Starting phenix.real_space_refine on Tue Aug 26 01:37:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c7h_45282/08_2025/9c7h_45282.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c7h_45282/08_2025/9c7h_45282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c7h_45282/08_2025/9c7h_45282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c7h_45282/08_2025/9c7h_45282.map" model { file = "/net/cci-nas-00/data/ceres_data/9c7h_45282/08_2025/9c7h_45282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c7h_45282/08_2025/9c7h_45282.cif" } resolution = 2.78 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= -0.001 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 171 5.16 5 C 20978 2.51 5 N 5636 2.21 5 O 5981 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32776 Number of models: 1 Model: "" Number of chains: 28 Chain: "0" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 561 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "1" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 493 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "2" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1513 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "3" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 47} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "4" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1515 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 185} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "5" Number of atoms: 3374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3374 Classifications: {'peptide': 435} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 417} Chain breaks: 1 Chain: "6" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3140 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain: "7" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3025 Classifications: {'peptide': 379} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 356} Chain: "8" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1903 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 217} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "9" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 893 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "u" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3373 Classifications: {'peptide': 435} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "v" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3140 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain: "w" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3025 Classifications: {'peptide': 379} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 356} Chain: "x" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1896 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 21, 'TRANS': 216} Chain: "y" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 893 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "z" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 666 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 6, 'TRANS': 72} Chain: "Af" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 275 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 34} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "Ae" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 271 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 34} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "Aa" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 666 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 6, 'TRANS': 72} Chain: "Ab" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 561 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "Ac" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 493 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "Ad" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 47} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "7" 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: "8" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "w" 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: "x" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2146 SG CYS 2 238 30.576 51.368 44.665 1.00 26.46 S ATOM 2282 SG CYS 2 257 31.363 48.215 42.852 1.00 17.26 S ATOM 4073 SG CYS 4 238 94.170 64.471 38.505 1.00 26.46 S ATOM 4209 SG CYS 4 257 92.442 66.977 36.934 1.00 17.26 S Time building chain proxies: 6.76, per 1000 atoms: 0.21 Number of scatterers: 32776 At special positions: 0 Unit cell: (124.12, 136.96, 174.41, 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 171 16.00 O 5981 8.00 N 5636 7.00 C 20978 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS 0 37 " - pdb=" SG CYS 0 43 " distance=2.05 Simple disulfide: pdb=" SG CYS 2 243 " - pdb=" SG CYS 2 259 " distance=2.04 Simple disulfide: pdb=" SG CYS 4 243 " - pdb=" SG CYS 4 259 " distance=2.04 Simple disulfide: pdb=" SG CYSAb 37 " - pdb=" SG CYSAb 43 " distance=2.04 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 301 " pdb="FE2 FES 2 301 " - pdb=" ND1 HIS 2 260 " pdb="FE2 FES 2 301 " - pdb=" ND1 HIS 2 240 " pdb="FE1 FES 2 301 " - pdb=" SG CYS 2 257 " pdb="FE1 FES 2 301 " - pdb=" SG CYS 2 238 " pdb=" FES 4 301 " pdb="FE2 FES 4 301 " - pdb=" NE2 HIS 4 240 " pdb="FE2 FES 4 301 " - pdb=" ND1 HIS 4 260 " pdb="FE1 FES 4 301 " - pdb=" SG CYS 4 257 " pdb="FE1 FES 4 301 " - pdb=" SG CYS 4 238 " Number of angles added : 6 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7720 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 19 sheets defined 59.8% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain '0' and resid 28 through 39 removed outlier: 3.983A pdb=" N THR 0 32 " --> pdb=" O ASP 0 28 " (cutoff:3.500A) Processing helix chain '0' and resid 40 through 60 Processing helix chain '0' and resid 67 through 86 Processing helix chain '0' and resid 87 through 89 No H-bonds generated for 'chain '0' and resid 87 through 89' Processing helix chain '1' and resid 5 through 14 Processing helix chain '1' and resid 17 through 48 Processing helix chain '1' and resid 52 through 60 removed outlier: 4.374A pdb=" N LYS 1 57 " --> pdb=" O LYS 1 54 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N HIS 1 58 " --> pdb=" O HIS 1 55 " (cutoff:3.500A) Processing helix chain '2' and resid 115 through 119 removed outlier: 4.149A pdb=" N ASP 2 119 " --> pdb=" O GLU 2 116 " (cutoff:3.500A) Processing helix chain '2' and resid 127 through 161 removed outlier: 3.758A pdb=" N MET 2 161 " --> pdb=" O PHE 2 157 " (cutoff:3.500A) Processing helix chain '2' and resid 164 through 170 Processing helix chain '2' and resid 178 through 180 No H-bonds generated for 'chain '2' and resid 178 through 180' Processing helix chain '2' and resid 201 through 210 Processing helix chain '2' and resid 221 through 226 Processing helix chain '3' and resid 2 through 6 Processing helix chain '3' and resid 7 through 37 Proline residue: 3 19 - end of helix Processing helix chain '3' and resid 47 through 51 Processing helix chain '4' and resid 114 through 118 removed outlier: 3.868A pdb=" N LEU 4 118 " --> pdb=" O ALA 4 115 " (cutoff:3.500A) Processing helix chain '4' and resid 124 through 161 removed outlier: 4.520A pdb=" N ASP 4 129 " --> pdb=" O LYS 4 125 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA 4 130 " --> pdb=" O GLU 4 126 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET 4 161 " --> pdb=" O PHE 4 157 " (cutoff:3.500A) Processing helix chain '4' and resid 164 through 170 removed outlier: 3.600A pdb=" N MET 4 170 " --> pdb=" O ASP 4 166 " (cutoff:3.500A) Processing helix chain '4' and resid 178 through 180 No H-bonds generated for 'chain '4' and resid 178 through 180' Processing helix chain '4' and resid 201 through 211 Processing helix chain '4' and resid 221 through 226 Processing helix chain '5' and resid 37 through 44 Processing helix chain '5' and resid 78 through 82 Processing helix chain '5' and resid 83 through 87 removed outlier: 4.134A pdb=" N ASN 5 87 " --> pdb=" O GLU 5 84 " (cutoff:3.500A) Processing helix chain '5' and resid 88 through 96 Processing helix chain '5' and resid 107 through 116 Processing helix chain '5' and resid 139 through 152 Processing helix chain '5' and resid 157 through 176 Processing helix chain '5' and resid 178 through 192 Processing helix chain '5' and resid 195 through 199 Processing helix chain '5' and resid 204 through 211 Processing helix chain '5' and resid 212 through 224 Processing helix chain '5' and resid 225 through 227 No H-bonds generated for 'chain '5' and resid 225 through 227' Processing helix chain '5' and resid 238 through 250 Processing helix chain '5' and resid 300 through 312 Processing helix chain '5' and resid 320 through 324 Processing helix chain '5' and resid 326 through 336 Processing helix chain '5' and resid 364 through 382 Processing helix chain '5' and resid 384 through 403 removed outlier: 3.705A pdb=" N LEU 5 403 " --> pdb=" O LEU 5 399 " (cutoff:3.500A) Processing helix chain '5' and resid 405 through 420 Processing helix chain '5' and resid 425 through 436 removed outlier: 3.600A pdb=" N VAL 5 436 " --> pdb=" O ARG 5 432 " (cutoff:3.500A) Processing helix chain '5' and resid 437 through 449 Processing helix chain '5' and resid 467 through 475 Processing helix chain '6' and resid 68 through 72 Processing helix chain '6' and resid 78 through 86 Processing helix chain '6' and resid 95 through 106 removed outlier: 3.704A pdb=" N VAL 6 106 " --> pdb=" O GLY 6 102 " (cutoff:3.500A) Processing helix chain '6' and resid 129 through 142 removed outlier: 3.509A pdb=" N LEU 6 133 " --> pdb=" O ASP 6 129 " (cutoff:3.500A) Processing helix chain '6' and resid 147 through 167 removed outlier: 4.541A pdb=" N SER 6 156 " --> pdb=" O ALA 6 152 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLN 6 157 " --> pdb=" O ALA 6 153 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU 6 158 " --> pdb=" O LEU 6 154 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG 6 159 " --> pdb=" O GLN 6 155 " (cutoff:3.500A) Processing helix chain '6' and resid 168 through 182 removed outlier: 4.255A pdb=" N GLN 6 172 " --> pdb=" O ASN 6 168 " (cutoff:3.500A) Processing helix chain '6' and resid 184 through 188 Processing helix chain '6' and resid 193 through 197 Processing helix chain '6' and resid 201 through 213 Processing helix chain '6' and resid 214 through 216 No H-bonds generated for 'chain '6' and resid 214 through 216' Processing helix chain '6' and resid 226 through 238 Processing helix chain '6' and resid 280 through 294 Processing helix chain '6' and resid 307 through 315 Processing helix chain '6' and resid 346 through 363 Processing helix chain '6' and resid 367 through 388 removed outlier: 4.065A pdb=" N SER 6 388 " --> pdb=" O MET 6 384 " (cutoff:3.500A) Processing helix chain '6' and resid 388 through 403 Processing helix chain '6' and resid 408 through 418 Processing helix chain '6' and resid 420 through 433 Processing helix chain '7' and resid 3 through 8 Processing helix chain '7' and resid 8 through 19 Processing helix chain '7' and resid 28 through 30 No H-bonds generated for 'chain '7' and resid 28 through 30' Processing helix chain '7' and resid 31 through 53 removed outlier: 4.651A pdb=" N SER 7 35 " --> pdb=" O TRP 7 31 " (cutoff:3.500A) Processing helix chain '7' and resid 61 through 72 Processing helix chain '7' and resid 75 through 104 removed outlier: 3.666A pdb=" N SER 7 88 " --> pdb=" O ALA 7 84 " (cutoff:3.500A) Processing helix chain '7' and resid 105 through 108 Processing helix chain '7' and resid 109 through 133 removed outlier: 3.629A pdb=" N VAL 7 132 " --> pdb=" O PHE 7 128 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU 7 133 " --> pdb=" O MET 7 129 " (cutoff:3.500A) Processing helix chain '7' and resid 136 through 150 removed outlier: 3.992A pdb=" N LEU 7 150 " --> pdb=" O ILE 7 146 " (cutoff:3.500A) Processing helix chain '7' and resid 151 through 153 No H-bonds generated for 'chain '7' and resid 151 through 153' Processing helix chain '7' and resid 156 through 166 Processing helix chain '7' and resid 171 through 202 Proline residue: 7 186 - end of helix Processing helix chain '7' and resid 213 through 215 No H-bonds generated for 'chain '7' and resid 213 through 215' Processing helix chain '7' and resid 220 through 246 removed outlier: 4.618A pdb=" N ILE 7 226 " --> pdb=" O PRO 7 222 " (cutoff:3.500A) Processing helix chain '7' and resid 252 through 257 Processing helix chain '7' and resid 271 through 284 removed outlier: 4.373A pdb=" N PHE 7 276 " --> pdb=" O TRP 7 272 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ALA 7 277 " --> pdb=" O TYR 7 273 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE 7 284 " --> pdb=" O ILE 7 280 " (cutoff:3.500A) Processing helix chain '7' and resid 286 through 304 removed outlier: 3.829A pdb=" N ILE 7 298 " --> pdb=" O LEU 7 294 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LEU 7 301 " --> pdb=" O SER 7 297 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE 7 302 " --> pdb=" O ILE 7 298 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU 7 303 " --> pdb=" O LEU 7 299 " (cutoff:3.500A) Processing helix chain '7' and resid 305 through 308 Processing helix chain '7' and resid 314 through 317 removed outlier: 4.020A pdb=" N PHE 7 317 " --> pdb=" O SER 7 314 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 314 through 317' Processing helix chain '7' and resid 318 through 341 Processing helix chain '7' and resid 344 through 364 removed outlier: 3.951A pdb=" N ILE 7 349 " --> pdb=" O HIS 7 345 " (cutoff:3.500A) Processing helix chain '7' and resid 364 through 377 Processing helix chain '8' and resid 107 through 122 Processing helix chain '8' and resid 123 through 125 No H-bonds generated for 'chain '8' and resid 123 through 125' Processing helix chain '8' and resid 132 through 137 Processing helix chain '8' and resid 142 through 153 removed outlier: 3.984A pdb=" N VAL 8 153 " --> pdb=" O LEU 8 149 " (cutoff:3.500A) Processing helix chain '8' and resid 182 through 190 Processing helix chain '8' and resid 208 through 218 Processing helix chain '8' and resid 263 through 280 Processing helix chain '8' and resid 282 through 317 Proline residue: 8 302 - end of helix removed outlier: 4.629A pdb=" N VAL 8 314 " --> pdb=" O HIS 8 310 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU 8 315 " --> pdb=" O LYS 8 311 " (cutoff:3.500A) Processing helix chain '9' and resid 12 through 25 Processing helix chain '9' and resid 33 through 37 Processing helix chain '9' and resid 41 through 50 Processing helix chain '9' and resid 52 through 72 Processing helix chain '9' and resid 77 through 81 removed outlier: 3.556A pdb=" N TRP 9 81 " --> pdb=" O LYS 9 78 " (cutoff:3.500A) Processing helix chain '9' and resid 91 through 111 removed outlier: 3.655A pdb=" N LYS 9 111 " --> pdb=" O GLU 9 107 " (cutoff:3.500A) Processing helix chain 'u' and resid 37 through 44 Processing helix chain 'u' and resid 78 through 82 Processing helix chain 'u' and resid 88 through 96 Processing helix chain 'u' and resid 105 through 116 removed outlier: 3.870A pdb=" N LEU u 109 " --> pdb=" O PRO u 105 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU u 110 " --> pdb=" O GLY u 106 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET u 116 " --> pdb=" O GLU u 112 " (cutoff:3.500A) Processing helix chain 'u' and resid 139 through 152 Processing helix chain 'u' and resid 157 through 176 Processing helix chain 'u' and resid 178 through 192 Processing helix chain 'u' and resid 195 through 199 Processing helix chain 'u' and resid 204 through 211 Processing helix chain 'u' and resid 212 through 224 Processing helix chain 'u' and resid 225 through 227 No H-bonds generated for 'chain 'u' and resid 225 through 227' Processing helix chain 'u' and resid 238 through 250 Processing helix chain 'u' and resid 300 through 312 Processing helix chain 'u' and resid 320 through 324 Processing helix chain 'u' and resid 326 through 336 Processing helix chain 'u' and resid 364 through 382 Processing helix chain 'u' and resid 384 through 403 Processing helix