Starting phenix.real_space_refine on Mon Sep 30 08:54:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8o_21107/09_2024/6v8o_21107.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8o_21107/09_2024/6v8o_21107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8o_21107/09_2024/6v8o_21107.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8o_21107/09_2024/6v8o_21107.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8o_21107/09_2024/6v8o_21107.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8o_21107/09_2024/6v8o_21107.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Zn 1 6.06 5 S 91 5.16 5 C 15930 2.51 5 N 4277 2.21 5 O 4804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 25103 Number of models: 1 Model: "" Number of chains: 23 Chain: "C" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 493 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "D" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 772 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain breaks: 1 Chain: "E" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 978 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "F" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 536 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 7, 'TRANS': 59} Chain breaks: 1 Chain: "G" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 422 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "H" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1083 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain breaks: 1 Chain: "I" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2416 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Chain: "J" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'TRANS': 114} Chain: "K" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 878 Classifications: {'peptide': 109} Link IDs: {'TRANS': 108} Chain breaks: 1 Chain: "L" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2445 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 2 Chain: "M" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2474 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 16, 'TRANS': 293} Chain breaks: 3 Chain: "N" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3275 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 18, 'TRANS': 393} Chain breaks: 1 Chain: "O" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3145 Classifications: {'peptide': 384} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 361} Chain breaks: 3 Chain: "Q" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2137 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 12, 'TRANS': 251} Chain breaks: 2 Chain: "R" Number of atoms: 2126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2126 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 11, 'TRANS': 250} Chain breaks: 1 Chain: "S" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 278 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "2" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 140 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'UNK:plan-1': 28} Unresolved non-hydrogen planarities: 28 Chain: "3" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "4" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "5" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "6" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "7" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 245 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'UNK:plan-1': 49} Unresolved non-hydrogen planarities: 49 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5813 SG CYS I 260 150.361 54.662 77.002 1.00 50.60 S ATOM 5836 SG CYS I 263 153.627 52.802 78.258 1.00 55.54 S ATOM 5999 SG CYS I 283 152.020 55.587 80.436 1.00 54.74 S ATOM 6022 SG CYS I 286 153.971 56.119 76.846 1.00 50.21 S Time building chain proxies: 14.35, per 1000 atoms: 0.57 Number of scatterers: 25103 At special positions: 0 Unit cell: (208.655, 130.949, 198.582, 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) Zn 1 29.99 S 91 16.00 O 4804 8.00 N 4277 7.00 C 15930 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: 6.87 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 601 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 260 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 263 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 286 