Starting phenix.real_space_refine on Tue May 5 23:34:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w2y_65584/05_2026/9w2y_65584.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w2y_65584/05_2026/9w2y_65584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w2y_65584/05_2026/9w2y_65584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w2y_65584/05_2026/9w2y_65584.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w2y_65584/05_2026/9w2y_65584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w2y_65584/05_2026/9w2y_65584.map" } resolution = 2.4 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= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 10 7.16 5 S 160 5.16 5 C 21276 2.51 5 N 5744 2.21 5 O 6076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 179 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33266 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3458 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain: "B" Number of atoms: 3181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3181 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 407} Chain: "C" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3003 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 355} Chain: "D" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1919 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 218} Chain: "E" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1519 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "F" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 911 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "G" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 628 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "H" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 548 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "I" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 406 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 5, 'TRANS': 51} Chain: "J" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 502 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "K" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 425 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "L" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3458 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain: "M" Number of atoms: 3181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3181 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 407} Chain: "N" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3003 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 355} Chain: "O" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1919 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 218} Chain: "P" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1519 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "Q" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 911 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "R" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 628 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "S" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 548 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "T" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 406 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 5, 'TRANS': 51} Chain: "U" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 502 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "V" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 425 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12655 SG CYS E 139 45.049 47.975 23.442 1.00115.95 S ATOM 12690 SG CYS E 144 48.862 48.558 21.139 1.00133.55 S ATOM 12791 SG CYS E 158 45.511 48.334 20.442 1.00120.13 S ATOM 12804 SG CYS E 160 48.892 46.229 21.505 1.00147.32 S ATOM 29155 SG CYS P 139 95.540 84.946 36.604 1.00175.81 S Time building chain proxies: 6.79, per 1000 atoms: 0.20 Number of scatterers: 33266 At special positions: 0 Unit cell: (131.89, 137.34, 172.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 10 26.01 S 160 16.00 O 6076 8.00 N 5744 7.00 C 21276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 24 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 54 " distance=2.03 Simple disulfide: pdb=" SG CYS P 144 " - pdb=" SG CYS P 160 " distance=2.04 Simple disulfide: pdb=" SG CYS S 24 " - pdb=" SG CYS S 30 " distance=2.06 Simple disulfide: pdb=" SG CYS S 24 " - pdb=" SG CYS S 68 " distance=2.04 Simple disulfide: pdb=" SG CYS S 40 " - pdb=" SG CYS S 54 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 200 " pdb="FE2 FES E 200 " - pdb=" ND1 HIS E 141 " pdb="FE2 FES E 200 " - pdb=" ND1 HIS E 161 " pdb="FE1 FES E 200 " - pdb=" SG CYS E 158 " pdb="FE1 FES E 200 " - pdb=" SG CYS E 160 " pdb="FE1 FES E 200 " - pdb=" SG CYS E 144 " pdb="FE1 FES E 200 " - pdb=" SG CYS E 139 " pdb=" FES P 200 " pdb="FE1 FES P 200 " - pdb=" NE2 HIS P 141 " pdb="FE1 FES P 200 " - pdb=" NE2 HIS P 161 " pdb="FE2 FES P 200 " - pdb=" SG CYS P 139 " pdb="FE2 FES P 200 " - pdb=" SG CYS P 158 " Number of angles added : 13 8324 Ramachandran restraints generated. 4162 Oldfield, 0 Emsley, 4162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7848 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 20 sheets defined 57.0% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 removed outlier: 3.643A pdb=" N GLN A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 48 Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.880A pdb=" N LEU A 75 " --> pdb=" O PRO A 71 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 119 Processing helix chain 'A' and resid 123 through 142 removed outlier: 3.704A pdb=" N ASP A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 178 through 190 removed outlier: 3.549A pdb=" N LEU A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.583A pdb=" N LEU A 290 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 330 through 348 Processing helix chain 'A' and resid 350 through 369 removed outlier: 3.591A pdb=" N VAL A 354 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 386 removed outlier: 3.730A pdb=" N VAL A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 400 Processing helix chain 'A' and resid 403 through 416 Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 64 through 72 removed outlier: 3.656A pdb=" N LEU B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 92 removed outlier: 3.869A pdb=" N VAL B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 129 removed outlier: 4.168A pdb=" N LEU B 119 " --> pdb=" O ASP B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 141 Processing helix chain 'B' and resid 142 through 152 removed outlier: 4.046A pdb=" N ILE B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 168 removed outlier: 3.926A pdb=" N HIS B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.585A pdb=" N LEU B 191 " --> pdb=" O THR B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 212 through 224 removed outlier: 3.608A pdb=" N LEU B 216 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 280 removed outlier: 4.081A pdb=" N ALA B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 301 removed outlier: 3.512A pdb=" N LYS B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 350 removed outlier: 3.715A pdb=" N VAL B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY B 350 " --> pdb=" O THR B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 372 removed outlier: 3.561A pdb=" N VAL B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 389 Processing helix chain 'B' and resid 394 through 403 Processing helix chain 'B' and resid 406 through 419 removed outlier: 3.661A pdb=" N VAL B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 7 Processing helix chain 'C' and resid 8 through 19 Processing helix chain 'C' and resid 28 through 31 Processing helix chain 'C' and resid 32 through 53 removed outlier: 3.657A pdb=" N LEU C 36 " --> pdb=" O ASN C 32 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY C 38 " --> pdb=" O GLY C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 72 Processing helix chain 'C' and resid 75 through 104 removed outlier: 3.574A pdb=" N ILE C 79 " --> pdb=" O TYR C 75 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 108 removed outlier: 3.967A pdb=" N THR C 108 " --> pdb=" O GLY C 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 105 through 108' Processing helix chain 'C' and resid 109 through 131 removed outlier: 3.688A pdb=" N TYR C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 148 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 156 through 166 Processing helix chain 'C' and resid 171 through 201 removed outlier: 3.523A pdb=" N ALA C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) Proline residue: C 186 - end of helix Processing helix chain 'C' and resid 220 through 246 removed outlier: 7.123A pdb=" N THR C 225 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.517A pdb=" N ILE C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 300 removed outlier: 4.034A pdb=" N ILE C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 308 Proline residue: C 305 - end of helix removed outlier: 3.909A pdb=" N HIS C 308 " --> pdb=" O PRO C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 317 removed outlier: 4.371A pdb=" N PHE C 317 " --> pdb=" O SER C 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 314 through 317' Processing helix chain 'C' and resid 318 through 340 removed outlier: 3.968A pdb=" N GLY C 340 " --> pdb=" O THR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 364 removed outlier: 3.666A pdb=" N PHE C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 377 removed outlier: 3.505A pdb=" N THR C 368 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 37 through 40 Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 57 through 66 Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 178 through 195 Processing helix chain 'D' and resid 197 through 232 Proline residue: D 217 - end of helix removed outlier: 3.570A pdb=" N LYS D 226 " --> pdb=" O MET D 222 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL D 229 " --> pdb=" O HIS D 225 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LEU D 230 " --> pdb=" O LYS D 226 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 5 removed outlier: 3.535A pdb=" N ASP E 4 " --> pdb=" O SER E 1 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 19 removed outlier: 3.575A pdb=" N LEU E 19 " --> pdb=" O PRO E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 61 removed outlier: 4.048A pdb=" N VAL E 39 " --> pdb=" O PHE E 35 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR E 40 " --> pdb=" O SER E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 70 removed outlier: 4.344A pdb=" N VAL E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU E 69 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 111 Processing helix chain 'E' and resid 122 through 127 Processing helix chain 'F' and resid 8 through 25 removed outlier: 3.763A pdb=" N TRP F 12 " --> pdb=" O ALA F 8 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY F 25 " --> pdb=" O TYR F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 32 through 37 removed outlier: 3.857A pdb=" N ILE F 37 " --> pdb=" O ASP F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 49 removed outlier: 3.601A pdb=" N ARG F 49 " --> pdb=" O GLU F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 71 removed outlier: 3.842A pdb=" N ARG F 71 " --> pdb=" O ASP F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 80 Processing helix chain 'F' and resid 90 through 110 removed outlier: 3.524A pdb=" N TRP F 107 " --> pdb=" O GLU F 103 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA F 108 " --> pdb=" O ARG F 104 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS F 110 " --> pdb=" O GLU F 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 23 removed outlier: 3.791A pdb=" N GLN G 23 " --> pdb=" O PRO G 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 20 through 23' Processing helix chain 'G' and resid 32 through 70 removed outlier: 3.793A pdb=" N CYS G 44 " --> pdb=" O ARG G 40 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU G 46 " --> pdb=" O ARG G 42 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ARG G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Proline residue: G 50 - end of helix removed outlier: 3.686A pdb=" N LYS G 70 " --> pdb=" O PHE G 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 25 removed outlier: 3.681A pdb=" N THR H 19 " --> pdb=" O ASP H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 47 removed outlier: 3.700A pdb=" N VAL