chain 'u' and resid 405 through 420 Processing helix chain 'u' and resid 425 through 434 Processing helix chain 'u' and resid 437 through 449 Processing helix chain 'u' and resid 467 through 475 Processing helix chain 'v' and resid 68 through 72 Processing helix chain 'v' and resid 73 through 77 removed outlier: 4.191A pdb=" N LEU v 77 " --> pdb=" O SER v 74 " (cutoff:3.500A) Processing helix chain 'v' and resid 78 through 86 Processing helix chain 'v' and resid 95 through 106 removed outlier: 3.702A pdb=" N VAL v 106 " --> pdb=" O GLY v 102 " (cutoff:3.500A) Processing helix chain 'v' and resid 129 through 141 removed outlier: 4.239A pdb=" N LEU v 133 " --> pdb=" O ASP v 129 " (cutoff:3.500A) Processing helix chain 'v' and resid 147 through 167 removed outlier: 4.662A pdb=" N SER v 156 " --> pdb=" O ALA v 152 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLN v 157 " --> pdb=" O ALA v 153 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU v 158 " --> pdb=" O LEU v 154 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG v 159 " --> pdb=" O GLN v 155 " (cutoff:3.500A) Processing helix chain 'v' and resid 168 through 182 removed outlier: 4.270A pdb=" N GLN v 172 " --> pdb=" O ASN v 168 " (cutoff:3.500A) Processing helix chain 'v' and resid 193 through 197 Processing helix chain 'v' and resid 201 through 213 Processing helix chain 'v' and resid 226 through 238 Processing helix chain 'v' and resid 280 through 294 removed outlier: 3.507A pdb=" N ASN v 284 " --> pdb=" O SER v 280 " (cutoff:3.500A) Processing helix chain 'v' and resid 307 through 315 Processing helix chain 'v' and resid 346 through 363 Processing helix chain 'v' and resid 367 through 386 Processing helix chain 'v' and resid 388 through 403 Processing helix chain 'v' and resid 408 through 419 removed outlier: 3.562A pdb=" N VAL v 419 " --> pdb=" O GLN v 415 " (cutoff:3.500A) Processing helix chain 'v' and resid 420 through 434 Processing helix chain 'w' and resid 3 through 8 Processing helix chain 'w' and resid 8 through 19 Processing helix chain 'w' and resid 28 through 30 No H-bonds generated for 'chain 'w' and resid 28 through 30' Processing helix chain 'w' and resid 31 through 53 removed outlier: 4.607A pdb=" N SER w 35 " --> pdb=" O TRP w 31 " (cutoff:3.500A) Processing helix chain 'w' and resid 61 through 70 Processing helix chain 'w' and resid 75 through 104 removed outlier: 3.615A pdb=" N SER w 88 " --> pdb=" O ALA w 84 " (cutoff:3.500A) Processing helix chain 'w' and resid 105 through 108 Processing helix chain 'w' and resid 109 through 133 Processing helix chain 'w' and resid 136 through 150 removed outlier: 3.981A pdb=" N LEU w 150 " --> pdb=" O ILE w 146 " (cutoff:3.500A) Processing helix chain 'w' and resid 151 through 153 No H-bonds generated for 'chain 'w' and resid 151 through 153' Processing helix chain 'w' and resid 156 through 166 Processing helix chain 'w' and resid 171 through 202 Proline residue: w 186 - end of helix Processing helix chain 'w' and resid 220 through 245 removed outlier: 4.383A pdb=" N ILE w 226 " --> pdb=" O PRO w 222 " (cutoff:3.500A) Processing helix chain 'w' and resid 252 through 257 removed outlier: 3.787A pdb=" N THR w 257 " --> pdb=" O ASP w 254 " (cutoff:3.500A) Processing helix chain 'w' and resid 271 through 284 removed outlier: 4.452A pdb=" N PHE w 276 " --> pdb=" O TRP w 272 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ALA w 277 " --> pdb=" O TYR w 273 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE w 284 " --> pdb=" O ILE w 280 " (cutoff:3.500A) Processing helix chain 'w' and resid 286 through 308 removed outlier: 3.865A pdb=" N ILE w 298 " --> pdb=" O LEU w 294 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU w 301 " --> pdb=" O SER w 297 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE w 302 " --> pdb=" O ILE w 298 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU w 303 " --> pdb=" O LEU w 299 " (cutoff:3.500A) Proline residue: w 305 - end of helix Processing helix chain 'w' and resid 314 through 317 removed outlier: 4.257A pdb=" N PHE w 317 " --> pdb=" O SER w 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 314 through 317' Processing helix chain 'w' and resid 318 through 341 Processing helix chain 'w' and resid 344 through 364 removed outlier: 3.850A pdb=" N ILE w 349 " --> pdb=" O HIS w 345 " (cutoff:3.500A) Processing helix chain 'w' and resid 364 through 377 Processing helix chain 'x' and resid 107 through 121 Processing helix chain 'x' and resid 122 through 125 Processing helix chain 'x' and resid 132 through 137 Processing helix chain 'x' and resid 142 through 152 Processing helix chain 'x' and resid 182 through 190 Processing helix chain 'x' and resid 200 through 205 Processing helix chain 'x' and resid 208 through 218 Processing helix chain 'x' and resid 263 through 280 Processing helix chain 'x' and resid 282 through 317 Proline residue: x 302 - end of helix removed outlier: 4.733A pdb=" N VAL x 314 " --> pdb=" O HIS x 310 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LEU x 315 " --> pdb=" O LYS x 311 " (cutoff:3.500A) Processing helix chain 'y' and resid 12 through 25 Processing helix chain 'y' and resid 26 through 31 Processing helix chain 'y' and resid 33 through 37 Processing helix chain 'y' and resid 41 through 50 Processing helix chain 'y' and resid 52 through 72 Processing helix chain 'y' and resid 77 through 81 removed outlier: 3.685A pdb=" N TRP y 81 " --> pdb=" O LYS y 78 " (cutoff:3.500A) Processing helix chain 'y' and resid 91 through 111 removed outlier: 3.502A pdb=" N LYS y 111 " --> pdb=" O GLU y 107 " (cutoff:3.500A) Processing helix chain 'z' and resid 21 through 24 removed outlier: 3.642A pdb=" N GLN z 24 " --> pdb=" O PRO z 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 21 through 24' Processing helix chain 'z' and resid 29 through 72 Proline residue: z 36 - end of helix removed outlier: 4.589A pdb=" N LEU z 47 " --> pdb=" O ARG z 43 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ARG z 48 " --> pdb=" O ALA z 44 " (cutoff:3.500A) Proline residue: z 51 - end of helix Processing helix chain 'z' and resid 74 through 79 removed outlier: 3.705A pdb=" N GLU z 79 " --> pdb=" O ALA z 76 " (cutoff:3.500A) Processing helix chain 'Af' and resid 71 through 76 removed outlier: 3.615A pdb=" N LEUAf 75 " --> pdb=" O LYSAf 71 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 71 through 75 removed outlier: 3.660A pdb=" N LEUAe 75 " --> pdb=" O ARGAe 72 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 33 through 72 removed outlier: 4.534A pdb=" N LEUAa 47 " --> pdb=" O ARGAa 43 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ARGAa 48 " --> pdb=" O ALAAa 44 " (cutoff:3.500A) Proline residue: Aa 51 - end of helix Processing helix chain 'Aa' and resid 74 through 79 Processing helix chain 'Ab' and resid 28 through 38 removed outlier: 3.869A pdb=" N THRAb 32 " --> pdb=" O ASPAb 28 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYSAb 37 " --> pdb=" O VALAb 33 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 40 through 60 Processing helix chain 'Ab' and resid 67 through 83 Processing helix chain 'Ab' and resid 85 through 90 removed outlier: 3.895A pdb=" N SERAb 89 " --> pdb=" O LYSAb 85 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 5 through 14 Processing helix chain 'Ac' and resid 17 through 48 removed outlier: 3.519A pdb=" N ARGAc 34 " --> pdb=" O LEUAc 30 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 52 through 61 removed outlier: 5.456A pdb=" N HISAc 58 " --> pdb=" O LYSAc 54 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LYSAc 59 " --> pdb=" O HISAc 55 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYRAc 60 " --> pdb=" O ILEAc 56 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 2 through 6 Processing helix chain 'Ad' and resid 7 through 37 Proline residue: Ad 19 - end of helix Processing helix chain 'Ad' and resid 47 through 51 Processing sheet with id=AA1, first strand: chain '2' and resid 174 through 176 removed outlier: 6.809A pdb=" N LEU 2 291 " --> pdb=" O THR 2 287 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 185 through 190 Processing sheet with id=AA3, first strand: chain '2' and resid 246 through 247 Processing sheet with id=AA4, first strand: chain '4' and resid 173 through 176 Processing sheet with id=AA5, first strand: chain '4' and resid 185 through 190 Processing sheet with id=AA6, first strand: chain '4' and resid 246 through 247 removed outlier: 3.872A pdb=" N LYS 4 272 " --> pdb=" O HIS 4 263 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '5' and resid 49 through 52 removed outlier: 3.596A pdb=" N ARG 5 58 " --> pdb=" O MET 5 229 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '5' and resid 313 through 315 removed outlier: 3.758A pdb=" N SER 5 340 " --> pdb=" O VAL 5 359 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N SER 5 273 " --> pdb=" O VAL 5 456 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N GLY 5 458 " --> pdb=" O SER 5 273 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE 5 275 " --> pdb=" O GLY 5 458 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N GLY 5 460 " --> pdb=" O ILE 5 275 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N HIS 5 277 " --> pdb=" O GLY 5 460 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU 5 274 " --> pdb=" O SERAa 18 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '6' and resid 39 through 42 removed outlier: 3.683A pdb=" N VAL 6 48 " --> pdb=" O MET 6 218 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER 6 118 " --> pdb=" O THR 6 115 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ALAAe 61 " --> pdb=" O LEU 6 110 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL 6 112 " --> pdb=" O ALAAe 61 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SERAe 63 " --> pdb=" O VAL 6 112 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N SER 6 114 " --> pdb=" O SERAe 63 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALAAe 51 " --> pdb=" O THRAe 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '6' and resid 257 through 261 removed outlier: 3.829A pdb=" N GLY 6 334 " --> pdb=" O SER 6 275 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '7' and resid 22 through 24 Processing sheet with id=AB3, first strand: chain '8' and resid 155 through 157 removed outlier: 3.852A pdb=" N PHE 8 166 " --> pdb=" O ASP 8 157 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'u' and resid 49 through 52 Processing sheet with id=AB5, first strand: chain 'u' and resid 313 through 315 removed outlier: 6.233A pdb=" N SER u 273 " --> pdb=" O VAL u 456 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N GLY u 458 " --> pdb=" O SER u 273 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE u 275 " --> pdb=" O GLY u 458 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY u 460 " --> pdb=" O ILE u 275 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N HIS u 277 " --> pdb=" O GLY u 460 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU u 274 " --> pdb=" O SER z 18 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL z 14 " --> pdb=" O ARG u 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'v' and resid 39 through 42 removed outlier: 6.633A pdb=" N VAL v 48 " --> pdb=" O LEU v 220 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N GLY v 222 " --> pdb=" O VAL v 48 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA v 50 " --> pdb=" O GLY v 222 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU v 110 " --> pdb=" O LEUAf 59 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ALAAf 61 " --> pdb=" O LEU v 110 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL v 112 " --> pdb=" O ALAAf 61 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALAAf 51 " --> pdb=" O THRAf 62 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'v' and resid 257 through 259 Processing sheet with id=AB8, first strand: chain 'w' and resid 22 through 24 Processing sheet with id=AB9, first strand: chain 'x' and resid 155 through 157 removed outlier: 3.974A pdb=" N PHE x 166 " --> pdb=" O ASP x 157 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'x' and resid 233 through 234 1934 hydrogen bonds defined for protein. 5499 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: 5.30 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.42: 14322 1.42 - 1.62: 18982 1.62 - 1.81: 260 1.81 - 2.01: 6 2.01 - 2.21: 32 Bond restraints: 33602 Sorted by residual: bond pdb=" CA ILE z 35 " pdb=" CB ILE z 35 " ideal model delta sigma weight residual 1.539 1.527 0.012 5.40e-03 3.43e+04 5.23e+00 bond pdb=" N THR w 225 " pdb=" CA THR w 225 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.20e-02 6.94e+03 4.22e+00 bond pdb=" CA ASN v 184 " pdb=" C ASN v 184 " ideal model delta sigma weight residual 1.523 1.499 0.024 1.34e-02 5.57e+03 3.32e+00 bond pdb=" CB CYS 0 37 " pdb=" SG CYS 0 37 " ideal model delta sigma weight residual 1.808 1.868 -0.060 3.30e-02 9.18e+02 3.28e+00 bond pdb=" C SERAe 65 " pdb=" N PROAe 66 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.54e+00 ... (remaining 33597 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 45534 3.18 - 6.37: 129 6.37 - 9.55: 7 9.55 - 12.74: 1 12.74 - 15.92: 4 Bond angle restraints: 45675 Sorted by residual: angle pdb=" C PRO w 154 " pdb=" N TYR w 155 " pdb=" CA TYR w 155 " ideal model delta sigma weight residual 121.54 128.31 -6.77 1.91e+00 2.74e-01 1.26e+01 angle pdb=" N ILE w 156 " pdb=" CA ILE w 156 " pdb=" C ILE w 156 " ideal model delta sigma weight residual 113.20 109.82 3.38 9.60e-01 1.09e+00 1.24e+01 angle pdb=" N THR w 225 " pdb=" CA THR w 225 " pdb=" C THR w 225 " ideal model delta sigma weight residual 111.14 107.35 3.79 1.08e+00 8.57e-01 1.23e+01 angle pdb=" C THR v 141 " pdb=" N ALA v 142 " pdb=" CA ALA v 142 " ideal model delta sigma weight residual 121.54 115.77 5.77 1.91e+00 2.74e-01 9.14e+00 angle pdb=" N VAL 6 106 " pdb=" CA VAL 6 106 " pdb=" C VAL 6 106 " ideal model delta sigma weight residual 112.80 109.50 3.30 1.15e+00 7.56e-01 8.25e+00 ... (remaining 45670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 18706 17.94 - 35.87: 933 35.87 - 53.81: 188 53.81 - 71.74: 56 71.74 - 89.68: 16 Dihedral angle restraints: 19899 sinusoidal: 7907 harmonic: 11992 Sorted by residual: dihedral pdb=" CA LYS 0 85 " pdb=" C LYS 0 85 " pdb=" N LEU 0 86 " pdb=" CA LEU 0 86 " ideal model delta harmonic sigma weight residual 180.00 -157.93 -22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ARGAd 39 " pdb=" C ARGAd 39 " pdb=" N LEUAd 40 " pdb=" CA LEUAd 40 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA HIS 7 221 " pdb=" C HIS 7 221 " pdb=" N PRO 7 222 " pdb=" CA PRO 7 222 " ideal model delta harmonic sigma weight residual 180.00 -162.60 -17.40 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 19896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3035 0.029 - 0.058: 1260 0.058 - 0.088: 455 0.088 - 0.117: 203 0.117 - 0.146: 40 Chirality restraints: 4993 Sorted by residual: chirality pdb=" CA ILE 6 341 " pdb=" N ILE 6 341 " pdb=" C ILE 6 341 " pdb=" CB ILE 6 341 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA ILE 7 153 " pdb=" N ILE 7 153 " pdb=" C ILE 7 153 " pdb=" CB ILE 7 153 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA VAL u 359 " pdb=" N VAL u 359 " pdb=" C VAL u 359 " pdb=" CB VAL u 359 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 4990 not shown) Planarity restraints: 5836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC 8 401 " 0.020 2.00e-02 2.50e+03 4.68e-02 4.93e+01 pdb=" C2C HEC 8 401 " -0.128 2.00e-02 2.50e+03 pdb=" C3C HEC 8 401 " 0.020 2.00e-02 2.50e+03 pdb=" C4C HEC 8 401 " 0.005 2.00e-02 2.50e+03 pdb=" CAC HEC 8 401 " 0.023 2.00e-02 2.50e+03 pdb=" CHC HEC 8 401 " 0.019 2.00e-02 2.50e+03 pdb=" CHD HEC 8 401 " -0.004 2.00e-02 2.50e+03 pdb=" CMC HEC 8 401 " 0.039 2.00e-02 2.50e+03 pdb=" NC HEC 8 401 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC x 401 " -0.014 2.00e-02 2.50e+03 3.99e-02 3.58e+01 pdb=" C2C HEC x 401 " 0.109 2.00e-02 2.50e+03 pdb=" C3C HEC x 401 " -0.019 2.00e-02 2.50e+03 pdb=" C4C HEC x 