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 283 " Number of angles added : 6 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6118 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 17 sheets defined 56.4% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'C' and resid 20 through 40 Processing helix chain 'C' and resid 45 through 54 Processing helix chain 'C' and resid 54 through 75 Processing helix chain 'D' and resid 7 through 18 Processing helix chain 'D' and resid 27 through 35 Processing helix chain 'D' and resid 72 through 79 Processing helix chain 'D' and resid 93 through 99 Processing helix chain 'D' and resid 101 through 113 removed outlier: 3.601A pdb=" N PHE D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 125 Processing helix chain 'E' and resid 318 through 343 Processing helix chain 'E' and resid 400 through 404 removed outlier: 4.236A pdb=" N SER E 403 " --> pdb=" O THR E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 411 removed outlier: 4.272A pdb=" N TYR E 410 " --> pdb=" O PRO E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 433 Processing helix chain 'F' and resid 862 through 867 Processing helix chain 'F' and resid 871 through 881 removed outlier: 3.765A pdb=" N MET F 881 " --> pdb=" O HIS F 877 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 196 removed outlier: 3.906A pdb=" N ILE G 177 " --> pdb=" O THR G 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 468 Processing helix chain 'I' and resid 58 through 72 Processing helix chain 'I' and resid 95 through 102 Processing helix chain 'I' and resid 103 through 106 Processing helix chain 'I' and resid 114 through 132 removed outlier: 3.756A pdb=" N SER I 132 " --> pdb=" O THR I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 146 removed outlier: 3.845A pdb=" N VAL I 142 " --> pdb=" O THR I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 163 removed outlier: 3.512A pdb=" N TRP I 163 " --> pdb=" O PHE I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 175 removed outlier: 4.099A pdb=" N LYS I 175 " --> pdb=" O PRO I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 244 Processing helix chain 'I' and resid 246 through 251 Processing helix chain 'I' and resid 283 through 289 Processing helix chain 'I' and resid 297 through 299 No H-bonds generated for 'chain 'I' and resid 297 through 299' Processing helix chain 'I' and resid 316 through 330 Processing helix chain 'I' and resid 333 through 342 removed outlier: 3.847A pdb=" N GLY I 342 " --> pdb=" O ALA I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 356 Processing helix chain 'I' and resid 360 through 368 Processing helix chain 'J' and resid 388 through 403 removed outlier: 3.624A pdb=" N CYS J 392 " --> pdb=" O LYS J 388 " (cutoff:3.500A) Processing helix chain 'J' and resid 406 through 490 removed outlier: 3.834A pdb=" N VAL J 410 " --> pdb=" O LYS J 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 388 through 402 Processing helix chain 'K' and resid 421 through 489 Processing helix chain 'L' and resid 59 through 76 Processing helix chain 'L' and resid 83 through 87 Processing helix chain 'L' and resid 96 through 102 Processing helix chain 'L' and resid 114 through 131 Processing helix chain 'L' and resid 138 through 145 removed outlier: 4.076A pdb=" N VAL L 142 " --> pdb=" O THR L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 163 Processing helix chain 'L' and resid 171 through 175 removed outlier: 3.541A pdb=" N LYS L 175 " --> pdb=" O PRO L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 292 Processing helix chain 'L' and resid 298 through 304 Processing helix chain 'L' and resid 316 through 330 Processing helix chain 'L' and resid 333 through 342 Processing helix chain 'L' and resid 346 through 356 Processing helix chain 'L' and resid 360 through 377 removed outlier: 3.583A pdb=" N ILE L 364 " --> pdb=" O GLU L 360 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 51 Processing helix chain 'M' and resid 237 through 242 removed outlier: 3.629A pdb=" N LEU M 241 " --> pdb=" O ASN M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 263 Processing helix chain 'M' and resid 268 through 275 Processing helix chain 'M' and resid 316 through 324 Processing helix chain 'M' and resid 331 through 342 removed outlier: 3.623A pdb=" N VAL M 335 " --> pdb=" O PRO M 331 " (cutoff:3.500A) Processing helix