: B 1033 ARG cc_start: 0.8251 (ttm-80) cc_final: 0.7666 (ttm-80) REVERT: B 1035 MET cc_start: 0.6100 (ptm) cc_final: 0.5771 (ppp) REVERT: B 1073 ARG cc_start: 0.7496 (ttt180) cc_final: 0.7230 (mtp-110) REVERT: B 1132 SER cc_start: 0.8762 (t) cc_final: 0.8295 (p) REVERT: B 1185 TYR cc_start: 0.9205 (t80) cc_final: 0.8704 (t80) REVERT: B 1186 ASN cc_start: 0.9124 (m-40) cc_final: 0.8716 (m110) REVERT: C 148 LYS cc_start: 0.8819 (ttpt) cc_final: 0.8587 (ttmm) REVERT: C 174 GLU cc_start: 0.8670 (tt0) cc_final: 0.8215 (tt0) REVERT: C 200 SER cc_start: 0.9296 (t) cc_final: 0.8790 (m) REVERT: C 231 ASN cc_start: 0.8608 (t0) cc_final: 0.8249 (t0) REVERT: D 5 GLU cc_start: 0.8564 (tt0) cc_final: 0.8215 (tt0) REVERT: D 179 ASN cc_start: 0.7929 (m-40) cc_final: 0.7590 (m110) REVERT: D 321 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8435 (tt) REVERT: D 436 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.6582 (m-10) REVERT: D 456 MET cc_start: 0.8207 (mmm) cc_final: 0.7940 (mmm) REVERT: D 526 GLN cc_start: 0.8601 (mt0) cc_final: 0.7951 (mp10) REVERT: D 527 ASN cc_start: 0.8675 (t0) cc_final: 0.7964 (t0) REVERT: D 530 PHE cc_start: 0.8127 (t80) cc_final: 0.7889 (t80) REVERT: D 543 ARG cc_start: 0.7652 (mtm-85) cc_final: 0.7390 (mtm-85) REVERT: D 722 MET cc_start: 0.8223 (ttm) cc_final: 0.7970 (ttm) REVERT: D 747 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.8113 (ptt-90) REVERT: D 754 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8380 (mp0) REVERT: D 778 THR cc_start: 0.8996 (p) cc_final: 0.8772 (p) REVERT: D 841 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8255 (tp) REVERT: D 935 ARG cc_start: 0.8158 (ptp90) cc_final: 0.7805 (ttp-110) REVERT: D 939 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7586 (pm20) REVERT: D 1073 ARG cc_start: 0.7498 (ttt180) cc_final: 0.7241 (mtp-110) REVERT: D 1132 SER cc_start: 0.8766 (t) cc_final: 0.8409 (m) REVERT: D 1156 ASN cc_start: 0.7569 (OUTLIER) cc_final: 0.7365 (p0) REVERT: D 1185 TYR cc_start: 0.9202 (t80) cc_final: 0.8703 (t80) REVERT: D 1186 ASN cc_start: 0.9130 (m-40) cc_final: 0.8747 (m110) outliers start: 75 outliers final: 55 residues processed: 370 average time/residue: 0.1643 time to fit residues: 94.9663 Evaluate side-chains 386 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 320 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 747 ARG Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 939 GLU Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1086 TRP Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1205 LYS Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 81 PHE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 436 PHE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 747 ARG Chi-restraints excluded: chain D residue 831 ILE Chi-restraints excluded: chain D residue 841 ILE Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 890 TRP Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 939 GLU Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1086 TRP Chi-restraints excluded: chain D residue 1090 CYS Chi-restraints excluded: chain D residue 1115 LEU Chi-restraints excluded: chain D residue 1156 ASN Chi-restraints excluded: chain D residue 1205 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 29 optimal weight: 6.9990 chunk 260 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 195 optimal weight: 0.0170 chunk 68 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 129 optimal weight: 0.2980 chunk 179 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 overall best weight: 