H 31 " --> pdb=" O LEU H 27 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG H 47 " --> pdb=" O ARG H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 73 removed outlier: 3.744A pdb=" N HIS H 67 " --> pdb=" O HIS H 63 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N HIS H 71 " --> pdb=" O HIS H 67 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS H 72 " --> pdb=" O CYS H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'I' and resid 29 through 33 Processing helix chain 'J' and resid 4 through 14 Processing helix chain 'J' and resid 16 through 47 Processing helix chain 'J' and resid 51 through 56 removed outlier: 3.535A pdb=" N ILE J 55 " --> pdb=" O LEU J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 59 No H-bonds generated for 'chain 'J' and resid 57 through 59' Processing helix chain 'K' and resid 2 through 6 removed outlier: 3.989A pdb=" N PHE K 5 " --> pdb=" O LEU K 2 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU K 6 " --> pdb=" O THR K 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 2 through 6' Processing helix chain 'K' and resid 7 through 37 Proline residue: K 19 - end of helix Processing helix chain 'K' and resid 38 through 43 Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 44 through 48 Processing helix chain 'L' and resid 54 through 63 Processing helix chain 'L' and resid 64 through 66 No H-bonds generated for 'chain 'L' and resid 64 through 66' Processing helix chain 'L' and resid 73 through 82 Processing helix chain 'L' and resid 105 through 119 Processing helix chain 'L' and resid 123 through 142 removed outlier: 3.759A pdb=" N ASP L 142 " --> pdb=" O LEU L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 158 removed outlier: 3.552A pdb=" N VAL L 148 " --> pdb=" O SER L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 165 removed outlier: 3.614A pdb=" N GLN L 165 " --> pdb=" O PRO L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 175 Processing helix chain 'L' and resid 178 through 190 removed outlier: 3.511A pdb=" N LEU L 182 " --> pdb=" O SER L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 193 No H-bonds generated for 'chain 'L' and resid 191 through 193' Processing helix chain 'L' and resid 204 through 216 Processing helix chain 'L' and resid 266 through 278 Processing helix chain 'L' and resid 286 through 290 removed outlier: 3.554A pdb=" N LEU L 290 " --> pdb=" O GLY L 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 302 Processing helix chain 'L' and resid 330 through 348 Processing helix chain 'L' and resid 350 through 369 removed outlier: 3.511A pdb=" N VAL L 354 " --> pdb=" O THR L 350 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 386 Processing helix chain 'L' and resid 391 through 400 Processing helix chain 'L' and resid 403 through 415 Processing helix chain 'L' and resid 433 through 439 Processing helix chain 'L' and resid 440 through 442 No H-bonds generated for 'chain 'L' and resid 440 through 442' Processing helix chain 'M' and resid 54 through 58 Processing helix chain 'M' and resid 64 through 72 Processing helix chain 'M' and resid 81 through 93 Processing helix chain 'M' and resid 115 through 129 removed outlier: 3.983A pdb=" N LEU M 119 " --> pdb=" O ASP M 115 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU M 121 " --> pdb=" O ASP M 117 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE M 122 " --> pdb=" O ILE M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 141 Processing helix chain 'M' and resid 142 through 152 removed outlier: 4.236A pdb=" N ILE M 146 " --> pdb=" O PRO M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 168 removed outlier: 3.965A pdb=" N HIS M 158 " --> pdb=" O ASN M 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 183 removed outlier: 3.579A pdb=" N ILE M 183 " --> pdb=" O ASP M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 199 Processing helix chain 'M' and resid 200 through 202 No H-bonds generated for 'chain 'M' and resid 200 through 202' Processing helix chain 'M' and resid 212 through 224 Processing helix chain 'M' and resid 266 through 280 removed outlier: 4.026A pdb=" N ASN M 270 " --> pdb=" O SER M 266 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA M 271 " --> pdb=" O ALA M 267 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 301 Processing helix chain 'M' and resid 332 through 350 removed outlier: 3.920A pdb=" N GLY M 350 " --> pdb=" O THR M 346 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 373 removed outlier: 3.668A pdb=" N VAL M 372 " --> pdb=" O TYR M 368 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU M 373 " --> pdb=" O LEU M 369 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 389 Processing helix chain 'M' and resid 394 through 404 Processing helix chain 'M' and resid 406 through 420 removed outlier: 3.696A pdb=" N VAL M 410 " --> pdb=" O ALA M 406 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 7 removed outlier: 3.535A pdb=" N SER N 7 " --> pdb=" O ILE N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 19 removed outlier: 3.751A pdb=" N ILE N 13 " --> pdb=" O PRO N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 31 Processing helix chain 'N' and resid 32 through 52 removed outlier: 3.633A pdb=" N LEU N 36 " --> pdb=" O ASN N 32 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY N 38 " --> pdb=" O GLY N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 72 Processing helix chain 'N' and resid 75 through 104 removed outlier: 3.615A pdb=" N ILE N 79 " --> pdb=" O TYR N 75 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER N 88 " --> pdb=" O ALA N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 108 removed outlier: 3.832A pdb=" N THR N 108 " --> pdb=" O GLY N 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 105 through 108' Processing helix chain 'N' and resid 109 through 131 removed outlier: 3.734A pdb=" N TYR N 131 " --> pdb=" O ALA N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 148 Processing helix chain 'N' and resid 149 through 153 Processing helix chain 'N' and resid 156 through 166 Processing helix chain 'N' and resid 171 through 204 Proline residue: N 186 - end of helix removed outlier: 3.565A pdb=" N VAL N 195 " --> pdb=" O ALA N 191 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU N 202 " --> pdb=" O LEU N 198 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR N 203 " --> pdb=" O PHE N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 222 through 246 Processing helix chain 'N' and resid 252 through 257 removed outlier: 3.615A pdb=" N THR N 257 " --> pdb=" O ASP N 254 " (cutoff:3.500A) Processing helix chain 'N' and resid 274 through 283 removed outlier: 3.508A pdb=" N ILE N 280 " --> pdb=" O PHE N 276 " (cutoff:3.500A) Processing helix chain 'N' and resid 286 through 300 removed outlier: 3.995A pdb=" N ILE N 298 " --> pdb=" O LEU N 294 " (cutoff:3.500A) Processing helix chain 'N' and resid 301 through 308 removed outlier: 3.511A pdb=" N ILE N 304 " --> pdb=" O LEU N 301 " (cutoff:3.500A) Proline residue: N 305 - end of helix removed outlier: 3.819A pdb=" N HIS N 308 " --> pdb=" O PRO N 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 301 through 308' Processing helix chain 'N' and resid 318 through 340 removed outlier: 3.967A pdb=" N GLY N 340 " --> pdb=" O THR N 336 " (cutoff:3.500A) Processing helix chain 'N' and resid 344 through 364 removed outlier: 4.119A pdb=" N THR N 349 " --> pdb=" O HIS N 345 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE N 359 " --> pdb=" O SER N 355 " (cutoff:3.500A) Processing helix chain 'N' and resid 364 through 377 Processing helix chain 'O' and resid 22 through 36 Processing helix chain 'O' and resid 37 through 40 Processing helix chain 'O' and resid 47 through 52 Processing helix chain 'O' and resid 57 through 66 Processing helix chain 'O' and resid 97 through 105 Processing helix chain 'O' and resid 122 through 132 Processing helix chain 'O' and resid 178 through 195 Processing helix chain 'O' and resid 197 through 232 Proline residue: O 217 - end of helix removed outlier: 4.900A pdb=" N VAL O 229 " --> pdb=" O HIS O 225 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU O 230 " --> pdb=" O LYS O 226 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER O 232 " --> pdb=" O SER O 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 5 removed outlier: 3.794A pdb=" N ASP P 4 " --> pdb=" O SER P 1 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE P 5 " --> pdb=" O HIS P 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 1 through 5' Processing helix chain 'P' and resid 15 through 19 Processing helix chain 'P' and resid 28 through 61 removed outlier: 3.932A pdb=" N THR P 40 " --> pdb=" O SER P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 70 Processing helix chain 'P' and resid 79 through 81 No H-bonds generated for 'chain 'P' and resid 79 through 81' Processing helix chain 'P' and resid 105 through 109 removed outlier: 3.948A pdb=" N GLU P 109 " --> pdb=" O ILE P 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 25 removed outlier: 3.821A pdb=" N GLY Q 25 " --> pdb=" O TYR Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 30 Processing helix chain 'Q' and resid 32 through 37 removed outlier: 3.703A pdb=" N ILE Q 37 " --> pdb=" O ASP Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 49 Processing helix chain 'Q' and resid 51 through 71 removed outlier: 3.796A pdb=" N ARG Q 71 " --> pdb=" O ASP Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 80 removed outlier: 3.561A pdb=" N TRP Q 80 " --> pdb=" O LYS Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 110 removed outlier: 3.912A pdb=" N LYS Q 110 " --> pdb=" O GLU Q 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 23 removed outlier: 3.751A pdb=" N GLN R 23 " --> pdb=" O PRO R 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 20 through 23' Processing helix chain 'R' and resid 32 through 43 removed outlier: 3.567A pdb=" N ASN R 36 " --> pdb=" O LYS R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 69 removed outlier: 3.613A pdb=" N VAL R 48 " --> pdb=" O CYS R 44 " (cutoff:3.500A) Proline residue: R 50 - end of helix Processing helix chain 'S' and resid 15 through 24 removed outlier: 3.794A pdb=" N THR S 19 " --> pdb=" O ASP S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 46 removed outlier: 3.516A pdb=" N SER S 46 " --> pdb=" O GLU S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 70 removed outlier: 4.141A pdb=" N LEU S 58 " --> pdb=" O CYS S 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 14 Processing helix chain 'U' and resid 16 through 47 Processing helix chain 'U' and resid 51 through 59 removed outlier: 4.311A pdb=" N LYS U 56 " --> pdb=" O LYS U 53 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N HIS U 57 " --> pdb=" O HIS U 54 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 37 Proline residue: V 19 - end of helix Processing helix chain 'V' and resid 38 through 43 Processing helix chain 'V' and resid 47 through 52 removed outlier: 3.585A pdb=" N GLY V 50 " --> pdb=" O TYR V 47 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE V 52 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 18 removed outlier: 6.487A pdb=" N ARG A 24 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ALA A 199 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA A 26 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N GLY A 201 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU A 28 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 280 through 281 removed outlier: 3.618A pdb=" N SER A 306 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 321 " --> pdb=" O PHE A 310 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 317 " --> pdb=" O TYR A 314 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A 240 " --> pdb=" O SER G 17 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL G 13 " --> pdb=" O ARG A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 28 removed outlier: 3.603A pdb=" N SER B 37 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL B 34 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N GLY B 208 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA B 36 " --> pdb=" O GLY B 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 243 through 247 removed outlier: 3.926A pdb=" N GLY B 320 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 24 Processing sheet with id=AA6, first strand: chain 'D' and resid 69 through 72 removed outlier: 4.100A pdb=" N PHE D 81 " --> pdb=" O ASP D 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 148 through 149 