chain 'M' and resid 372 through 377 Processing helix chain 'M' and resid 387 through 425 Processing helix chain 'M' and resid 425 through 445 Processing helix chain 'M' and resid 452 through 457 Processing helix chain 'M' and resid 470 through 472 No H-bonds generated for 'chain 'M' and resid 470 through 472' Processing helix chain 'M' and resid 473 through 480 Processing helix chain 'N' and resid 40 through 46 Processing helix chain 'N' and resid 65 through 70 removed outlier: 3.923A pdb=" N SER N 70 " --> pdb=" O VAL N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 92 removed outlier: 3.995A pdb=" N GLY N 92 " --> pdb=" O ALA N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 111 Processing helix chain 'N' and resid 123 through 140 removed outlier: 3.664A pdb=" N PHE N 127 " --> pdb=" O LEU N 123 " (cutoff:3.500A) Proline residue: N 133 - end of helix Processing helix chain 'N' and resid 148 through 170 Processing helix chain 'N' and resid 171 through 180 removed outlier: 3.691A pdb=" N LYS N 180 " --> pdb=" O GLN N 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 201 Processing helix chain 'N' and resid 208 through 210 No H-bonds generated for 'chain 'N' and resid 208 through 210' Processing helix chain 'N' and resid 211 through 231 removed outlier: 3.878A pdb=" N SER N 231 " --> pdb=" O GLU N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 240 through 253 Processing helix chain 'N' and resid 255 through 269 removed outlier: 3.614A pdb=" N VAL N 259 " --> pdb=" O ASP N 255 " (cutoff:3.500A) Processing helix chain 'N' and resid 279 through 284 removed outlier: 3.521A pdb=" N ASP N 282 " --> pdb=" O SER N 279 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU N 284 " --> pdb=" O ALA N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 285 through 298 removed outlier: 3.565A pdb=" N LEU N 298 " --> pdb=" O SER N 294 " (cutoff:3.500A) Processing helix chain 'N' and resid 301 through 317 Processing helix chain 'N' and resid 320 through 329 removed outlier: 4.334A pdb=" N SER N 329 " --> pdb=" O GLU N 325 " (cutoff:3.500A) Processing helix chain 'N' and resid 329 through 345 Proline residue: N 341 - end of helix removed outlier: 3.681A pdb=" N SER N 345 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'N' and resid 353 through 359 removed outlier: 3.800A pdb=" N GLN N 357 " --> pdb=" O TYR N 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 524 through 539 removed outlier: 3.651A pdb=" N ASN N 539 " --> pdb=" O CYS N 535 " (cutoff:3.500A) Processing helix chain 'N' and resid 546 through 564 removed outlier: 3.749A pdb=" N CYS N 550 " --> pdb=" O GLY N 546 " (cutoff:3.500A) Proline residue: N 555 - end of helix Processing helix chain 'N' and resid 564 through 571 removed outlier: 3.513A pdb=" N THR N 568 " --> pdb=" O ILE N 564 " (cutoff:3.500A) Processing helix chain 'N' and resid 571 through 577 Processing helix chain 'O' and resid 10 through 25 Processing helix chain 'O' and resid 29 through 33 Processing helix chain 'O' and resid 43 through 45 No H-bonds generated for 'chain 'O' and resid 43 through 45' Processing helix chain 'O' and resid 46 through 61 Processing helix chain 'O' and resid 75 through 82 removed outlier: 3.518A pdb=" N ARG O 79 " --> pdb=" O THR O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 110 removed outlier: 3.500A pdb=" N PHE O 92 " --> pdb=" O ILE O 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 114 through 138 removed outlier: 3.532A pdb=" N GLN O 118 " --> pdb=" O THR O 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 170 through 179 Processing helix chain 'O' and resid 243 through 248 removed outlier: 4.029A pdb=" N VAL O 247 " --> pdb=" O ARG O 243 " (cutoff:3.500A) Processing helix chain 'O' and resid 302 through 314 Processing helix chain 'O' and resid 389 through 394 Processing helix chain 'O' and resid 403 through 412 removed outlier: 3.659A pdb=" N ILE O 407 " --> pdb=" O GLY O 403 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 436 removed outlier: 3.656A pdb=" N ASN O 436 " --> pdb=" O GLU O 432 " (cutoff:3.500A) Processing helix chain 'O' and resid 442 through 462 Processing helix chain 'Q' and resid 3 through 7 Processing helix chain 'Q' and resid 15 through 22 Processing helix chain 'Q' and resid 161 through 167 Processing helix chain 'Q' and resid 168 through 177 Processing helix