Starting phenix.real_space_refine on Mon Aug 25 13:05:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ovw_17224/08_2025/8ovw_17224.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ovw_17224/08_2025/8ovw_17224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ovw_17224/08_2025/8ovw_17224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ovw_17224/08_2025/8ovw_17224.map" model { file = "/net/cci-nas-00/data/ceres_data/8ovw_17224/08_2025/8ovw_17224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ovw_17224/08_2025/8ovw_17224.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 P 54 5.49 5 S 109 5.16 5 C 17953 2.51 5 N 4873 2.21 5 O 5472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 149 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: 28461 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 822 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain: "B" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 1, 'TRANS': 105} Chain: "D" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 553 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "H" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1412 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 167} Chain breaks: 1 Chain: "I" Number of atoms: 5496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5496 Classifications: {'peptide': 679} Link IDs: {'PTRANS': 27, 'TRANS': 651} Chain breaks: 4 Chain: "K" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1762 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1941 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 9, 'TRANS': 231} Chain: "N" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3166 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 369} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1979 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 6, 'TRANS': 234} Chain breaks: 1 Chain: "P" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2116 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 250} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "Q" Number of atoms: 2144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2144 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "T" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 761 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "U" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1485 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 181} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "W" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 551 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Chain: "Y" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1663 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 4, 'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "Z" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1180 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 2, 'TRANS': 148} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 2, 'TYR:plan': 1, 'GLU:plan': 2, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 554 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Time building chain proxies: 5.15, per 1000 atoms: 0.18 Number of scatterers: 28461 At special positions: 0 Unit cell: (131.152, 187.36, 176.821, 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) S 109 16.00 P 54 15.00 O 5472 8.00 N 4873 7.00 C 17953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 929.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6548 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 16 sheets defined 67.1% alpha, 9.5% beta 25 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'A' and resid 229 through 249 removed outlier: 3.619A pdb=" N ARG A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 320 Processing helix chain 'B' and resid 219 through 248 Processing helix chain 'B' and resid 255 through 324 Processing helix chain 'H' and resid 5 through 39 Processing helix chain 'H' and resid 46 through 74 removed outlier: 3.846A pdb=" N LEU H 52 " --> pdb=" O THR H 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 94 removed outlier: 3.648A pdb=" N THR H 84 " --> pdb=" O ASN H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 133 removed outlier: 3.543A pdb=" N LEU H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU H 101 " --> pdb=" O ASP H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 172 removed outlier: 3.806A pdb=" N GLU H 153 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 13 Processing helix chain 'I' and resid 26 through 38 Processing helix chain 'I' and resid 41 through 55 removed outlier: 3.570A pdb=" N THR I 55 " --> pdb=" O LEU I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 70 Processing helix chain 'I' and resid 78 through 89 removed outlier: 3.615A pdb=" N LEU I 82 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 117 Processing helix chain 'I' and resid 131 through 139 Processing helix chain 'I' and resid 145 through 157 removed outlier: 4.005A pdb=" N THR I 150 " --> pdb=" O GLN I 146 " (cutoff:3.500A) Proline residue: I 151 - end of helix Processing helix chain 'I' and resid 164 through 176 Processing helix chain 'I' and resid 182 through 199 removed outlier: 3.857A pdb=" N GLY I 199 " --> pdb=" O GLN I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 211 Processing helix chain 'I' and resid 216 through 222 Processing helix chain 'I' and resid 227 through 241 Processing helix chain 'I' and resid 247 through 264 removed outlier: 3.655A pdb=" N ILE I 262 " --> pdb=" O TYR I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 267 No H-bonds generated for 'chain 'I' and resid 265 through 267' Processing helix chain 'I' and resid 295 through 302 removed outlier: 3.819A pdb=" N LEU I 299 " --> pdb=" O SER I 295 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA I 300 " --> pdb=" O LEU I 296 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN I 301 " --> pdb=" O GLU I 297 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN I 302 " --> pdb=" O GLN I 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 295 through 302' Processing helix chain 'I' and resid 311 through 317 Processing helix chain 'I' and resid 332 through 337 removed outlier: 3.800A pdb=" N LEU I 336 " --> pdb=" O ARG I 333 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS I 337 " --> pdb=" O ASP I 334 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 348 Processing helix chain 'I' and resid 354 through 369 Processing helix chain 'I' and resid 378 through 387 Processing helix chain 'I' and resid 389 through 401 removed outlier: 3.527A pdb=" N SER I 393 " --> pdb=" O ASP I 389 " (cutoff:3.500A) Processing helix chain 'I' and resid 402 through 409 Processing helix chain 'I' and resid 409 through 421 removed outlier: 3.534A pdb=" N LEU I 413 " --> pdb=" O ASP I 409 " (cutoff:3.500A) Processing helix chain 'I' and resid 422 through 424 No H-bonds generated for 'chain 'I' and resid 422 through 424' Processing helix chain 'I' and resid 431 through 450 removed outlier: 4.200A pdb=" N ASP I 450 " --> pdb=" O TRP I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 456 through 475 removed outlier: 3.896A pdb=" N ASP I 475 " --> pdb=" O ASN I 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 494 Processing helix chain 'I' and resid 505 through 524 removed outlier: 3.532A pdb=" N LYS I 524 " --> pdb=" O THR I 520 " (cutoff:3.500A) Processing helix chain 'I' and resid 531 through 535 removed outlier: 3.623A pdb=" N TYR I 534 " --> pdb=" O ALA I 531 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU I 535 " --> pdb=" O ILE I 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 531 through 535' Processing helix chain 'I' and resid 538 through 548 removed outlier: 3.798A pdb=" N MET I 542 " --> pdb=" O GLY I 538 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS I 544 " --> pdb=" O ASP I 540 " (cutoff:3.500A) Processing helix chain 'I' and resid 550 through 569 Processing helix chain 'I' and resid 577 through 593 Processing helix chain 'I' and resid 607 through 616 removed outlier: 3.763A pdb=" N PHE I 611 " --> pdb=" O SER I 607 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU I 615 " --> pdb=" O PHE I 611 " (cutoff:3.500A) Processing helix chain 'I' and resid 639 through 654 removed outlier: 3.526A pdb=" N CYS I 643 " --> pdb=" O LEU I 639 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE I 644 " --> pdb=" O SER I 640 " (cutoff:3.500A) Processing helix chain 'I' and resid 666 through 677 removed outlier: 3.586A pdb=" N HIS I 677 " --> pdb=" O PHE I 673 " (cutoff:3.500A) Processing helix chain 'I' and resid 677 through 684 removed outlier: 3.667A pdb=" N GLN I 683 " --> pdb=" O ASP I 679 " (cutoff:3.500A) Processing helix chain 'I' and resid 692 through 705 Processing helix chain 'I' and resid 711 through 721 removed outlier: 4.120A pdb=" N ALA I 715 " --> pdb=" O TYR I 711 " (cutoff:3.500A) Processing helix chain 'I' and resid 725 through 729 removed outlier: 3.767A pdb=" N SER I 729 " --> pdb=" O SER I 726 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 40 Processing helix chain 'K' and resid 49 through 58 Processing helix chain 'K' and resid 70 through 130 removed outlier: 3.875A pdb=" N SER K 130 " --> pdb=" O THR K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 159 Processing helix chain 'K' and resid 159 through 165 Processing helix chain 'K' and resid 166 through 169 Processing helix chain 'K' and resid 170 through 187 removed outlier: 3.840A pdb=" N LEU K 174 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU K 177 " --> pdb=" O SER K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 211 Processing helix chain 'L' and resid 19 through 28 removed outlier: 3.738A pdb=" N LEU L 23 " --> pdb=" O GLY L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 47 removed outlier: 3.526A pdb=" N GLY L 47 " --> pdb=" O PRO L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 108 removed outlier: 3.922A pdb=" N VAL L 98 " --> pdb=" O ASN L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 128 Processing helix chain 'L' and resid 153 through 157 Processing helix chain 'L' and resid 166 through 178 Processing helix chain 'L' and resid 182 through 187 Processing helix chain 'L' and resid 187 through 197 Processing helix chain 'L' and resid 229 through 240 Processing helix chain 'N' and resid 16 through 25 Processing helix chain 'N' and resid 28 through 43 Processing helix chain 'N' and resid 50 through 