Processing sheet with id=AA8, first strand: chain 'E' and resid 74 through 77 removed outlier: 3.715A pdb=" N ILE E 74 " --> pdb=" O VAL E 195 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL E 195 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE E 76 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL E 193 " --> pdb=" O ILE E 76 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 86 through 91 removed outlier: 3.565A pdb=" N VAL E 98 " --> pdb=" O MET E 87 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 147 through 148 removed outlier: 3.791A pdb=" N LYS E 173 " --> pdb=" O HIS E 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 15 through 18 removed outlier: 6.636A pdb=" N ARG L 24 " --> pdb=" O LEU L 197 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ALA L 199 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA L 26 " --> pdb=" O ALA L 199 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLY L 201 " --> pdb=" O ALA L 26 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU L 28 " --> pdb=" O GLY L 201 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 280 through 281 removed outlier: 3.668A pdb=" N SER L 306 " --> pdb=" O VAL L 325 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY L 321 " --> pdb=" O PHE L 310 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN L 240 " --> pdb=" O SER R 17 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 25 through 28 removed outlier: 6.425A pdb=" N VAL M 34 " --> pdb=" O LEU M 206 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N GLY M 208 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA M 36 " --> pdb=" O GLY M 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 243 through 247 removed outlier: 3.745A pdb=" N GLY M 320 " --> pdb=" O SER M 261 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 22 through 24 Processing sheet with id=AB7, first strand: chain 'O' and resid 69 through 72 removed outlier: 4.143A pdb=" N PHE O 81 " --> pdb=" O ASP O 72 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'O' and resid 148 through 149 Processing sheet with id=AB9, first strand: chain 'P' and resid 74 through 77 removed outlier: 6.715A pdb=" N MET P 192 " --> pdb=" O THR P 188 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR P 188 " --> pdb=" O MET P 192 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 86 through 91 Processing sheet with id=AC2, first strand: chain 'P' and resid 147 through 148 removed outlier: 6.737A pdb=" N HIS P 164 " --> pdb=" O ARG P 172 " (cutoff:3.500A) 1812 hydrogen bonds defined for protein. 5145 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.21 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.42: 14472 1.42 - 1.62: 19360 1.62 - 1.82: 242 1.82 - 2.02: 2 2.02 - 2.22: 32 Bond restraints: 34108 Sorted by residual: bond pdb=" CAB HEC O 301 " pdb=" CBB HEC O 301 " ideal model delta sigma weight residual 1.544 1.334 0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C2D HEC O 301 " pdb=" C3D HEC O 301 " ideal model delta sigma weight residual 1.544 1.334 0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C2D HEC D 301 " pdb=" C3D HEC D 301 " ideal model delta sigma weight residual 1.544 1.334 0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" CAC HEC D 301 " pdb=" CBC HEC D 301 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" CAC HEC O 301 " pdb=" CBC HEC O 301 " ideal model delta sigma weight residual 1.544 1.337 0.207 2.00e-02 2.50e+03 1.07e+02 ... (remaining 34103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 46090 3.43 - 6.86: 259 6.86 - 10.30: 34 10.30 - 13.73: 6 13.73 - 17.16: 9 Bond angle restraints: 46398 Sorted by residual: angle pdb=" CA CYS S 24 " pdb=" CB CYS S 24 " pdb=" SG CYS S 24 " ideal model delta sigma weight residual 114.40 128.14 -13.74 2.30e+00 1.89e-01 3.57e+01 angle pdb=" C3B HEC D 301 " pdb=" CAB HEC D 301 " pdb=" CBB HEC D 301 " ideal model delta sigma weight residual 109.00 126.16 -17.16 3.00e+00 1.11e-01 3.27e+01 angle pdb=" CA PRO T 13 " pdb=" N PRO T 13 " pdb=" CD PRO T 13 " ideal model delta sigma weight residual 112.00 104.41 7.59 1.40e+00 5.10e-01 2.94e+01 angle pdb=" C3C HEC O 301 " pdb=" CAC HEC O 301 " pdb=" CBC HEC O 301 " ideal model delta sigma weight residual 109.00 124.08 -15.08 3.00e+00 1.11e-01 2.53e+01 angle pdb=" C3C HEC D 301 " pdb=" CAC HEC D 301 " pdb=" CBC HEC D 301 " ideal model delta sigma weight residual 109.00 123.88 -14.88 3.00e+00 1.11e-01 2.46e+01 ... (remaining 46393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 17471 17.96 - 35.92: 1946 35.92 - 53.88: 645 53.88 - 71.84: 127 71.84 - 89.80: 47 Dihedral angle restraints: 20236 sinusoidal: 8036 harmonic: 12200 Sorted by residual: dihedral pdb=" CB CYS S 24 " pdb=" SG CYS S 24 " pdb=" SG CYS S 68 " pdb=" CB CYS S 68 " ideal model delta sinusoidal sigma weight residual -86.00 -155.82 69.82 1 1.00e+01 1.00e-02 6.29e+01 dihedral pdb=" CB CYS S 24 " pdb=" SG CYS S 24 " pdb=" SG CYS S 30 " pdb=" CB CYS S 30 " ideal model delta sinusoidal sigma weight residual -86.00 -20.42 -65.58 1 1.00e+01 1.00e-02 5.63e+01 dihedral pdb=" CA CYS S 24 " pdb=" C CYS S 24 " pdb=" N GLU S 25 " pdb=" CA GLU S 25 " ideal model delta harmonic sigma weight residual 180.00 143.73 36.27 0 5.00e+00 4.00e-02 5.26e+01 ... (remaining 20233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4029 0.051 - 0.103: 883 0.103 - 0.154: 166 0.154 - 0.206: 11 0.206 - 0.257: 1 Chirality restraints: 5090 Sorted by residual: chirality pdb=" CA ASP V 37 " pdb=" N ASP V 37 " pdb=" C ASP V 37 " pdb=" CB ASP V 37 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB THR U 23 " pdb=" CA THR U 23 " pdb=" OG1 THR U 23 " pdb=" CG2 THR U 23 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CB ILE C 284 " pdb=" CA ILE C 284 " pdb=" CG1 ILE C 284 " pdb=" CG2 ILE C 284 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.16e-01 ... (remaining 5087 not shown) Planarity restraints: 5944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 81 " 0.066 5.00e-02 4.00e+02 9.94e-02 1.58e+01 pdb=" N PRO E 82 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO E 82 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO E 82 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 221 " -0.018 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" CD GLU B 221 " 0.065 2.00e-02 2.50e+03 pdb=" OE1 GLU B 221 " -0.023 2.00e-02 2.50e+03 pdb=" OE2 GLU B 221 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA O 161 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO O 162 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO O 162 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO O 162 " 0.032 5.00e-02 4.00e+02 ... (remaining 5941 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 797 2.71 - 3.26: 30822 3.26 - 3.80: 51315 3.80 - 4.35: 64634 4.35 - 4.90: 112386 Nonbonded interactions: 259954 Sorted by model distance: nonbonded pdb=" OH TYR D 152 " pdb=" OD2 ASP H 66 " model vdw 2.160 3.040 nonbonded pdb=" OH TYR O 152 " pdb=" OD2 ASP S 66 " model vdw 2.181 3.040 nonbonded pdb=" OG SER E 65 " pdb=" OD1 ASP E 67 " model vdw 2.224 3.040 nonbonded pdb=" ND1 HIS P 161 " pdb="FE1 FES P 200 " model vdw 2.225 2.464 nonbonded pdb=" OD2 ASP A 433 " pdb=" OH TYR C 223 " model vdw 2.235 3.040 ... (remaining 259949 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'E' selection = chain 'P' } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = chain 'H' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'U' } ncs_group { reference = chain 'K' selection = chain 'V' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 30.530 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.871 34133 Z= 0.237 Angle : 0.876 48.322 46423 Z= 0.377 Chirality : 0.043 0.257 5090 Planarity : 0.005 0.099 5944 Dihedral : 17.501 89.802 12370 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.21 % Allowed : 24.56 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.62 (0.13), residues: 4162 helix: 1.52 (0.11), residues: 2064 sheet: 0.26 (0.25), residues: 422 loop : -0.96 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG T 52 TYR 0.017 0.001 TYR O 165 PHE 0.023 0.001 PHE E 89 TRP 0.013 0.001 TRP D 192 HIS 0.008 0.001 HIS P 100 Details of bonding type rmsd covalent geometry : bond 0.00443 (34108) covalent geometry : angle 0.72947 (46398) SS BOND : bond 0.01203 ( 6) SS BOND : angle 5.00060 ( 12) hydrogen bonds : bond 0.17449 ( 1812) hydrogen bonds : angle 5.36485 ( 5145) metal coordination : bond 0.28192 ( 10) metal coordination : angle 28.55818 ( 13) Misc. bond : bond 0.08380 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8324 Ramachandran restraints generated. 4162 Oldfield, 0 Emsley, 4162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8324 Ramachandran restraints generated. 4162 Oldfield, 0 Emsley, 4162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 438 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 MET cc_start: 0.8798 (mtp) cc_final: 0.8515 (mtp) REVERT: E 113 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7688 (tm-30) REVERT: F 14 GLU cc_start: 0.8791 (tp30) cc_final: 0.8587 (tp30) REVERT: G 31 SER cc_start: 0.9050 (m) cc_final: 0.8774 (p) REVERT: H 23 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8210 (tt0) REVERT: L 429 GLU cc_start: 0.8568 (tt0) cc_final: 0.8355 (tt0) REVERT: P 109 GLU cc_start: 0.7027 (pm20) cc_final: 0.5828 (mp0) REVERT: R 65 GLU cc_start: 0.8417 (tp30) cc_final: 0.8133 (tp30) REVERT: V 51 LYS cc_start: 0.8898 (ptmt) cc_final: 0.7596 (pptt) outliers start: 78 outliers final: 68 residues processed: 508 average time/residue: 0.7651 time to fit residues: 452.0806 Evaluate side-chains 473 residues out of total 3530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 405 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 184 GLU Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 352 SER Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 226 ILE Chi-restraints excluded: chain M residue 247 GLN Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain N residue 147 THR Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 205 SER Chi-restraints excluded: chain N residue 282 ARG Chi-restraints excluded: chain N residue 283 SER Chi-restraints excluded: chain N residue 345 HIS Chi-restraints excluded: chain O residue 168 VAL Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 110 LYS Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain S residue 35 GLU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 11 PHE Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 47 ARG Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain T residue 56 ARG Chi-restraints excluded: chain U residue 4 THR Chi-restraints excluded: chain U residue 17 THR Chi-restraints excluded: chain V residue 3 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.1980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 GLN C 312 GLN L 53 ASN M 248 ASN P 53 ASN ** P 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.102772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.074896 restraints weight = 50252.579| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.27 r_work: 0.2830 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.187 34133 Z= 0.227 Angle : 0.841 48.765 46423 Z= 0.355 Chirality : 0.046 0.228 5090 Planarity : 0.005 0.069 5944 Dihedral : 8.386 155.262 4762 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.84 % Allowed : 20.57 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.91 (0.13), residues: 4162 helix: 1.75 (0.11), residues: 2079 sheet: 0.41 (0.24), residues: 423 loop : -0.81 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 206 TYR 0.025 0.002 TYR C 81 PHE 0.020 0.002 PHE C 91 TRP 0.013 0.002 TRP D 192 HIS 0.012 0.001 HIS N 196 Details of bonding type rmsd covalent geometry : bond 0.00561 (34108) covalent geometry : angle 0.68553 (46398) SS BOND : bond 0.01322 ( 6) SS BOND : angle 2.82630 ( 12) hydrogen bonds : bond 0.07638 ( 1812) hydrogen bonds : angle 4.37745 ( 5145) metal coordination : bond 0.04831 ( 10) metal coordination : angle 29.03272 ( 13) Misc. bond : bond 0.08284 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8324 Ramachandran restraints generated. 4162 Oldfield, 0 Emsley, 4162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8324 Ramachandran restraints generated. 