chain 'Q' and resid 231 through 244 Processing helix chain 'Q' and resid 247 through 265 removed outlier: 3.553A pdb=" N LEU Q 265 " --> pdb=" O GLN Q 261 " (cutoff:3.500A) Processing helix chain 'Q' and resid 265 through 270 removed outlier: 3.629A pdb=" N ALA Q 270 " --> pdb=" O GLU Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 319 Processing helix chain 'Q' and resid 323 through 345 removed outlier: 4.018A pdb=" N LEU Q 327 " --> pdb=" O GLU Q 323 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER Q 329 " --> pdb=" O ILE Q 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 66 Processing helix chain 'R' and resid 68 through 73 Processing helix chain 'R' and resid 74 through 102 removed outlier: 3.502A pdb=" N ALA R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 127 Processing helix chain 'R' and resid 132 through 136 removed outlier: 4.081A pdb=" N LEU R 136 " --> pdb=" O ASP R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 172 removed outlier: 3.548A pdb=" N LEU R 172 " --> pdb=" O LYS R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 179 removed outlier: 4.106A pdb=" N PHE R 178 " --> pdb=" O GLU R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 208 Processing helix chain 'R' and resid 236 through 250 Processing helix chain 'R' and resid 250 through 267 Processing helix chain 'R' and resid 268 through 273 Processing helix chain 'R' and resid 273 through 278 Processing helix chain 'R' and resid 279 through 290 removed outlier: 3.635A pdb=" N GLN R 290 " --> pdb=" O GLN R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 318 Processing helix chain 'S' and resid 204 through 227 removed outlier: 3.744A pdb=" N GLN S 227 " --> pdb=" O LEU S 223 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 20 Processing helix chain '4' and resid 1 through 18 Processing helix chain '5' and resid 4 through 16 Processing helix chain '6' and resid 421 through 434 Processing sheet with id=AA1, first strand: chain 'E' and resid 349 through 351 removed outlier: 3.734A pdb=" N GLY L 180 " --> pdb=" O ILE E 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 368 through 373 removed outlier: 6.977A pdb=" N VAL E 368 " --> pdb=" O ASP I 192 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASP I 192 " --> pdb=" O VAL E 368 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY E 370 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL E 385 " --> pdb=" O PHE I 187 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL I 189 " --> pdb=" O VAL E 385 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU E 387 " --> pdb=" O VAL I 189 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU I 191 " --> pdb=" O GLU E 387 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL E 389 " --> pdb=" O LEU I 191 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS I 231 " --> pdb=" O THR E 388 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE E 390 " --> pdb=" O THR I 229 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N THR I 229 " --> pdb=" O ILE E 390 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 157 through 160 removed outlier: 3.503A pdb=" N SER S 201 " --> pdb=" O ASN G 157 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 589 through 594 removed outlier: 4.072A pdb=" N HIS H 514 " --> pdb=" O GLN H 453 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLN H 453 " --> pdb=" O HIS H 514 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER H 458 " --> pdb=" O VAL H 482 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL H 482 " --> pdb=" O SER H 458 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP H 481 " --> pdb=" O ILE L 259 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N HIS L 261 " --> pdb=" O TRP H 481 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU H 483 " --> pdb=" O HIS L 261 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR L 262 " --> pdb=" O ASN L 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 522 through 526 removed outlier: 6.052A pdb=" N PHE H 498 " --> pdb=" O TRP H 620 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ASN H 622 " --> pdb=" O PHE H 498 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE H 500 " --> pdb=" O ASN H 622 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA H 497 " --> pdb=" O ILE O 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 80 through 83 