401 " -0.005 2.00e-02 2.50e+03 pdb=" CAC HEC x 401 " -0.017 2.00e-02 2.50e+03 pdb=" CHC HEC x 401 " -0.017 2.00e-02 2.50e+03 pdb=" CHD HEC x 401 " 0.002 2.00e-02 2.50e+03 pdb=" CMC HEC x 401 " -0.035 2.00e-02 2.50e+03 pdb=" NC HEC x 401 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR 7 224 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C TYR 7 224 " 0.037 2.00e-02 2.50e+03 pdb=" O TYR 7 224 " -0.014 2.00e-02 2.50e+03 pdb=" N THR 7 225 " -0.013 2.00e-02 2.50e+03 ... (remaining 5833 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3818 2.75 - 3.29: 33852 3.29 - 3.82: 58613 3.82 - 4.36: 70948 4.36 - 4.90: 120664 Nonbonded interactions: 287895 Sorted by model distance: nonbonded pdb=" OH TYR 8 237 " pdb=" OD2 ASPAb 79 " model vdw 2.209 3.040 nonbonded pdb=" O GLU 5 112 " pdb=" OG SER 5 115 " model vdw 2.221 3.040 nonbonded pdb=" NH2 ARG 4 225 " pdb=" O LEU 4 279 " model vdw 2.222 3.120 nonbonded pdb=" OD1 ASP 9 36 " pdb=" OH TYR 9 90 " model vdw 2.223 3.040 nonbonded pdb=" OG SER 5 273 " pdb=" O SERAa 18 " model vdw 2.231 3.040 ... (remaining 287890 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'Ab' } ncs_group { reference = chain '1' selection = chain 'Ac' } ncs_group { reference = (chain '2' and (resid 100 through 217 or (resid 218 and (name N or name CA or na \ me C or name O or name CB )) or resid 219 through 301)) selection = (chain '4' and (resid 100 through 294 or resid 301)) } ncs_group { reference = chain '3' selection = chain 'Ad' } ncs_group { reference = (chain '5' and (resid 36 through 156 or (resid 157 and (name N or name CA or nam \ e C or name O or name CB )) or resid 158 through 254 or resid 266 through 480)) selection = (chain 'u' and resid 36 through 480) } ncs_group { reference = chain '6' selection = chain 'v' } ncs_group { reference = chain '7' selection = chain 'w' } ncs_group { reference = (chain '8' and (resid 88 through 325 or resid 401)) selection = (chain 'x' and (resid 88 through 288 or (resid 289 and (name N or name CA or nam \ e C or name O or name CB )) or resid 290 through 401)) } ncs_group { reference = chain '9' selection = chain 'y' } ncs_group { reference = chain 'Aa' selection = chain 'z' } ncs_group { reference = chain 'Ae' selection = (chain 'Af' and (resid 38 through 70 or (resid 71 and (name N or name CA or name \ C or name O or name CB )) or resid 72 through 76)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.350 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.090 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:8.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.477 33619 Z= 0.150 Angle : 0.547 15.923 45689 Z= 0.273 Chirality : 0.040 0.146 4993 Planarity : 0.004 0.048 5836 Dihedral : 11.829 89.677 12167 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.48 % Favored : 97.50 % Rotamer: Outliers : 3.45 % Allowed : 4.69 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.14), residues: 4080 helix: 1.98 (0.11), residues: 2104 sheet: -0.15 (0.27), residues: 384 loop : 0.15 (0.17), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG z 25 TYR 0.020 0.001 TYR w 81 PHE 0.017 0.001 PHE v 326 TRP 0.015 0.001 TRP w 141 HIS 0.004 0.001 HIS 7 196 Details of bonding type rmsd covalent geometry : bond 0.00333 (33602) covalent geometry : angle 0.53440 (45675) SS BOND : bond 0.01320 ( 4) SS BOND : angle 2.74866 ( 8) hydrogen bonds : bond 0.12872 ( 1934) hydrogen bonds : angle 5.75989 ( 5499) metal coordination : bond 0.01998 ( 8) metal coordination : angle 9.66482 ( 6) Misc. bond : bond 0.35655 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 776 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 39 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7122 (ttt180) REVERT: 5 247 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7992 (tm-30) REVERT: 6 250 LYS cc_start: 0.8742 (ttmm) cc_final: 0.7607 (ptmm) REVERT: 6 414 GLN cc_start: 0.7941 (mt0) cc_final: 0.7694 (mt0) REVERT: 8 263 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8743 (p) REVERT: u 311 ILE cc_start: 0.8399 (mm) cc_final: 0.8104 (mp) REVERT: v 129 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7773 (p0) REVERT: v 421 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7563 (m-30) REVERT: x 162 ASP cc_start: 0.8933 (m-30) cc_final: 0.8026 (m-30) REVERT: x 172 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8399 (pp) REVERT: y 33 MET cc_start: 0.7932 (mtp) cc_final: 0.7688 (mtt) REVERT: z 33 LYS cc_start: 0.9004 (mttm) cc_final: 0.8762 (mttp) REVERT: Aa 66 GLU cc_start: 0.8308 (tp30) cc_final: 0.7954 (tm-30) REVERT: Ab 50 LEU cc_start: 0.9302 (tp) cc_final: 0.8934 (tp) REVERT: Ad 39 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.6961 (ptt-90) REVERT: Ad 44 TRP cc_start: 0.7499 (m100) cc_final: 0.7245 (m-10) outliers start: 120 outliers final: 21 residues processed: 848 average time/residue: 0.7074 time to fit residues: 699.9655 Evaluate side-chains 512 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 484 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 39 ARG Chi-restraints excluded: chain 4 residue 104 ILE Chi-restraints excluded: chain 5 residue 95 HIS Chi-restraints excluded: chain 5 residue 247 GLN Chi-restraints excluded: chain 5 residue 327 THR Chi-restraints excluded: chain 5 residue 362 ASN Chi-restraints excluded: chain 6 residue 133 LEU Chi-restraints excluded: chain 6 residue 240 MET Chi-restraints excluded: chain 6 residue 401 LEU Chi-restraints excluded: chain 8 residue 263 THR Chi-restraints excluded: chain 9 residue 75 ILE Chi-restraints excluded: chain u residue 341 PHE Chi-restraints excluded: chain v residue 83 LEU Chi-restraints excluded: chain v residue 124 GLU Chi-restraints excluded: chain v residue 129 ASP Chi-restraints excluded: chain v residue 342 SER Chi-restraints excluded: chain v residue 421 ASP Chi-restraints excluded: chain x residue 122 CYS Chi-restraints excluded: chain x residue 172 LEU Chi-restraints excluded: chain Af residue 59 LEU Chi-restraints excluded: chain Af residue 68 LEU Chi-restraints excluded: chain Af residue 72 ARG Chi-restraints excluded: chain Ae residue 46 LEU Chi-restraints excluded: chain Ae residue 59 LEU Chi-restraints excluded: chain Ae residue 68 LEU Chi-restraints excluded: chain Aa residue 19 LEU Chi-restraints excluded: chain Ab residue 60 ARG Chi-restraints excluded: chain Ad residue 39 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 36 GLN 0 55 GLN 1 55 HIS 2 221 HIS 2 248 ASN ** 2 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 221 HIS ** 4 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 GLN 5 170 GLN 5 175 ASN 5 222 GLN 5 342 GLN 6 157 GLN ** 6 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 232 GLN 6 327 ASN 6 357 GLN 7 3 ASN 7 97 HIS 7 196 HIS 7 207 ASN 7 255 ASN 7 260 ASN 8 91 HIS 8 310 HIS u 153 ASN u 247 GLN u 345 ASN u 375 GLN v 157 GLN v 168 ASN ** v 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 268 HIS v 290 GLN v 304 ASN v 311 GLN v 372 GLN w 85 ASN w 97 HIS ** w 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 255 ASN w 260 ASN w 312 GLN x 191 ASN Af 39 HIS Af 56 HIS Ae 39 HIS Ab 88 ASN Ac 49 GLN Ac 55 HIS Ad 16 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.091922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.072283 restraints weight = 53815.593| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.01 r_work: 0.2682 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.574 33619 Z= 0.182 Angle : 0.597 15.562 45689 Z= 0.298 Chirality : 0.041 0.169 4993 Planarity : 0.005 0.055 5836 Dihedral : 7.574 88.927 4633 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.35 % Favored : 97.62 % Rotamer: Outliers : 3.39 % Allowed : 12.66 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.13), residues: 4080 helix: 2.24 (0.11), residues: 2133 sheet: -0.16 (0.26), residues: 396 loop : 0.21 (0.17), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGAb 47 TYR 0.018 0.001 TYR 7 224 PHE 0.014 0.001 PHE 7 91 TRP 0.013 0.001 TRP w 141 HIS 0.008 0.001 HIS u 95 Details of bonding type rmsd covalent geometry : bond 0.00417 (33602) covalent geometry : angle 0.58714 (45675) SS BOND : bond 0.02702 ( 4) SS BOND : angle 5.60394 ( 8) hydrogen bonds : bond 0.04611 ( 1934) hydrogen bonds : angle 4.67359 ( 5499) metal coordination : bond 0.01519 ( 8) metal coordination : angle 7.05964 ( 6) Misc. bond : bond 0.37115 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 537 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 38 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7428 (mm-30) REVERT: 0 39 GLN cc_start: 0.8658 (pt0) cc_final: 0.8180 (mm-40) REVERT: 0 45 LYS cc_start: 0.8653 (mmpt) cc_final: 0.8452 (mtpp) REVERT: 0 73 ASP cc_start: 0.8924 (m-30) cc_final: 0.8248 (m-30) REVERT: 0 78 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8878 (tmm-80) REVERT: 1 9 ARG cc_start: 0.9110 (mmt90) cc_final: 0.8872 (mtt-85) REVERT: 2 207 GLN cc_start: 0.8213 (pp30) cc_final: 0.7965 (pp30) REVERT: 2 285 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7282 (pp20) REVERT: 3 6 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8543 (mp) REVERT: 3 43 ASP cc_start: 0.9256 (m-30) cc_final: 0.8988 (m-30) REVERT: 4 271 ARG cc_start: 0.8609 (mmm-85) cc_final: 0.8264 (mmm-85) REVERT: 5 111 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7882 (mtmm) REVERT: 5 206 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7849 (pp20) REVERT: 5 247 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8257 (tp40) REVERT: 6 370 ASP cc_start: 0.8813 (m-30) cc_final: 0.8248 (m-30) REVERT: 6 417 ASP cc_start: 0.8812 (p0) cc_final: 0.8523 (p0) REVERT: 7 202 GLU cc_start: 0.8799 (tp30) cc_final: 0.8431 (tp30) REVERT: 8 143 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8466 (tm-30) REVERT: 8 191 ASN cc_start: 0.8520 (t0) cc_final: 0.8225 (t0) REVERT: 9 68 ASP cc_start: 0.8982 (t70) cc_final: 0.8706 (t70) REVERT: u 114 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8651 (mt-10) REVERT: u 206 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8200 (tm-30) REVERT: u 354 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9302 (tp) REVERT: u 411 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8755 (tm-30) REVERT: v 129 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8302 (p0) REVERT: v 262 ASN cc_start: 0.8853 (p0) cc_final: 0.8545 (p0) REVERT: v 352 LYS cc_start: 0.8891 (mmmm) cc_final: 0.8497 (tmmt) REVERT: w 11 MET cc_start: 0.8729 (mmm) cc_final: 0.8433 (mmm) REVERT: w 203 THR cc_start: 0.9562 (p) cc_final: 0.9221 (t) REVERT: w 344 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8613 (mm-30) REVERT: x 157 ASP cc_start: 0.8389 (t0) cc_final: 0.8180 (t0) REVERT: x 172 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8521 (pp) REVERT: x 258 ASP cc_start: 0.8221 (t0) cc_final: 0.7984 (t0) REVERT: y 22 TYR cc_start: 0.9493 (t80) cc_final: 0.9285 (t80) REVERT: y 33 MET cc_start: 0.9102 (mtp) cc_final: 0.8776 (mtt) REVERT: y 74 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8536 (mt0) REVERT: z 33 LYS cc_start: 0.9109 (mttm) cc_final: 0.8673 (mttp) REVERT: z 72 ARG cc_start: 0.8674 (ttm-80) cc_final: 0.8135 (tpt-90) REVERT: Aa 65 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7423 (mp10) REVERT: Aa 66 GLU cc_start: 0.8704 (tp30) cc_final: 0.8198 (tm-30) REVERT: Ab 70 GLU cc_start: 0.8802 (mp0) cc_final: 0.8030 (mp0) REVERT: Ac 54 LYS cc_start: 0.8803 (ptmm) cc_final: 0.8533 (ptmm) REVERT: Ad 39 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.6694 (ptt-90) REVERT: Ad 44 TRP cc_start: 0.7819 (m100) cc_final: 0.6776 (m-10) outliers start: 118 outliers final: 42 residues processed: 607 average time/residue: 0.6996 time to fit residues: 498.0399 Evaluate side-chains 525 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 469 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 38 GLU Chi-restraints excluded: chain 0 residue 58 SER Chi-restraints excluded: chain 0 residue 78 ARG Chi-restraints excluded: chain 1 residue 10 LEU Chi-restraints excluded: chain 2 residue 118 LEU Chi-restraints excluded: chain 2 residue 285 GLU Chi-restraints excluded: chain 2 residue 291 LEU Chi-restraints excluded: chain 3 residue 6 LEU Chi-restraints excluded: chain 4 residue 206 ASP Chi-restraints excluded: chain 4 residue 246 ILE Chi-restraints excluded: chain 5 residue 95 HIS Chi-restraints excluded: chain 5 residue 111 LYS Chi-restraints excluded: chain 5 residue 206 GLU Chi-restraints excluded: chain 5 residue 247 GLN Chi-restraints excluded: chain 5 residue 313 HIS Chi-restraints excluded: chain 5 residue 327 THR Chi-restraints excluded: chain 5 residue 338 CYS Chi-restraints excluded: chain 6 residue 238 LEU Chi-restraints excluded: chain 6 residue 401 LEU Chi-restraints excluded: chain 6 residue 450 VAL Chi-restraints excluded: chain 7 residue 269 LYS Chi-restraints excluded: chain 8 residue 136 LEU Chi-restraints excluded: chain 8 residue 173 SER Chi-restraints excluded: chain 9 residue 75 ILE Chi-restraints excluded: chain u residue 79 SER Chi-restraints excluded: chain u residue 273 SER Chi-restraints excluded: chain u residue 341 PHE Chi-restraints excluded: chain u residue 354 LEU Chi-restraints excluded: chain u residue 411 GLU Chi-restraints excluded: chain v residue 83 LEU Chi-restraints excluded: chain v residue 124 GLU Chi-restraints excluded: chain v residue 129 ASP Chi-restraints excluded: chain v residue 342 SER Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain x residue 122 CYS Chi-restraints excluded: chain x residue 172 LEU Chi-restraints excluded: chain x residue 265 SER Chi-restraints excluded: chain x residue 320 LEU Chi-restraints excluded: chain y residue 74 GLN Chi-restraints excluded: chain z residue 16 THR Chi-restraints excluded: chain z residue 47 LEU Chi-restraints excluded: chain Af residue 59 LEU Chi-restraints excluded: chain Af residue 68 LEU Chi-restraints excluded: chain Af residue 72 ARG Chi-restraints excluded: chain Ae residue 46 LEU Chi-restraints excluded: chain Ae residue 59 LEU Chi-restraints excluded: chain Ae residue 68 LEU Chi-restraints excluded: chain Aa residue 19 LEU Chi-restraints excluded: chain Aa residue 58 LEU Chi-restraints excluded: chain Aa residue 65 GLN Chi-restraints excluded: chain Ab residue 27 VAL Chi-restraints excluded: chain Ab residue 60 ARG Chi-restraints excluded: chain Ab residue 68 THR Chi-restraints excluded: chain Ab residue 89 SER Chi-restraints excluded: chain Ad residue 3 SER Chi-restraints excluded: chain Ad residue 39 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 224 optimal weight: 0.6980 chunk 305 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 333 optimal weight: 0.0270 chunk 116 optimal weight: 3.9990 chunk 302 optimal weight: 0.6980 chunk 275 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 197 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 55 GLN ** 2 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 221 HIS ** 2 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 175 ASN 5 362 ASN ** 6 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 207 ASN 8 91 HIS u 345 ASN u 375 GLN ** v 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 54 HIS w 97 HIS ** w 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 352 GLN Ad 16 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.093491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.073751 restraints weight = 55014.486| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.93 r_work: 0.2768 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.483 33619 Z= 0.135 Angle : 0.545 14.722 45689 Z= 0.272 Chirality : 0.040 0.209 4993 Planarity : 0.004 0.054 5836 Dihedral : 7.352 89.695 4617 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.18 % Favored : 97.79 % Rotamer: Outliers : 3.05 % Allowed : 14.04 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.13), residues: 4080 helix: 2.31 (0.11), residues: 2146 sheet: -0.11 (0.26), residues: 400 loop : 0.24 (0.17), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAb 47 TYR 0.017 0.001 TYRAa 60 PHE 0.013 0.001 PHE v 326 TRP 0.013 0.001 TRP 7 141 HIS 0.008 