4162 Oldfield, 0 Emsley, 4162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 422 time to evaluate : 1.293 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 224 ASP cc_start: 0.5217 (OUTLIER) cc_final: 0.5012 (t0) REVERT: B 110 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8343 (tp30) REVERT: B 221 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: B 223 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7489 (m-80) REVERT: B 305 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7522 (mp10) REVERT: C 12 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7543 (tttt) REVERT: C 366 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7209 (mmt) REVERT: C 373 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8396 (mt-10) REVERT: C 379 TRP cc_start: 0.7777 (OUTLIER) cc_final: 0.5977 (m-10) REVERT: E 13 TYR cc_start: 0.9133 (m-80) cc_final: 0.8892 (m-80) REVERT: E 73 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8666 (mtmt) REVERT: E 99 ARG cc_start: 0.7879 (ttp-170) cc_final: 0.7599 (tpp80) REVERT: H 23 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8044 (tt0) REVERT: H 38 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7705 (pt0) REVERT: H 42 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7762 (pm20) REVERT: K 6 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7116 (mm) REVERT: L 28 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8613 (tt0) REVERT: L 50 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8224 (tm-30) REVERT: L 245 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.7541 (tp30) REVERT: N 194 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8849 (mmm) REVERT: N 366 MET cc_start: 0.8804 (mmm) cc_final: 0.8335 (mmm) REVERT: N 379 TRP cc_start: 0.8303 (OUTLIER) cc_final: 0.7694 (t60) REVERT: O 58 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8029 (tp30) REVERT: P 30 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7760 (mt-10) REVERT: P 166 ASP cc_start: 0.6236 (OUTLIER) cc_final: 0.5892 (p0) REVERT: P 181 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7165 (tt0) REVERT: S 54 CYS cc_start: 0.6667 (OUTLIER) cc_final: 0.6246 (p) REVERT: S 56 GLU cc_start: 0.7206 (pm20) cc_final: 0.6748 (pm20) REVERT: S 57 GLU cc_start: 0.8259 (mp0) cc_final: 0.7623 (mp0) REVERT: T 44 ASP cc_start: 0.5658 (t0) cc_final: 0.5304 (t0) REVERT: V 51 LYS cc_start: 0.8594 (ptmt) cc_final: 0.7532 (pptt) outliers start: 171 outliers final: 74 residues processed: 545 average time/residue: 0.7393 time to fit residues: 471.6969 Evaluate side-chains 489 residues out of total 3530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 395 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 305 GLN Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 366 MET Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 379 TRP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 6 HIS Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain J residue 11 SER Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 184 GLU Chi-restraints excluded: chain L residue 245 GLU Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 353 GLU Chi-restraints excluded: chain L residue 369 LEU Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 223 PHE Chi-restraints excluded: chain M residue 326 THR Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 194 MET Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 282 ARG Chi-restraints excluded: chain N residue 283 SER Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 345 HIS Chi-restraints excluded: chain N residue 379 TRP Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 58 GLU Chi-restraints excluded: chain O residue 168 VAL Chi-restraints excluded: chain O residue 173 ASP Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain P residue 30 GLU Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 166 ASP Chi-restraints excluded: chain P residue 181 GLU Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain R residue 3 GLN Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 44 CYS Chi-restraints excluded: chain S residue 54 CYS Chi-restraints excluded: chain T residue 2 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 46 LYS Chi-restraints excluded: chain U residue 4 THR Chi-restraints excluded: chain U residue 11 SER Chi-restraints excluded: chain U residue 18 SER Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 37 ASP Chi-restraints excluded: chain V residue 40 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 338 optimal weight: 2.9990 chunk 247 optimal weight: 0.4980 chunk 360 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 chunk 362 optimal weight: 3.9990 chunk 308 optimal weight: 0.7980 chunk 334 optimal weight: 4.9990 chunk 354 optimal weight: 6.9990 chunk 188 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 53 ASN M 248 ASN P 53 ASN ** P 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.106013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.078181 restraints weight = 50195.533| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.29 r_work: 0.2890 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.162 34133 Z= 0.132 Angle : 0.740 44.647 46423 Z= 0.300 Chirality : 0.041 0.190 5090 Planarity : 0.004 0.051 5944 Dihedral : 7.285 86.264 4710 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.97 % Allowed : 21.50 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.20 (0.13), residues: 4162 helix: 1.97 (0.11), residues: 2093 sheet: 0.62 (0.24), residues: 422 loop : -0.70 (0.16), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 8 TYR 0.015 0.001 TYR N 224 PHE 0.014 0.001 PHE C 91 TRP 0.013 0.001 TRP D 192 HIS 0.007 0.001 HIS P 100 Details of bonding type rmsd covalent geometry : bond 0.00292 (34108) covalent geometry : angle 0.58694 (46398) SS BOND : bond 0.01166 ( 6) SS BOND : angle 3.10134 ( 12) hydrogen bonds : bond 0.05610 ( 1812) hydrogen bonds : angle 4.14042 ( 5145) metal coordination : bond 0.06602 ( 10) metal coordination : angle 26.73101 ( 13) Misc. bond : bond 0.08679 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8324 Ramachandran restraints generated. 4162 Oldfield, 0 Emsley, 4162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8324 Ramachandran restraints generated. 4162 Oldfield, 0 Emsley, 4162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 435 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8178 (ttt180) REVERT: B 25 GLU cc_start: 0.8064 (pt0) cc_final: 0.7775 (pt0) REVERT: B 110 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8347 (tp30) REVERT: B 221 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: B 223 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.7427 (m-80) REVERT: B 305 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7470 (mp10) REVERT: C 379 TRP cc_start: 0.7736 (OUTLIER) cc_final: 0.5900 (m-10) REVERT: D 234 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8413 (mttm) REVERT: E 13 TYR cc_start: 0.9151 (m-80) cc_final: 0.8897 (m-80) REVERT: E 99 ARG cc_start: 0.7946 (ttp-170) cc_final: 0.7658 (tpp80) REVERT: H 23 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8062 (tt0) REVERT: H 38 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7777 (pt0) REVERT: H 42 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7757 (pm20) REVERT: H 52 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.5188 (mm-30) REVERT: K 6 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7115 (mm) REVERT: L 28 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8580 (tt0) REVERT: L 50 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8226 (tt0) REVERT: L 206 ARG cc_start: 0.8449 (mmm160) cc_final: 0.7983 (mmm160) REVERT: L 245 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7499 (tp30) REVERT: L 332 ASP cc_start: 0.8540 (t70) cc_final: 0.8071 (m-30) REVERT: L 429 GLU cc_start: 0.8795 (tt0) cc_final: 0.8508 (tt0) REVERT: M 185 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8094 (mmtp) REVERT: N 112 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8522 (m) REVERT: N 171 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8240 (m-30) REVERT: N 366 MET cc_start: 0.8701 (mmm) cc_final: 0.8182 (mmm) REVERT: O 58 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7988 (tp30) REVERT: O 80 MET cc_start: 0.8847 (mmm) cc_final: 0.8479 (mmm) REVERT: P 105 GLU cc_start: 0.1668 (tt0) cc_final: 0.1338 (tt0) REVERT: P 109 GLU cc_start: 0.7051 (pm20) cc_final: 0.5879 (mp0) REVERT: P 181 GLU cc_start: 0.7637 (mp0) cc_final: 0.7244 (tt0) REVERT: R 22 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: S 15 ASP cc_start: 0.8353 (t0) cc_final: 0.8039 (t70) REVERT: S 32 LYS cc_start: 0.7535 (mppt) cc_final: 0.7299 (mppt) REVERT: S 54 CYS cc_start: 0.6715 (OUTLIER) cc_final: 0.6112 (p) REVERT: S 56 GLU cc_start: 0.7361 (pm20) cc_final: 0.6938 (pm20) REVERT: S 57 GLU cc_start: 0.8374 (mp0) cc_final: 0.7716 (mp0) REVERT: T 44 ASP cc_start: 0.5297 (t0) cc_final: 0.4946 (t0) REVERT: U 1 VAL cc_start: -0.0341 (OUTLIER) cc_final: -0.0624 (p) REVERT: U 44 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: V 51 LYS cc_start: 0.8403 (ptmt) cc_final: 0.7451 (pptt) outliers start: 140 outliers final: 54 residues processed: 535 average time/residue: 0.7509 time to fit residues: 470.0820 Evaluate side-chains 489 residues out of total 3530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 415 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 305 GLN Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 379 TRP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 144 CYS Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 6 HIS Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 184 GLU Chi-restraints excluded: chain L residue 245 GLU Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 353 GLU Chi-restraints excluded: chain L residue 369 LEU Chi-restraints excluded: chain L residue 381 ARG Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 176 LEU Chi-restraints excluded: chain M residue 185 LYS Chi-restraints excluded: chain M residue 223 PHE Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 171 ASP Chi-restraints excluded: chain N residue 172 LYS Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 345 HIS Chi-restraints excluded: chain O residue 58 GLU Chi-restraints excluded: chain O residue 168 VAL Chi-restraints excluded: chain P residue 9 ASP Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain R residue 3 GLN Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 22 GLU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain S residue 54 CYS Chi-restraints excluded: chain T residue 2 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 56 ARG Chi-restraints excluded: chain U residue 1 VAL Chi-restraints excluded: chain U residue 18 SER Chi-restraints excluded: chain U residue 44 GLU Chi-restraints excluded: chain V residue 40 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 18 optimal weight: 0.2980 chunk 347 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 275 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 313 optimal weight: 1.9990 chunk 303 optimal weight: 0.0770 chunk 319 optimal weight: 4.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN M 248 ASN P 53 ASN ** P 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.079751 restraints weight = 50126.708| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.29 r_work: 0.2919 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 34133 Z= 0.117 Angle : 0.713 43.701 46423 Z= 0.283 Chirality : 0.041 0.196 5090 Planarity : 0.004 0.050 5944 Dihedral : 6.885 86.655 4691 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.71 % Allowed : 21.87 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.40 (0.13), residues: 4162 helix: 2.15 (0.11), residues: 2099 sheet: 0.71 (0.25), residues: 410 loop : -0.63 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 43 TYR 0.015 0.001 TYR N 224 PHE 0.012 0.001 PHE C 91 TRP 0.012 0.001 TRP D 192 HIS 0.007 0.001 HIS P 100 Details of bonding type rmsd covalent geometry : bond 0.00255 (34108) covalent geometry : angle 0.55664 (46398) SS BOND : bond 0.01154 ( 6) SS BOND : angle 3.01575 ( 12) hydrogen bonds : bond 0.04937 ( 1812) hydrogen bonds : angle 4.00304 ( 5145) metal coordination : bond 0.05426 ( 10) metal coordination : angle 26.46410 ( 13) Misc. bond : bond 0.08195 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8324 Ramachandran restraints generated. 4162 Oldfield, 0 Emsley, 4162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8324 Ramachandran restraints generated. 