1.2624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 889 ASN ** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.162466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.109085 restraints weight = 39692.258| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.95 r_work: 0.3318 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23488 Z= 0.139 Angle : 0.715 11.101 31818 Z= 0.346 Chirality : 0.052 0.483 3436 Planarity : 0.003 0.048 3876 Dihedral : 11.053 147.114 3478 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.66 % Allowed : 24.23 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.17), residues: 2612 helix: 0.31 (0.16), residues: 1136 sheet: -2.07 (0.33), residues: 256 loop : -1.91 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1033 TYR 0.026 0.001 TYR D 115 PHE 0.018 0.001 PHE B1027 TRP 0.015 0.001 TRP D 362 HIS 0.003 0.001 HIS D 797 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (23488) covalent geometry : angle 0.71486 / 0.35 (31818) hydrogen bonds : bond 0.03107 / 2.01 ( 868) hydrogen bonds : angle 4.73229 / 3.23 ( 2434) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 332 time to evaluate : 0.871 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 148 LYS cc_start: 0.8772 (ttpt) cc_final: 0.8542 (ttmm) REVERT: A 166 ASP cc_start: 0.7523 (t70) cc_final: 0.7213 (p0) REVERT: A 174 GLU cc_start: 0.8609 (tt0) cc_final: 0.8254 (tt0) REVERT: A 176 GLU cc_start: 0.8402 (pm20) cc_final: 0.7947 (pm20) REVERT: A 200 SER cc_start: 0.9283 (t) cc_final: 0.8759 (m) REVERT: A 231 ASN cc_start: 0.8574 (t0) cc_final: 0.8216 (t0) REVERT: B 5 GLU cc_start: 0.8520 (tt0) cc_final: 0.8162 (tt0) REVERT: B 260 ASN cc_start: 0.9055 (t0) cc_final: 0.8823 (m-40) REVERT: B 262 TYR cc_start: 0.6942 (t80) cc_final: 0.6689 (t80) REVERT: B 321 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8364 (tt) REVERT: B 436 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.6521 (m-10) REVERT: B 456 MET cc_start: 0.8126 (mmm) cc_final: 0.7824 (mmp) REVERT: B 527 ASN cc_start: 0.8567 (t0) cc_final: 0.7969 (t0) REVERT: B 754 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8367 (mp0) REVERT: B 778 THR cc_start: 0.8977 (p) cc_final: 0.8760 (p) REVERT: B 841 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8215 (tp) REVERT: B 858 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8376 (mt-10) REVERT: B 935 ARG cc_start: 0.8134 (ptp90) cc_final: 0.7774 (ttp-110) REVERT: B 939 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7474 (pm20) REVERT: B 1033 ARG cc_start: 0.8169 (ttm-80) cc_final: 0.7608 (ttm-80) REVERT: B 1035 MET cc_start: 0.6011 (ptm) cc_final: 0.5687 (ppp) REVERT: B 1064 LYS cc_start: 0.7419 (ttmm) cc_final: 0.7188 (ttmm) REVERT: B 1073 ARG cc_start: 0.7455 (ttt180) cc_final: 0.7187 (mtp-110) REVERT: B 1132 SER cc_start: 0.8773 (t) cc_final: 0.8438 (m) REVERT: B 1156 ASN cc_start: 0.7479 (OUTLIER) cc_final: 0.7256 (p0) REVERT: B 1185 TYR cc_start: 0.9192 (t80) cc_final: 0.8686 (t80) REVERT: B 1186 ASN cc_start: 0.9142 (m-40) cc_final: 0.8707 (m110) REVERT: C 148 LYS cc_start: 0.8789 (ttpt) cc_final: 0.8567 (ttmm) REVERT: C 166 ASP cc_start: 0.7498 (t70) cc_final: 0.7154 (p0) REVERT: C 174 GLU cc_start: 0.8648 (tt0) cc_final: 0.8214 (tt0) REVERT: C 200 SER cc_start: 0.9259 (t) cc_final: 0.8766 (m) REVERT: C 231 ASN cc_start: 0.8604 (t0) cc_final: 0.8243 (t0) REVERT: D 5 GLU cc_start: 0.8559 (tt0) cc_final: 0.8214 (tt0) REVERT: D 262 TYR cc_start: 0.6953 (t80) cc_final: 0.6706 (t80) REVERT: D 321 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8362 (tt) REVERT: D 436 PHE cc_start: 0.7028 (OUTLIER) cc_final: 