64 Processing helix chain 'N' and resid 67 through 78 removed outlier: 3.892A pdb=" N ILE N 71 " --> pdb=" O ARG N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 100 removed outlier: 3.713A pdb=" N ASP N 93 " --> pdb=" O LEU N 89 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 103 No H-bonds generated for 'chain 'N' and resid 101 through 103' Processing helix chain 'N' and resid 124 through 137 Processing helix chain 'N' and resid 218 through 234 removed outlier: 3.777A pdb=" N SER N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU N 234 " --> pdb=" O ARG N 230 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 258 removed outlier: 3.565A pdb=" N ILE N 254 " --> pdb=" O SER N 250 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 269 No H-bonds generated for 'chain 'N' and resid 267 through 269' Processing helix chain 'N' and resid 270 through 276 removed outlier: 3.587A pdb=" N ALA N 274 " --> pdb=" O TRP N 270 " (cutoff:3.500A) Processing helix chain 'N' and resid 289 through 294 Processing helix chain 'N' and resid 318 through 335 Processing helix chain 'N' and resid 408 through 419 Processing helix chain 'N' and resid 428 through 433 Processing helix chain 'O' and resid 134 through 139 removed outlier: 4.142A pdb=" N THR O 138 " --> pdb=" O THR O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 139 through 148 removed outlier: 3.709A pdb=" N ARG O 143 " --> pdb=" O SER O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 154 through 172 Processing helix chain 'O' and resid 182 through 184 No H-bonds generated for 'chain 'O' and resid 182 through 184' Processing helix chain 'O' and resid 245 through 253 Processing helix chain 'O' and resid 254 through 256 No H-bonds generated for 'chain 'O' and resid 254 through 256' Processing helix chain 'O' and resid 260 through 291 removed outlier: 3.754A pdb=" N GLN O 274 " --> pdb=" O ARG O 270 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 348 Processing helix chain 'O' and resid 352 through 364 removed outlier: 3.764A pdb=" N ALA O 364 " --> pdb=" O ASN O 360 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 112 Processing helix chain 'P' and resid 133 through 140 Processing helix chain 'P' and resid 149 through 160 Processing helix chain 'P' and resid 224 through 232 Processing helix chain 'P' and resid 236 through 266 removed outlier: 3.618A pdb=" N CYS P 240 " --> pdb=" O ASN P 236 " (cutoff:3.500A) Processing helix chain 'P' and resid 333 through 349 Processing helix chain 'P' and resid 350 through 363 Processing helix chain 'P' and resid 364 through 368 removed outlier: 3.838A pdb=" N ALA P 368 " --> pdb=" O ASP P 365 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 141 removed outlier: 3.728A pdb=" N VAL Q 133 " --> pdb=" O GLU Q 129 " (cutoff:3.500A) Processing helix chain 'Q' and resid 155 through 181 Processing helix chain 'Q' and resid 181 through 190 removed outlier: 3.549A pdb=" N MET Q 185 " --> pdb=" O TYR Q 181 " (cutoff:3.500A) Processing helix chain 'Q' and resid 192 through 220 removed outlier: 3.551A pdb=" N VAL Q 196 " --> pdb=" O ASP Q 192 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN Q 220 " --> pdb=" O LYS Q 216 " (cutoff:3.500A) Processing helix chain 'Q' and resid 233 through 290 removed outlier: 3.576A pdb=" N ILE Q 237 " --> pdb=" O ASP Q 233 " (cutoff:3.500A) Processing helix chain 'Q' and resid 297 through 299 No H-bonds generated for 'chain 'Q' and resid 297 through 299' Processing helix chain 'Q' and resid 300 through 308 Processing helix chain 'Q' and resid 321 through 332 removed outlier: 4.045A pdb=" N HIS Q 330 " --> pdb=" O ARG Q 326 " (cutoff:3.500A) Processing helix chain 'Q' and resid 349 through 357 Processing helix chain 'Q' and resid 358 through 382 removed outlier: 4.019A pdb=" N GLU Q 362 " --> pdb=" O PRO Q 358 " (cutoff:3.500A) Processing helix chain 'Q' and resid 382 through 389 removed outlier: 3.642A pdb=" N VAL Q 389 " --> pdb=" O GLU Q 385 " (cutoff:3.500A) Processing helix chain 'T' and resid 274 through 283 Processing helix chain 'T' and resid 284 through 289 Processing helix chain 'T' and resid 294 through 316 removed outlier: 4.112A pdb=" N LEU T 306 " --> pdb=" O GLN T 302 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN T 307 " --> pdb=" O GLU T 303 " (cutoff:3.500A) Processing helix chain 'T' and resid 320 through 331 removed outlier: 3.863A pdb=" N LEU T 324 " --> pdb=" O GLN T 320 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL T 325 " --> pdb=" O LYS T 321 " (cutoff:3.500A) Processing helix chain 'T' and resid 336 through 344 Processing helix chain 'T' and resid 349 through 360 Processing helix chain 'U' and resid 134 through 149 Processing helix chain 'U' and resid 150 through 161 Processing helix chain 'U' and resid 164 through 232 removed outlier: 3.995A pdb=" N ASN U 200 " --> pdb=" O ASN U 196 " (cutoff:3.500A) Processing helix chain 'U' and resid 233 through 265 removed outlier: 3.599A pdb=" N HIS U 237 " --> pdb=" O GLY U 233 " (cutoff:3.500A) Processing helix chain 'U' and resid 286 through 299 removed outlier: 3.506A pdb=" N LEU U 290 " --> pdb=" O ASP U 286 " (cutoff:3.500A) Processing helix chain 'U' and resid 305 through 321 Processing helix chain 'W' and resid 2 through 15 Processing helix chain 'W' and resid 37 through 69 Processing helix chain 'W' and resid 74 through 88 Processing helix chain 'Y' and resid 3 through 16 removed outlier: 3.673A pdb=" N SER Y 7 " --> pdb=" O ASP Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 30 Processing helix chain 'Y' and resid 36 through 50 Processing helix chain 'Y' and resid 55 through 84 Processing helix chain 'Y' and resid 94 through 102 Processing helix chain 'Y' and resid 109 through 119 removed outlier: 3.623A pdb=" N LYS Y 119 " --> pdb=" O GLU Y 115 " (cutoff:3.500A) Processing helix chain 'Y' and resid 137 through 186 removed outlier: 3.595A pdb=" N GLU Y 186 " --> pdb=" O LYS Y 182 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 219 removed outlier: 4.528A pdb=" N ALA Y 195 " --> pdb=" O SER Y 191 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE Y 219 " --> pdb=" O ALA Y 215 " (cutoff:3.500A) Processing helix chain 'Y' and resid 222 through 238 Processing helix chain 'Z' and resid 4 through 13 Processing helix chain 'Z' and resid 15 through 20 Processing helix chain 'Z' and resid 21 through 29 Processing helix chain 'Z' and resid 35 through 84 Processing helix chain 'Z' and resid 86 through 127 removed outlier: 3.540A pdb=" N LEU Z 90 " --> pdb=" O SER Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 134 through 153 removed outlier: 3.547A pdb=" N ASN Z 153 " --> pdb=" O LEU Z 149 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 288 through 289 removed outlier: 6.510A pdb=" N VAL I 288 " --> pdb=" O HIS I 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'K' and resid 214 through 218 removed outlier: 3.699A pdb=" N LYS K 229 " --> pdb=" O THR K 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 35 through 36 removed outlier: 3.798A pdb=" N MET L 85 " --> pdb=" O ILE L 10 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP L 112 " --> pdb=" O GLY L 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 35 through 36 removed outlier: 3.798A pdb=" N MET L 85 " --> pdb=" O ILE L 10 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER L 220 " --> pdb=" O MET L 217 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL L 222 " --> pdb=" O LYS L 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 130 through 132 Processing sheet with id=AA6, first strand: chain 'N' and resid 141 through 148 removed outlier: 3.943A pdb=" N HIS N 141 " --> pdb=" O PHE N 162 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL N 202 " --> pdb=" O THR N 157 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TYR N 201 " --> pdb=" O SER N 214 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ILE N 210 " --> pdb=" O PRO N 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 141 through 148 removed outlier: 3.943A pdb=" N HIS N 141 " --> pdb=" O PHE N 162 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL N 202 " --> pdb=" O THR N 157 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TYR N 201 " --> pdb=" O SER N 214 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ILE N 210 " --> pdb=" O PRO N 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 295 through 298 Processing sheet with id=AA9, first strand: chain 'O' and resid 175 through 180 removed outlier: 4.360A pdb=" N LEU O 180 " --> pdb=" O MET O 201 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET O 201 " --> pdb=" O LEU O 180 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS O 225 " --> pdb=" O LEU O 235 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU O 235 " --> pdb=" O LYS O 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 186 through 188 Processing sheet with id=AB2, first strand: chain 'O' and resid 209 through 210 Processing sheet with id=AB3, first strand: chain 'O' and resid 305 through 309 removed outlier: 6.212A pdb=" N LYS O 320 " --> pdb=" O ILE O 324 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE O 324 " --> pdb=" O LYS O 320 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 165 through 171 removed outlier: 3.518A pdb=" N GLN P 170 " --> pdb=" O VAL P 184 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL P 184 " --> pdb=" O GLN P 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 165 through 171 removed outlier: 3.518A pdb=" N GLN P 170 " --> pdb=" O VAL P 184 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL P 184 " --> pdb=" O GLN P 170 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE P 197 " --> pdb=" O PHE P 189 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLU P 198 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE P 220 " --> pdb=" O GLU P 198 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLN P 200 " --> pdb=" O LEU P 218 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LYS P 214 " --> pdb=" O PHE P 204 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 270 through 274 removed outlier: 3.550A pdb=" N SER P 322 " --> pdb=" O ASN P 299 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 270 through 274 removed outlier: 3.550A pdb=" N SER P 322 " --> pdb=" O ASN P 299 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER P 319 " --> pdb=" O MET Q 335 " (cutoff:3.500A) 1869 hydrogen bonds defined for protein. 