4162 Oldfield, 0 Emsley, 4162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 437 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8123 (ttt180) REVERT: B 25 GLU cc_start: 0.8020 (pt0) cc_final: 0.7756 (pt0) REVERT: B 110 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8293 (tp30) REVERT: B 221 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: B 305 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7429 (mp10) REVERT: C 171 ASP cc_start: 0.8671 (t0) cc_final: 0.8460 (t0) REVERT: C 379 TRP cc_start: 0.7695 (OUTLIER) cc_final: 0.5887 (m-10) REVERT: D 144 ARG cc_start: 0.6366 (OUTLIER) cc_final: 0.5878 (ptp-170) REVERT: D 234 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8327 (mttm) REVERT: E 13 TYR cc_start: 0.9161 (m-80) cc_final: 0.8906 (m-80) REVERT: E 99 ARG cc_start: 0.7929 (ttp-170) cc_final: 0.7649 (tpp80) REVERT: H 22 GLU cc_start: 0.8486 (tp30) cc_final: 0.7973 (mm-30) REVERT: H 23 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8053 (tt0) REVERT: H 38 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7799 (pt0) REVERT: H 42 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7705 (pm20) REVERT: I 1 MET cc_start: 0.6432 (tpt) cc_final: 0.4666 (pmm) REVERT: K 6 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7125 (mm) REVERT: L 28 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8549 (tt0) REVERT: L 50 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8225 (tt0) REVERT: L 206 ARG cc_start: 0.8461 (mmm160) cc_final: 0.7995 (mmm160) REVERT: L 245 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7461 (tp30) REVERT: L 429 GLU cc_start: 0.8799 (tt0) cc_final: 0.8496 (tt0) REVERT: M 185 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8085 (mmtp) REVERT: M 245 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7662 (ptm160) REVERT: N 171 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8279 (m-30) REVERT: O 15 ARG cc_start: 0.8747 (tpt-90) cc_final: 0.8515 (ttm-80) REVERT: O 58 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7976 (tp30) REVERT: O 80 MET cc_start: 0.8775 (mmm) cc_final: 0.8418 (mmm) REVERT: P 30 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: P 181 GLU cc_start: 0.7585 (mp0) cc_final: 0.7260 (tt0) REVERT: R 22 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8011 (mt-10) REVERT: S 15 ASP cc_start: 0.8353 (t0) cc_final: 0.8017 (t70) REVERT: S 22 GLU cc_start: 0.8580 (mm-30) cc_final: 0.7953 (mt-10) REVERT: S 32 LYS cc_start: 0.7475 (mppt) cc_final: 0.7239 (mppt) REVERT: S 54 CYS cc_start: 0.6658 (OUTLIER) cc_final: 0.5365 (p) REVERT: S 56 GLU cc_start: 0.7429 (pm20) cc_final: 0.6952 (pm20) REVERT: S 57 GLU cc_start: 0.8492 (mp0) cc_final: 0.7639 (mp0) REVERT: U 1 VAL cc_start: -0.0797 (OUTLIER) cc_final: -0.1047 (p) REVERT: U 16 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6197 (mtt180) REVERT: U 44 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7774 (mt-10) REVERT: V 51 LYS cc_start: 0.8277 (ptmt) cc_final: 0.7417 (pptt) outliers start: 131 outliers final: 52 residues processed: 528 average time/residue: 0.7590 time to fit residues: 468.6830 Evaluate side-chains 488 residues out of total 3530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 415 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 305 GLN Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 379 TRP Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 6 HIS Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 184 GLU Chi-restraints excluded: chain L residue 245 GLU Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 369 LEU Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 185 LYS Chi-restraints excluded: chain M residue 219 VAL Chi-restraints excluded: chain M residue 223 PHE Chi-restraints excluded: chain M residue 245 ARG Chi-restraints excluded: chain N residue 171 ASP Chi-restraints excluded: chain N residue 172 LYS Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 212 SER Chi-restraints excluded: chain N residue 282 ARG Chi-restraints excluded: chain N residue 345 HIS Chi-restraints excluded: chain O residue 58 GLU Chi-restraints excluded: chain O residue 168 VAL Chi-restraints excluded: chain O residue 173 ASP Chi-restraints excluded: chain P residue 9 ASP Chi-restraints excluded: chain P residue 30 GLU Chi-restraints excluded: chain R residue 3 GLN Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 22 GLU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain S residue 54 CYS Chi-restraints excluded: chain T residue 2 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 56 ARG Chi-restraints excluded: chain U residue 1 VAL Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 16 ARG Chi-restraints excluded: chain U residue 18 SER Chi-restraints excluded: chain U residue 44 GLU Chi-restraints excluded: chain V residue 37 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 169 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 329 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 chunk 286 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 397 optimal weight: 0.2980 chunk 300 optimal weight: 1.9990 chunk 220 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 308 GLN M 248 ASN P 53 ASN ** P 161 HIS ** 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 = 0.3410 r_free = 0.3410 target = 0.105869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.078040 restraints weight = 50093.440| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.29 r_work: 0.2888 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 34133 Z= 0.141 Angle : 0.728 43.265 46423 Z= 0.296 Chirality : 0.042 0.208 5090 Planarity : 0.004 0.050 5944 Dihedral : 6.931 86.448 4687 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.80 % Allowed : 21.81 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % 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: 1.41 (0.13), residues: 4162 helix: 2.18 (0.11), residues: 2093 sheet: 0.68 (0.25), residues: 410 loop : -0.64 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 8 TYR 0.016 0.001 TYR C 81 PHE 0.015 0.001 PHE C 91 TRP 0.010 0.001 TRP C 141 HIS 0.008 0.001 HIS P 100 Details of bonding type rmsd covalent geometry : bond 0.00328 (34108) covalent geometry : angle 0.58097 (46398) SS BOND : bond 0.01072 ( 6) SS BOND : angle 3.10135 ( 12) hydrogen bonds : bond 0.05639 ( 1812) hydrogen bonds : angle 3.99968 ( 5145) metal coordination : bond 0.05680 ( 10) metal coordination : angle 26.09740 ( 13) Misc. bond : bond 0.07855 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8324 Ramachandran restraints generated. 4162 Oldfield, 0 Emsley, 4162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8324 Ramachandran restraints generated. 4162 Oldfield, 0 Emsley, 4162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 425 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.5860 (mp10) REVERT: A 188 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8138 (ttt180) REVERT: B 25 GLU cc_start: 0.8045 (pt0) cc_final: 0.7779 (pt0) REVERT: B 110 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8359 (tp30) REVERT: B 221 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: B 223 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7440 (m-80) REVERT: B 305 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7450 (mp10) REVERT: C 171 ASP cc_start: 0.8794 (t0) cc_final: 0.8546 (t0) REVERT: C 379 TRP cc_start: 0.7779 (OUTLIER) cc_final: 0.5939 (m-10) REVERT: D 66 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: D 144 ARG cc_start: 0.6421 (OUTLIER) cc_final: 0.5870 (ptp90) REVERT: D 234 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8415 (mttm) REVERT: E 13 TYR cc_start: 0.9083 (m-80) cc_final: 0.8787 (m-80) REVERT: E 99 ARG cc_start: 0.7961 (ttp-170) cc_final: 0.7649 (tpp80) REVERT: H 22 GLU cc_start: 0.8516 (tp30) cc_final: 0.8035 (mm-30) REVERT: H 23 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8020 (tt0) REVERT: H 42 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7690 (pm20) REVERT: H 52 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.5109 (mm-30) REVERT: I 1 MET cc_start: 0.6389 (tpt) cc_final: 0.4666 (pmm) REVERT: K 6 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7151 (mm) REVERT: L 28 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8550 (tt0) REVERT: L 145 MET cc_start: 0.8087 (mmm) cc_final: 0.7752 (mtt) REVERT: L 206 ARG cc_start: 0.8531 (mmm160) cc_final: 0.8092 (mmm160) REVERT: L 245 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.7582 (tp30) REVERT: L 429 GLU cc_start: 0.8810 (tt0) cc_final: 0.8506 (tt0) REVERT: M 185 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8081 (mmtp) REVERT: M 245 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.7592 (ptm160) REVERT: N 112 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8515 (m) REVERT: N 171 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8298 (m-30) REVERT: O 15 ARG cc_start: 0.8729 (tpt-90) cc_final: 0.8490 (ttm-80) REVERT: O 58 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7996 (tp30) REVERT: O 80 MET cc_start: 0.8786 (mmm) cc_final: 0.8475 (mmm) REVERT: P 30 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7499 (mt-10) REVERT: P 181 GLU cc_start: 0.7645 (mp0) cc_final: 0.7312 (tt0) REVERT: R 22 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: S 15 ASP cc_start: 0.8372 (t0) cc_final: 0.8074 (t70) REVERT: S 22 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8004 (mt-10) REVERT: S 54 CYS cc_start: 0.6286 (OUTLIER) cc_final: 0.4806 (p) REVERT: S 56 GLU cc_start: 0.7435 (pm20) cc_final: 0.7105 (pm20) REVERT: S 57 GLU cc_start: 0.8545 (mp0) cc_final: 0.7606 (mp0) REVERT: T 44 ASP cc_start: 0.5208 (t0) cc_final: 0.4816 (t0) REVERT: U 1 VAL cc_start: -0.0695 (OUTLIER) cc_final: -0.0972 (p) REVERT: U 16 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6198 (mtt180) REVERT: U 44 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: V 39 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.2935 (mpp-170) REVERT: V 51 LYS cc_start: 0.8282 (ptmt) cc_final: 0.7437 (pptt) outliers start: 134 outliers final: 67 residues processed: 522 average time/residue: 0.7426 time to fit residues: 453.8180 Evaluate side-chains 504 residues out of total 3530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 410 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 305 GLN Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 379 TRP Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 6 HIS Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 184 GLU Chi-restraints excluded: chain L residue 245 GLU Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 369 LEU Chi-restraints excluded: chain L residue 412 SER Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 185 LYS Chi-restraints excluded: chain M residue 219 VAL Chi-restraints excluded: chain M residue 223 PHE Chi-restraints excluded: chain M residue 245 ARG Chi-restraints excluded: chain M residue 326 THR Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 171 ASP Chi-restraints excluded: chain N residue 172 LYS Chi-restraints excluded: chain N residue 194 MET Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 212 SER Chi-restraints excluded: chain N residue 282 ARG Chi-restraints excluded: chain N residue 345 HIS Chi-restraints excluded: chain O residue 58 GLU Chi-restraints excluded: chain O residue 168 VAL Chi-restraints excluded: chain O residue 173 ASP Chi-restraints excluded: chain P residue 9 ASP Chi-restraints excluded: chain P residue 30 GLU Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain Q residue 110 LYS Chi-restraints excluded: chain R residue 3 GLN Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 22 GLU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain S residue 54 CYS Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 56 ARG Chi-restraints excluded: chain U residue 1 VAL Chi-restraints excluded: chain U residue 16 ARG Chi-restraints excluded: chain U residue 18 SER Chi-restraints excluded: chain U residue 44 GLU Chi-restraints excluded: chain V residue 37 ASP Chi-restraints excluded: chain V residue 39 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 204 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 364 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 409 optimal weight: 1.9990 chunk 337 optimal weight: 2.9990 chunk 368 optimal weight: 0.9980 chunk 344 optimal weight: 0.7980 chunk 360 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 308 GLN F 38 HIS L 139 GLN L 341 GLN M 248 ASN P 53 ASN ** P 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.102532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.074752 restraints weight = 50185.765| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.26 r_work: 0.2828 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.187 34133 Z= 0.216 Angle : 0.792 42.308 46423 Z= 0.336 Chirality : 0.045 0.227 5090 Planarity : 0.005 0.054 5944 Dihedral : 7.237 86.700 4687 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.31 % Allowed : 21.25 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.19 (0.13), residues: 4162 helix: 2.01 (0.11), residues: 2093 sheet: 0.81 (0.25), residues: 387 loop : -0.80 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 8 TYR 0.024 0.002 TYR C 81 PHE 0.018 0.002 PHE C 91 TRP 0.009 0.001 TRP C 141 HIS 0.011 0.001 HIS N 196 Details of bonding type rmsd covalent geometry : bond 0.00528 (34108) covalent geometry : angle 0.65610 (46398) SS BOND : bond 0.01281 ( 6) SS BOND : angle 3.81207 ( 12) hydrogen bonds : bond 0.07296 ( 1812) hydrogen bonds : angle 4.16396 ( 5145) metal coordination : bond 0.06261 ( 10) metal coordination : angle 26.29897 ( 13) Misc. bond : bond 0.07986 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8324 Ramachandran restraints generated. 