0.001 HIS 2 101 Details of bonding type rmsd covalent geometry : bond 0.00308 (33602) covalent geometry : angle 0.53951 (45675) SS BOND : bond 0.01624 ( 4) SS BOND : angle 4.26635 ( 8) hydrogen bonds : bond 0.04105 ( 1934) hydrogen bonds : angle 4.44956 ( 5499) metal coordination : bond 0.01051 ( 8) metal coordination : angle 4.95929 ( 6) Misc. bond : bond 0.31165 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 541 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 39 GLN cc_start: 0.8285 (pt0) cc_final: 0.7835 (pm20) REVERT: 0 62 GLN cc_start: 0.8511 (tp-100) cc_final: 0.8100 (tp-100) REVERT: 0 73 ASP cc_start: 0.8691 (m-30) cc_final: 0.8095 (m-30) REVERT: 0 78 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8448 (tmm-80) REVERT: 1 9 ARG cc_start: 0.8602 (mmt90) cc_final: 0.8398 (mtt-85) REVERT: 1 45 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8538 (mt-10) REVERT: 2 101 HIS cc_start: 0.8767 (OUTLIER) cc_final: 0.8567 (p90) REVERT: 2 207 GLN cc_start: 0.8261 (pp30) cc_final: 0.7970 (pp30) REVERT: 2 285 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.7004 (pp20) REVERT: 3 6 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8120 (mp) REVERT: 3 43 ASP cc_start: 0.9263 (m-30) cc_final: 0.8921 (m-30) REVERT: 4 271 ARG cc_start: 0.8291 (mmm-85) cc_final: 0.8089 (mmm-85) REVERT: 4 278 ASN cc_start: 0.7836 (m-40) cc_final: 0.7633 (m-40) REVERT: 5 179 MET cc_start: 0.8503 (mmm) cc_final: 0.8270 (mmp) REVERT: 5 206 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7644 (pp20) REVERT: 5 213 ARG cc_start: 0.8166 (ttt90) cc_final: 0.7828 (ttm-80) REVERT: 5 240 ARG cc_start: 0.8185 (mmm160) cc_final: 0.7739 (mmm160) REVERT: 5 247 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8099 (tp40) REVERT: 5 324 MET cc_start: 0.8451 (mtp) cc_final: 0.8057 (mtp) REVERT: 5 412 ASP cc_start: 0.8682 (t70) cc_final: 0.8452 (t70) REVERT: 6 124 GLU cc_start: 0.8439 (tt0) cc_final: 0.8171 (tt0) REVERT: 6 370 ASP cc_start: 0.8749 (m-30) cc_final: 0.8283 (m-30) REVERT: 6 417 ASP cc_start: 0.8610 (p0) cc_final: 0.8158 (p0) REVERT: 7 171 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8358 (m-30) REVERT: 7 202 GLU cc_start: 0.8472 (tp30) cc_final: 0.8112 (tp30) REVERT: 7 287 LYS cc_start: 0.8817 (mmtm) cc_final: 0.8516 (mppt) REVERT: 8 120 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8590 (mt0) REVERT: 8 143 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8176 (tm-30) REVERT: 8 174 ASP cc_start: 0.8943 (m-30) cc_final: 0.8526 (m-30) REVERT: 8 191 ASN cc_start: 0.8550 (t0) cc_final: 0.8101 (t0) REVERT: 8 229 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.6978 (ttm170) REVERT: 8 323 ARG cc_start: 0.9090 (mtp85) cc_final: 0.8840 (mtp85) REVERT: 9 68 ASP cc_start: 0.8738 (t70) cc_final: 0.8454 (t70) REVERT: u 114 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8342 (mt-10) REVERT: u 206 GLU cc_start: 0.8602 (mm-30) cc_final: 0.7978 (tm-30) REVERT: u 218 GLU cc_start: 0.8894 (tt0) cc_final: 0.8472 (tp30) REVERT: u 240 ARG cc_start: 0.8574 (ttm-80) cc_final: 0.8004 (tpp80) REVERT: u 244 ASP cc_start: 0.8512 (m-30) cc_final: 0.8257 (m-30) REVERT: u 354 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9165 (tp) REVERT: u 411 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8029 (tm-30) REVERT: v 129 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8086 (p0) REVERT: v 262 ASN cc_start: 0.8464 (p0) cc_final: 0.8135 (p0) REVERT: v 352 LYS cc_start: 0.8723 (mmmm) cc_final: 0.8501 (mmmm) REVERT: w 11 MET cc_start: 0.8376 (mmm) cc_final: 0.8026 (mmm) REVERT: w 344 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8514 (mm-30) REVERT: x 143 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8109 (tm-30) REVERT: x 157 ASP cc_start: 0.8032 (t0) cc_final: 0.7830 (t0) REVERT: x 172 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8227 (pp) REVERT: z 33 LYS cc_start: 0.8715 (mttm) cc_final: 0.8266 (mttp) REVERT: z 72 ARG cc_start: 0.8405 (ttm-80) cc_final: 0.7789 (tpt-90) REVERT: Aa 65 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7012 (mp10) REVERT: Aa 66 GLU cc_start: 0.8624 (tp30) cc_final: 0.8125 (tm-30) REVERT: Ab 40 ILE cc_start: 0.8161 (tt) cc_final: 0.7730 (pt) REVERT: Ab 42 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8377 (mttp) REVERT: Ab 51 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8254 (mp0) REVERT: Ab 79 ASP cc_start: 0.9356 (m-30) cc_final: 0.9120 (m-30) REVERT: Ac 54 LYS cc_start: 0.8659 (ptmm) cc_final: 0.8375 (ptmm) REVERT: Ad 15 ARG cc_start: 0.8329 (ttp-170) cc_final: 0.8125 (ttp-110) REVERT: Ad 39 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.6265 (ptt-90) REVERT: Ad 44 TRP cc_start: 0.7491 (m100) cc_final: 0.6306 (m-10) outliers start: 106 outliers final: 47 residues processed: 603 average time/residue: 0.7039 time to fit residues: 498.1008 Evaluate side-chains 549 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 486 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 27 VAL Chi-restraints excluded: chain 0 residue 40 ILE Chi-restraints excluded: chain 0 residue 59 SER Chi-restraints excluded: chain 0 residue 78 ARG Chi-restraints excluded: chain 1 residue 10 LEU Chi-restraints excluded: chain 1 residue 45 GLU Chi-restraints excluded: chain 2 residue 101 HIS Chi-restraints excluded: chain 2 residue 285 GLU Chi-restraints excluded: chain 2 residue 291 LEU Chi-restraints excluded: chain 3 residue 6 LEU Chi-restraints excluded: chain 4 residue 104 ILE Chi-restraints excluded: chain 4 residue 176 LYS Chi-restraints excluded: chain 5 residue 95 HIS Chi-restraints excluded: chain 5 residue 206 GLU Chi-restraints excluded: chain 5 residue 247 GLN Chi-restraints excluded: chain 5 residue 327 THR Chi-restraints excluded: chain 6 residue 346 SER Chi-restraints excluded: chain 6 residue 386 VAL Chi-restraints excluded: chain 6 residue 416 ILE Chi-restraints excluded: chain 6 residue 441 SER Chi-restraints excluded: chain 7 residue 171 ASP Chi-restraints excluded: chain 7 residue 345 HIS Chi-restraints excluded: chain 8 residue 136 LEU Chi-restraints excluded: chain 8 residue 229 ARG Chi-restraints excluded: chain 9 residue 17 ILE Chi-restraints excluded: chain 9 residue 75 ILE Chi-restraints excluded: chain u residue 79 SER Chi-restraints excluded: chain u residue 253 LEU Chi-restraints excluded: chain u residue 341 PHE Chi-restraints excluded: chain u residue 354 LEU Chi-restraints excluded: chain u residue 411 GLU Chi-restraints excluded: chain v residue 83 LEU Chi-restraints excluded: chain v residue 124 GLU Chi-restraints excluded: chain v residue 129 ASP Chi-restraints excluded: chain w residue 110 LEU Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 281 LEU Chi-restraints excluded: chain w residue 297 SER Chi-restraints excluded: chain x residue 162 ASP Chi-restraints excluded: chain x residue 172 LEU Chi-restraints excluded: chain x residue 265 SER Chi-restraints excluded: chain x residue 320 LEU Chi-restraints excluded: chain z residue 16 THR Chi-restraints excluded: chain z residue 47 LEU Chi-restraints excluded: chain Af residue 53 VAL Chi-restraints excluded: chain Af residue 59 LEU Chi-restraints excluded: chain Af residue 62 THR Chi-restraints excluded: chain Af residue 68 LEU Chi-restraints excluded: chain Ae residue 46 LEU Chi-restraints excluded: chain Ae residue 53 VAL Chi-restraints excluded: chain Ae residue 59 LEU Chi-restraints excluded: chain Ae residue 62 THR Chi-restraints excluded: chain Ae residue 68 LEU Chi-restraints excluded: chain Aa residue 19 LEU Chi-restraints excluded: chain Aa residue 65 GLN Chi-restraints excluded: chain Ab residue 27 VAL Chi-restraints excluded: chain Ab residue 42 LYS Chi-restraints excluded: chain Ab residue 68 THR Chi-restraints excluded: chain Ab residue 89 SER Chi-restraints excluded: chain Ad residue 3 SER Chi-restraints excluded: chain Ad residue 13 LEU Chi-restraints excluded: chain Ad residue 32 LEU Chi-restraints excluded: chain Ad residue 39 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 189 optimal weight: 0.8980 chunk 230 optimal weight: 0.9990 chunk 315 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 245 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 203 optimal weight: 0.0980 chunk 103 optimal weight: 3.9990 chunk 269 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 55 GLN ** 2 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 221 HIS 2 248 ASN ** 2 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 175 ASN ** 6 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 357 GLN 8 91 HIS u 43 GLN u 345 ASN u 402 HIS ** v 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 446 HIS w 97 HIS ** w 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.093346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.073607 restraints weight = 55029.101| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.12 r_work: 0.2742 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.483 33619 Z= 0.138 Angle : 0.541 15.147 45689 Z= 0.268 Chirality : 0.040 0.233 4993 Planarity : 0.004 0.056 5836 Dihedral : 7.153 89.988 4605 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.08 % Favored : 97.89 % Rotamer: Outliers : 3.11 % Allowed : 14.64 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.13), residues: 4080 helix: 2.34 (0.11), residues: 2146 sheet: -0.05 (0.26), residues: 400 loop : 0.26 (0.17), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 0 49 TYR 0.018 0.001 TYRAa 60 PHE 0.014 0.001 PHE w 91 TRP 0.013 0.001 TRP w 141 HIS 0.007 0.001 HIS 2 101 Details of bonding type rmsd covalent geometry : bond 0.00322 (33602) covalent geometry : angle 0.53644 (45675) SS BOND : bond 0.02724 ( 4) SS BOND : angle 3.81839 ( 8) hydrogen bonds : bond 0.03994 ( 1934) hydrogen bonds : angle 4.36893 ( 5499) metal coordination : bond 0.01022 ( 8) metal coordination : angle 4.00769 ( 6) Misc. bond : bond 0.30697 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 524 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 39 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7657 (pm20) REVERT: 0 62 GLN cc_start: 0.8575 (tp-100) cc_final: 0.8145 (tp-100) REVERT: 0 73 ASP cc_start: 0.8694 (m-30) cc_final: 0.8134 (m-30) REVERT: 1 9 ARG cc_start: 0.8611 (mmt90) cc_final: 0.8349 (mmm-85) REVERT: 1 45 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8529 (mt-10) REVERT: 2 204 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7098 (mt-10) REVERT: 2 207 GLN cc_start: 0.8277 (pp30) cc_final: 0.7949 (pp30) REVERT: 2 285 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.7013 (pp20) REVERT: 3 6 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8316 (mt) REVERT: 3 43 ASP cc_start: 0.9302 (m-30) cc_final: 0.8964 (m-30) REVERT: 5 206 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7700 (pp20) REVERT: 5 213 ARG cc_start: 0.8233 (ttt90) cc_final: 0.7861 (ttm-80) REVERT: 5 240 ARG cc_start: 0.8277 (mmm160) cc_final: 0.7819 (mmm160) REVERT: 5 247 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8099 (tp40) REVERT: 5 324 MET cc_start: 0.8443 (mtp) cc_final: 0.8077 (mtp) REVERT: 5 412 ASP cc_start: 0.8708 (t70) cc_final: 0.8469 (t70) REVERT: 6 124 GLU cc_start: 0.8601 (tt0) cc_final: 0.8128 (tt0) REVERT: 6 370 ASP cc_start: 0.8753 (m-30) cc_final: 0.8269 (m-30) REVERT: 7 171 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8655 (t0) REVERT: 7 202 GLU cc_start: 0.8484 (tp30) cc_final: 0.8134 (tp30) REVERT: 7 287 LYS cc_start: 0.8812 (mmtm) cc_final: 0.8522 (mppt) REVERT: 8 120 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8741 (mt0) REVERT: 8 143 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8238 (tm-30) REVERT: 8 147 LYS cc_start: 0.8300 (tptm) cc_final: 0.8001 (ttmp) REVERT: 8 174 ASP cc_start: 0.8943 (m-30) cc_final: 0.8588 (m-30) REVERT: 8 191 ASN cc_start: 0.8613 (t0) cc_final: 0.8114 (t0) REVERT: 8 229 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.6992 (ttm170) REVERT: 9 68 ASP cc_start: 0.8789 (t70) cc_final: 0.8522 (t70) REVERT: u 114 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8339 (mt-10) REVERT: u 206 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8025 (tm-30) REVERT: u 218 GLU cc_start: 0.8944 (tt0) cc_final: 0.8507 (tp30) REVERT: u 240 ARG cc_start: 0.8621 (ttm-80) cc_final: 0.8070 (tpp80) REVERT: u 244 ASP cc_start: 0.8550 (m-30) cc_final: 0.8299 (m-30) REVERT: u 354 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9136 (tp) REVERT: u 411 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: u 430 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8172 (tp30) REVERT: v 129 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8138 (p0) REVERT: v 175 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: v 352 LYS cc_start: 0.8742 (mmmm) cc_final: 0.8183 (tmmt) REVERT: w 11 MET cc_start: 0.8442 (mmm) cc_final: 0.8092 (mmm) REVERT: w 344 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8596 (mm-30) REVERT: x 143 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8208 (tm-30) REVERT: x 172 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8251 (pp) REVERT: x 174 ASP cc_start: 0.8887 (m-30) cc_final: 0.8588 (m-30) REVERT: y 74 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8447 (mt0) REVERT: z 33 LYS cc_start: 0.8694 (mttm) cc_final: 0.8099 (mttt) REVERT: z 72 ARG cc_start: 0.8412 (ttm-80) cc_final: 0.7763 (tpt-90) REVERT: Aa 65 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7123 (mp10) REVERT: Aa 66 GLU cc_start: 0.8639 (tp30) cc_final: 0.8161 (tm-30) REVERT: Ab 79 ASP cc_start: 0.9357 (m-30) cc_final: 0.9068 (m-30) REVERT: Ac 16 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.6703 (ttp-170) REVERT: Ac 17 ARG cc_start: 0.7786 (mtm180) cc_final: 0.7527 (mtm-85) REVERT: Ac 54 LYS cc_start: 0.8786 (ptmm) cc_final: 0.8416 (ptmm) REVERT: Ad 6 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8159 (mm) REVERT: Ad 15 ARG cc_start: 0.8323 (ttp-170) cc_final: 0.8030 (ttp-110) REVERT: Ad 39 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.6197 (ptt-90) REVERT: Ad 44 TRP cc_start: 0.7519 (m100) cc_final: 0.6268 (m-10) outliers start: 108 outliers final: 51 residues processed: 588 average time/residue: 0.6606 time to fit residues: 457.0255 Evaluate side-chains 563 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 493 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 27 VAL Chi-restraints excluded: chain 0 residue 39 GLN Chi-restraints excluded: chain 0 residue 40 ILE Chi-restraints excluded: chain 1 residue 10 LEU Chi-restraints excluded: chain 1 residue 45 GLU Chi-restraints excluded: chain 2 residue 118 LEU Chi-restraints excluded: chain 2 residue 204 GLU Chi-restraints excluded: chain 2 residue 285 GLU Chi-restraints excluded: chain 2 residue 291 LEU Chi-restraints excluded: chain 3 residue 6 LEU Chi-restraints excluded: chain 4 residue 104 ILE Chi-restraints excluded: chain 5 residue 95 HIS Chi-restraints excluded: chain 5 residue 206 GLU Chi-restraints excluded: chain 5 residue 247 GLN Chi-restraints excluded: chain 5 residue 327 THR Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 238 LEU Chi-restraints excluded: chain 6 residue 244 LEU Chi-restraints excluded: chain 6 residue 346 SER Chi-restraints excluded: chain 6 residue 386 VAL Chi-restraints excluded: chain 6 residue 401 LEU Chi-restraints excluded: chain 6 residue 416 ILE Chi-restraints excluded: chain 6 residue 441 SER Chi-restraints excluded: chain 7 residue 171 ASP Chi-restraints excluded: chain 7 residue 345 HIS Chi-restraints excluded: chain 8 residue 136 LEU Chi-restraints excluded: chain 8 residue 229 ARG Chi-restraints excluded: chain 9 residue 17 ILE Chi-restraints excluded: chain 9 residue 75 ILE Chi-restraints excluded: chain u residue 79 SER Chi-restraints excluded: chain u residue 341 PHE Chi-restraints excluded: chain u residue 354 LEU Chi-restraints excluded: chain u residue 411 GLU Chi-restraints excluded: chain u residue 417 LEU Chi-restraints excluded: chain v residue 83 LEU Chi-restraints excluded: chain v residue 124 GLU Chi-restraints excluded: chain v residue 129 ASP Chi-restraints excluded: chain v residue 175 GLU Chi-restraints