5517 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 4.72 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4921 1.32 - 1.45: 7342 1.45 - 1.57: 16490 1.57 - 1.70: 106 1.70 - 1.82: 182 Bond restraints: 29041 Sorted by residual: bond pdb=" N ARG P 308 " pdb=" CA ARG P 308 " ideal model delta sigma weight residual 1.458 1.531 -0.073 1.90e-02 2.77e+03 1.47e+01 bond pdb=" C ALA I 241 " pdb=" N HIS I 242 " ideal model delta sigma weight residual 1.328 1.377 -0.049 1.44e-02 4.82e+03 1.15e+01 bond pdb=" N LYS Q 222 " pdb=" CA LYS Q 222 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.21e-02 6.83e+03 1.10e+01 bond pdb=" N ALA Q 221 " pdb=" CA ALA Q 221 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.29e-02 6.01e+03 9.61e+00 bond pdb=" N HIS I 242 " pdb=" CA HIS I 242 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.29e-02 6.01e+03 8.68e+00 ... (remaining 29036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 38794 2.56 - 5.11: 483 5.11 - 7.67: 94 7.67 - 10.22: 25 10.22 - 12.78: 7 Bond angle restraints: 39403 Sorted by residual: angle pdb=" N PRO Y 223 " pdb=" CA PRO Y 223 " pdb=" CB PRO Y 223 " ideal model delta sigma weight residual 103.44 110.05 -6.61 1.12e+00 7.97e-01 3.48e+01 angle pdb=" N PRO Z 137 " pdb=" CA PRO Z 137 " pdb=" CB PRO Z 137 " ideal model delta sigma weight residual 103.44 110.02 -6.58 1.12e+00 7.97e-01 3.45e+01 angle pdb=" N GLN Y 45 " pdb=" CA GLN Y 45 " pdb=" CB GLN Y 45 " ideal model delta sigma weight residual 110.30 118.32 -8.02 1.54e+00 4.22e-01 2.71e+01 angle pdb=" N GLN H 14 " pdb=" CA GLN H 14 " pdb=" CB GLN H 14 " ideal model delta sigma weight residual 110.28 118.15 -7.87 1.55e+00 4.16e-01 2.58e+01 angle pdb=" CA ILE Z 136 " pdb=" C ILE Z 136 " pdb=" N PRO Z 137 " ideal model delta sigma weight residual 121.00 117.30 3.70 8.30e-01 1.45e+00 1.98e+01 ... (remaining 39398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 15566 17.95 - 35.90: 1595 35.90 - 53.85: 406 53.85 - 71.79: 90 71.79 - 89.74: 53 Dihedral angle restraints: 17710 sinusoidal: 7703 harmonic: 10007 Sorted by residual: dihedral pdb=" CA ASP Y 187 " pdb=" C ASP Y 187 " pdb=" N ASP Y 188 " pdb=" CA ASP Y 188 " ideal model delta harmonic sigma weight residual -180.00 -134.75 -45.25 0 5.00e+00 4.00e-02 8.19e+01 dihedral pdb=" CD ARG U 167 " pdb=" NE ARG U 167 " pdb=" CZ ARG U 167 " pdb=" NH1 ARG U 167 " ideal model delta sinusoidal sigma weight residual 0.00 79.94 -79.94 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CA SER I 202 " pdb=" C SER I 202 " pdb=" N GLN I 203 " pdb=" CA GLN I 203 " ideal model delta harmonic sigma weight residual -180.00 -142.38 -37.62 0 5.00e+00 4.00e-02 5.66e+01 ... (remaining 17707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4078 0.073 - 0.146: 410 0.146 - 0.219: 31 0.219 - 0.292: 9 0.292 - 0.365: 2 Chirality restraints: 4530 Sorted by residual: chirality pdb=" CG LEU H 114 " pdb=" CB LEU H 114 " pdb=" CD1 LEU H 114 " pdb=" CD2 LEU H 114 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB VAL H 43 " pdb=" CA VAL H 43 " pdb=" CG1 VAL H 43 " pdb=" CG2 VAL H 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB THR K 140 " pdb=" CA THR K 140 " pdb=" OG1 THR K 140 " pdb=" CG2 THR K 140 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 4527 not shown) Planarity restraints: 4802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG U 167 " -1.083 9.50e-02 1.11e+02 4.86e-01 1.42e+02 pdb=" NE ARG U 167 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG U 167 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG U 167 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG U 167 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG Q 219 " -0.035 2.00e-02 2.50e+03 6.86e-02 4.70e+01 pdb=" C ARG Q 219 " 0.119 2.00e-02 2.50e+03 pdb=" O ARG Q 219 " -0.045 2.00e-02 2.50e+03 pdb=" N GLN Q 220 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA I 241 " 0.029 2.00e-02 2.50e+03 5.67e-02 3.21e+01 pdb=" C ALA I 241 " -0.098 2.00e-02 2.50e+03 pdb=" O ALA I 241 " 0.037 2.00e-02 2.50e+03 pdb=" N HIS I 242 " 0.032 2.00e-02 2.50e+03 ... (remaining 4799 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2684 2.75 - 3.29: 28468 3.29 - 3.82: 49026 3.82 - 4.36: 55544 4.36 - 4.90: 95211 Nonbonded interactions: 230933 Sorted by model distance: nonbonded pdb=" OG SER N 233 " pdb=" O GLU N 236 " model vdw 2.212 3.040 nonbonded pdb=" O ILE K 171 " pdb=" OG1 THR K 175 " model vdw 2.232 3.040 nonbonded pdb=" OG SER Q 249 " pdb=" OD1 ASN Y 6 " model vdw 2.264 3.040 nonbonded pdb=" O ILE I 204 " pdb=" OG SER I 207 " model vdw 2.272 3.040 nonbonded pdb=" OH TYR L 148 " pdb=" OE1 GLN L 160 " model vdw 2.277 3.040 ... (remaining 230928 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 221 through 321) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.760 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 29041 Z= 0.193 Angle : 0.784 12.777 39403 Z= 0.432 Chirality : 0.046 0.365 4530 Planarity : 0.009 0.486 4802 Dihedral : 16.453 89.742 11162 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.13 % Allowed : 0.52 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.14), residues: 3318 helix: 0.74 (0.11), residues: 2094 sheet: -0.72 (0.33), residues: 246 loop : -1.45 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG K 139 TYR 0.052 0.001 TYR Q 363 PHE 0.054 0.002 PHE H 83 TRP 0.023 0.001 TRP I 136 HIS 0.007 0.001 HIS L 131 Details of bonding type rmsd covalent geometry : bond 0.00375 (29041) covalent geometry : angle 0.78422 (39403) hydrogen bonds : bond 0.13988 ( 1870) hydrogen bonds : angle 5.97988 ( 5641) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 639 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ASP cc_start: 0.6166 (m-30) cc_final: 0.5694 (t70) REVERT: B 219 TRP cc_start: 0.6206 (t-100) cc_final: 0.5852 (t60) REVERT: B 222 GLN cc_start: 0.7065 (tp40) cc_final: 0.6751 (tp40) REVERT: B 223 ARG cc_start: 0.7279 (mtt180) cc_final: 0.6953 (mtt-85) REVERT: B 315 TYR cc_start: 0.6057 (t80) cc_final: 0.5396 (t80) REVERT: B 316 MET cc_start: 0.7176 (mmm) cc_final: 0.6904 (mmm) REVERT: B 322 LYS cc_start: 0.6868 (mttm) cc_final: 0.6503 (tmmt) REVERT: H 7 LYS cc_start: 0.7832 (mttt) cc_final: 0.7552 (mptt) REVERT: H 14 GLN cc_start: 0.6559 (pm20) cc_final: 0.5898 (tt0) REVERT: H 31 ASP cc_start: 0.8071 (m-30) cc_final: 0.7829 (m-30) REVERT: H 51 ARG cc_start: 0.7721 (tpp80) cc_final: 0.7330 (tpp80) REVERT: H 60 GLN cc_start: 0.8071 (tt0) cc_final: 0.7751 (tt0) REVERT: H 71 ARG cc_start: 0.5774 (ttm-80) cc_final: 0.4947 (mtt180) REVERT: H 74 GLU cc_start: 0.5251 (tt0) cc_final: 0.4724 (tp30) REVERT: H 75 LYS cc_start: 0.5610 (mtpp) cc_final: 0.5041 (pttm) REVERT: H 125 MET cc_start: 0.7738 (tpp) cc_final: 0.7435 (tpp) REVERT: H 127 LYS cc_start: 0.7646 (mmtp) cc_final: 0.7250 (mmmt) REVERT: H 154 VAL cc_start: 0.7556 (p) cc_final: 0.7115 (p) REVERT: H 166 ILE cc_start: 0.6657 (mm) cc_final: 0.6403 (mt) REVERT: I 148 TRP cc_start: 0.7275 (m100) cc_final: 0.6195 (m100) REVERT: I 264 GLN cc_start: 0.7613 (pt0) cc_final: 0.6961 (tt0) REVERT: I 311 ASP cc_start: 0.6961 (t0) cc_final: 0.6563 (t0) REVERT: I 331 MET cc_start: 0.4962 (mmp) cc_final: 0.4165 (mtm) REVERT: I 438 LYS cc_start: 0.8093 (tttm) cc_final: 0.7871 (mmtm) REVERT: I 533 GLN cc_start: 0.8034 (pt0) cc_final: 0.7432 (tt0) REVERT: I 582 ASN cc_start: 0.6435 (m-40) cc_final: 0.5829 (m-40) REVERT: I 677 HIS cc_start: 0.5532 (m90) cc_final: 0.5014 (m170) REVERT: K 13 LYS cc_start: 0.8061 (mttt) cc_final: 0.7769 (tptp) REVERT: K 54 THR cc_start: 0.8246 (m) cc_final: 0.7968 (m) REVERT: K 56 LEU cc_start: 0.8490 (tp) cc_final: 0.8195 (tt) REVERT: K 94 ASN cc_start: 0.7341 (m-40) cc_final: 0.6938 (t0) REVERT: K 149 TRP cc_start: 0.5691 (m100) cc_final: 0.5423 (m100) REVERT: K 179 MET cc_start: 0.7303 (mmm) cc_final: 0.6850 (mmp) REVERT: K 183 LYS cc_start: 0.5806 (mptt) cc_final: 0.5118 (tppt) REVERT: L 215 LYS cc_start: 0.7877 (ptmm) cc_final: 0.7652 (ptpt) REVERT: N 25 MET cc_start: 0.7741 (mmm) cc_final: 0.7445 (mmm) REVERT: O 123 MET cc_start: 0.1781 (tpt) cc_final: 0.0536 (ptp) REVERT: O 124 PHE cc_start: 0.6335 (m-80) cc_final: 0.5886 (m-10) REVERT: O 360 ASN cc_start: 0.7756 (t0) cc_final: 0.6386 (p0) REVERT: O 361 HIS cc_start: 0.7432 (t70) cc_final: 0.7130 (t70) REVERT: P 136 LYS cc_start: 0.8636 (tttp) cc_final: 0.8414 (tttm) REVERT: Q 153 LYS cc_start: 0.6675 (mttt) cc_final: 0.6331 (pttp) REVERT: Q 200 TYR cc_start: 0.6478 (t80) cc_final: 0.6107 (t80) REVERT: Q 222 LYS cc_start: 0.4327 (OUTLIER) cc_final: 0.3958 (mtmm) REVERT: Q 380 ASP cc_start: 0.8649 (m-30) cc_final: 0.8295 (m-30) REVERT: T 288 GLU cc_start: 0.6931 (tt0) cc_final: 0.6521 (tt0) REVERT: T 291 ILE cc_start: 0.4658 (mm) cc_final: 0.4447 (mm) REVERT: T 316 ILE cc_start: 0.5882 (mp) cc_final: 0.5634 (pt) REVERT: T 338 ASP cc_start: 0.5412 (t0) cc_final: 0.4837 (m-30) REVERT: T 340 MET cc_start: 0.6350 (mmm) cc_final: 0.5626 (mmm) REVERT: U 176 ARG cc_start: 0.5424 (mmp80) cc_final: 0.5076 (mmp-170) REVERT: W 8 ASN cc_start: 0.6095 (m-40) cc_final: 0.5875 (m-40) REVERT: W 41 ASN cc_start: 0.6916 (m-40) cc_final: 0.6666 (m-40) REVERT: W 64 ARG cc_start: 0.6703 (mtt-85) cc_final: 0.6374 (mtt-85) REVERT: Y 60 ASP cc_start: 0.7278 (t70) cc_final: 0.6790 (t70) REVERT: Z 30 GLN cc_start: 0.4786 (mt0) cc_final: 0.4213 (mm-40) REVERT: Z 36 GLU cc_start: 0.6485 (tt0) cc_final: 0.5818 (mm-30) REVERT: Z 50 ASP cc_start: 0.4097 (p0) cc_final: 0.3665 (p0) REVERT: Z 77 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7247 (mt-10) REVERT: Z 81 LEU cc_start: 0.8214 (tt) cc_final: 0.7977 (pp) outliers start: 4 outliers final: 0 residues processed: 643 average time/residue: 0.1847 time to fit residues: 181.4432 Evaluate side-chains 381 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 380 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 222 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 GLN ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 ASN ** H 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 338 HIS K 30 GLN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 HIS N 73 ASN N 435 ASN O 231 ASN P 166 GLN Q 135 GLN Q 169 ASN ** T 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 165 GLN Y 59 GLN Y 106 GLN Y 170 GLN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.133969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.097209 restraints weight = 59695.961| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.26 r_work: 