4162 Oldfield, 0 Emsley, 4162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8324 Ramachandran restraints generated. 4162 Oldfield, 0 Emsley, 4162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 415 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.6110 (mp10) REVERT: B 110 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8360 (tp30) REVERT: B 221 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: B 305 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7492 (mp10) REVERT: C 171 ASP cc_start: 0.8893 (t0) cc_final: 0.8642 (t0) REVERT: C 177 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8495 (ttm170) REVERT: C 269 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8212 (ptmm) REVERT: C 379 TRP cc_start: 0.7957 (OUTLIER) cc_final: 0.6579 (m-10) REVERT: D 144 ARG cc_start: 0.6467 (OUTLIER) cc_final: 0.5993 (ptp90) REVERT: D 234 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8526 (mttm) REVERT: E 13 TYR cc_start: 0.9103 (m-80) cc_final: 0.8717 (m-80) REVERT: E 99 ARG cc_start: 0.8005 (ttp-170) cc_final: 0.7634 (tpp80) REVERT: H 23 GLN cc_start: 0.8497 (tm-30) cc_final: 0.7983 (tt0) REVERT: H 34 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.7524 (tpp-160) REVERT: H 42 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7625 (pm20) REVERT: H 52 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.5140 (mm-30) REVERT: I 1 MET cc_start: 0.6474 (tpt) cc_final: 0.4729 (pmm) REVERT: K 6 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7134 (mm) REVERT: K 39 ARG cc_start: 0.6365 (mpp-170) cc_final: 0.4761 (mmm-85) REVERT: L 28 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8624 (tt0) REVERT: L 206 ARG cc_start: 0.8556 (mmm160) cc_final: 0.8132 (mmm160) REVERT: L 245 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.7684 (tp30) REVERT: M 185 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8095 (mmtp) REVERT: M 245 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7581 (ptm160) REVERT: N 366 MET cc_start: 0.8827 (mmm) cc_final: 0.8403 (mmm) REVERT: O 15 ARG cc_start: 0.8725 (tpt-90) cc_final: 0.8466 (ttm-80) REVERT: O 58 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7980 (tp30) REVERT: O 77 ASP cc_start: 0.8020 (t0) cc_final: 0.7733 (m-30) REVERT: O 80 MET cc_start: 0.8657 (mmm) cc_final: 0.8450 (mmm) REVERT: P 30 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7750 (mt-10) REVERT: P 181 GLU cc_start: 0.7674 (mp0) cc_final: 0.7256 (tt0) REVERT: R 22 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.7962 (mm-30) REVERT: S 15 ASP cc_start: 0.8442 (t0) cc_final: 0.8208 (t70) REVERT: S 22 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8089 (mt-10) REVERT: S 54 CYS cc_start: 0.6600 (OUTLIER) cc_final: 0.5584 (p) REVERT: S 56 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7236 (pm20) REVERT: S 57 GLU cc_start: 0.8617 (mp0) cc_final: 0.7874 (mp0) REVERT: T 44 ASP cc_start: 0.5594 (t0) cc_final: 0.5227 (t0) REVERT: U 1 VAL cc_start: -0.0744 (OUTLIER) cc_final: -0.0995 (p) REVERT: U 16 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6293 (mtp180) REVERT: U 44 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8000 (mp0) REVERT: V 39 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.2991 (mpp-170) outliers start: 152 outliers final: 81 residues processed: 521 average time/residue: 0.7469 time to fit residues: 454.1910 Evaluate side-chains 515 residues out of total 3530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 409 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 305 GLN Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 379 TRP Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 6 HIS Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain J residue 11 SER Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 245 GLU Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 352 SER Chi-restraints excluded: chain L residue 369 LEU Chi-restraints excluded: chain L residue 412 SER Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 176 LEU Chi-restraints excluded: chain M residue 185 LYS Chi-restraints excluded: chain M residue 219 VAL Chi-restraints excluded: chain M residue 223 PHE Chi-restraints excluded: chain M residue 245 ARG Chi-restraints excluded: chain M residue 326 THR Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 171 ASP Chi-restraints excluded: chain N residue 172 LYS Chi-restraints excluded: chain N residue 194 MET Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 212 SER Chi-restraints excluded: chain N residue 282 ARG Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain N residue 345 HIS Chi-restraints excluded: chain O residue 58 GLU Chi-restraints excluded: chain O residue 168 VAL Chi-restraints excluded: chain O residue 173 ASP Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain P residue 9 ASP Chi-restraints excluded: chain P residue 30 GLU Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 110 LYS Chi-restraints excluded: chain R residue 3 GLN Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 22 GLU Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain S residue 54 CYS Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 56 ARG Chi-restraints excluded: chain U residue 1 VAL Chi-restraints excluded: chain U residue 4 THR Chi-restraints excluded: chain U residue 16 ARG Chi-restraints excluded: chain U residue 18 SER Chi-restraints excluded: chain U residue 44 GLU Chi-restraints excluded: chain V residue 37 ASP Chi-restraints excluded: chain V residue 39 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 292 optimal weight: 0.6980 chunk 379 optimal weight: 0.6980 chunk 256 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 139 optimal weight: 5.9990 chunk 123 optimal weight: 0.0570 chunk 346 optimal weight: 1.9990 chunk 402 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 345 optimal weight: 4.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 308 GLN C 15 ASN ** P 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.105131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.077285 restraints weight = 50238.144| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.29 r_work: 0.2874 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.180 34133 Z= 0.136 Angle : 0.730 42.573 46423 Z= 0.301 Chirality : 0.042 0.205 5090 Planarity : 0.004 0.051 5944 Dihedral : 6.938 87.126 4684 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.68 % Allowed : 22.12 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.13), residues: 4162 helix: 2.12 (0.11), residues: 2095 sheet: 0.62 (0.25), residues: 410 loop : -0.72 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 8 TYR 0.016 0.001 TYR N 224 PHE 0.014 0.001 PHE C 91 TRP 0.012 0.001 TRP D 192 HIS 0.008 0.001 HIS P 100 Details of bonding type rmsd covalent geometry : bond 0.00307 (34108) covalent geometry : angle 0.59069 (46398) SS BOND : bond 0.01237 ( 6) SS BOND : angle 3.36742 ( 12) hydrogen bonds : bond 0.05738 ( 1812) hydrogen bonds : angle 4.05011 ( 5145) metal coordination : bond 0.05613 ( 10) metal coordination : angle 25.43023 ( 13) Misc. bond : bond 0.08494 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8324 Ramachandran restraints generated. 4162 Oldfield, 0 Emsley, 4162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8324 Ramachandran restraints generated. 4162 Oldfield, 0 Emsley, 4162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 426 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.5882 (mp10) REVERT: B 110 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8383 (tp30) REVERT: B 221 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: B 223 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: B 305 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7437 (mp10) REVERT: C 171 ASP cc_start: 0.8811 (t0) cc_final: 0.8534 (t0) REVERT: C 269 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8165 (ptmm) REVERT: C 379 TRP cc_start: 0.7879 (OUTLIER) cc_final: 0.6239 (m-10) REVERT: D 234 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8413 (mttm) REVERT: E 13 TYR cc_start: 0.9102 (m-80) cc_final: 0.8736 (m-80) REVERT: E 99 ARG cc_start: 0.8042 (ttp-170) cc_final: 0.7698 (tpp80) REVERT: H 22 GLU cc_start: 0.8557 (tp30) cc_final: 0.8065 (mm-30) REVERT: H 23 GLN cc_start: 0.8474 (tm-30) cc_final: 0.7955 (tt0) REVERT: H 34 ARG cc_start: 0.7898 (ttm-80) cc_final: 0.7609 (tpp-160) REVERT: H 42 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7667 (pm20) REVERT: H 52 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.5088 (mm-30) REVERT: I 1 MET cc_start: 0.6469 (tpt) cc_final: 0.4735 (pmm) REVERT: K 6 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7170 (mm) REVERT: K 39 ARG cc_start: 0.6408 (mpp-170) cc_final: 0.4784 (mmm-85) REVERT: L 28 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8553 (tt0) REVERT: L 184 GLU cc_start: 0.8492 (tp30) cc_final: 0.8151 (mp0) REVERT: L 206 ARG cc_start: 0.8522 (mmm160) cc_final: 0.8066 (mmm160) REVERT: L 245 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.7643 (tp30) REVERT: L 381 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8041 (ttm-80) REVERT: L 429 GLU cc_start: 0.8805 (tt0) cc_final: 0.8510 (tt0) REVERT: M 185 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8088 (mmtp) REVERT: M 245 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.7600 (ptm160) REVERT: N 112 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8537 (m) REVERT: N 171 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8327 (m-30) REVERT: O 15 ARG cc_start: 0.8714 (tpt-90) cc_final: 0.8467 (ttm-80) REVERT: O 58 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7986 (tp30) REVERT: O 77 ASP cc_start: 0.8049 (t0) cc_final: 0.7734 (m-30) REVERT: O 80 MET cc_start: 0.8732 (mmm) cc_final: 0.8496 (mmm) REVERT: P 30 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7638 (mt-10) REVERT: P 181 GLU cc_start: 0.7671 (mp0) cc_final: 0.7268 (tt0) REVERT: R 22 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7919 (mm-30) REVERT: S 15 ASP cc_start: 0.8476 (t0) cc_final: 0.8198 (t70) REVERT: S 22 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8210 (mt-10) REVERT: S 54 CYS cc_start: 0.6492 (OUTLIER) cc_final: 0.5080 (p) REVERT: S 56 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7077 (pm20) REVERT: S 57 GLU cc_start: 0.8629 (mp0) cc_final: 0.7776 (mp0) REVERT: T 44 ASP cc_start: 0.5478 (t0) cc_final: 0.5082 (t0) REVERT: U 1 VAL cc_start: -0.1018 (OUTLIER) cc_final: -0.1241 (p) REVERT: U 16 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.6241 (mtt180) REVERT: U 44 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: V 39 ARG cc_start: 0.6855 (OUTLIER) cc_final: 0.2987 (mpp-170) outliers start: 130 outliers final: 69 residues processed: 517 average time/residue: 0.7489 time to fit residues: 451.8273 Evaluate side-chains 503 residues out of total 3530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 407 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 305 GLN Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 379 TRP Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 6 HIS Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 222 THR Chi-restraints excluded: chain L residue 245 GLU Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 369 LEU Chi-restraints excluded: chain L residue 381 ARG Chi-restraints excluded: chain L residue 412 SER Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 176 LEU Chi-restraints excluded: chain M residue 185 LYS Chi-restraints excluded: chain M residue 219 VAL Chi-restraints excluded: chain M residue 223 PHE Chi-restraints excluded: chain M residue 245 ARG Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 171 ASP Chi-restraints excluded: chain N residue 172 LYS Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 212 SER Chi-restraints excluded: chain N residue 282 ARG Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain N residue 345 HIS Chi-restraints excluded: chain O residue 58 GLU Chi-restraints excluded: chain O residue 168 VAL Chi-restraints excluded: chain O residue 173 ASP Chi-restraints excluded: chain P residue 9 ASP Chi-restraints excluded: chain P residue 30 GLU Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 110 LYS Chi-restraints excluded: chain R residue 3 GLN Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 22 GLU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain S residue 54 CYS Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain U residue 1 VAL Chi-restraints excluded: chain U residue 4 THR Chi-restraints excluded: chain U residue 16 ARG Chi-restraints excluded: chain U residue 18 SER Chi-restraints excluded: chain U residue 44 GLU Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 37 ASP Chi-restraints excluded: chain V residue 39 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 212 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 387 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 365 optimal weight: 0.7980 chunk 245 optimal weight: 0.0170 chunk 408 optimal weight: 3.9990 chunk 345 optimal weight: 2.9990 chunk 296 optimal weight: 1.9990 chunk 348 optimal weight: 4.9990 chunk 256 optimal weight: 3.