excluded: chain v residue 282 GLU Chi-restraints excluded: chain v residue 306 THR Chi-restraints excluded: chain v residue 342 SER Chi-restraints excluded: chain w residue 110 LEU Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 297 SER Chi-restraints excluded: chain x residue 122 CYS Chi-restraints excluded: chain x residue 172 LEU Chi-restraints excluded: chain x residue 265 SER Chi-restraints excluded: chain x residue 320 LEU Chi-restraints excluded: chain y residue 74 GLN Chi-restraints excluded: chain z residue 16 THR Chi-restraints excluded: chain z residue 47 LEU Chi-restraints excluded: chain z residue 59 VAL Chi-restraints excluded: chain Af residue 53 VAL Chi-restraints excluded: chain Af residue 59 LEU Chi-restraints excluded: chain Af residue 62 THR Chi-restraints excluded: chain Af residue 68 LEU Chi-restraints excluded: chain Ae residue 46 LEU Chi-restraints excluded: chain Ae residue 53 VAL Chi-restraints excluded: chain Ae residue 59 LEU Chi-restraints excluded: chain Ae residue 62 THR Chi-restraints excluded: chain Ae residue 68 LEU Chi-restraints excluded: chain Aa residue 19 LEU Chi-restraints excluded: chain Aa residue 32 THR Chi-restraints excluded: chain Aa residue 65 GLN Chi-restraints excluded: chain Ab residue 27 VAL Chi-restraints excluded: chain Ab residue 89 SER Chi-restraints excluded: chain Ac residue 16 ARG Chi-restraints excluded: chain Ad residue 3 SER Chi-restraints excluded: chain Ad residue 6 LEU Chi-restraints excluded: chain Ad residue 39 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 27 optimal weight: 4.9990 chunk 325 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 237 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 351 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 GLN 5 175 ASN ** 6 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 365 ASN 8 91 HIS 8 251 ASN u 43 GLN u 345 ASN u 402 HIS ** v 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 284 ASN w 97 HIS ** w 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 120 GLN ** Ab 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.092996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.073033 restraints weight = 55114.788| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.97 r_work: 0.2735 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.500 33619 Z= 0.147 Angle : 0.550 15.414 45689 Z= 0.271 Chirality : 0.040 0.163 4993 Planarity : 0.004 0.055 5836 Dihedral : 7.151 89.705 4605 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.21 % Favored : 97.77 % Rotamer: Outliers : 3.02 % Allowed : 15.19 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.13), residues: 4080 helix: 2.33 (0.11), residues: 2146 sheet: 0.01 (0.26), residues: 399 loop : 0.24 (0.16), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAb 47 TYR 0.019 0.001 TYRAa 60 PHE 0.015 0.001 PHE w 91 TRP 0.012 0.001 TRP w 141 HIS 0.006 0.001 HIS 2 101 Details of bonding type rmsd covalent geometry : bond 0.00347 (33602) covalent geometry : angle 0.54631 (45675) SS BOND : bond 0.02125 ( 4) SS BOND : angle 3.90319 ( 8) hydrogen bonds : bond 0.04001 ( 1934) hydrogen bonds : angle 4.34261 ( 5499) metal coordination : bond 0.01088 ( 8) metal coordination : angle 3.65277 ( 6) Misc. bond : bond 0.30411 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 500 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: 0 62 GLN cc_start: 0.8770 (tp-100) cc_final: 0.8270 (tp-100) REVERT: 0 73 ASP cc_start: 0.8691 (m-30) cc_final: 0.8117 (m-30) REVERT: 1 9 ARG cc_start: 0.8611 (mmt90) cc_final: 0.8360 (mmm-85) REVERT: 2 204 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7375 (mt-10) REVERT: 2 207 GLN cc_start: 0.8275 (pp30) cc_final: 0.7866 (tm-30) REVERT: 2 221 HIS cc_start: 0.7653 (t-90) cc_final: 0.7310 (t-90) REVERT: 2 285 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.7014 (pp20) REVERT: 3 6 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8341 (mt) REVERT: 3 13 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8716 (mp) REVERT: 3 23 MET cc_start: 0.8842 (tpp) cc_final: 0.8636 (tpp) REVERT: 3 43 ASP cc_start: 0.9303 (m-30) cc_final: 0.8918 (m-30) REVERT: 4 271 ARG cc_start: 0.8240 (mmm-85) cc_final: 0.7975 (mmm-85) REVERT: 5 179 MET cc_start: 0.8582 (mmm) cc_final: 0.8352 (mmp) REVERT: 5 206 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7658 (pp20) REVERT: 5 213 ARG cc_start: 0.8254 (ttt90) cc_final: 0.7813 (ttm-80) REVERT: 5 240 ARG cc_start: 0.8295 (mmm160) cc_final: 0.7865 (mmm160) REVERT: 5 247 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8111 (tp40) REVERT: 5 324 MET cc_start: 0.8492 (mtp) cc_final: 0.8122 (mtp) REVERT: 5 412 ASP cc_start: 0.8723 (t70) cc_final: 0.8471 (t70) REVERT: 6 124 GLU cc_start: 0.8515 (tt0) cc_final: 0.8018 (tt0) REVERT: 6 370 ASP cc_start: 0.8692 (m-30) cc_final: 0.8234 (m-30) REVERT: 7 171 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.8641 (t0) REVERT: 7 202 GLU cc_start: 0.8446 (tp30) cc_final: 0.8117 (tp30) REVERT: 7 287 LYS cc_start: 0.8791 (mmtm) cc_final: 0.8526 (mppt) REVERT: 8 120 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8654 (mt0) REVERT: 8 143 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8258 (tm-30) REVERT: 8 147 LYS cc_start: 0.8322 (tptm) cc_final: 0.8065 (tttp) REVERT: 8 191 ASN cc_start: 0.8690 (t0) cc_final: 0.8188 (t0) REVERT: 8 229 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6995 (ttm170) REVERT: 9 68 ASP cc_start: 0.8764 (t70) cc_final: 0.8503 (t70) REVERT: u 114 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8292 (mt-10) REVERT: u 206 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8060 (tm-30) REVERT: u 218 GLU cc_start: 0.8931 (tt0) cc_final: 0.8289 (tp30) REVERT: u 240 ARG cc_start: 0.8622 (ttm-80) cc_final: 0.8189 (tpp80) REVERT: u 361 ASP cc_start: 0.8107 (t0) cc_final: 0.7782 (t0) REVERT: u 411 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: u 430 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8185 (tp30) REVERT: v 129 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8152 (p0) REVERT: v 175 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8029 (mp0) REVERT: v 352 LYS cc_start: 0.8719 (mmmm) cc_final: 0.8182 (tmmt) REVERT: w 11 MET cc_start: 0.8450 (mmm) cc_final: 0.8108 (mmm) REVERT: w 344 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8602 (mm-30) REVERT: x 143 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8296 (tm-30) REVERT: x 172 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8229 (pp) REVERT: x 245 MET cc_start: 0.9119 (ttm) cc_final: 0.8524 (ttm) REVERT: y 74 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8435 (mt0) REVERT: z 33 LYS cc_start: 0.8734 (mttm) cc_final: 0.8132 (mttt) REVERT: z 72 ARG cc_start: 0.8439 (ttm-80) cc_final: 0.7813 (tpt-90) REVERT: Aa 58 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8800 (mp) REVERT: Aa 65 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7808 (mp10) REVERT: Aa 66 GLU cc_start: 0.8651 (tp30) cc_final: 0.8186 (tm-30) REVERT: Ab 42 LYS cc_start: 0.8519 (mttp) cc_final: 0.8311 (mtpt) REVERT: Ac 16 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.6747 (ttp-170) REVERT: Ac 17 ARG cc_start: 0.7754 (mtm180) cc_final: 0.7425 (mtm180) REVERT: Ac 54 LYS cc_start: 0.8828 (ptmm) cc_final: 0.8452 (ptmm) REVERT: Ad 15 ARG cc_start: 0.8274 (ttp-170) cc_final: 0.7977 (ttp-110) REVERT: Ad 39 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.6125 (ptt-90) REVERT: Ad 44 TRP cc_start: 0.7513 (m100) cc_final: 0.6192 (m-10) outliers start: 105 outliers final: 58 residues processed: 559 average time/residue: 0.6681 time to fit residues: 438.2493 Evaluate side-chains 538 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 463 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 27 VAL Chi-restraints excluded: chain 0 residue 43 CYS Chi-restraints excluded: chain 0 residue 59 SER Chi-restraints excluded: chain 1 residue 10 LEU Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 118 LEU Chi-restraints excluded: chain 2 residue 204 GLU Chi-restraints excluded: chain 2 residue 212 GLU Chi-restraints excluded: chain 2 residue 285 GLU Chi-restraints excluded: chain 2 residue 291 LEU Chi-restraints excluded: chain 3 residue 6 LEU Chi-restraints excluded: chain 3 residue 13 LEU Chi-restraints excluded: chain 4 residue 104 ILE Chi-restraints excluded: chain 4 residue 239 THR Chi-restraints excluded: chain 5 residue 79 SER Chi-restraints excluded: chain 5 residue 95 HIS Chi-restraints excluded: chain 5 residue 206 GLU Chi-restraints excluded: chain 5 residue 247 GLN Chi-restraints excluded: chain 5 residue 327 THR Chi-restraints excluded: chain 5 residue 338 CYS Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 241 ARG Chi-restraints excluded: chain 6 residue 346 SER Chi-restraints excluded: chain 6 residue 386 VAL Chi-restraints excluded: chain 6 residue 401 LEU Chi-restraints excluded: chain 6 residue 416 ILE Chi-restraints excluded: chain 6 residue 441 SER Chi-restraints excluded: chain 7 residue 171 ASP Chi-restraints excluded: chain 7 residue 345 HIS Chi-restraints excluded: chain 8 residue 136 LEU Chi-restraints excluded: chain 8 residue 229 ARG Chi-restraints excluded: chain 9 residue 75 ILE Chi-restraints excluded: chain u residue 79 SER Chi-restraints excluded: chain u residue 156 LEU Chi-restraints excluded: chain u residue 253 LEU Chi-restraints excluded: chain u residue 341 PHE Chi-restraints excluded: chain u residue 411 GLU Chi-restraints excluded: chain u residue 417 LEU Chi-restraints excluded: chain v residue 83 LEU Chi-restraints excluded: chain v residue 124 GLU Chi-restraints excluded: chain v residue 129 ASP Chi-restraints excluded: chain v residue 175 GLU Chi-restraints excluded: chain v residue 282 GLU Chi-restraints excluded: chain v residue 306 THR Chi-restraints excluded: chain w residue 110 LEU Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 297 SER Chi-restraints excluded: chain x residue 162 ASP Chi-restraints excluded: chain x residue 172 LEU Chi-restraints excluded: chain x residue 265 SER Chi-restraints excluded: chain x residue 320 LEU Chi-restraints excluded: chain y residue 74 GLN Chi-restraints excluded: chain z residue 16 THR Chi-restraints excluded: chain z residue 47 LEU Chi-restraints excluded: chain z residue 59 VAL Chi-restraints excluded: chain z residue 68 GLU Chi-restraints excluded: chain Af residue 53 VAL Chi-restraints excluded: chain Af residue 59 LEU Chi-restraints excluded: chain Af residue 62 THR Chi-restraints excluded: chain Af residue 68 LEU Chi-restraints excluded: chain Ae residue 53 VAL Chi-restraints excluded: chain Ae residue 59 LEU Chi-restraints excluded: chain Ae residue 62 THR Chi-restraints excluded: chain Ae residue 68 LEU Chi-restraints excluded: chain Aa residue 19 LEU Chi-restraints excluded: chain Aa residue 32 THR Chi-restraints excluded: chain Aa residue 58 LEU Chi-restraints excluded: chain Aa residue 65 GLN Chi-restraints excluded: chain Ab residue 27 VAL Chi-restraints excluded: chain Ab residue 89 SER Chi-restraints excluded: chain Ac residue 16 ARG Chi-restraints excluded: chain Ad residue 3 SER Chi-restraints excluded: chain Ad residue 6 LEU Chi-restraints excluded: chain Ad residue 32 LEU Chi-restraints excluded: chain Ad residue 39 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 285 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 324 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 chunk 136 optimal weight: 3.9990 chunk 307 optimal weight: 0.6980 chunk 352 optimal weight: 0.8980 chunk 237 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 55 GLN ** 2 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 156 GLN ** 2 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 170 GLN 5 175 ASN ** 6 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 91 HIS 8 251 ASN 9 23 ASN u 43 GLN u 247 GLN u 345 ASN u 402 HIS v 212 HIS ** v 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 97 HIS ** w 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 23 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.092969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.073037 restraints weight = 55103.660| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.17 r_work: 0.2715 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.501 33619 Z= 0.150 Angle : 0.557 15.300 45689 Z= 0.275 Chirality : 0.040 0.239 4993 Planarity : 0.004 0.056 5836 Dihedral : 7.146 89.849 4603 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.18 % Favored : 97.79 % Rotamer: Outliers : 3.08 % Allowed : 15.54 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.13), residues: 4080 helix: 2.32 (0.11), residues: 2141 sheet: 0.02 (0.26), residues: 399 loop : 0.24 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAb 49 TYR 0.018 0.001 TYR 7 224 PHE 0.014 0.001 PHE w 91 TRP 0.013 0.001 TRP w 141 HIS 0.007 0.001 HIS u 95 Details of bonding type rmsd covalent geometry : bond 0.00358 (33602) covalent geometry : angle 0.55257 (45675) SS BOND : bond 0.02258 ( 4) SS BOND : angle 4.44070 ( 8) hydrogen bonds : bond 0.03992 ( 1934) hydrogen bonds : angle 4.33088 ( 5499) metal coordination : bond 0.01012 ( 8) metal coordination : angle 3.37292 ( 6) Misc. bond : bond 0.30044 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 490 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: 0 62 GLN cc_start: 0.8827 (tp-100) cc_final: 0.8280 (tp-100) REVERT: 0 73 ASP cc_start: 0.8696 (m-30) cc_final: 0.8128 (m-30) REVERT: 1 9 ARG cc_start: 0.8629 (mmt90) cc_final: 0.8382 (mmm-85) REVERT: 2 208 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7122 (mm-30) REVERT: 2 221 HIS cc_start: 0.7660 (t-90) cc_final: 0.7190 (t-90) REVERT: 2 285 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.7008 (pp20) REVERT: 3 6 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8332 (mt) REVERT: 3 13 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8644 (mp) REVERT: 3 23 MET cc_start: 0.8835 (tpp) cc_final: 0.8579 (tpp) REVERT: 3 43 ASP cc_start: 0.9308 (m-30) cc_final: 0.8927 (m-30) REVERT: 4 271 ARG cc_start: 0.8259 (mmm-85) cc_final: 0.8017 (mmm-85) REVERT: 5 114 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8224 (mt-10) REVERT: 5 116 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8234 (mtm) REVERT: 5 179 MET cc_start: 0.8558 (mmm) cc_final: 0.8328 (mmp) REVERT: 5 206 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7691 (pp20) REVERT: 5 240 ARG cc_start: 0.8320 (mmm160) cc_final: 0.7915 (mmm160) REVERT: 5 247 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8129 (tp40) REVERT: 5 324 MET cc_start: 0.8487 (mtp) cc_final: 0.8088 (mtp) REVERT: 5 412 ASP cc_start: 0.8721 (t70) cc_final: 0.8463 (t70) REVERT: 6 124 GLU cc_start: 0.8560 (tt0) cc_final: 0.8116 (tt0) REVERT: 6 131 GLU cc_start: 0.7332 (tm-30) cc_final: 0.7039 (tm-30) REVERT: 7 171 ASP cc_start: 0.8860 (OUTLIER) cc_final: 0.8659 (t0) REVERT: 7 202 GLU cc_start: 0.8471 (tp30) cc_final: 0.8157 (tp30) REVERT: 7 287 LYS cc_start: 0.8791 (mmtm) cc_final: 0.8531 (mppt) REVERT: 8 143 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8226 (tm-30) REVERT: 8 147 LYS cc_start: 0.8337 (tptm) cc_final: 0.7951 (ttmm) REVERT: 8 174 ASP cc_start: 0.9022 (m-30) cc_final: 0.8658 (m-30) REVERT: 8 191 ASN cc_start: 0.8711 (t0) cc_final: 0.8194 (t0) REVERT: 8 229 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6977 (ttm170) REVERT: 9 68 ASP cc_start: 0.8770 (t70) cc_final: 0.8532 (t70) REVERT: u 114 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8307 (mt-10) REVERT: u 206 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8074 (tm-30) REVERT: u 218 GLU cc_start: 0.8942 (tt0) cc_final: 0.8260 (tp30) REVERT: u 240 ARG cc_start: 0.8676 (ttm-80) cc_final: 0.8071 (tpp80) REVERT: u 244 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8296 (m-30) REVERT: u 361 ASP cc_start: 0.8201 (t0) cc_final: 0.7877 (t0) REVERT: u 411 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.7926 (tm-30) REVERT: u 430 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8208 (tp30) REVERT: v 129 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8178 (p0) REVERT: v 134 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8534 (mtp) REVERT: v 175 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: v 352 LYS cc_start: 0.8729 (mmmm) cc_final: 0.8183 (tmmt) REVERT: w 11 MET cc_start: 0.8441 (mmm) cc_final: 0.8151 (mmm) REVERT: w 129 MET cc_start: 0.9062 (mtm) cc_final: 0.8783 (mtp) REVERT: w 344 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8624 (mm-30) REVERT: x 143 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8327 (tm-30) REVERT: x 172 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8234 (pp) REVERT: x 174 ASP cc_start: 0.8869 (m-30) cc_final: 0.8569 (m-30) REVERT: x 191 ASN cc_start: 0.9074 (m110) cc_final: 0.8258 (t0) REVERT: x 245 MET cc_start: 0.9175 (ttm) cc_final: 0.8578 (ttm) REVERT: y 71 MET cc_start: 0.9309 (ttp) cc_final: 0.9098 (tmm) REVERT: y 74 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8500 (mt0) REVERT: z 33 LYS cc_start: 0.8724 (mttm) cc_final: 0.8105 (mttt) REVERT: z 72 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.7836 (tpt-90) REVERT: z 80 ASN cc_start: 0.7615 (p0) cc_final: 0.7396 (p0) REVERT: Aa 58 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8789 (mp) REVERT: Aa 65 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7846 (mp10) REVERT: Aa 66 GLU cc_start: 0.8646 (tp30) cc_final: 0.8112 (tm-30) REVERT: Ab 54 ASP cc_start: 0.8773 (p0) cc_final: 0.8475 (p0) REVERT: Ab 62 GLN cc_start: 0.7429 (pm20) cc_final: 0.6677 (pp30) REVERT: Ab 78 ARG cc_start: 0.8684 (ttp80) cc_final: 0.8476 (ttp80) REVERT: Ac 16 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.6789 (ttp-170) REVERT: Ac 17 ARG cc_start: 0.7813 (mtm180) cc_final: 0.7470 (mtm180) REVERT: Ac 54 LYS cc_start: 0.8802 (ptmm) cc_final: 0.8412 (ptmm) REVERT: Ad 15 ARG cc_start: 0.8294 (ttp-170) cc_final: 0.7987 (ttp-110) REVERT: Ad 39 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.6132 (ptt-90) REVERT: Ad 44 TRP cc_start: 0.7531 (m100) cc_final: 0.6209 (m-10) outliers start: 107 outliers final: 59 residues processed: 554 average time/residue: 0.6421 time to fit residues: 421.9080 Evaluate side-chains 548 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 470 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 27 VAL Chi-restraints excluded: chain 0 residue 59 SER Chi-restraints excluded: chain 1 residue 10 LEU Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 118 LEU Chi-restraints excluded: chain 2 residue 285 GLU Chi-restraints excluded: chain 2 residue 291 LEU Chi-restraints excluded: chain 3 residue 6 LEU Chi-restraints excluded: chain 3 residue 13 LEU Chi-restraints excluded: chain 4 residue 104 ILE Chi-restraints excluded: chain 4 residue 239 THR Chi-restraints excluded: chain 5 residue 79 SER Chi-restraints excluded: chain 5 residue 95 HIS Chi-restraints excluded: chain 5 residue 116 MET Chi-restraints excluded: chain 5 residue 206 GLU Chi-restraints excluded: chain 5 residue 247 GLN Chi-restraints excluded: chain 5 residue 327 THR Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 241 ARG Chi-restraints excluded: chain 6 residue 244 LEU Chi-restraints excluded: chain 6 residue 346 SER Chi-restraints excluded: chain 6 residue 386 VAL Chi-restraints excluded: chain 6 residue 401 LEU Chi-restraints excluded: chain 6 residue 441 SER Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 171 ASP Chi-restraints excluded: chain 7 residue 345 HIS Chi-restraints excluded: chain 8 residue 136 LEU Chi-restraints excluded: chain 8 residue 173 SER Chi-restraints excluded: chain 8 residue 229 ARG Chi-restraints excluded: chain 9 residue 75 ILE Chi-restraints excluded: chain u residue 79 SER Chi-restraints excluded: chain u residue 92 PHE Chi-restraints excluded: chain u residue 244 ASP Chi-restraints excluded: chain u residue 253 LEU Chi-restraints excluded: chain u residue 341 PHE Chi-restraints excluded: chain u residue 411 GLU Chi-restraints excluded: chain u residue 417 LEU Chi-restraints excluded: chain v residue 83 LEU Chi-restraints excluded: chain v residue 124 GLU Chi-restraints excluded: chain v residue 129 ASP Chi-restraints excluded: chain v residue 134 MET Chi-restraints excluded: chain v residue 175 GLU Chi-restraints excluded: chain v residue 282 GLU Chi-restraints excluded: chain v residue 306 THR Chi-restraints excluded: chain v residue 342 SER Chi-restraints excluded: chain w residue 110 LEU Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 264 THR Chi-restraints excluded: chain w residue 297 SER Chi-restraints excluded: chain x residue 122 CYS Chi-restraints excluded: chain x residue 172 LEU Chi-restraints excluded: chain x residue 265 SER Chi-restraints excluded: chain x residue 320 LEU Chi-restraints excluded: chain y residue 74 GLN Chi-restraints excluded: chain z residue 16 THR Chi-restraints excluded: chain z residue 18 SER Chi-restraints excluded: chain z residue 47 LEU Chi-restraints excluded: chain z residue 59 VAL Chi-restraints excluded: chain z residue 68 GLU Chi-restraints excluded: chain Af residue 53 VAL Chi-restraints excluded: chain Af residue 59 LEU Chi-restraints excluded: chain Af residue 62 THR Chi-restraints excluded: chain Af residue 68 LEU Chi-restraints excluded: chain Ae residue 53 VAL Chi-restraints excluded: chain Ae residue 59 LEU Chi-restraints excluded: chain Ae residue 62 THR Chi-restraints excluded: chain Ae residue 68 LEU Chi-restraints excluded: chain Aa residue 19 LEU Chi-restraints excluded: chain Aa residue 32 THR Chi-restraints excluded: chain Aa residue 58 LEU Chi-restraints excluded: chain Aa residue 65 GLN Chi-restraints excluded: chain Ab residue 27 VAL Chi-restraints excluded: chain Ac residue 10 LEU Chi-restraints excluded: chain Ac residue 16 ARG Chi-restraints excluded: chain Ad residue 3 SER Chi-restraints excluded: chain Ad residue 6 LEU Chi-restraints excluded: chain Ad residue 39 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 388 optimal weight: 1.9990 chunk 398 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 327 optimal weight: 0.9990 chunk 331 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 247 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 175 ASN ** 6 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 251 ASN u 43 GLN u 222 GLN u 345 ASN u 373 GLN u 402 HIS ** v 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 97 HIS ** w 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 120 GLN z 80 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.091951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.071857 restraints weight = 55378.691| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.23 r_work: 0.2715 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.560 33619 Z= 0.177 Angle : 0.573 15.762 45689 Z= 0.282 Chirality : 0.041 0.166 4993 Planarity : 0.004 0.056 5836 Dihedral : 7.158 89.629 4603 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.25 % Favored : 97.72 % Rotamer: Outliers : 3.14 % Allowed : 15.88 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.13), residues: 4080 helix: 2.28 (0.11), residues: 2144 sheet: 0.08 (0.26), residues: 395 loop : 0.23 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG y 100 TYR 0.019 0.001 TYR 7 224 PHE 0.017 0.001 PHE w 91 TRP 0.012 0.001 TRP w 141 HIS 0.007 0.001 HIS 2 101 Details of bonding type rmsd covalent geometry : bond 0.00422 (33602) covalent geometry : angle 0.56900 (45675) SS BOND : bond 0.02394 ( 4) SS BOND : angle 4.03212 ( 8) hydrogen bonds : bond 0.04136 ( 1934) hydrogen bonds : angle 4.36010 ( 5499) metal coordination : bond 0.01211 ( 8) metal coordination : angle 3.24978 ( 6) Misc. bond : bond 0.32969 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 486 time to evaluate : 1.282 Fit side-chains revert: symmetry clash REVERT: 0 55 GLN cc_start: 0.8734 (tp40) cc_final: 0.8273 (tp-100) REVERT: 0 62 GLN cc_start: 0.8858 (tp-100) cc_final: 0.8299 (tp-100) REVERT: 0 73 ASP cc_start: 0.8744 (m-30) cc_final: 0.8181 (m-30) REVERT: 1 9 ARG cc_start: 0.8698 (mmt90) cc_final: 0.8457 (mmm-85) REVERT: 1 45 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8355 (mt-10) REVERT: 2 203 LYS cc_start: 0.8575 (pptt) cc_final: 0.8200 (pptt) REVERT: 2 221 HIS cc_start: 0.7766 (t-90) cc_final: 0.7260 (t-90) REVERT: 2 285 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7130 (pp20) REVERT: 3 6 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8420 (mt) REVERT: 3 13 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8779 (mp) REVERT: 3 23 MET cc_start: 0.8952 (tpp) cc_final: 0.8673 (tpp) REVERT: 3 43 ASP cc_start: 0.9332 (m-30) cc_final: 0.8947 (m-30) REVERT: 4 225 ARG cc_start: 0.6065 (mtp85) cc_final: 0.5823 (mtp85) REVERT: 4 271 ARG cc_start: 0.8303 (mmm-85) cc_final: 0.8065 (mmm-85) REVERT: 5 114 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8289 (mt-10) REVERT: 5 179 MET cc_start: 0.8645 (mmm) cc_final: 0.8408 (mmp) REVERT: 5 206 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7777 (pp20) REVERT: 5 240 ARG cc_start: 0.8382 (mmm160) cc_final: 0.7954 (mmm160) REVERT: 5 247 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8104 (tp40) REVERT: 5 324 MET cc_start: 0.8597 (mtp) cc_final: 0.8182 (mtp) REVERT: 5 368 MET cc_start: 0.9229 (mmm) cc_final: 0.9001 (tpp) REVERT: 5 412 ASP cc_start: 0.8821 (t70) cc_final: 0.8572 (t70) REVERT: 6 124 GLU cc_start: 0.8645 (tt0) cc_final: 0.8224 (tt0) REVERT: 6 131 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7215 (tm-30) REVERT: 7 171 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8751 (t0) REVERT: 7 202 GLU cc_start: 0.8519 (tp30) cc_final: 0.8210 (tp30) REVERT: 7 287 LYS cc_start: 0.8839 (mmtm) cc_final: 0.8569 (mppt) REVERT: 8 120 GLN cc_start: 0.9079 (mt0) cc_final: 0.8714 (mt0) REVERT: 8 143 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8270 (tm-30) REVERT: 8 147 LYS cc_start: 0.8423 (tptm) cc_final: 0.8039 (ttmm) REVERT: 8 229 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7074 (ttm170) REVERT: 9 68 ASP cc_start: 0.8858 (t70) cc_final: 0.8627 (t70) REVERT: u 114 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8401 (mt-10) REVERT: u 206 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8188 (tm-30) REVERT: u 218 GLU cc_start: 0.8989 (tt0) cc_final: 0.8348 (tp30) REVERT: u 240 ARG cc_start: 0.8725 (ttm-80) cc_final: 0.8118 (tpp80) REVERT: u 244 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8342 (m-30) REVERT: u 361 ASP cc_start: 0.8380 (t0) cc_final: 0.8050 (t0) REVERT: u 411 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.7999 (tm-30) REVERT: v 129 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8250 (p0) REVERT: v 175 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: v 352 LYS cc_start: 0.8783 (mmmm) cc_final: 0.8247 (tmmt) REVERT: w 11 MET cc_start: 0.8684 (mmm) cc_final: 0.8367 (mmm) REVERT: w 344 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8696 (mm-30) REVERT: x 143 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8453 (tm-30) REVERT: x 172 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8334 (pp) REVERT: x 191 ASN cc_start: 0.9097 (m110) cc_final: 0.8311 (t0) REVERT: x 245 MET cc_start: 0.9205 (ttm) cc_final: 0.8599 (ttm) REVERT: y 71 MET cc_start: 0.9389 (ttp) cc_final: 0.9175 (tmm) REVERT: y 74 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8551 (mt0) REVERT: z 33 LYS cc_start: 0.8802 (mttm) cc_final: 0.8177 (mttt) REVERT: z 72 ARG cc_start: 0.8517 (ttm-80) cc_final: 0.7928 (tpt-90) REVERT: Aa 58 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8876 (mp) REVERT: Aa 65 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7893 (mp10) REVERT: Aa 66 GLU cc_start: 0.8709 (tp30) cc_final: 0.8184 (tm-30) REVERT: Ab 47 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7339 (ttm170) REVERT: Ab 54 ASP cc_start: 0.8641 (p0) cc_final: 0.8326 (p0) REVERT: Ac 16 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.6906 (ttp-170) REVERT: Ac 17 ARG cc_start: 0.8055 (mtm180) cc_final: 0.7702 (mtm-85) REVERT: Ac 54 LYS cc_start: 0.8874 (ptmm) cc_final: 0.8512 (ptmm) REVERT: Ad 15 ARG cc_start: 0.8360 (ttp-170) cc_final: 0.8058 (ttp-110) REVERT: Ad 39 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.6243 (pmt-80) REVERT: Ad 44 TRP cc_start: 0.7854 (m100) cc_final: 0.6458 (m-10) outliers start: 109 outliers final: 58 residues processed: 551 average time/residue: 0.6578 time to fit residues: 427.6925 Evaluate side-chains 542 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 466 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 27 VAL Chi-restraints excluded: chain 0 residue 59 SER Chi-restraints excluded: chain 1 residue 10 LEU Chi-restraints excluded: chain 1 residue 45 GLU Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 118 LEU Chi-restraints excluded: chain 2 residue 121 THR Chi-restraints excluded: chain 2 residue 285 GLU Chi-restraints excluded: chain 2 residue 291 LEU Chi-restraints excluded: chain 3 residue 6 LEU Chi-restraints excluded: chain 3 residue 13 LEU Chi-restraints excluded: chain 4 residue 239 THR Chi-restraints excluded: chain 5 residue 79 SER Chi-restraints excluded: chain 5 residue 95 HIS Chi-restraints excluded: chain 5 residue 183 VAL Chi-restraints excluded: chain 5 residue 206 GLU Chi-restraints excluded: chain 5 residue 247 GLN Chi-restraints excluded: chain 5 residue 327 THR Chi-restraints excluded: chain 5 residue 341 PHE Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 241 ARG Chi-restraints excluded: chain 6 residue 346 SER Chi-restraints excluded: chain 6 residue 386 VAL Chi-restraints excluded: chain 6 residue 401 LEU Chi-restraints excluded: chain 6 residue 441 SER Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 171 ASP Chi-restraints excluded: chain 7 residue 345 HIS Chi-restraints excluded: chain 8 residue 136 LEU Chi-restraints excluded: chain 8 residue 173 SER Chi-restraints excluded: chain 8 residue 229 ARG Chi-restraints excluded: chain 9 residue 75 ILE Chi-restraints excluded: chain u residue 79 SER Chi-restraints excluded: chain u residue 92 PHE Chi-restraints excluded: chain u residue 244 ASP Chi-restraints excluded: chain u residue 341 PHE Chi-restraints excluded: chain u residue 411 GLU Chi-restraints excluded: chain u residue 417 LEU Chi-restraints excluded: chain v residue 83 LEU Chi-restraints excluded: chain v residue 124 GLU Chi-restraints excluded: chain v residue 129 ASP Chi-restraints excluded: chain v residue 175 GLU Chi-restraints excluded: chain v residue 282 GLU Chi-restraints excluded: chain v residue 306 THR Chi-restraints excluded: chain v residue 342 SER Chi-restraints excluded: chain w residue 110 LEU Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 264 THR Chi-restraints excluded: chain w residue 297 SER Chi-restraints excluded: chain x residue 109 THR Chi-restraints excluded: chain x residue 122 CYS Chi-restraints excluded: chain x residue 172 LEU Chi-restraints excluded: chain x residue 265 SER Chi-restraints excluded: chain y residue 74 GLN Chi-restraints excluded: chain z residue 16 THR Chi-restraints excluded: chain z residue 18 SER Chi-restraints excluded: chain z residue 47 LEU Chi-restraints excluded: chain z residue 59 VAL Chi-restraints excluded: chain z residue 68 GLU Chi-restraints excluded: chain Af residue 53 VAL Chi-restraints excluded: chain Af residue 59 LEU Chi-restraints excluded: chain Af residue 62 THR Chi-restraints excluded: chain Af residue 68 LEU Chi-restraints excluded: chain Ae residue 53 VAL Chi-restraints excluded: chain Ae residue 59 LEU Chi-restraints excluded: chain Ae residue 62 THR Chi-restraints excluded: chain Ae residue 68 LEU Chi-restraints excluded: chain Aa residue 19 LEU Chi-restraints excluded: chain Aa residue 32 THR Chi-restraints excluded: chain Aa residue 58 LEU Chi-restraints excluded: chain Aa residue 65 GLN Chi-restraints excluded: chain Ab residue 27 VAL Chi-restraints excluded: chain Ac residue 16 ARG Chi-restraints excluded: chain Ad residue 3 SER Chi-restraints excluded: chain Ad residue 6 LEU Chi-restraints excluded: chain Ad residue 39 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 280 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 