0.3230 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 29041 Z= 0.231 Angle : 0.660 10.320 39403 Z= 0.349 Chirality : 0.043 0.250 4530 Planarity : 0.005 0.061 4802 Dihedral : 13.627 79.765 4214 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.86 % Allowed : 8.44 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.15), residues: 3318 helix: 1.42 (0.11), residues: 2126 sheet: -0.85 (0.32), residues: 250 loop : -1.16 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 167 TYR 0.030 0.002 TYR Q 306 PHE 0.029 0.002 PHE T 341 TRP 0.012 0.002 TRP Q 128 HIS 0.008 0.001 HIS K 123 Details of bonding type rmsd covalent geometry : bond 0.00537 (29041) covalent geometry : angle 0.65974 (39403) hydrogen bonds : bond 0.04549 ( 1870) hydrogen bonds : angle 4.39389 ( 5641) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 375 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8072 (mt-10) REVERT: B 222 GLN cc_start: 0.7371 (tp-100) cc_final: 0.7088 (tp40) REVERT: H 7 LYS cc_start: 0.7746 (mttt) cc_final: 0.7442 (mptt) REVERT: H 14 GLN cc_start: 0.6960 (pm20) cc_final: 0.6476 (tm-30) REVERT: H 23 TYR cc_start: 0.8254 (t80) cc_final: 0.7780 (t80) REVERT: H 51 ARG cc_start: 0.7866 (tpp80) cc_final: 0.7405 (tpp80) REVERT: H 60 GLN cc_start: 0.8337 (tt0) cc_final: 0.8051 (tt0) REVERT: H 74 GLU cc_start: 0.5522 (tt0) cc_final: 0.4688 (tp30) REVERT: H 75 LYS cc_start: 0.5703 (mtpp) cc_final: 0.5287 (pttm) REVERT: H 97 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.6935 (p0) REVERT: H 127 LYS cc_start: 0.7392 (mmtp) cc_final: 0.7142 (mmmt) REVERT: I 264 GLN cc_start: 0.7766 (pt0) cc_final: 0.7293 (tt0) REVERT: I 311 ASP cc_start: 0.7754 (t0) cc_final: 0.7368 (t0) REVERT: I 533 GLN cc_start: 0.8114 (pt0) cc_final: 0.7641 (tt0) REVERT: I 578 VAL cc_start: 0.7473 (t) cc_final: 0.7201 (p) REVERT: I 582 ASN cc_start: 0.5984 (m-40) cc_final: 0.5616 (m-40) REVERT: I 586 MET cc_start: 0.7066 (ptm) cc_final: 0.6836 (ptp) REVERT: I 596 LYS cc_start: 0.7203 (ptpt) cc_final: 0.6923 (mmtm) REVERT: I 622 THR cc_start: 0.5507 (m) cc_final: 0.4997 (p) REVERT: I 629 LYS cc_start: 0.6102 (ttmt) cc_final: 0.5846 (ttmt) REVERT: I 641 TYR cc_start: 0.7217 (t80) cc_final: 0.6839 (t80) REVERT: K 125 MET cc_start: 0.5894 (OUTLIER) cc_final: 0.5691 (tpp) REVERT: K 183 LYS cc_start: 0.6160 (mptt) cc_final: 0.5507 (tppt) REVERT: O 123 MET cc_start: 0.2633 (tpt) cc_final: 0.0768 (ptp) REVERT: O 361 HIS cc_start: 0.7966 (t70) cc_final: 0.7732 (t-90) REVERT: Q 153 LYS cc_start: 0.6746 (mttt) cc_final: 0.6349 (pttp) REVERT: Q 188 MET cc_start: 0.6004 (OUTLIER) cc_final: 0.5321 (ptp) REVERT: Q 222 LYS cc_start: 0.3626 (OUTLIER) cc_final: 0.2782 (mtmm) REVERT: Q 259 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8464 (tp30) REVERT: Q 271 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7870 (tm-30) REVERT: T 277 ASP cc_start: 0.6964 (m-30) cc_final: 0.6754 (m-30) REVERT: T 290 ARG cc_start: 0.7685 (mtm180) cc_final: 0.7406 (mtp85) REVERT: T 309 MET cc_start: 0.7005 (ppp) cc_final: 0.6607 (ppp) REVERT: T 338 ASP cc_start: 0.5491 (t0) cc_final: 0.5054 (m-30) REVERT: T 340 MET cc_start: 0.6767 (mmm) cc_final: 0.5920 (mmm) REVERT: U 166 PHE cc_start: 0.4005 (t80) cc_final: 0.3732 (t80) REVERT: U 176 ARG cc_start: 0.5561 (mmp80) cc_final: 0.4120 (mmt-90) REVERT: Y 41 LEU cc_start: 0.6441 (mt) cc_final: 0.6162 (tt) REVERT: Z 30 GLN cc_start: 0.5342 (mt0) cc_final: 0.4670 (mm-40) REVERT: Z 77 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7358 (mt-10) outliers start: 57 outliers final: 29 residues processed: 412 average time/residue: 0.1821 time to fit residues: 117.6018 Evaluate side-chains 338 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 305 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain I residue 242 HIS Chi-restraints excluded: chain I residue 466 LEU Chi-restraints excluded: chain I residue 526 THR Chi-restraints excluded: chain I residue 579 ARG Chi-restraints excluded: chain I residue 610 PHE Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 126 THR Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 131 HIS Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain O residue 213 THR Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 198 GLU Chi-restraints excluded: chain Q residue 188 MET Chi-restraints excluded: chain Q residue 217 LYS Chi-restraints excluded: chain Q residue 222 LYS Chi-restraints excluded: chain Q residue 277 MET Chi-restraints excluded: chain T residue 305 SER Chi-restraints excluded: chain U residue 223 VAL Chi-restraints excluded: chain W residue 73 VAL Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 205 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 258 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 333 optimal weight: 8.9990 chunk 257 optimal weight: 4.9990 chunk 306 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 296 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 338 HIS ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 HIS P 230 GLN T 289 ASN ** U 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 196 ASN W 41 ASN Y 79 GLN Y 170 GLN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.134092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.098119 restraints weight = 59007.057| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.19 r_work: 0.3236 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29041 Z= 0.169 Angle : 0.570 13.068 39403 Z= 0.301 Chirality : 0.040 0.246 4530 Planarity : 0.004 0.052 4802 Dihedral : 13.423 74.879 4214 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.25 % Allowed : 11.87 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.16 (0.15), residues: 3318 helix: 1.79 (0.11), residues: 2127 sheet: -0.79 (0.32), residues: 244 loop : -1.15 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 39 TYR 0.024 0.002 TYR Q 306 PHE 0.024 0.002 PHE Q 325 TRP 0.013 0.001 TRP T 298 HIS 0.009 0.001 HIS K 123 Details of bonding type rmsd covalent geometry : bond 0.00386 (29041) covalent geometry : angle 0.57027 (39403) hydrogen bonds : bond 0.04199 ( 1870) hydrogen bonds : angle 4.17072 ( 5641) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 338 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 GLU cc_start: 0.8254 (mt-10) cc_final: 0.8053 (mt-10) REVERT: A 313 ILE cc_start: 0.8544 (mm) cc_final: 0.8319 (tt) REVERT: B 222 GLN cc_start: 0.7337 (tp-100) cc_final: 0.7056 (tp40) REVERT: B 315 TYR cc_start: 0.6125 (t80) cc_final: 0.5646 (t80) REVERT: H 7 LYS cc_start: 0.7873 (mttt) cc_final: 0.7528 (mptt) REVERT: H 14 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6581 (tm-30) REVERT: H 23 TYR cc_start: 0.8151 (t80) cc_final: 0.7796 (t80) REVERT: H 51 ARG cc_start: 0.7931 (tpp80) cc_final: 0.7430 (tpp80) REVERT: H 60 GLN cc_start: 0.8238 (tt0) cc_final: 0.7958 (tt0) REVERT: H 75 LYS cc_start: 0.5761 (mtpp) cc_final: 0.5149 (pttm) REVERT: H 97 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.6799 (p0) REVERT: H 98 TYR cc_start: 0.7188 (t80) cc_final: 0.6885 (t80) REVERT: H 166 ILE cc_start: 0.6939 (mm) cc_final: 0.6694 (mt) REVERT: I 264 GLN cc_start: 0.7785 (pt0) cc_final: 0.7362 (tt0) REVERT: I 311 ASP cc_start: 0.7763 (t0) cc_final: 0.7410 (t0) REVERT: I 331 MET cc_start: 0.5497 (mmp) cc_final: 0.4690 (mtm) REVERT: I 533 GLN cc_start: 0.8073 (pt0) cc_final: 0.7815 (mt0) REVERT: I 578 VAL cc_start: 0.7416 (t) cc_final: 0.7145 (p) REVERT: I 580 MET cc_start: 0.8078 (mtp) cc_final: 0.7736 (ttt) REVERT: I 582 ASN cc_start: 0.6404 (m-40) cc_final: 0.5972 (m-40) REVERT: I 586 MET cc_start: 0.7083 (ptm) cc_final: 0.6853 (ptp) REVERT: I 622 THR cc_start: 0.5541 (m) cc_final: 0.5025 (p) REVERT: K 53 PHE cc_start: 0.7423 (t80) cc_final: 0.7170 (t80) REVERT: K 125 MET cc_start: 0.5917 (OUTLIER) cc_final: 0.5566 (tmm) REVERT: K 183 LYS cc_start: 0.6170 (mptt) cc_final: 0.5496 (tppt) REVERT: N 5 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7239 (tt) REVERT: N 317 GLU cc_start: 0.7588 (tp30) cc_final: 0.6921 (mp0) REVERT: O 123 MET cc_start: 0.2637 (tpt) cc_final: 0.0839 (ptp) REVERT: P 136 LYS cc_start: 0.8704 (tttp) cc_final: 0.8459 (tttm) REVERT: P 253 LYS cc_start: 0.8667 (mmtm) cc_final: 0.8368 (mmtm) REVERT: Q 153 LYS cc_start: 0.6723 (mttt) cc_final: 0.6226 (pttp) REVERT: Q 222 LYS cc_start: 0.4309 (OUTLIER) cc_final: 0.3572 (mtmm) REVERT: Q 271 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7897 (tm-30) REVERT: T 277 ASP cc_start: 0.7014 (m-30) cc_final: 0.6763 (m-30) REVERT: T 290 ARG cc_start: 0.7666 (mtm180) cc_final: 0.7308 (mtp85) REVERT: T 309 MET cc_start: 0.7131 (ppp) cc_final: 0.6821 (ppp) REVERT: T 324 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.6183 (tp) REVERT: T 338 ASP cc_start: 0.5485 (t0) cc_final: 0.5069 (m-30) REVERT: T 340 MET cc_start: 0.6894 (mmm) cc_final: 0.6010 (mmm) REVERT: U 170 LEU cc_start: 0.5734 (OUTLIER) cc_final: 0.5466 (tt) REVERT: U 176 ARG cc_start: 0.5688 (mmp80) cc_final: 0.4268 (mmt-90) REVERT: U 228 GLN cc_start: 0.8405 (mm110) cc_final: 0.7969 (mt0) REVERT: Y 41 LEU cc_start: 0.6497 (mt) cc_final: 0.6016 (tt) REVERT: Z 30 GLN cc_start: 0.5371 (mt0) cc_final: 0.4698 (mm-40) outliers start: 69 outliers final: 39 residues processed: 386 average time/residue: 0.2128 time to fit residues: 128.3076 Evaluate side-chains 344 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 298 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 242 HIS Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 466 LEU Chi-restraints excluded: chain I residue 526 THR Chi-restraints excluded: chain I residue 579 ARG Chi-restraints excluded: chain I residue 610 PHE Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 126 THR Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 131 HIS Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 125 ASP Chi-restraints excluded: chain O residue 213 THR Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 198 GLU Chi-restraints excluded: chain Q residue 130 PHE Chi-restraints excluded: chain Q residue 217 LYS Chi-restraints excluded: chain Q residue 222 LYS Chi-restraints excluded: chain Q residue 277 MET Chi-restraints excluded: chain T residue 305 SER Chi-restraints excluded: chain T residue 324 LEU Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 223 VAL Chi-restraints excluded: chain W residue 73 VAL Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 205 LEU Chi-restraints excluded: chain Z residue 50 ASP Chi-restraints excluded: chain