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 308 GLN L 271 GLN M 248 ASN ** P 161 HIS ** 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 = 0.3383 r_free = 0.3383 target = 0.103978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.076274 restraints weight = 50096.766| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.27 r_work: 0.2856 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.190 34133 Z= 0.169 Angle : 0.753 41.785 46423 Z= 0.315 Chirality : 0.043 0.215 5090 Planarity : 0.005 0.051 5944 Dihedral : 6.937 86.925 4680 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.99 % Allowed : 21.70 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.28 (0.13), residues: 4162 helix: 2.08 (0.11), residues: 2093 sheet: 0.82 (0.25), residues: 387 loop : -0.76 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 8 TYR 0.019 0.001 TYR C 81 PHE 0.023 0.002 PHE P 153 TRP 0.010 0.001 TRP D 192 HIS 0.009 0.001 HIS P 100 Details of bonding type rmsd covalent geometry : bond 0.00406 (34108) covalent geometry : angle 0.61772 (46398) SS BOND : bond 0.01366 ( 6) SS BOND : angle 3.62322 ( 12) hydrogen bonds : bond 0.06336 ( 1812) hydrogen bonds : angle 4.07182 ( 5145) metal coordination : bond 0.05643 ( 10) metal coordination : angle 25.54878 ( 13) Misc. bond : bond 0.08383 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8324 Ramachandran restraints generated. 4162 Oldfield, 0 Emsley, 4162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8324 Ramachandran restraints generated. 4162 Oldfield, 0 Emsley, 4162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 407 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.5997 (mp10) REVERT: A 104 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8598 (mtmt) REVERT: B 110 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8384 (tp30) REVERT: B 221 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: B 305 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7446 (mp10) REVERT: C 171 ASP cc_start: 0.8850 (t0) cc_final: 0.8579 (t0) REVERT: C 269 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8194 (ptmm) REVERT: C 379 TRP cc_start: 0.7877 (OUTLIER) cc_final: 0.6292 (m-10) REVERT: D 80 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.6624 (mmp) REVERT: D 234 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8446 (mttm) REVERT: E 13 TYR cc_start: 0.9108 (m-80) cc_final: 0.8739 (m-80) REVERT: E 99 ARG cc_start: 0.8091 (ttp-170) cc_final: 0.7736 (tpp80) REVERT: H 22 GLU cc_start: 0.8571 (tp30) cc_final: 0.8072 (mm-30) REVERT: H 23 GLN cc_start: 0.8495 (tm-30) cc_final: 0.7965 (tt0) REVERT: H 34 ARG cc_start: 0.7903 (ttm-80) cc_final: 0.7603 (tpp-160) REVERT: H 52 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.5150 (mm-30) REVERT: I 1 MET cc_start: 0.6468 (tpt) cc_final: 0.4788 (pmm) REVERT: I 20 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6647 (mpt-90) REVERT: K 6 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7178 (mm) REVERT: K 39 ARG cc_start: 0.6525 (mpp-170) cc_final: 0.4808 (mmm-85) REVERT: L 28 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8579 (tt0) REVERT: L 184 GLU cc_start: 0.8502 (tp30) cc_final: 0.8147 (mp0) REVERT: L 206 ARG cc_start: 0.8545 (mmm160) cc_final: 0.8090 (mmm160) REVERT: L 245 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.7664 (tp30) REVERT: L 429 GLU cc_start: 0.8828 (tt0) cc_final: 0.8481 (tt0) REVERT: M 185 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8095 (mmtp) REVERT: M 245 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.7587 (ptm160) REVERT: N 194 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8427 (mpp) REVERT: O 15 ARG cc_start: 0.8736 (tpt-90) cc_final: 0.8482 (ttm-80) REVERT: O 58 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7999 (tp30) REVERT: O 77 ASP cc_start: 0.8064 (t0) cc_final: 0.7797 (m-30) REVERT: P 30 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: P 181 GLU cc_start: 0.7677 (mp0) cc_final: 0.7273 (tt0) REVERT: R 22 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: S 15 ASP cc_start: 0.8469 (t0) cc_final: 0.8181 (t70) REVERT: S 22 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8216 (mt-10) REVERT: S 54 CYS cc_start: 0.6454 (OUTLIER) cc_final: 0.5093 (p) REVERT: S 56 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7119 (pm20) REVERT: S 57 GLU cc_start: 0.8621 (mp0) cc_final: 0.7720 (mp0) REVERT: T 44 ASP cc_start: 0.5567 (t0) cc_final: 0.5206 (t0) REVERT: U 16 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6266 (mtt180) REVERT: U 44 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7949 (mp0) REVERT: V 39 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.3030 (mpp-170) outliers start: 141 outliers final: 82 residues processed: 516 average time/residue: 0.7646 time to fit residues: 460.9679 Evaluate side-chains 512 residues out of total 3530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 405 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 305 GLN Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 379 TRP Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 6 HIS Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain I residue 20 ARG Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain J residue 11 SER Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 222 THR Chi-restraints excluded: chain L residue 245 GLU Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 352 SER Chi-restraints excluded: chain L residue 369 LEU Chi-restraints excluded: chain L residue 381 ARG Chi-restraints excluded: chain L residue 412 SER Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 176 LEU Chi-restraints excluded: chain M residue 185 LYS Chi-restraints excluded: chain M residue 219 VAL Chi-restraints excluded: chain M residue 223 PHE Chi-restraints excluded: chain M residue 245 ARG Chi-restraints excluded: chain M residue 326 THR Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 171 ASP Chi-restraints excluded: chain N residue 172 LYS Chi-restraints excluded: chain N residue 190 MET Chi-restraints excluded: chain N residue 194 MET Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 212 SER Chi-restraints excluded: chain N residue 282 ARG Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain N residue 345 HIS Chi-restraints excluded: chain N residue 378 LYS Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 58 GLU Chi-restraints excluded: chain O residue 168 VAL Chi-restraints excluded: chain O residue 173 ASP Chi-restraints excluded: chain P residue 9 ASP Chi-restraints excluded: chain P residue 30 GLU Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 110 LYS Chi-restraints excluded: chain R residue 3 GLN Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 22 GLU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain S residue 54 CYS Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain U residue 4 THR Chi-restraints excluded: chain U residue 16 ARG Chi-restraints excluded: chain U residue 18 SER Chi-restraints excluded: chain U residue 44 GLU Chi-restraints excluded: chain V residue 37 ASP Chi-restraints excluded: chain V residue 39 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 137 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 23 optimal weight: 0.4980 chunk 252 optimal weight: 1.9990 chunk 389 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 340 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN ** P 161 HIS ** 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 = 0.3398 r_free = 0.3398 target = 0.104732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.076960 restraints weight = 49983.686| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.26 r_work: 0.2871 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.184 34133 Z= 0.155 Angle : 0.746 41.997 46423 Z= 0.313 Chirality : 0.043 0.211 5090 Planarity : 0.004 0.052 5944 Dihedral : 6.907 87.143 4680 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.57 % Allowed : 22.15 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.28 (0.13), residues: 4162 helix: 2.09 (0.11), residues: 2095 sheet: 0.61 (0.25), residues: 410 loop : -0.71 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 8 TYR 0.017 0.001 TYR C 81 PHE 0.020 0.002 PHE P 153 TRP 0.011 0.001 TRP D 192 HIS 0.010 0.001 HIS P 100 Details of bonding type rmsd covalent geometry : bond 0.00366 (34108) covalent geometry : angle 0.61309 (46398) SS BOND : bond 0.01219 ( 6) SS BOND : angle 3.54700 ( 12) hydrogen bonds : bond 0.06053 ( 1812) hydrogen bonds : angle 4.05556 ( 5145) metal coordination : bond 0.05457 ( 10) metal coordination : angle 25.22972 ( 13) Misc. bond : bond 0.08496 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8324 Ramachandran restraints generated. 4162 Oldfield, 0 Emsley, 4162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8324 Ramachandran restraints generated. 4162 Oldfield, 0 Emsley, 4162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 417 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.6061 (mp10) REVERT: A 104 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8604 (mtmt) REVERT: B 25 GLU cc_start: 0.8109 (pt0) cc_final: 0.7833 (pt0) REVERT: B 221 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: B 305 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7454 (mp10) REVERT: C 171 ASP cc_start: 0.8853 (t0) cc_final: 0.8609 (t0) REVERT: C 269 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8165 (ptmm) REVERT: C 379 TRP cc_start: 0.7869 (OUTLIER) cc_final: 0.6269 (m-10) REVERT: D 72 ASP cc_start: 0.8480 (t0) cc_final: 0.7942 (t0) REVERT: D 80 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.6696 (mmp) REVERT: D 234 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8472 (mttm) REVERT: E 13 TYR cc_start: 0.9198 (m-80) cc_final: 0.8806 (m-80) REVERT: E 99 ARG cc_start: 0.8131 (ttp-170) cc_final: 0.7796 (tpp80) REVERT: H 22 GLU cc_start: 0.8558 (tp30) cc_final: 0.8091 (mm-30) REVERT: H 23 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8008 (tt0) REVERT: H 34 ARG cc_start: 0.7939 (ttm-80) cc_final: 0.7642 (tpp-160) REVERT: H 52 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.5066 (mm-30) REVERT: I 1 MET cc_start: 0.6439 (tpt) cc_final: 0.4864 (pmm) REVERT: K 6 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7233 (mm) REVERT: K 39 ARG cc_start: 0.6687 (mpp-170) cc_final: 0.5128 (mtp180) REVERT: L 28 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8604 (tt0) REVERT: L 184 GLU cc_start: 0.8554 (tp30) cc_final: 0.8202 (mp0) REVERT: L 206 ARG cc_start: 0.8549 (mmm160) cc_final: 0.8102 (mmm160) REVERT: L 245 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.7594 (tp30) REVERT: L 429 GLU cc_start: 0.8838 (tt0) cc_final: 0.8514 (tt0) REVERT: M 185 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8153 (mmtp) REVERT: M 245 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.7640 (ptm160) REVERT: N 112 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8671 (m) REVERT: N 194 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8531 (mpp) REVERT: O 15 ARG cc_start: 0.8773 (tpt-90) cc_final: 0.8546 (ttm-80) REVERT: O 58 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8066 (tp30) REVERT: O 77 ASP cc_start: 0.8083 (t0) cc_final: 