Processing sheet with id=AA7, first strand: chain 'I' and resid 256 through 257 removed outlier: 3.664A pdb=" N VAL N 47 " --> pdb=" O VAL I 257 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 281 through 282 Processing sheet with id=AA9, first strand: chain 'K' and resid 493 through 497 Processing sheet with id=AB1, first strand: chain 'M' and resid 368 through 369 removed outlier: 3.543A pdb=" N LEU M 368 " --> pdb=" O ILE M 76 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG M 75 " --> pdb=" O UNK 7 24 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR M 77 " --> pdb=" O UNK 7 26 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR M 79 " --> pdb=" O UNK 7 28 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 349 through 352 removed outlier: 6.582A pdb=" N SER M 219 " --> pdb=" O UNK 7 62 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N UNK 7 64 " --> pdb=" O SER M 219 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR M 221 " --> pdb=" O UNK 7 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 246 through 247 Processing sheet with id=AB4, first strand: chain 'M' and resid 313 through 314 removed outlier: 3.531A pdb=" N LEU M 330 " --> pdb=" O VAL M 313 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 476 through 477 Processing sheet with id=AB6, first strand: chain 'Q' and resid 13 through 14 removed outlier: 3.566A pdb=" N LYS Q 179 " --> pdb=" O SER Q 14 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 203 through 212 Processing sheet with id=AB8, first strand: chain 'Q' and resid 278 through 286 1297 hydrogen bonds defined for protein. 3765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.39 Time building geometry restraints manager: 7.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8274 1.34 - 1.46: 4234 1.46 - 1.57: 12890 1.57 - 1.69: 0 1.69 - 1.81: 145 Bond restraints: 25543 Sorted by residual: bond pdb=" CB TRP I 163 " pdb=" CG TRP I 163 " ideal model delta sigma weight residual 1.498 1.463 0.035 3.10e-02 1.04e+03 1.30e+00 bond pdb=" CA LEU N 132 " pdb=" C LEU N 132 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.26e-02 6.30e+03 1.20e+00 bond pdb=" C TYR O 85 " pdb=" N GLU O 86 " ideal model delta sigma weight residual 1.329 1.297 0.031 3.03e-02 1.09e+03 1.08e+00 bond pdb=" C LEU N 132 " pdb=" O LEU N 132 " ideal model delta sigma weight residual 1.238 1.251 -0.013 1.28e-02 6.10e+03 1.07e+00 bond pdb=" C PHE R 135 " pdb=" N LEU R 136 " ideal model delta sigma weight residual 1.332 1.318 0.014 1.40e-02 5.10e+03 9.94e-01 ... (remaining 25538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 34433 2.96 - 5.92: 112 5.92 - 8.87: 8 8.87 - 11.83: 1 11.83 - 14.79: 1 Bond angle restraints: 34555 Sorted by residual: angle pdb=" N SER Q 374 " pdb=" CA SER Q 374 " pdb=" C SER Q 374 " ideal model delta sigma weight residual 110.80 120.59 -9.79 2.13e+00 2.20e-01 2.11e+01 angle pdb=" C ILE H 528 " pdb=" N ASN H 529 " pdb=" CA ASN H 529 " ideal model delta sigma weight residual 121.54 129.75 -8.21 1.91e+00 2.74e-01 1.85e+01 angle pdb=" C GLY Q 373 " pdb=" N SER Q 374 " pdb=" CA SER Q 374 " ideal model delta sigma weight residual 121.54 129.11 -7.57 1.91e+00 2.74e-01 1.57e+01 angle pdb=" N PRO O 415 " pdb=" CA PRO O 415 " pdb=" C PRO O 415 " ideal model delta sigma weight residual 114.18 110.44 3.74 1.39e+00 5.18e-01 7.23e+00 angle pdb=" C SER Q 374 " pdb=" CA SER Q 374 " pdb=" CB SER Q 374 " ideal model delta sigma weight residual 110.42 105.22 5.20 1.99e+00 2.53e-01 6.84e+00 ... (remaining 34550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 14796 17.77 - 35.54: 707 35.54 - 53.31: 140 53.31 - 71.09: 34 71.09 - 88.86: 6 Dihedral angle restraints: 15683 sinusoidal: 6343 harmonic: 9340 Sorted by residual: dihedral pdb=" CA GLU Q 371 " pdb=" C GLU Q 371 " pdb=" N LEU Q 372 " pdb=" CA LEU Q 372 " ideal model delta harmonic sigma weight residual -180.00 -153.93 -26.07 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ASN H 529 " pdb=" C ASN H 529 " pdb=" N LYS H 530 " pdb=" CA LYS H 530 " ideal model delta harmonic sigma weight residual 180.00 155.34 24.66 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLY Q 373 " pdb=" C GLY Q 373 " pdb=" N SER Q 374 " pdb=" CA SER Q 374 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 15680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2642 0.033 - 0.066: 973 0.066 - 