Z residue 81 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 173 optimal weight: 0.6980 chunk 312 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 212 optimal weight: 7.9990 chunk 323 optimal weight: 7.9990 chunk 309 optimal weight: 8.9990 chunk 243 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 305 optimal weight: 0.0040 chunk 13 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 HIS ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 467 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN K 123 HIS P 230 GLN T 289 ASN ** U 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 170 GLN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.135034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.099237 restraints weight = 58635.384| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.18 r_work: 0.3260 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29041 Z= 0.127 Angle : 0.527 12.327 39403 Z= 0.279 Chirality : 0.039 0.244 4530 Planarity : 0.003 0.051 4802 Dihedral : 13.213 72.690 4214 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.15 % Allowed : 13.37 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.47 (0.15), residues: 3318 helix: 2.05 (0.11), residues: 2124 sheet: -0.62 (0.32), residues: 244 loop : -1.10 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 23 TYR 0.041 0.001 TYR I 641 PHE 0.022 0.001 PHE Q 325 TRP 0.014 0.001 TRP T 298 HIS 0.010 0.001 HIS K 123 Details of bonding type rmsd covalent geometry : bond 0.00274 (29041) covalent geometry : angle 0.52739 (39403) hydrogen bonds : bond 0.03838 ( 1870) hydrogen bonds : angle 3.96609 ( 5641) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 342 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 ILE cc_start: 0.8552 (mm) cc_final: 0.8334 (tt) REVERT: B 222 GLN cc_start: 0.7484 (tp-100) cc_final: 0.7195 (tp40) REVERT: B 315 TYR cc_start: 0.6098 (t80) cc_final: 0.5612 (t80) REVERT: H 7 LYS cc_start: 0.7866 (mttt) cc_final: 0.7515 (mptt) REVERT: H 14 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6461 (tm-30) REVERT: H 23 TYR cc_start: 0.7916 (t80) cc_final: 0.7613 (t80) REVERT: H 51 ARG cc_start: 0.8060 (tpp80) cc_final: 0.7640 (tpp80) REVERT: H 60 GLN cc_start: 0.8220 (tt0) cc_final: 0.7940 (tt0) REVERT: H 75 LYS cc_start: 0.5582 (mtpp) cc_final: 0.4986 (pttm) REVERT: H 98 TYR cc_start: 0.7181 (t80) cc_final: 0.6957 (t80) REVERT: H 166 ILE cc_start: 0.7278 (mm) cc_final: 0.6983 (mt) REVERT: I 176 MET cc_start: 0.7035 (mtp) cc_final: 0.6753 (mmm) REVERT: I 264 GLN cc_start: 0.7679 (pt0) cc_final: 0.7245 (tt0) REVERT: I 311 ASP cc_start: 0.7742 (t0) cc_final: 0.7325 (t0) REVERT: I 578 VAL cc_start: 0.7421 (t) cc_final: 0.7152 (p) REVERT: I 582 ASN cc_start: 0.6283 (m-40) cc_final: 0.5843 (m-40) REVERT: I 586 MET cc_start: 0.7065 (ptm) cc_final: 0.6850 (ptp) REVERT: K 79 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7392 (mp) REVERT: K 90 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7435 (mm) REVERT: K 94 ASN cc_start: 0.7374 (m-40) cc_final: 0.7065 (t0) REVERT: K 183 LYS cc_start: 0.6221 (mptt) cc_final: 0.5708 (pptt) REVERT: K 231 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7598 (mt) REVERT: N 5 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7209 (tt) REVERT: N 317 GLU cc_start: 0.7595 (tp30) cc_final: 0.6878 (mp0) REVERT: O 123 MET cc_start: 0.2540 (tpt) cc_final: 0.0790 (ptm) REVERT: O 125 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.6262 (m-30) REVERT: P 136 LYS cc_start: 0.8740 (tttp) cc_final: 0.8470 (tttm) REVERT: P 253 LYS cc_start: 0.8608 (mmtm) cc_final: 0.8325 (mmtm) REVERT: Q 188 MET cc_start: 0.5517 (OUTLIER) cc_final: 0.4720 (tpt) REVERT: Q 222 LYS cc_start: 0.3983 (OUTLIER) cc_final: 0.3247 (mtmm) REVERT: Q 271 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7841 (tm-30) REVERT: T 290 ARG cc_start: 0.7680 (mtm180) cc_final: 0.7381 (mtp85) REVERT: T 309 MET cc_start: 0.7163 (ppp) cc_final: 0.6834 (ppp) REVERT: T 331 MET cc_start: 0.5877 (mmm) cc_final: 0.5632 (mtt) REVERT: T 338 ASP cc_start: 0.5439 (t0) cc_final: 0.5039 (m-30) REVERT: T 340 MET cc_start: 0.6902 (mmm) cc_final: 0.6059 (mmm) REVERT: U 167 ARG cc_start: 0.3029 (tpt170) cc_final: 0.1896 (mmt180) REVERT: U 178 PHE cc_start: 0.7610 (m-80) cc_final: 0.7104 (t80) REVERT: U 228 GLN cc_start: 0.8307 (mm110) cc_final: 0.7933 (mt0) REVERT: U 302 TYR cc_start: 0.8755 (m-80) cc_final: 0.8350 (m-80) REVERT: Y 3 ASP cc_start: 0.7466 (t0) cc_final: 0.7211 (m-30) REVERT: Y 45 GLN cc_start: 0.6347 (OUTLIER) cc_final: 0.5998 (mp10) REVERT: Z 30 GLN cc_start: 0.5361 (mt0) cc_final: 0.4711 (mm-40) REVERT: Z 46 LEU cc_start: 0.7323 (mt) cc_final: 0.6955 (mm) outliers start: 66 outliers final: 40 residues processed: 386 average time/residue: 0.2098 time to fit residues: 127.7021 Evaluate side-chains 352 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 303 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 242 HIS Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 466 LEU Chi-restraints excluded: chain I residue 526 THR Chi-restraints excluded: chain I residue 579 ARG Chi-restraints excluded: chain I residue 610 PHE Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain K residue 123 HIS Chi-restraints excluded: chain K residue 126 THR Chi-restraints excluded: chain K residue 231 ILE Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain O residue 125 ASP Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 278 VAL Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain Q residue 188 MET Chi-restraints excluded: chain Q residue 217 LYS Chi-restraints excluded: chain Q residue 222 LYS Chi-restraints excluded: chain Q residue 277 MET Chi-restraints excluded: chain Q residue 335 MET Chi-restraints excluded: chain T residue 305 SER Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 170 GLN Chi-restraints excluded: chain Y residue 205 LEU Chi-restraints excluded: chain Z residue 81 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 244 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 326 optimal weight: 6.9990 chunk 51 optimal weight: 0.0980 chunk 130 optimal weight: 7.9990 chunk 322 optimal weight: 10.0000 chunk 159 optimal weight: 0.8980 chunk 212 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 240 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 HIS I 338 HIS I 533 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 238 GLN O 231 ASN ** O 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 79 GLN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.130447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.093923 restraints weight = 58613.712| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.38 r_work: 0.3147 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 29041 Z= 0.293 Angle : 0.678 11.419 39403 Z= 0.354 Chirality : 0.045 0.234 4530 Planarity : 0.005 0.068 4802 Dihedral : 13.605 74.591 4214 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.06 % Allowed : 15.23 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.09 (0.15), residues: 3318 helix: 1.76 (0.11), residues: 2122 sheet: -0.93 (0.31), residues: 250 loop : -1.21 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 71 TYR 0.030 0.002 TYR Q 306 PHE 0.027 0.002 PHE T 341 TRP 0.012 0.002 TRP I 291 HIS 0.018 0.001 HIS K 123 Details of bonding type rmsd covalent geometry : bond 0.00692 (29041) covalent geometry : angle 0.67803 (39403) hydrogen bonds : bond 0.04607 ( 1870) hydrogen bonds : angle 4.26653 ( 5641) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 296 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8631 (tt) REVERT: B 222 GLN cc_start: 0.7343 (tp-100) cc_final: 0.7082 (tp40) REVERT: B 315 TYR cc_start: 0.6010 (t80) cc_final: 0.5624 (t80) REVERT: H 14 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6598 (tm-30) REVERT: H 60 GLN cc_start: 0.8223 (tt0) cc_final: 0.7995 (tt0) REVERT: H 75 LYS cc_start: 0.5601 (mtpp) cc_final: 0.5025 (pttm) REVERT: H 166 ILE cc_start: 0.7255 (mm) cc_final: 0.6947 (mt) REVERT: I 264 GLN cc_start: 0.7701 (pt0) cc_final: 0.7412 (tt0) REVERT: I 311 ASP cc_start: 0.7800 (t0) cc_final: 0.7573 (t70) REVERT: I 331 MET cc_start: 0.5307 (mmp) cc_final: 0.4678 (mtm) REVERT: I 445 MET cc_start: 0.7723 (mmp) cc_final: 0.7395 (mtp) REVERT: I 578 VAL cc_start: 0.7281 (t) cc_final: 0.7047 (p) REVERT: I 580 MET cc_start: 0.7907 (mtp) cc_final: 0.7580 (ttt) REVERT: I 582 ASN cc_start: 0.6202 (m-40) cc_final: 0.5743 (m110) REVERT: I 586 MET cc_start: 0.6999 (ptm) cc_final: 0.6770 (ptp) REVERT: I 698 VAL cc_start: 0.5342 (t) cc_final: 0.5065 (m) REVERT: K 90 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7849 (mm) REVERT: K 100 GLN cc_start: 0.7600 (mt0) cc_final: 0.7223 (mt0) REVERT: K 125 MET cc_start: 0.5983 (OUTLIER) cc_final: 0.5781 (tmm) REVERT: K 183 LYS cc_start: 0.6279 (mptt) cc_final: 0.5629 (tptm) REVERT: N 5 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7343 (tt) REVERT: O 123 MET cc_start: 0.2611 (tpt) cc_final: 0.0967 (ptm) REVERT: Q 223 PHE cc_start: 0.5237 (m-80) cc_final: 0.4923 (m-80) REVERT: Q 271 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7630 (tm-30) REVERT: Q 276 CYS cc_start: 0.8697 (t) cc_final: 0.8359 (m) REVERT: Q 374 MET cc_start: 0.8960 (mtt) cc_final: 0.8756 (mtt) REVERT: T 301 ILE cc_start: 0.7646 (pt) cc_final: 0.7431 (tp) REVERT: T 309 MET cc_start: 0.7205 (ppp) cc_final: 0.6807 (ppp) REVERT: U 167 ARG cc_start: 0.2672 (tpt170) cc_final: 0.2298 (mmt180) REVERT: U 171 TYR cc_start: 0.5828 (m-10) cc_final: 0.5454 (m-10) REVERT: U 178 PHE cc_start: 0.7744 (m-80) cc_final: 0.7150 (t80) REVERT: Y 19 LEU cc_start: 0.6763 (tt) cc_final: 0.6545 (tp) REVERT: Y 45 GLN cc_start: 0.6468 (OUTLIER) cc_final: 0.5848 (mp10) outliers start: 94 outliers final: 60 residues processed: 368 average time/residue: 0.1946 time to fit residues: 115.8565 Evaluate side-chains 339 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 273 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 242 HIS Chi-restraints excluded: chain I residue 255 ILE Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 466 LEU Chi-restraints excluded: chain I residue 526 THR Chi-restraints excluded: chain I residue 579 ARG Chi-restraints excluded: chain I residue 610 PHE Chi-restraints excluded: chain I residue 665 ILE Chi-restraints excluded: chain I residue 687 ILE Chi-restraints excluded: chain I residue 714 ILE Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain K residue 231 ILE Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 131 HIS Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 10 ASN Chi-restraints excluded: chain N residue 195 ILE Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 125 ASP Chi-restraints excluded: chain O residue 159 GLU Chi-restraints excluded: chain O residue 213 THR Chi-restraints excluded: chain O residue 258 VAL Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 278 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 301 ILE Chi-restraints excluded: chain Q residue 217 LYS Chi-restraints excluded: chain Q residue 222 LYS Chi-restraints excluded: chain Q residue 277 MET Chi-restraints excluded: chain T residue 291 ILE Chi-restraints excluded: chain T residue 305 SER Chi-restraints excluded: chain U residue 223 VAL Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 205 LEU Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 81 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 40 optimal weight: 0.9990 chunk 262 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 325 optimal weight: 9.9990 chunk 187 optimal weight: 0.7980 chunk 287 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 166 optimal weight: 0.7980 chunk 68 optimal weight: 0.2980 chunk 18 optimal weight: 4.9990 chunk 204 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: ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 338 HIS I 500 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 HIS N 165 ASN N 284 HIS P 200 GLN Q 150 HIS ** Q 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 79 GLN Y 170 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.134076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.098715 restraints weight = 57689.588| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.21 r_work: 0.3248 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29041 Z= 0.119 Angle : 0.532 11.381 39403 Z= 0.281 Chirality : 0.039 0.227 4530 Planarity : 0.004 0.072 4802 Dihedral : 13.229 71.336 4214 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.04 % Favored : 96.93 % Rotamer: Outliers : 1.83 % Allowed : 16.89 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.58 (0.15), residues: 3318 helix: 2.14 (0.11), residues: 2129 sheet: -0.62 (0.32), residues: 242 loop : -1.08 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 71 TYR 0.026 0.002 TYR T 359 PHE 0.023 0.001 PHE Q 325 TRP 0.015 0.001 TRP L 102 HIS 0.008 0.001 HIS K 123 Details of bonding type rmsd covalent geometry : bond 0.00251 (29041) covalent geometry : angle 0.53192 (39403) hydrogen bonds : bond 0.03850 ( 1870) hydrogen bonds : angle 3.94939 ( 5641) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 313 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 222 GLN cc_start: 0.7465 (tp-100) cc_final: 0.7188 (tp40) REVERT: B 315 TYR cc_start: 0.5844 (t80) cc_final: 0.5567 (t80) REVERT: H 14 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6319 (tm-30) REVERT: H 60 GLN cc_start: 0.8163 (tt0) cc_final: 0.7938 (tt0) REVERT: H 75 LYS cc_start: 0.5477 (mtpp) cc_final: 0.4964 (pttm) REVERT: H 166 ILE cc_start: 0.7091 (mm) cc_final: 0.6825 (mt) REVERT: H 175 THR cc_start: 0.7148 (p) cc_final: 0.6860 (p) REVERT: I 176 MET cc_start: 0.7073 (mtp) cc_final: 0.6841 (mmm) REVERT: I 264 GLN cc_start: 0.7709 (pt0) cc_final: 0.7326 (tt0) REVERT: I 311 ASP cc_start: 0.7835 (t0) cc_final: 0.7460 (t0) REVERT: I 331 MET cc_start: 0.5527 (mmp) cc_final: 0.4690 (mtm) REVERT: I 578 VAL cc_start: 0.7216 (t) cc_final: 0.6981 (p) REVERT: I 580 MET cc_start: 0.8019 (mtp) cc_final: 0.7659 (ttt) REVERT: I 582 ASN cc_start: 0.6236 (m-40) cc_final: 0.5758 (m110) REVERT: I 586 MET cc_start: 0.6975 (ptm) cc_final: 0.6772 (ptp) REVERT: K 90 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7725 (mm) REVERT: K 94 ASN cc_start: 0.7582 (m-40) cc_final: 0.7350 (t0) REVERT: K 125 MET cc_start: 0.6044 (OUTLIER) cc_final: 0.5763 (tmm) REVERT: K 183 LYS cc_start: 0.6367 (mptt) cc_final: 0.5546 (tttp) REVERT: K 231 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7269 (mt) REVERT: N 5 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7217 (tt) REVERT: N 317 GLU cc_start: 0.7534 (tp30) cc_final: 0.6857 (mp0) REVERT: O 123 MET cc_start: 0.2765 (tpt) cc_final: 0.0964 (ptm) REVERT: O 125 ASP cc_start: 0.6836 (OUTLIER) cc_final: 0.6516 (m-30) REVERT: P 136 LYS cc_start: 0.8670 (tttp) cc_final: 0.8464 (tttm) REVERT: P 253 LYS cc_start: 0.8629 (mmtm) cc_final: 0.8326 (mmtm) REVERT: Q 222 LYS cc_start: 0.4088 (OUTLIER) cc_final: 0.3461 (mtmm) REVERT: Q 223 PHE cc_start: 0.5150 (m-80) cc_final: 0.4930 (m-80) REVERT: Q 271 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7786 (tm-30) REVERT: Q 387 LYS cc_start: 0.7885 (ttmt) cc_final: 0.7241 (tppt) REVERT: T 276 MET cc_start: 0.7315 (ptt) cc_final: 0.7098 (ptp) REVERT: T 290 ARG cc_start: 0.7791 (mtm180) cc_final: 0.7492 (mtp85) REVERT: T 291 ILE cc_start: 0.6167 (OUTLIER) cc_final: 0.5916 (mm) REVERT: T 309 MET cc_start: 0.7298 (ppp) cc_final: 0.6884 (ppp) REVERT: T 338 ASP cc_start: 0.5266 (t0) cc_final: 0.4908 (m-30) REVERT: U 167 ARG cc_start: 0.3029 (tpt170) cc_final: 0.2547 (mmt180) REVERT: U 171 TYR cc_start: 0.5730 (m-10) cc_final: 0.5471 (m-10) REVERT: U 176 ARG cc_start: 0.5720 (mmp-170) cc_final: 0.5266 (tpp-160) REVERT: U 178 PHE cc_start: 0.7702 (m-80) cc_final: 0.7145 (t80) REVERT: U 228 GLN cc_start: 0.8285 (mm110) cc_final: 0.7824 (mt0) REVERT: W 1 MET cc_start: 0.4073 (tmm) cc_final: 0.2808 (ttm) REVERT: Y 3 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7155 (m-30) REVERT: Y 41 LEU cc_start: 0.6243 (mt) cc_final: 0.5587 (tt) REVERT: Y 79 GLN cc_start: 0.7608 (mt0) cc_final: 0.7405 (mt0) REVERT: Z 15 LEU cc_start: 0.6207 (mt) cc_final: 0.5795 (tp) outliers start: 56 outliers final: 31 residues processed: 352 average time/residue: 0.1851 time to fit residues: 105.6778 Evaluate side-chains 325 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 285 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 242 HIS Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 466 LEU Chi-restraints excluded: chain I residue 610 PHE Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain K residue 123 HIS Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain K residue 231 ILE Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 195 ILE Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 125 ASP Chi-restraints excluded: chain O residue 278 VAL Chi-restraints excluded: chain O residue 305 MET Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain Q residue 222 LYS Chi-restraints excluded: chain T residue 291 ILE Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain Y residue 3 ASP Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 170 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 147 optimal weight: 0.9980 chunk 196 optimal weight: 5.9990 chunk 194 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 81 optimal weight: 0.1980 chunk 174 optimal weight: 0.0870 chunk 84 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 312 optimal weight: 1.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 338 HIS ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 HIS ** U 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.134745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.098387 restraints weight = 58718.675| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.45 r_work: 0.3224 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29041 Z= 0.117 Angle : 0.527 11.054 39403 Z= 0.276 Chirality : 0.039 0.224 4530 Planarity : 0.003 0.072 4802 Dihedral : 13.135 70.705 4214 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.79 % Allowed : 17.77 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.73 (0.15), residues: 3318 helix: 2.24 (0.11), residues: 2132 sheet: -0.48 (0.32), residues: 242 loop : -1.01 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 71 TYR 0.023 0.001 TYR T 359 PHE 0.020 0.001 PHE Q 325 TRP 0.012 0.001 TRP L 102 HIS 0.021 0.001 HIS K 123 Details of bonding type rmsd covalent geometry : bond 0.00251 (29041) covalent geometry : angle 0.52717 (39403) hydrogen bonds : bond 0.03752 ( 1870) hydrogen bonds : angle 3.86471 ( 5641) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 299 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8755 (tt) REVERT: B 222 GLN cc_start: 0.7336 (tp-100) cc_final: 0.7060 (tp40) REVERT: B 315 TYR cc_start: 0.5776 (t80) cc_final: 0.5503 (t80) REVERT: H 14 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.6302 (tm-30) REVERT: H 60 GLN cc_start: 0.8127 (tt0) cc_final: 0.7844 (tt0) REVERT: H 75 LYS cc_start: 0.5439 (mtpp) cc_final: 0.4924 (pttm) REVERT: H 166 ILE cc_start: 0.7021 (mm) cc_final: 0.6770 (mt) REVERT: H 175 THR cc_start: 0.6968 (p) cc_final: 0.6718 (p) REVERT: I 264 GLN cc_start: 0.7588 (pt0) cc_final: 0.7190 (tt0) REVERT: I 311 ASP cc_start: 0.7690 (t0) cc_final: 0.7287 (t0) REVERT: I 331 MET cc_start: 0.5346 (mmp) cc_final: 0.4824 (mtm) REVERT: I 578 VAL cc_start: 0.7250 (t) cc_final: 0.7015 (p) REVERT: I 580 MET cc_start: 0.8062 (mtp) cc_final: 0.7682 (ttt) REVERT: I 582 ASN cc_start: 0.6136 (m-40) cc_final: 0.5659 (m110) REVERT: I 586 MET cc_start: 0.6946 (ptm) cc_final: 0.6726 (ptp) REVERT: I 641 TYR cc_start: 0.7196 (t80) cc_final: 0.6933 (t80) REVERT: K 90 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7581 (mm) REVERT: K 183 LYS cc_start: 0.6224 (mptt) cc_final: 0.5672 (pptt) REVERT: K 231 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7241 (mt) REVERT: N 5 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7138 (tt) REVERT: N 317 GLU cc_start: 0.7453 (tp30) cc_final: 0.6873 (mp0) REVERT: O 123 MET cc_start: 0.2601 (tpt) cc_final: 0.0938 (ptm) REVERT: O 125 ASP cc_start: 0.6791 (OUTLIER) cc_final: 0.6484 (m-30) REVERT: P 136 LYS cc_start: 0.8614 (tttp) cc_final: 0.8344 (tttm) REVERT: P 253 LYS cc_start: 0.8524 (mmtm) cc_final: 0.8249 (mmtm) REVERT: Q 222 LYS cc_start: 0.4279 (OUTLIER) cc_final: 0.3747 (mtmm) REVERT: Q 223 PHE cc_start: 0.5228 (m-80) cc_final: 0.4963 (m-80) REVERT: Q 271 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7544 (tm-30) REVERT: Q 387 LYS cc_start: 0.7683 (ttmt) cc_final: 0.7179 (tppt) REVERT: T 276 MET cc_start: 0.7291 (ptt) cc_final: 0.7058 (ptp) REVERT: T 290 ARG cc_start: 0.7741 (mtm180) cc_final: 0.7461 (mtp85) REVERT: T 309 MET cc_start: 0.7348 (ppp) cc_final: 0.6918 (ppp) REVERT: U 167 ARG cc_start: 0.2962 (tpt170) cc_final: 