0.6430 (m-10) REVERT: D 526 GLN cc_start: 0.8564 (mt0) cc_final: 0.7928 (mp10) REVERT: D 527 ASN cc_start: 0.8662 (t0) cc_final: 0.7817 (t0) REVERT: D 722 MET cc_start: 0.8235 (ttm) cc_final: 0.7970 (ttm) REVERT: D 754 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8366 (mp0) REVERT: D 778 THR cc_start: 0.8958 (p) cc_final: 0.8737 (p) REVERT: D 841 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8213 (tp) REVERT: D 858 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8351 (mt-10) REVERT: D 935 ARG cc_start: 0.8137 (ptp90) cc_final: 0.7781 (ttp-110) REVERT: D 939 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7495 (pm20) REVERT: D 1064 LYS cc_start: 0.7281 (ttmm) cc_final: 0.7077 (ttmm) REVERT: D 1073 ARG cc_start: 0.7464 (ttt180) cc_final: 0.7201 (mtp-110) REVERT: D 1132 SER cc_start: 0.8774 (t) cc_final: 0.8435 (m) REVERT: D 1156 ASN cc_start: 0.7483 (OUTLIER) cc_final: 0.7278 (p0) REVERT: D 1185 TYR cc_start: 0.9192 (t80) cc_final: 0.8678 (t80) REVERT: D 1186 ASN cc_start: 0.9156 (m-40) cc_final: 0.8725 (m110) outliers start: 64 outliers final: 52 residues processed: 367 average time/residue: 0.1686 time to fit residues: 96.9613 Evaluate side-chains 380 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 318 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 939 GLU Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1156 ASN Chi-restraints excluded: chain B residue 1205 LYS Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 436 PHE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 819 LEU Chi-restraints excluded: chain D residue 831 ILE Chi-restraints excluded: chain D residue 841 ILE Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 890 TRP Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 939 GLU Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1115 LEU Chi-restraints excluded: chain D residue 1156 ASN Chi-restraints excluded: chain D residue 1205 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 139 optimal weight: 4.9990 chunk 111 optimal weight: 0.0470 chunk 51 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 237 optimal weight: 0.6980 chunk 201 optimal weight: 0.9990 chunk 194 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 803 ASN ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 GLN ** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 803 ASN ** D 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 889 ASN D 975 GLN ** D1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.164850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.111805 restraints weight = 39822.063| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.98 r_work: 0.3343 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23488 Z= 0.119 Angle : 0.700 11.182 31818 Z= 0.339 Chirality : 0.050 0.516 3436 Planarity : 0.003 0.043 3876 Dihedral : 10.985 146.019 3478 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.58 % Allowed : 24.31 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.17), residues: 2612 helix: 0.37 (0.16), residues: 1140 sheet: -1.91 (0.33), residues: 256 loop : -1.85 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1033 TYR 0.030 0.001 TYR B 115 PHE 0.018 0.001 PHE D1027 TRP 0.012 0.001 TRP D 362 HIS 0.005 0.001 HIS B 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (23488) covalent geometry : angle 0.69987 / 0.34 (31818) hydrogen bonds : bond 0.02955 / 1.91 ( 868) hydrogen bonds : angle 4.60143 / 3.14 ( 2434) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6200.00 seconds wall clock time: 107 minutes 1.71 seconds (6421.71 seconds total)