0.7865 (m-30) REVERT: P 30 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: P 181 GLU cc_start: 0.7695 (mp0) cc_final: 0.7290 (tt0) REVERT: R 22 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8010 (mt-10) REVERT: S 15 ASP cc_start: 0.8540 (t0) cc_final: 0.8271 (t70) REVERT: S 22 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8252 (mt-10) REVERT: S 54 CYS cc_start: 0.6410 (OUTLIER) cc_final: 0.5011 (p) REVERT: S 56 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7143 (pm20) REVERT: S 57 GLU cc_start: 0.8643 (mp0) cc_final: 0.7731 (mp0) REVERT: T 44 ASP cc_start: 0.5568 (t0) cc_final: 0.5203 (t0) REVERT: U 16 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6428 (mtt180) REVERT: U 44 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: V 39 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.3024 (mpp-170) outliers start: 126 outliers final: 81 residues processed: 509 average time/residue: 0.7572 time to fit residues: 449.8065 Evaluate side-chains 509 residues out of total 3530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 404 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 305 GLN Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 379 TRP Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 6 HIS Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain J residue 11 SER Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 222 THR Chi-restraints excluded: chain L residue 245 GLU Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 369 LEU Chi-restraints excluded: chain L residue 381 ARG Chi-restraints excluded: chain L residue 412 SER Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 176 LEU Chi-restraints excluded: chain M residue 185 LYS Chi-restraints excluded: chain M residue 219 VAL Chi-restraints excluded: chain M residue 223 PHE Chi-restraints excluded: chain M residue 245 ARG Chi-restraints excluded: chain M residue 326 THR Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 171 ASP Chi-restraints excluded: chain N residue 172 LYS Chi-restraints excluded: chain N residue 194 MET Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 212 SER Chi-restraints excluded: chain N residue 282 ARG Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain N residue 345 HIS Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 58 GLU Chi-restraints excluded: chain O residue 168 VAL Chi-restraints excluded: chain O residue 173 ASP Chi-restraints excluded: chain P residue 9 ASP Chi-restraints excluded: chain P residue 30 GLU Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 110 LYS Chi-restraints excluded: chain R residue 3 GLN Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 22 GLU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain S residue 54 CYS Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain U residue 4 THR Chi-restraints excluded: chain U residue 16 ARG Chi-restraints excluded: chain U residue 17 THR Chi-restraints excluded: chain U residue 18 SER Chi-restraints excluded: chain U residue 44 GLU Chi-restraints excluded: chain V residue 37 ASP Chi-restraints excluded: chain V residue 39 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 99 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 388 optimal weight: 3.9990 chunk 347 optimal weight: 0.6980 chunk 229 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 318 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 308 GLN M 248 ASN ** P 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.106026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.078315 restraints weight = 50280.121| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.27 r_work: 0.2896 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.177 34133 Z= 0.133 Angle : 0.724 40.269 46423 Z= 0.300 Chirality : 0.042 0.204 5090 Planarity : 0.004 0.052 5944 Dihedral : 6.791 87.604 4680 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.14 % Allowed : 22.63 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % 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: 1.37 (0.13), residues: 4162 helix: 2.13 (0.11), residues: 2101 sheet: 0.64 (0.25), residues: 410 loop : -0.63 (0.16), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 36 TYR 0.019 0.001 TYR P 157 PHE 0.018 0.001 PHE P 153 TRP 0.012 0.001 TRP D 192 HIS 0.010 0.001 HIS P 100 Details of bonding type rmsd covalent geometry : bond 0.00303 (34108) covalent geometry : angle 0.58920 (46398) SS BOND : bond 0.01033 ( 6) SS BOND : angle 3.17544 ( 12) hydrogen bonds : bond 0.05429 ( 1812) hydrogen bonds : angle 4.00072 ( 5145) metal coordination : bond 0.05245 ( 10) metal coordination : angle 25.00869 ( 13) Misc. bond : bond 0.08563 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8324 Ramachandran restraints generated. 4162 Oldfield, 0 Emsley, 4162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8324 Ramachandran restraints generated. 4162 Oldfield, 0 Emsley, 4162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 419 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.5776 (mp10) REVERT: B 25 GLU cc_start: 0.7952 (pt0) cc_final: 0.7693 (pt0) REVERT: B 221 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: B 305 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7419 (mp10) REVERT: C 269 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8153 (ptmm) REVERT: C 287 LYS cc_start: 0.8521 (mtpp) cc_final: 0.8259 (mtmm) REVERT: C 379 TRP cc_start: 0.7730 (OUTLIER) cc_final: 0.6058 (m-10) REVERT: D 72 ASP cc_start: 0.8458 (t0) cc_final: 0.7868 (t0) REVERT: D 80 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.6790 (mmp) REVERT: D 234 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8400 (mttm) REVERT: E 13 TYR cc_start: 0.9161 (m-80) cc_final: 0.8759 (m-80) REVERT: E 99 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7727 (tpp80) REVERT: G 64 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: H 22 GLU cc_start: 0.8529 (tp30) cc_final: 0.8057 (mm-30) REVERT: H 23 GLN cc_start: 0.8464 (tm-30) cc_final: 0.8032 (tt0) REVERT: H 34 ARG cc_start: 0.7865 (ttm-80) cc_final: 0.7564 (tpp-160) REVERT: H 52 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.5058 (mm-30) REVERT: H 57 GLU cc_start: 0.8510 (mp0) cc_final: 0.8062 (mp0) REVERT: I 1 MET cc_start: 0.6381 (tpt) cc_final: 0.4821 (pmm) REVERT: I 20 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.6585 (mpt-90) REVERT: K 6 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7225 (mm) REVERT: K 39 ARG cc_start: 0.6569 (mpp-170) cc_final: 0.5064 (mtp180) REVERT: L 28 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8555 (tt0) REVERT: L 184 GLU cc_start: 0.8507 (tp30) cc_final: 0.8159 (mp0) REVERT: L 206 ARG cc_start: 0.8509 (mmm160) cc_final: 0.8054 (mmm160) REVERT: L 245 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.7546 (tp30) REVERT: L 429 GLU cc_start: 0.8816 (tt0) cc_final: 0.8465 (tt0) REVERT: M 185 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8135 (mmtp) REVERT: M 245 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.7601 (ptm160) REVERT: N 112 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8574 (m) REVERT: N 171 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8316 (m-30) REVERT: N 194 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8483 (mpp) REVERT: O 15 ARG cc_start: 0.8736 (tpt-90) cc_final: 0.8510 (ttm-80) REVERT: O 58 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8041 (tp30) REVERT: P 30 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7564 (mt-10) REVERT: P 181 GLU cc_start: 0.7658 (mp0) cc_final: 0.7265 (tt0) REVERT: R 22 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8004 (mt-10) REVERT: S 15 ASP cc_start: 0.8485 (t0) cc_final: 0.8189 (t70) REVERT: S 22 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8243 (mt-10) REVERT: S 38 GLU cc_start: 0.7602 (pp20) cc_final: 0.7196 (pp20) REVERT: S 43 ARG cc_start: 0.7707 (tmm-80) cc_final: 0.7280 (ttm170) REVERT: S 54 CYS cc_start: 0.6321 (OUTLIER) cc_final: 0.4830 (p) REVERT: S 56 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7159 (pm20) REVERT: S 57 GLU cc_start: 0.8645 (mp0) cc_final: 0.7780 (mp0) REVERT: T 44 ASP cc_start: 0.5498 (t0) cc_final: 0.5140 (t0) REVERT: U 16 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6291 (mtt180) REVERT: U 44 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7980 (mp0) REVERT: V 39 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.2987 (mpp-170) outliers start: 111 outliers final: 79 residues processed: 499 average time/residue: 0.7617 time to fit residues: 443.9021 Evaluate side-chains 518 residues out of total 3530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 412 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 305 GLN Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 379 TRP Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 6 HIS Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 64 GLN Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain I residue 20 ARG Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain J residue 11 SER Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 222 THR Chi-restraints excluded: chain L residue 245 GLU Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 369 LEU Chi-restraints excluded: chain L residue 381 ARG Chi-restraints excluded: chain L residue 412 SER Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 185 LYS Chi-restraints excluded: chain M residue 219 VAL Chi-restraints excluded: chain M residue 223 PHE Chi-restraints excluded: chain M residue 245 ARG Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 171 ASP Chi-restraints excluded: chain N residue 172 LYS Chi-restraints excluded: chain N residue 194 MET Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 212 SER Chi-restraints excluded: chain N residue 282 ARG Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain N residue 345 HIS Chi-restraints excluded: chain O residue 58 GLU Chi-restraints excluded: chain O residue 168 VAL Chi-restraints excluded: chain O residue 173 ASP Chi-restraints excluded: chain P residue 9 ASP Chi-restraints excluded: chain P residue 30 GLU Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 110 LYS Chi-restraints excluded: chain R residue 3 GLN Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 22 GLU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain S residue 54 CYS Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 11 PHE Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain U residue 16 ARG Chi-restraints excluded: chain U residue 17 THR Chi-restraints excluded: chain U residue 18 SER Chi-restraints excluded: chain U residue 44 GLU Chi-restraints excluded: chain V residue 37 ASP Chi-restraints excluded: chain V residue 39 ARG Chi-restraints excluded: chain V residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 409 optimal weight: 5.9990 chunk 227 optimal weight: 8.9990 chunk 54 optimal weight: 0.4980 chunk 305 optimal weight: 1.9990 chunk 368 optimal weight: 9.9990 chunk 208 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 276 optimal weight: 7.9990 chunk 407 optimal weight: 0.8980 chunk 245 optimal weight: 0.0470 chunk 308 optimal weight: 0.2980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN C 15 ASN M 198 HIS ** P 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.108495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.081014 restraints weight = 49925.611| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.26 r_work: 0.2950 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.135 34133 Z= 0.114 Angle : 0.698 39.898 46423 Z= 0.286 Chirality : 0.041 0.195 5090 Planarity : 0.004 0.053 5944 Dihedral : 6.597 88.055 4680 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.92 % Allowed : 23.09 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % 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: 1.50 (0.13), residues: 4162 helix: 2.26 (0.11), residues: 2095 sheet: 0.84 (0.25), residues: 395 loop : -0.61 (0.16), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 421 TYR 0.014 0.001 TYR N 224 PHE 0.017 0.001 PHE P 153 TRP 0.013 0.001 TRP D 192 HIS 0.010 0.001 HIS P 100 Details of bonding type rmsd covalent geometry : bond 0.00251 (34108) covalent geometry : angle 0.56320 (46398) SS BOND : bond 0.01119 ( 6) SS BOND : angle 3.03138 ( 12) hydrogen bonds : bond 0.04527 ( 1812) hydrogen bonds : angle 3.90897 ( 5145) metal coordination : bond 0.04964 ( 10) metal coordination : angle 24.51579 ( 13) Misc. bond : bond 0.08076 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15394.64 seconds wall clock time: 261 minutes 2.54 seconds (15662.54 seconds total)