0.2564 (mmt180) REVERT: U 171 TYR cc_start: 0.5711 (m-10) cc_final: 0.5451 (m-10) REVERT: U 178 PHE cc_start: 0.7690 (m-80) cc_final: 0.7209 (t80) REVERT: U 228 GLN cc_start: 0.8143 (mm110) cc_final: 0.7830 (mt0) REVERT: Y 3 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6930 (m-30) REVERT: Y 45 GLN cc_start: 0.6141 (OUTLIER) cc_final: 0.5514 (mp10) REVERT: Z 15 LEU cc_start: 0.6087 (mt) cc_final: 0.5709 (tp) outliers start: 55 outliers final: 37 residues processed: 336 average time/residue: 0.1925 time to fit residues: 104.3638 Evaluate side-chains 335 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 289 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 242 HIS Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 466 LEU Chi-restraints excluded: chain I residue 579 ARG Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain K residue 123 HIS Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain K residue 231 ILE Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 195 ILE Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 125 ASP Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 278 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 355 LEU Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 301 ILE Chi-restraints excluded: chain Q residue 222 LYS Chi-restraints excluded: chain T residue 291 ILE Chi-restraints excluded: chain T residue 305 SER Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain Y residue 3 ASP Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Z residue 81 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 172 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 297 optimal weight: 0.6980 chunk 227 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 chunk 243 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 chunk 335 optimal weight: 7.9990 chunk 334 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 338 HIS ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 HIS O 295 HIS ** U 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 170 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.133521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.098806 restraints weight = 58705.335| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.31 r_work: 0.3230 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 29041 Z= 0.156 Angle : 0.553 10.739 39403 Z= 0.289 Chirality : 0.040 0.227 4530 Planarity : 0.004 0.066 4802 Dihedral : 13.175 70.945 4214 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.38 % Allowed : 17.22 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.71 (0.15), residues: 3318 helix: 2.23 (0.11), residues: 2128 sheet: -0.49 (0.32), residues: 242 loop : -1.01 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 71 TYR 0.023 0.002 TYR K 205 PHE 0.024 0.002 PHE K 53 TRP 0.013 0.001 TRP T 298 HIS 0.021 0.001 HIS K 123 Details of bonding type rmsd covalent geometry : bond 0.00357 (29041) covalent geometry : angle 0.55297 (39403) hydrogen bonds : bond 0.03852 ( 1870) hydrogen bonds : angle 3.90004 ( 5641) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 291 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8807 (tt) REVERT: B 222 GLN cc_start: 0.7411 (tp-100) cc_final: 0.7098 (tp40) REVERT: B 315 TYR cc_start: 0.5755 (t80) cc_final: 0.5473 (t80) REVERT: H 14 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6260 (tm-30) REVERT: H 23 TYR cc_start: 0.8478 (t80) cc_final: 0.7831 (t80) REVERT: H 60 GLN cc_start: 0.8125 (tt0) cc_final: 0.7855 (tt0) REVERT: H 75 LYS cc_start: 0.5443 (mtpp) cc_final: 0.4892 (pttm) REVERT: H 166 ILE cc_start: 0.7258 (mm) cc_final: 0.6956 (mt) REVERT: I 235 LYS cc_start: 0.6810 (OUTLIER) cc_final: 0.6598 (tppt) REVERT: I 264 GLN cc_start: 0.7572 (pt0) cc_final: 0.7246 (tt0) REVERT: I 311 ASP cc_start: 0.7852 (t0) cc_final: 0.7464 (t0) REVERT: I 331 MET cc_start: 0.5506 (mmp) cc_final: 0.4708 (mtm) REVERT: I 578 VAL cc_start: 0.7283 (t) cc_final: 0.7057 (p) REVERT: I 582 ASN cc_start: 0.6264 (m-40) cc_final: 0.5787 (m110) REVERT: I 586 MET cc_start: 0.6974 (ptm) cc_final: 0.6760 (ptp) REVERT: I 641 TYR cc_start: 0.7427 (t80) cc_final: 0.7110 (t80) REVERT: K 79 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7306 (mp) REVERT: K 90 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7656 (mm) REVERT: K 125 MET cc_start: 0.6205 (OUTLIER) cc_final: 0.5930 (tmm) REVERT: K 183 LYS cc_start: 0.6230 (mptt) cc_final: 0.5452 (tttp) REVERT: L 101 GLN cc_start: 0.6242 (OUTLIER) cc_final: 0.5444 (mm-40) REVERT: N 5 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7377 (tt) REVERT: N 317 GLU cc_start: 0.7612 (tp30) cc_final: 0.6871 (mp0) REVERT: O 123 MET cc_start: 0.2423 (tpt) cc_final: 0.0729 (ptm) REVERT: O 125 ASP cc_start: 0.6625 (OUTLIER) cc_final: 0.6378 (m-30) REVERT: P 136 LYS cc_start: 0.8694 (tttp) cc_final: 0.8405 (tttm) REVERT: P 253 LYS cc_start: 0.8660 (mmtm) cc_final: 0.8383 (mmtm) REVERT: Q 222 LYS cc_start: 0.4192 (OUTLIER) cc_final: 0.3495 (mtmm) REVERT: Q 223 PHE cc_start: 0.5286 (m-80) cc_final: 0.5007 (m-80) REVERT: Q 271 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7803 (tm-30) REVERT: Q 387 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7189 (tptt) REVERT: T 309 MET cc_start: 0.7338 (ppp) cc_final: 0.6875 (ppp) REVERT: T 331 MET cc_start: 0.6662 (OUTLIER) cc_final: 0.6130 (mtt) REVERT: U 167 ARG cc_start: 0.2976 (tpt170) cc_final: 0.2553 (mmt180) REVERT: U 171 TYR cc_start: 0.5697 (m-10) cc_final: 0.5446 (m-10) REVERT: U 176 ARG cc_start: 0.5960 (tpp-160) cc_final: 0.5396 (tpp-160) REVERT: U 178 PHE cc_start: 0.7713 (m-80) cc_final: 0.7217 (t80) REVERT: U 228 GLN cc_start: 0.8398 (mm110) cc_final: 0.7907 (mt0) REVERT: W 1 MET cc_start: 0.3969 (tmm) cc_final: 0.2729 (ttm) REVERT: Y 3 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7150 (m-30) REVERT: Y 45 GLN cc_start: 0.6323 (OUTLIER) cc_final: 0.5666 (mp10) REVERT: Y 79 GLN cc_start: 0.7081 (mt0) cc_final: 0.6579 (mt0) outliers start: 73 outliers final: 47 residues processed: 344 average time/residue: 0.1891 time to fit residues: 105.5193 Evaluate side-chains 342 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 282 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 235 LYS Chi-restraints excluded: chain I residue 242 HIS Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 308 ILE Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 466 LEU Chi-restraints excluded: chain I residue 579 ARG Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain K residue 123 HIS Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain K residue 231 ILE Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 10 ASN Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 195 ILE Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 125 ASP Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 278 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 355 LEU Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 301 ILE Chi-restraints excluded: chain Q residue 222 LYS Chi-restraints excluded: chain T residue 291 ILE Chi-restraints excluded: chain T residue 305 SER Chi-restraints excluded: chain T residue 331 MET Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain Y residue 3 ASP Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 141 SER Chi-restraints excluded: chain Y residue 205 LEU Chi-restraints excluded: chain Z residue 81 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 214 optimal weight: 0.5980 chunk 200 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 221 optimal weight: 4.9990 chunk 266 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 318 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 338 HIS I 683 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 435 ASN ** Q 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 170 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.132110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.096618 restraints weight = 58756.382| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.22 r_work: 0.3211 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 29041 Z= 0.202 Angle : 0.590 10.463 39403 Z= 0.308 Chirality : 0.041 0.230 4530 Planarity : 0.004 0.067 4802 Dihedral : 13.287 72.035 4214 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.41 % Allowed : 17.31 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.59 (0.15), residues: 3318 helix: 2.13 (0.11), residues: 2128 sheet: -0.60 (0.32), residues: 243 loop : -1.02 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 71 TYR 0.024 0.002 TYR K 205 PHE 0.023 0.002 PHE Q 325 TRP 0.018 0.001 TRP I 136 HIS 0.039 0.001 HIS K 123 Details of bonding type rmsd covalent geometry : bond 0.00473 (29041) covalent geometry : angle 0.59024 (39403) hydrogen bonds : bond 0.04064 ( 1870) hydrogen bonds : angle 3.98551 ( 5641) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 286 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8757 (tt) REVERT: B 222 GLN cc_start: 0.7363 (tp-100) cc_final: 0.7034 (tp40) REVERT: B 315 TYR cc_start: 0.5987 (t80) cc_final: 0.5691 (t80) REVERT: H 14 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.6407 (tm-30) REVERT: H 23 TYR cc_start: 0.8429 (t80) cc_final: 0.7804 (t80) REVERT: H 60 GLN cc_start: 0.8148 (tt0) cc_final: 0.7896 (tt0) REVERT: H 75 LYS cc_start: 0.5436 (mtpp) cc_final: 0.4887 (pttm) REVERT: H 166 ILE cc_start: 0.7264 (mm) cc_final: 0.6984 (mt) REVERT: I 176 MET cc_start: 0.7113 (mtp) cc_final: 0.6827 (mmm) REVERT: I 235 LYS cc_start: 0.6829 (OUTLIER) cc_final: 0.6612 (tppt) REVERT: I 264 GLN cc_start: 0.7562 (pt0) cc_final: 0.7251 (tt0) REVERT: I 311 ASP cc_start: 0.7955 (t0) cc_final: 0.7713 (t0) REVERT: I 331 MET cc_start: 0.5361 (mmp) cc_final: 0.4778 (mtm) REVERT: I 578 VAL cc_start: 0.7221 (t) cc_final: 0.6993 (p) REVERT: I 580 MET cc_start: 0.7901 (mtp) cc_final: 0.7682 (ttt) REVERT: I 582 ASN cc_start: 0.6339 (m-40) cc_final: 0.5855 (m110) REVERT: I 586 MET cc_start: 0.6960 (ptm) cc_final: 0.6744 (ptp) REVERT: I 641 TYR cc_start: 0.7455 (t80) cc_final: 0.7210 (t80) REVERT: K 79 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7454 (mp) REVERT: K 90 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7806 (mm) REVERT: K 179 MET cc_start: 0.7401 (mmm) cc_final: 0.7123 (mmm) REVERT: K 183 LYS cc_start: 0.6221 (mptt) cc_final: 0.5554 (tptm) REVERT: L 101 GLN cc_start: 0.6263 (OUTLIER) cc_final: 0.5434 (mm-40) REVERT: N 5 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7426 (tt) REVERT: N 317 GLU cc_start: 0.7583 (tp30) cc_final: 0.6858 (mp0) REVERT: N 435 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8671 (p0) REVERT: O 123 MET cc_start: 0.2605 (tpt) cc_final: 0.2351 (tpt) REVERT: O 125 ASP cc_start: 0.6709 (OUTLIER) cc_final: 0.6377 (m-30) REVERT: P 136 LYS cc_start: 0.8690 (tttp) cc_final: 0.8450 (tttm) REVERT: P 253 LYS cc_start: 0.8685 (mmtm) cc_final: 0.8391 (mmtm) REVERT: Q 188 MET cc_start: 0.5656 (ttp) cc_final: 0.5343 (ptp) REVERT: Q 222 LYS cc_start: 0.4062 (OUTLIER) cc_final: 0.3409 (mtmm) REVERT: Q 271 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7805 (tm-30) REVERT: Q 387 LYS cc_start: 0.7897 (ttmt) cc_final: 0.7197 (tptt) REVERT: T 309 MET cc_start: 0.7365 (ppp) cc_final: 0.6969 (ppp) REVERT: U 167 ARG cc_start: 0.3014 (tpt170) cc_final: 0.2539 (mmt180) REVERT: U 171 TYR cc_start: 0.5755 (m-10) cc_final: 0.5525 (m-10) REVERT: U 176 ARG cc_start: 0.6076 (tpp-160) cc_final: 0.5489 (tpp-160) REVERT: U 178 PHE cc_start: 0.7727 (m-80) cc_final: 0.7195 (t80) REVERT: U 228 GLN cc_start: 0.8413 (mm110) cc_final: 0.7920 (mt0) REVERT: W 1 MET cc_start: 0.4051 (tmm) cc_final: 0.2805 (ttm) REVERT: Y 3 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7118 (m-30) REVERT: Y 45 GLN cc_start: 0.6354 (OUTLIER) cc_final: 0.5765 (mp10) outliers start: 74 outliers final: 49 residues processed: 345 average time/residue: 0.1966 time to fit residues: 108.6803 Evaluate side-chains 344 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 283 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 235 LYS Chi-restraints excluded: chain I residue 242 HIS Chi-restraints excluded: chain I residue 308 ILE Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 466 LEU Chi-restraints excluded: chain I residue 526 THR Chi-restraints excluded: chain I residue 579 ARG Chi-restraints excluded: chain I residue 665 ILE Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain K residue 231 ILE Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 10 ASN Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 195 ILE Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain N residue 435 ASN Chi-restraints excluded: chain O residue 125 ASP Chi-restraints excluded: chain O residue 188 ILE Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 278 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 355 LEU Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 301 ILE Chi-restraints excluded: chain Q residue 222 LYS Chi-restraints excluded: chain T residue 291 ILE Chi-restraints excluded: chain T residue 305 SER Chi-restraints excluded: chain U residue 278 SER Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain Y residue 3 ASP Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 141 SER Chi-restraints excluded: chain Y residue 205 LEU Chi-restraints excluded: chain Z residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 140 optimal weight: 6.9990 chunk 205 optimal weight: 2.9990 chunk 251 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 97 optimal weight: 0.0020 chunk 98 optimal weight: 0.9990 chunk 266 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 176 optimal weight: 0.9980 chunk 190 optimal weight: 20.0000 chunk 172 optimal weight: 3.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 338 HIS ** I 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 HIS L 238 GLN N 435 ASN ** Q 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 170 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.132203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.096383 restraints weight = 58579.570| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.16 r_work: 0.3218 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.178 29041 Z= 0.207 Angle : 0.706 59.186 39403 Z= 0.390 Chirality : 0.041 0.428 4530 Planarity : 0.004 0.069 4802 Dihedral : 13.289 72.073 4214 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.31 % Allowed : 17.70 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.59 (0.15), residues: 3318 helix: 2.14 (0.11), residues: 2128 sheet: -0.62 (0.32), residues: 243 loop : -1.03 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 197 TYR 0.044 0.002 TYR L 148 PHE 0.024 0.002 PHE Q 325 TRP 0.015 0.001 TRP I 136 HIS 0.029 0.001 HIS K 123 Details of bonding type rmsd covalent geometry : bond 0.00486 (29041) covalent geometry : angle 0.70641 (39403) hydrogen bonds : bond 0.04045 ( 1870) hydrogen bonds : angle 3.98455 ( 5641) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 282 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8759 (tt) REVERT: B 222 GLN cc_start: 0.7349 (tp-100) cc_final: 0.7019 (tp40) REVERT: B 315 TYR cc_start: 0.5984 (t80) cc_final: 0.5689 (t80) REVERT: H 14 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.6402 (tm-30) REVERT: H 23 TYR cc_start: 0.8420 (t80) cc_final: 0.7812 (t80) REVERT: H 60 GLN cc_start: 0.8172 (tt0) cc_final: 0.7911 (tt0) REVERT: H 75 LYS cc_start: 0.5432 (mtpp) cc_final: 0.4883 (pttm) REVERT: H 166 ILE cc_start: 0.7267 (mm) cc_final: 0.6991 (mt) REVERT: I 176 MET cc_start: 0.7110 (mtp) cc_final: 0.6829 (mmm) REVERT: I 235 LYS cc_start: 0.6827 (OUTLIER) cc_final: 0.6610 (tppt) REVERT: I 264 GLN cc_start: 0.7574 (pt0) cc_final: 0.7261 (tt0) REVERT: I 311 ASP cc_start: 0.7929 (t0) cc_final: 0.7691 (t0) REVERT: I 331 MET cc_start: 0.5358 (mmp) cc_final: 0.4775 (mtm) REVERT: I 578 VAL cc_start: 0.7212 (t) cc_final: 0.6981 (p) REVERT: I 582 ASN cc_start: 0.6337 (m-40) cc_final: 0.5852 (m110) REVERT: I 586 MET cc_start: 0.6957 (ptm) cc_final: 0.6741 (ptp) REVERT: I 641 TYR cc_start: 0.7508 (t80) cc_final: 0.7276 (t80) REVERT: K 79 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7446 (mp) REVERT: K 90 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7822 (mm) REVERT: K 183 LYS cc_start: 0.6217 (mptt) cc_final: 0.5568 (tptm) REVERT: L 101 GLN cc_start: 0.6242 (OUTLIER) cc_final: 0.5409 (mm-40) REVERT: N 5 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7416 (tt) REVERT: N 317 GLU cc_start: 0.7586 (tp30) cc_final: 0.6858 (mp0) REVERT: O 123 MET cc_start: 0.2774 (tpt) cc_final: 0.2527 (tpt) REVERT: O 125 ASP cc_start: 0.6716 (OUTLIER) cc_final: 0.6381 (m-30) REVERT: P 136 LYS cc_start: 0.8692 (tttp) cc_final: 0.8454 (tttm) REVERT: P 253 LYS cc_start: 0.8677 (mmtm) cc_final: 0.8381 (mmtm) REVERT: Q 188 MET cc_start: 0.5629 (ttp) cc_final: 0.5338 (ptp) REVERT: Q 222 LYS cc_start: 0.4057 (OUTLIER) cc_final: 0.3405 (mtmm) REVERT: Q 271 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7776 (tm-30) REVERT: Q 387 LYS cc_start: 0.7878 (ttmt) cc_final: 0.7188 (tptt) REVERT: T 309 MET cc_start: 0.7363 (ppp) cc_final: 0.6971 (ppp) REVERT: U 167 ARG cc_start: 0.2990 (tpt170) cc_final: 0.2538 (mmt180) REVERT: U 171 TYR cc_start: 0.5747 (m-10) cc_final: 0.5523 (m-10) REVERT: U 176 ARG cc_start: 0.6078 (tpp-160) cc_final: 0.5493 (tpp-160) REVERT: U 178 PHE cc_start: 0.7728 (m-80) cc_final: 0.7190 (t80) REVERT: U 228 GLN cc_start: 0.8378 (mm110) cc_final: 0.7890 (mt0) REVERT: W 1 MET cc_start: 0.4044 (tmm) cc_final: 0.2804 (ttm) REVERT: Y 3 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7111 (m-30) REVERT: Y 45 GLN cc_start: 0.6346 (OUTLIER) cc_final: 0.5756 (mp10) outliers start: 71 outliers final: 53 residues processed: 340 average time/residue: 0.1792 time to fit residues: 98.2107 Evaluate side-chains 345 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 281 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 235 LYS Chi-restraints excluded: chain I residue 242 HIS Chi-restraints excluded: chain I residue 308 ILE Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 466 LEU Chi-restraints excluded: chain I residue 526 THR Chi-restraints excluded: chain I residue 579 ARG Chi-restraints excluded: chain I residue 665 ILE Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain K residue 123 HIS Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain K residue 231 ILE Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 10 ASN Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 195 ILE Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 125 ASP Chi-restraints excluded: chain O residue 159 GLU Chi-restraints excluded: chain O residue 188 ILE Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 278 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 355 LEU Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 301 ILE Chi-restraints excluded: chain Q residue 130 PHE Chi-restraints excluded: chain Q residue 222 LYS Chi-restraints excluded: chain T residue 291 ILE Chi-restraints excluded: chain T residue 305 SER Chi-restraints excluded: chain U residue 278 SER Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain Y residue 3 ASP Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 141 SER Chi-restraints excluded: chain Y residue 205 LEU Chi-restraints excluded: chain Z residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 232 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 301 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 311 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 25 optimal weight: 0.0980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 338 HIS ** I 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 HIS L 238 GLN ** U 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 170 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.134059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.096882 restraints weight = 58914.779| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.18 r_work: 0.3256 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29041 Z= 0.127 Angle : 0.551 11.746 39403 Z= 0.288 Chirality : 0.039 0.227 4530 Planarity : 0.003 0.065 4802 Dihedral : 13.166 71.155 4214 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.99 % Allowed : 18.03 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.73 (0.15), residues: 3318 helix: 2.23 (0.11), residues: 2130 sheet: -0.46 (0.32), residues: 242 loop : -0.97 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 71 TYR 0.028 0.001 TYR N 220 PHE 0.022 0.001 PHE Q 325 TRP 0.013 0.001 TRP T 298 HIS 0.012 0.001 HIS K 123 Details of bonding type rmsd covalent geometry : bond 0.00276 (29041) covalent geometry : angle 0.55139 (39403) hydrogen bonds : bond 0.03796 ( 1870) hydrogen bonds : angle 3.87588 ( 5641) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8663.84 seconds wall clock time: 148 minutes 49.90 seconds (8929.90 seconds total)