211 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 264 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 263 optimal weight: 0.7980 chunk 316 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 207 ASN 5 373 GLN ** 6 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 251 ASN u 345 ASN u 402 HIS ** v 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 97 HIS ** w 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 80 ASN Ac 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.092911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.072843 restraints weight = 55270.918| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.25 r_work: 0.2738 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.505 33619 Z= 0.145 Angle : 0.566 15.102 45689 Z= 0.280 Chirality : 0.040 0.286 4993 Planarity : 0.004 0.057 5836 Dihedral : 7.127 89.966 4603 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.33 % Favored : 97.65 % Rotamer: Outliers : 2.88 % Allowed : 16.43 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.13), residues: 4080 helix: 2.29 (0.11), residues: 2145 sheet: 0.09 (0.26), residues: 393 loop : 0.25 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAc 34 TYR 0.019 0.001 TYRAa 60 PHE 0.016 0.001 PHE 5 341 TRP 0.013 0.001 TRP w 141 HIS 0.007 0.001 HIS u 95 Details of bonding type rmsd covalent geometry : bond 0.00344 (33602) covalent geometry : angle 0.56120 (45675) SS BOND : bond 0.02645 ( 4) SS BOND : angle 5.17009 ( 8) hydrogen bonds : bond 0.03970 ( 1934) hydrogen bonds : angle 4.33486 ( 5499) metal coordination : bond 0.00962 ( 8) metal coordination : angle 2.94252 ( 6) Misc. bond : bond 0.30249 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 500 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: 0 55 GLN cc_start: 0.8745 (tp40) cc_final: 0.8284 (tp-100) REVERT: 0 62 GLN cc_start: 0.8901 (tp-100) cc_final: 0.8384 (tp-100) REVERT: 0 73 ASP cc_start: 0.8698 (m-30) cc_final: 0.8145 (m-30) REVERT: 1 45 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8255 (mt-10) REVERT: 2 203 LYS cc_start: 0.8554 (pptt) cc_final: 0.8140 (pptt) REVERT: 2 206 ASP cc_start: 0.8711 (m-30) cc_final: 0.8375 (t0) REVERT: 2 221 HIS cc_start: 0.7748 (t-90) cc_final: 0.7241 (t-90) REVERT: 2 285 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7103 (pp20) REVERT: 3 6 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8342 (mt) REVERT: 3 13 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8677 (mp) REVERT: 3 23 MET cc_start: 0.8818 (tpp) cc_final: 0.8535 (tpp) REVERT: 3 43 ASP cc_start: 0.9305 (m-30) cc_final: 0.8905 (m-30) REVERT: 4 271 ARG cc_start: 0.8317 (mmm-85) cc_final: 0.8085 (mmm-85) REVERT: 5 179 MET cc_start: 0.8568 (mmm) cc_final: 0.8351 (mmp) REVERT: 5 240 ARG cc_start: 0.8347 (mmm160) cc_final: 0.7948 (mmm160) REVERT: 5 247 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8123 (tp40) REVERT: 5 324 MET cc_start: 0.8530 (mtp) cc_final: 0.8106 (mtp) REVERT: 5 368 MET cc_start: 0.9190 (mmm) cc_final: 0.8958 (tpp) REVERT: 5 412 ASP cc_start: 0.8765 (t70) cc_final: 0.8502 (t70) REVERT: 6 124 GLU cc_start: 0.8614 (tt0) cc_final: 0.8180 (tt0) REVERT: 6 131 GLU cc_start: 0.7400 (tm-30) cc_final: 0.7140 (tm-30) REVERT: 6 233 VAL cc_start: 0.9188 (OUTLIER) cc_final: 0.8922 (m) REVERT: 6 370 ASP cc_start: 0.8637 (m-30) cc_final: 0.8208 (m-30) REVERT: 7 202 GLU cc_start: 0.8462 (tp30) cc_final: 0.8134 (tp30) REVERT: 7 287 LYS cc_start: 0.8803 (mmtm) cc_final: 0.8539 (mppt) REVERT: 8 109 THR cc_start: 0.9048 (m) cc_final: 0.8798 (p) REVERT: 8 120 GLN cc_start: 0.9048 (mt0) cc_final: 0.8695 (mt0) REVERT: 8 143 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8234 (tm-30) REVERT: 8 147 LYS cc_start: 0.8341 (tptm) cc_final: 0.7991 (ttmm) REVERT: 8 174 ASP cc_start: 0.9021 (m-30) cc_final: 0.8661 (m-30) REVERT: 8 229 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7019 (ttm170) REVERT: u 114 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8287 (mt-10) REVERT: u 206 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8123 (tm-30) REVERT: u 218 GLU cc_start: 0.8965 (tt0) cc_final: 0.8314 (tp30) REVERT: u 240 ARG cc_start: 0.8701 (ttm-80) cc_final: 0.8079 (tpp80) REVERT: u 244 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8287 (m-30) REVERT: u 361 ASP cc_start: 0.8370 (t0) cc_final: 0.8004 (t0) REVERT: u 411 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: u 430 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8217 (tp30) REVERT: v 129 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8238 (p0) REVERT: v 352 LYS cc_start: 0.8753 (mmmm) cc_final: 0.8207 (tmmt) REVERT: w 11 MET cc_start: 0.8639 (mmm) cc_final: 0.8319 (mmm) REVERT: w 344 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8623 (mm-30) REVERT: x 143 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8386 (tm-30) REVERT: x 172 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8264 (pp) REVERT: x 174 ASP cc_start: 0.8883 (m-30) cc_final: 0.8564 (m-30) REVERT: x 191 ASN cc_start: 0.9106 (m110) cc_final: 0.8282 (t0) REVERT: x 245 MET cc_start: 0.9177 (ttm) cc_final: 0.8519 (ttm) REVERT: y 22 TYR cc_start: 0.9263 (t80) cc_final: 0.8954 (t80) REVERT: y 74 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8518 (mt0) REVERT: z 33 LYS cc_start: 0.8739 (mttm) cc_final: 0.8114 (mttt) REVERT: z 72 ARG cc_start: 0.8477 (ttm-80) cc_final: 0.7886 (tpt-90) REVERT: Aa 58 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8801 (mp) REVERT: Aa 65 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7888 (mp10) REVERT: Aa 66 GLU cc_start: 0.8660 (tp30) cc_final: 0.8158 (tm-30) REVERT: Ab 47 ARG cc_start: 0.8125 (ttm-80) cc_final: 0.7271 (ttm170) REVERT: Ab 54 ASP cc_start: 0.8619 (p0) cc_final: 0.8263 (p0) REVERT: Ab 62 GLN cc_start: 0.7366 (pm20) cc_final: 0.6656 (pp30) REVERT: Ab 70 GLU cc_start: 0.8883 (mp0) cc_final: 0.8311 (mp0) REVERT: Ac 54 LYS cc_start: 0.8812 (ptmm) cc_final: 0.8455 (ptmm) REVERT: Ad 6 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8110 (mm) REVERT: Ad 15 ARG cc_start: 0.8257 (ttp-170) cc_final: 0.7959 (ttp-110) REVERT: Ad 39 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.6138 (pmt-80) REVERT: Ad 44 TRP cc_start: 0.7760 (m100) cc_final: 0.6368 (m-10) outliers start: 100 outliers final: 61 residues processed: 564 average time/residue: 0.6710 time to fit residues: 447.5602 Evaluate side-chains 558 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 481 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 27 VAL Chi-restraints excluded: chain 0 residue 40 ILE Chi-restraints excluded: chain 0 residue 59 SER Chi-restraints excluded: chain 1 residue 10 LEU Chi-restraints excluded: chain 1 residue 45 GLU Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 118 LEU Chi-restraints excluded: chain 2 residue 121 THR Chi-restraints excluded: chain 2 residue 285 GLU Chi-restraints excluded: chain 2 residue 291 LEU Chi-restraints excluded: chain 3 residue 6 LEU Chi-restraints excluded: chain 3 residue 13 LEU Chi-restraints excluded: chain 4 residue 239 THR Chi-restraints excluded: chain 5 residue 79 SER Chi-restraints excluded: chain 5 residue 95 HIS Chi-restraints excluded: chain 5 residue 183 VAL Chi-restraints excluded: chain 5 residue 247 GLN Chi-restraints excluded: chain 5 residue 327 THR Chi-restraints excluded: chain 5 residue 341 PHE Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 346 SER Chi-restraints excluded: chain 6 residue 386 VAL Chi-restraints excluded: chain 6 residue 416 ILE Chi-restraints excluded: chain 6 residue 441 SER Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 345 HIS Chi-restraints excluded: chain 8 residue 136 LEU Chi-restraints excluded: chain 8 residue 173 SER Chi-restraints excluded: chain 8 residue 202 VAL Chi-restraints excluded: chain 8 residue 229 ARG Chi-restraints excluded: chain 8 residue 258 ASP Chi-restraints excluded: chain 9 residue 75 ILE Chi-restraints excluded: chain u residue 79 SER Chi-restraints excluded: chain u residue 92 PHE Chi-restraints excluded: chain u residue 244 ASP Chi-restraints excluded: chain u residue 341 PHE Chi-restraints excluded: chain u residue 411 GLU Chi-restraints excluded: chain u residue 417 LEU Chi-restraints excluded: chain v residue 83 LEU Chi-restraints excluded: chain v residue 124 GLU Chi-restraints excluded: chain v residue 129 ASP Chi-restraints excluded: chain v residue 282 GLU Chi-restraints excluded: chain v residue 306 THR Chi-restraints excluded: chain v residue 342 SER Chi-restraints excluded: chain w residue 7 SER Chi-restraints excluded: chain w residue 110 LEU Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 238 ILE Chi-restraints excluded: chain w residue 264 THR Chi-restraints excluded: chain w residue 297 SER Chi-restraints excluded: chain x residue 109 THR Chi-restraints excluded: chain x residue 122 CYS Chi-restraints excluded: chain x residue 172 LEU Chi-restraints excluded: chain x residue 265 SER Chi-restraints excluded: chain y residue 74 GLN Chi-restraints excluded: chain z residue 16 THR Chi-restraints excluded: chain z residue 18 SER Chi-restraints excluded: chain z residue 47 LEU Chi-restraints excluded: chain z residue 68 GLU Chi-restraints excluded: chain Af residue 53 VAL Chi-restraints excluded: chain Af residue 59 LEU Chi-restraints excluded: chain Af residue 62 THR Chi-restraints excluded: chain Af residue 68 LEU Chi-restraints excluded: chain Ae residue 53 VAL Chi-restraints excluded: chain Ae residue 59 LEU Chi-restraints excluded: chain Ae residue 62 THR Chi-restraints excluded: chain Ae residue 68 LEU Chi-restraints excluded: chain Aa residue 19 LEU Chi-restraints excluded: chain Aa residue 32 THR Chi-restraints excluded: chain Aa residue 58 LEU Chi-restraints excluded: chain Aa residue 65 GLN Chi-restraints excluded: chain Ab residue 27 VAL Chi-restraints excluded: chain Ab residue 40 ILE Chi-restraints excluded: chain Ac residue 5 THR Chi-restraints excluded: chain Ad residue 3 SER Chi-restraints excluded: chain Ad residue 6 LEU Chi-restraints excluded: chain Ad residue 39 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 355 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 298 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 314 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 220 GLN ** 4 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 175 ASN ** 6 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 251 ASN u 345 ASN u 402 HIS ** v 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 97 HIS ** w 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 267 HIS z 80 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.092174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.072052 restraints weight = 54981.371| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.25 r_work: 0.2721 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.558 33619 Z= 0.178 Angle : 0.597 19.981 45689 Z= 0.294 Chirality : 0.041 0.289 4993 Planarity : 0.004 0.056 5836 Dihedral : 7.148 89.842 4603 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.33 % Favored : 97.65 % Rotamer: Outliers : 2.82 % Allowed : 16.69 % Favored : 80.49 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.13), residues: 4080 helix: 2.23 (0.11), residues: 2150 sheet: 0.05 (0.26), residues: 395 loop : 0.24 (0.17), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGAb 49 TYR 0.019 0.001 TYR 7 224 PHE 0.017 0.001 PHE w 91 TRP 0.012 0.001 TRP w 141 HIS 0.008 0.001 HIS u 95 Details of bonding type rmsd covalent geometry : bond 0.00428 (33602) covalent geometry : angle 0.59147 (45675) SS BOND : bond 0.02346 ( 4) SS BOND : angle 5.62007 ( 8) hydrogen bonds : bond 0.04124 ( 1934) hydrogen bonds : angle 4.37876 ( 5499) metal coordination : bond 0.01115 ( 8) metal coordination : angle 3.11084 ( 6) Misc. bond : bond 0.32739 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 492 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: 0 43 CYS cc_start: 0.7035 (m) cc_final: 0.6659 (m) REVERT: 0 55 GLN cc_start: 0.8792 (tp40) cc_final: 0.8343 (tp-100) REVERT: 0 62 GLN cc_start: 0.8935 (tp-100) cc_final: 0.8442 (tp-100) REVERT: 0 73 ASP cc_start: 0.8725 (m-30) cc_final: 0.8164 (m-30) REVERT: 1 45 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8324 (mt-10) REVERT: 2 203 LYS cc_start: 0.8537 (pptt) cc_final: 0.8164 (pptt) REVERT: 2 221 HIS cc_start: 0.7815 (t-90) cc_final: 0.7281 (t-90) REVERT: 2 285 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7126 (pp20) REVERT: 3 6 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8415 (mt) REVERT: 3 13 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8762 (mp) REVERT: 3 23 MET cc_start: 0.8868 (tpp) cc_final: 0.8572 (tpp) REVERT: 3 43 ASP cc_start: 0.9246 (m-30) cc_final: 0.8848 (m-30) REVERT: 4 271 ARG cc_start: 0.8301 (mmm-85) cc_final: 0.8085 (mmm-85) REVERT: 5 114 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8279 (mt-10) REVERT: 5 179 MET cc_start: 0.8634 (mmm) cc_final: 0.8412 (mmp) REVERT: 5 240 ARG cc_start: 0.8393 (mmm160) cc_final: 0.7975 (mmm160) REVERT: 5 247 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8110 (tp40) REVERT: 5 324 MET cc_start: 0.8655 (mtp) cc_final: 0.8227 (mtp) REVERT: 5 368 MET cc_start: 0.9253 (mmm) cc_final: 0.9026 (tpp) REVERT: 5 412 ASP cc_start: 0.8822 (t70) cc_final: 0.8566 (t70) REVERT: 6 124 GLU cc_start: 0.8645 (tt0) cc_final: 0.8194 (tt0) REVERT: 6 131 GLU cc_start: 0.7494 (tm-30) cc_final: 0.7225 (tm-30) REVERT: 6 370 ASP cc_start: 0.8670 (m-30) cc_final: 0.8264 (m-30) REVERT: 7 202 GLU cc_start: 0.8556 (tp30) cc_final: 0.8230 (tp30) REVERT: 7 287 LYS cc_start: 0.8831 (mmtm) cc_final: 0.8577 (mppt) REVERT: 8 120 GLN cc_start: 0.9088 (mt0) cc_final: 0.8729 (mt0) REVERT: 8 143 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8284 (tm-30) REVERT: 8 147 LYS cc_start: 0.8423 (tptm) cc_final: 0.8037 (ttmm) REVERT: 8 174 ASP cc_start: 0.9072 (m-30) cc_final: 0.8709 (m-30) REVERT: 8 229 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7080 (ttm170) REVERT: u 114 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8386 (mt-10) REVERT: u 206 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8207 (tm-30) REVERT: u 218 GLU cc_start: 0.8983 (tt0) cc_final: 0.8340 (tp30) REVERT: u 240 ARG cc_start: 0.8725 (ttm-80) cc_final: 0.8117 (tpp80) REVERT: u 244 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8293 (m-30) REVERT: u 354 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9223 (tp) REVERT: u 361 ASP cc_start: 0.8467 (t0) cc_final: 0.8109 (t0) REVERT: u 411 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8042 (tm-30) REVERT: v 129 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8242 (p0) REVERT: v 134 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8590 (mtp) REVERT: v 352 LYS cc_start: 0.8794 (mmmm) cc_final: 0.8256 (tmmt) REVERT: w 11 MET cc_start: 0.8687 (mmm) cc_final: 0.8447 (mmm) REVERT: w 344 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8671 (mm-30) REVERT: x 143 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8468 (tm-30) REVERT: x 172 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8315 (pp) REVERT: x 191 ASN cc_start: 0.9092 (m110) cc_final: 0.8310 (t0) REVERT: x 245 MET cc_start: 0.9210 (ttm) cc_final: 0.8614 (ttm) REVERT: y 74 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8559 (mt0) REVERT: z 33 LYS cc_start: 0.8798 (mttm) cc_final: 0.8143 (mtmt) REVERT: z 72 ARG cc_start: 0.8523 (ttm-80) cc_final: 0.7931 (tpt-90) REVERT: Aa 58 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8878 (mp) REVERT: Aa 65 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7909 (mp10) REVERT: Aa 66 GLU cc_start: 0.8711 (tp30) cc_final: 0.8213 (tm-30) REVERT: Ab 47 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7301 (ttm170) REVERT: Ab 54 ASP cc_start: 0.8654 (p0) cc_final: 0.8275 (p0) REVERT: Ac 54 LYS cc_start: 0.8858 (ptmm) cc_final: 0.8484 (ptmm) REVERT: Ad 6 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8103 (mm) REVERT: Ad 15 ARG cc_start: 0.8321 (ttp-170) cc_final: 0.8022 (ttp-110) REVERT: Ad 39 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.6186 (pmt-80) REVERT: Ad 44 TRP cc_start: 0.7846 (m100) cc_final: 0.6491 (m-10) outliers start: 98 outliers final: 61 residues processed: 555 average time/residue: 0.6604 time to fit residues: 432.6543 Evaluate side-chains 552 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 474 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 27 VAL Chi-restraints excluded: chain 0 residue 40 ILE Chi-restraints excluded: chain 0 residue 59 SER Chi-restraints excluded: chain 1 residue 10 LEU Chi-restraints excluded: chain 1 residue 45 GLU Chi-restraints excluded: chain 2 residue 118 LEU Chi-restraints excluded: chain 2 residue 121 THR Chi-restraints excluded: chain 2 residue 285 GLU Chi-restraints excluded: chain 2 residue 291 LEU Chi-restraints excluded: chain 3 residue 6 LEU Chi-restraints excluded: chain 3 residue 13 LEU Chi-restraints excluded: chain 4 residue 239 THR Chi-restraints excluded: chain 5 residue 79 SER Chi-restraints excluded: chain 5 residue 95 HIS Chi-restraints excluded: chain 5 residue 183 VAL Chi-restraints excluded: chain 5 residue 247 GLN Chi-restraints excluded: chain 5 residue 327 THR Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 346 SER Chi-restraints excluded: chain 6 residue 386 VAL Chi-restraints excluded: chain 6 residue 441 SER Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 281 LEU Chi-restraints excluded: chain 7 residue 345 HIS Chi-restraints excluded: chain 8 residue 136 LEU Chi-restraints excluded: chain 8 residue 173 SER Chi-restraints excluded: chain 8 residue 202 VAL Chi-restraints excluded: chain 8 residue 229 ARG Chi-restraints excluded: chain 8 residue 254 LEU Chi-restraints excluded: chain 9 residue 75 ILE Chi-restraints excluded: chain u residue 79 SER Chi-restraints excluded: chain u residue 92 PHE Chi-restraints excluded: chain u residue 244 ASP Chi-restraints excluded: chain u residue 341 PHE Chi-restraints excluded: chain u residue 354 LEU Chi-restraints excluded: chain u residue 411 GLU Chi-restraints excluded: chain u residue 417 LEU Chi-restraints excluded: chain v residue 83 LEU Chi-restraints excluded: chain v residue 124 GLU Chi-restraints excluded: chain v residue 129 ASP Chi-restraints excluded: chain v residue 134 MET Chi-restraints excluded: chain v residue 282 GLU Chi-restraints excluded: chain v residue 306 THR Chi-restraints excluded: chain v residue 342 SER Chi-restraints excluded: chain w residue 7 SER Chi-restraints excluded: chain w residue 110 LEU Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 238 ILE Chi-restraints excluded: chain w residue 264 THR Chi-restraints excluded: chain w residue 297 SER Chi-restraints excluded: chain x residue 109 THR Chi-restraints excluded: chain x residue 122 CYS Chi-restraints excluded: chain x residue 172 LEU Chi-restraints excluded: chain x residue 265 SER Chi-restraints excluded: chain y residue 74 GLN Chi-restraints excluded: chain z residue 16 THR Chi-restraints excluded: chain z residue 18 SER Chi-restraints excluded: chain z residue 47 LEU Chi-restraints excluded: chain z residue 68 GLU Chi-restraints excluded: chain Af residue 53 VAL Chi-restraints excluded: chain Af residue 59 LEU Chi-restraints excluded: chain Af residue 62 THR Chi-restraints excluded: chain Af residue 68 LEU Chi-restraints excluded: chain Ae residue 53 VAL Chi-restraints excluded: chain Ae residue 59 LEU Chi-restraints excluded: chain Ae residue 62 THR Chi-restraints excluded: chain Ae residue 68 LEU Chi-restraints excluded: chain Aa residue 19 LEU Chi-restraints excluded: chain Aa residue 32 THR Chi-restraints excluded: chain Aa residue 47 LEU Chi-restraints excluded: chain Aa residue 58 LEU Chi-restraints excluded: chain Aa residue 65 GLN Chi-restraints excluded: chain Ab residue 27 VAL Chi-restraints excluded: chain Ab residue 40 ILE Chi-restraints excluded: chain Ac residue 5 THR Chi-restraints excluded: chain Ad residue 3 SER Chi-restraints excluded: chain Ad residue 6 LEU Chi-restraints excluded: chain Ad residue 39 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 349 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 380 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 301 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 308 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 175 ASN ** 6 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 251 ASN u 345 ASN u 402 HIS ** v 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 97 HIS ** w 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 37 ASN z 80 ASN Ac 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.091992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.071845 restraints weight = 55457.213| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.25 r_work: 0.2720 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.564 33619 Z= 0.178 Angle : 0.595 15.698 45689 Z= 0.292 Chirality : 0.041 0.212 4993 Planarity : 0.004 0.056 5836 Dihedral : 7.146 89.596 4603 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.28 % Favored : 97.70 % Rotamer: Outliers : 2.50 % Allowed : 17.38 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.13), residues: 4080 helix: 2.22 (0.11), residues: 2149 sheet: 0.04 (0.26), residues: 395 loop : 0.24 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGAb 49 TYR 0.020 0.001 TYRAa 60 PHE 0.016 0.001 PHE w 91 TRP 0.012 0.001 TRP w 141 HIS 0.008 0.001 HIS u 95 Details of bonding type rmsd covalent geometry : bond 0.00428 (33602) covalent geometry : angle 0.59061 (45675) SS BOND : bond 0.02207 ( 4) SS BOND : angle 4.60152 ( 8) hydrogen bonds : bond 0.04132 ( 1934) hydrogen bonds : angle 4.39182 ( 5499) metal coordination : bond 0.01099 ( 8) metal coordination : angle 3.22780 ( 6) Misc. bond : bond 0.32844 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 485 time to evaluate : 1.358 Fit side-chains revert: symmetry clash REVERT: 0 55 GLN cc_start: 0.8795 (tp40) cc_final: 0.8338 (tp-100) REVERT: 0 62 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8420 (tp-100) REVERT: 0 73 ASP cc_start: 0.8733 (m-30) cc_final: 0.8174 (m-30) REVERT: 1 45 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8330 (mt-10) REVERT: 2 203 LYS cc_start: 0.8538 (pptt) cc_final: 0.8167 (pptt) REVERT: 2 221 HIS cc_start: 0.7842 (t-90) cc_final: 0.7299 (t-90) REVERT: 2 285 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7119 (pp20) REVERT: 3 6 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8412 (mt) REVERT: 3 13 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8765 (mp) REVERT: 3 23 MET cc_start: 0.8869 (tpp) cc_final: 0.8575 (tpp) REVERT: 3 43 ASP cc_start: 0.9250 (m-30) cc_final: 0.8865 (m-30) REVERT: 4 271 ARG cc_start: 0.8319 (mmm-85) cc_final: 0.8097 (mmm-85) REVERT: 5 114 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8281 (mt-10) REVERT: 5 179 MET cc_start: 0.8644 (mmm) cc_final: 0.8424 (mmp) REVERT: 5 206 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7916 (pp20) REVERT: 5 240 ARG cc_start: 0.8402 (mmm160) cc_final: 0.7979 (mmm160) REVERT: 5 247 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8116 (tp40) REVERT: 5 324 MET cc_start: 0.8666 (mtp) cc_final: 0.8246 (mtp) REVERT: 5 368 MET cc_start: 0.9266 (mmm) cc_final: 0.9050 (tpp) REVERT: 5 412 ASP cc_start: 0.8826 (t70) cc_final: 0.8566 (t70) REVERT: 6 124 GLU cc_start: 0.8648 (tt0) cc_final: 0.8191 (tt0) REVERT: 6 131 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7248 (tm-30) REVERT: 6 370 ASP cc_start: 0.8678 (m-30) cc_final: 0.8249 (m-30) REVERT: 7 202 GLU cc_start: 0.8549 (tp30) cc_final: 0.8222 (tp30) REVERT: 7 287 LYS cc_start: 0.8831 (mmtm) cc_final: 0.8579 (mppt) REVERT: 8 120 GLN cc_start: 0.9084 (mt0) cc_final: 0.8721 (mt0) REVERT: 8 143 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8297 (tm-30) REVERT: 8 147 LYS cc_start: 0.8440 (tptm) cc_final: 0.8050 (ttmm) REVERT: 8 174 ASP cc_start: 0.9064 (m-30) cc_final: 0.8702 (m-30) REVERT: 8 229 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7086 (ttm170) REVERT: u 114 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8423 (mt-10) REVERT: u 206 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8195 (tm-30) REVERT: u 218 GLU cc_start: 0.8989 (tt0) cc_final: 0.8348 (tp30) REVERT: u 240 ARG cc_start: 0.8721 (ttm-80) cc_final: 0.8127 (tpp80) REVERT: u 244 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8309 (m-30) REVERT: u 354 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9213 (tp) REVERT: u 361 ASP cc_start: 0.8474 (t0) cc_final: 0.8127 (t0) REVERT: u 411 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8043 (tm-30) REVERT: v 129 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8274 (p0) REVERT: v 134 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8570 (mtp) REVERT: v 352 LYS cc_start: 0.8796 (mmmm) cc_final: 0.8261 (tmmt) REVERT: w 11 MET cc_start: 0.8693 (mmm) cc_final: 0.8449 (mmm) REVERT: w 344 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8673 (mm-30) REVERT: x 143 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8472 (tm-30) REVERT: x 172 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8324 (pp) REVERT: x 191 ASN cc_start: 0.9138 (m110) cc_final: 0.8347 (t0) REVERT: x 245 MET cc_start: 0.9214 (ttm) cc_final: 0.8620 (ttm) REVERT: y 74 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8555 (mt0) REVERT: z 33 LYS cc_start: 0.8847 (mttm) cc_final: 0.8202 (mtmt) REVERT: z 66 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8441 (mm-30) REVERT: z 72 ARG cc_start: 0.8518 (ttm-80) cc_final: 0.7926 (tpt-90) REVERT: Aa 58 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8853 (mp) REVERT: Aa 65 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7908 (mp10) REVERT: Aa 66 GLU cc_start: 0.8714 (tp30) cc_final: 0.8217 (tm-30) REVERT: Ab 47 ARG cc_start: 0.8127 (ttm-80) cc_final: 0.7283 (ttm170) REVERT: Ab 54 ASP cc_start: 0.8681 (p0) cc_final: 0.8256 (p0) REVERT: Ac 54 LYS cc_start: 0.8864 (ptmm) cc_final: 0.8491 (ptmm) REVERT: Ad 6 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8103 (mm) REVERT: Ad 15 ARG cc_start: 0.8313 (ttp-170) cc_final: 0.8010 (ttp-110) REVERT: Ad 39 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.6170 (pmt-80) REVERT: Ad 44 TRP cc_start: 0.7933 (m100) cc_final: 0.6543 (m-10) outliers start: 87 outliers final: 62 residues processed: 538 average time/residue: 0.6637 time to fit residues: 425.0723 Evaluate side-chains 547 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 467 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 40 ILE Chi-restraints excluded: chain 0 residue 59 SER Chi-restraints excluded: chain 1 residue 10 LEU Chi-restraints excluded: chain 1 residue 45 GLU Chi-restraints excluded: chain 2 residue 118 LEU Chi-restraints excluded: chain 2 residue 121 THR Chi-restraints excluded: chain 2 residue 285 GLU Chi-restraints excluded: chain 2 residue 291 LEU Chi-restraints excluded: chain 3 residue 6 LEU Chi-restraints excluded: chain 3 residue 13 LEU Chi-restraints excluded: chain 4 residue 239 THR Chi-restraints excluded: chain 5 residue 79 SER Chi-restraints excluded: chain 5 residue 95 HIS Chi-restraints excluded: chain 5 residue 183 VAL Chi-restraints excluded: chain 5 residue 206 GLU Chi-restraints excluded: chain 5 residue 247 GLN Chi-restraints excluded: chain 5 residue 327 THR Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 346 SER Chi-restraints excluded: chain 6 residue 386 VAL Chi-restraints excluded: chain 6 residue 441 SER Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 171 ASP Chi-restraints excluded: chain 7 residue 281 LEU Chi-restraints excluded: chain 7 residue 345 HIS Chi-restraints excluded: chain 8 residue 136 LEU Chi-restraints excluded: chain 8 residue 173 SER Chi-restraints excluded: chain 8 residue 202 VAL Chi-restraints excluded: chain 8 residue 229 ARG Chi-restraints excluded: chain 8 residue 254 LEU Chi-restraints excluded: chain 9 residue 75 ILE Chi-restraints excluded: chain u residue 79 SER Chi-restraints excluded: chain u residue 92 PHE Chi-restraints excluded: chain u residue 244 ASP Chi-restraints excluded: chain u residue 289 ILE Chi-restraints excluded: chain u residue 341 PHE Chi-restraints excluded: chain u residue 354 LEU Chi-restraints excluded: chain u residue 411 GLU Chi-restraints excluded: chain u residue 417 LEU Chi-restraints excluded: chain v residue 83 LEU Chi-restraints excluded: chain v residue 124 GLU Chi-restraints excluded: chain v residue 129 ASP Chi-restraints excluded: chain v residue 134 MET Chi-restraints excluded: chain v residue 282 GLU Chi-restraints excluded: chain v residue 306 THR Chi-restraints excluded: chain v residue 342 SER Chi-restraints excluded: chain w residue 7 SER Chi-restraints excluded: chain w residue 110 LEU Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 238 ILE Chi-restraints excluded: chain w residue 264 THR Chi-restraints excluded: chain w residue 297 SER Chi-restraints excluded: chain x residue 109 THR Chi-restraints excluded: chain x residue 122 CYS Chi-restraints excluded: chain x residue 172 LEU Chi-restraints excluded: chain x residue 265 SER Chi-restraints excluded: chain y residue 74 GLN Chi-restraints excluded: chain z residue 16 THR Chi-restraints excluded: chain z residue 18 SER Chi-restraints excluded: chain z residue 47 LEU Chi-restraints excluded: chain z residue 68 GLU Chi-restraints excluded: chain Af residue 53 VAL Chi-restraints excluded: chain Af residue 59 LEU Chi-restraints excluded: chain Af residue 62 THR Chi-restraints excluded: chain Af residue 68 LEU Chi-restraints excluded: chain Ae residue 53 VAL Chi-restraints excluded: chain Ae residue 59 LEU Chi-restraints excluded: chain Ae residue 62 THR Chi-restraints excluded: chain Ae residue 68 LEU Chi-restraints excluded: chain Aa residue 19 LEU Chi-restraints excluded: chain Aa residue 32 THR Chi-restraints excluded: chain Aa residue 47 LEU Chi-restraints excluded: chain Aa residue 58 LEU Chi-restraints excluded: chain Aa residue 65 GLN Chi-restraints excluded: chain Ab residue 27 VAL Chi-restraints excluded: chain Ab residue 40 ILE Chi-restraints excluded: chain Ac residue 5 THR Chi-restraints excluded: chain Ad residue 3 SER Chi-restraints excluded: chain Ad residue 6 LEU Chi-restraints excluded: chain Ad residue 39 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 169 optimal weight: 1.9990 chunk 317 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 88 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 323 optimal weight: 2.9990 chunk 243 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 175 ASN ** 6 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 251 ASN u 43 GLN u 345 ASN u 402 HIS ** v 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 97 HIS ** w 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 80 ASN Ac 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.092976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.072842 restraints weight = 55370.908| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.24 r_work: 0.2745 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.515 33619 Z= 0.148 Angle : 0.587 15.074 45689 Z= 0.289 Chirality : 0.041 0.305 4993 Planarity : 0.004 0.057 5836 Dihedral : 7.116 89.754 4603 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.33 % Favored : 97.65 % Rotamer: Outliers : 2.50 % Allowed : 17.61 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.13), residues: 4080 helix: 2.22 (0.11), residues: 2152 sheet: 0.05 (0.26), residues: 395 loop : 0.25 (0.17), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 4 225 TYR 0.021 0.001 TYRAa 60 PHE 0.015 0.001 PHE 5 341 TRP 0.013 0.001 TRP w 141 HIS 0.008 0.001 HIS u 95 Details of bonding type rmsd covalent geometry : bond 0.00354 (33602) covalent geometry : angle 0.58188 (45675) SS BOND : bond 0.01882 ( 4) SS BOND : angle 5.50677 ( 8) hydrogen bonds : bond 0.03968 ( 1934) hydrogen bonds : angle 4.35334 ( 5499) metal coordination : bond 0.00909 ( 8) metal coordination : angle 3.04127 ( 6) Misc. bond : bond 0.30609 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11666.98 seconds wall clock time: 199 minutes 8.61 seconds (11948.61 seconds total)