0.099: 233 0.099 - 0.133: 118 0.133 - 0.166: 5 Chirality restraints: 3971 Sorted by residual: chirality pdb=" CA ILE E 359 " pdb=" N ILE E 359 " pdb=" C ILE E 359 " pdb=" CB ILE E 359 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA ILE N 514 " pdb=" N ILE N 514 " pdb=" C ILE N 514 " pdb=" CB ILE N 514 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA SER Q 374 " pdb=" N SER Q 374 " pdb=" C SER Q 374 " pdb=" CB SER Q 374 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 3968 not shown) Planarity restraints: 4440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE N 564 " -0.048 5.00e-02 4.00e+02 7.37e-02 8.70e+00 pdb=" N PRO N 565 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO N 565 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO N 565 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN M 6 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO M 7 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO M 7 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO M 7 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU N 124 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO N 125 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO N 125 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO N 125 " -0.025 5.00e-02 4.00e+02 ... (remaining 4437 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 668 2.70 - 3.25: 25129 3.25 - 3.80: 37366 3.80 - 4.35: 48918 4.35 - 4.90: 82429 Nonbonded interactions: 194510 Sorted by model distance: nonbonded pdb=" O GLU N 227 " pdb=" OG SER N 230 " model vdw 2.149 3.040 nonbonded pdb=" OH TYR Q 184 " pdb=" OD1 ASP Q 242 " model vdw 2.150 3.040 nonbonded pdb=" OE2 GLU O 41 " pdb=" OG SER O 50 " model vdw 2.163 3.040 nonbonded pdb=" O LYS H 449 " pdb=" OG1 THR H 516 " model vdw 2.164 3.040 nonbonded pdb=" OD1 ASN Q 282 " pdb=" ND2 ASN Q 295 " model vdw 2.201 3.120 ... (remaining 194505 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 '3' selection = chain '4' } ncs_group { reference = chain '5' selection = (chain '6' and resid 421 through 434) } ncs_group { reference = (chain 'I' and (resid 58 through 304 or resid 312 through 368)) selection = (chain 'L' and (resid 58 through 202 or resid 222 through 368)) } ncs_group { reference = (chain 'J' and (resid 387 through 402 or resid 420 through 501)) selection = (chain 'K' and resid 387 through 501) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 1.020 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 58.530 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.110 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:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 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 0.050 25543 Z= 0.272 Angle : 0.549 14.790 34555 Z= 0.299 Chirality : 0.039 0.166 3971 Planarity : 0.003 0.074 4440 Dihedral : 11.206 88.857 9565 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.89 % Favored : 93.01 % Rotamer: Outliers : 2.31 % Allowed : 5.62 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.14), residues: 2946 helix: 0.34 (0.13), residues: 1511 sheet: -0.89 (0.36), residues: 187 loop : -2.91 (0.15), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP O 273 HIS 0.004 0.001 HIS N 220 PHE 0.012 0.001 PHE I 85 TYR 0.015 0.001 TYR I 272 ARG 0.003 0.000 ARG Q 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 682 time to evaluate : 3.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 ARG cc_start: 0.7326 (ttt90) cc_final: 0.7065 (tmt170) REVERT: D 94 ARG cc_start: 0.6705 (ttt180) cc_final: 0.6372 (ttt-90) REVERT: D 107 HIS cc_start: 0.7234 (t70) cc_final: 0.6968 (t-90) REVERT: E 329 ARG cc_start: 0.7079 (mtm110) cc_final: 0.6539 (mmt180) REVERT: E 353 TYR cc_start: 0.8604 (m-80) cc_final: 0.8031 (m-80) REVERT: E 430 LYS cc_start: 0.8227 (mttt) cc_final: 0.8021 (mtmt) REVERT: F 817 ARG cc_start: 0.6858 (mtp180) cc_final: 0.6477 (mtp85) REVERT: G 167 MET cc_start: 0.8383 (ttm) cc_final: 0.7454 (mtp) REVERT: G 189 LEU cc_start: 0.7023 (mt) cc_final: 0.6772 (mt) REVERT: I 191 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7780 (pp) REVERT: I 255 HIS cc_start: 0.6476 (p-80) cc_final: 0.6193 (m170) REVERT: I 281 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8570 (m-40) REVERT: J 388 LYS cc_start: 0.7808 (mttt) cc_final: 0.7329 (mppt) REVERT: J 390 MET cc_start: 0.7978 (mmm) cc_final: 0.7726 (mmm) REVERT: J 394 ASN cc_start: 0.8741 (m-40) cc_final: 0.8443 (m110) REVERT: J 437 MET cc_start: 0.7769 (mmm) cc_final: 0.7245 (mmt) REVERT: K 475 LEU cc_start: 0.7844 (tp) cc_final: 0.7631 (mm) REVERT: K 485 SER cc_start: 0.7064 (t) cc_final: 0.6522 (p) REVERT: K 501 GLN cc_start: 0.6941 (mt0) cc_final: 0.6576 (mt0) REVERT: K 503 ASP cc_start: 0.6895 (OUTLIER) cc_final: 0.5326 (m-30) REVERT: L 317 ASP cc_start: 0.7461 (m-30) cc_final: 0.7225 (m-30) REVERT: M 40 ASP cc_start: 0.8293 (t70) cc_final: 0.8087 (t70) REVERT: M 391 THR cc_start: 0.6244 (m) cc_final: 0.5833 (p) REVERT: N 85 MET cc_start: 0.8801 (mtm) cc_final: 0.8126 (mtm) REVERT: N 102 LYS cc_start: 0.8000 (mttt) cc_final: 0.7671 (mtpp) REVERT: N 104 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.6830 (m-10) REVERT: N 170 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8454 (mp10) REVERT: N 293 VAL cc_start: 0.8319 (t) cc_final: 0.8014 (t) REVERT: N 329 SER cc_start: 0.8300 (t) cc_final: 0.7858 (m) REVERT: N 551 GLN cc_start: 0.8485 (mt0) cc_final: 0.8272 (mt0) REVERT: N 553 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8393 (tt) REVERT: O 122 LYS cc_start: 0.6902 (tttt) cc_final: 0.6296 (tmtt) REVERT: Q 173 ASP cc_start: 0.6972 (m-30) cc_final: 0.6599 (t0) REVERT: Q 203 MET cc_start: 0.8732 (mmt) cc_final: 0.8357 (mmt) REVERT: Q 266 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7333 (pt0) REVERT: Q 294 ASP cc_start: 0.7805 (t0) cc_final: 0.7351 (t0) REVERT: Q 303 LYS cc_start: 0.8529 (mttt) cc_final: 0.8305 (mmtt) REVERT: R 193 ILE cc_start: 0.8099 (mt) cc_final: 0.7825 (pt) REVERT: R 306 GLU cc_start: 0.6363 (mt-10) cc_final: 0.6040 (pt0) REVERT: S 218 ASN cc_start: 0.6751 (m-40) cc_final: 0.6270 (t0) outliers start: 64 outliers final: 16 residues processed: 729 average time/residue: 0.4080 time to fit residues: 455.4974 Evaluate side-chains 407 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 385 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 281 ASN Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain K residue 503 ASP Chi-restraints excluded: chain M residue 316 ASP Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 170 GLN Chi-restraints excluded: chain N residue 553 ILE Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain Q residue 342 ASP Chi-restraints excluded: chain Q residue 345 ASP Chi-restraints excluded: chain Q residue 368 ASP Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 262 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.0980 chunk 231 optimal weight: 0.8980 chunk 128 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 239 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 277 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 HIS D 64 HIS D 108 HIS D 122 HIS E 331 ASN E 425 GLN E 432 ASN F 816 ASN F 855 ASN H 452 GLN H 494 ASN H 506 GLN H 514 HIS H 529 ASN H 601 HIS I 167 ASN I 253 GLN I 314 ASN J 430 GLN K 430 GLN K 501 GLN L 145 ASN ** L 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 318 GLN M 340 ASN M 378 GLN M 380 GLN N 43 GLN N 69 GLN N 286 HIS N 512 ASN N 559 HIS O 18 GLN O 22 ASN O 97 HIS O 193 GLN O 482 ASN O 484 ASN Q 5 ASN ** Q 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 158 GLN Q 164 ASN Q 220 GLN Q 261 GLN Q 352 HIS R 116 ASN R 123 GLN R 204 ASN R 270 HIS R 290 GLN S 227 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25543 Z= 0.191 Angle : 0.561 14.684 34555 Z= 0.287 Chirality : 0.040 0.233 3971 Planarity : 0.004 0.073 4440 Dihedral : 5.308 59.953 3399 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.67 % Favored : 94.26 % Rotamer: Outliers : 2.63 % Allowed : 11.06 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 2946 helix: 1.59 (0.13), residues: 1529 sheet: -0.55 (0.35), residues: 196 loop : -2.33 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 273 HIS 0.009 0.001 HIS N 220 PHE 0.031 0.001 PHE R 83 TYR 0.019 0.001 TYR O 178 ARG 0.006 0.000 ARG O 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 410 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 ARG cc_start: 0.7512 (ttt90) cc_final: 0.7153 (tmt170) REVERT: C 64 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7379 (tp30) REVERT: D 94 ARG cc_start: 0.6838 (ttt180) cc_final: 0.6539 (ttt-90) REVERT: D 107 HIS cc_start: 0.7299 (t70) cc_final: 0.6974 (t-90) REVERT: E 329 ARG cc_start: 0.7580 (mtm110) cc_final: 0.6551 (mmt180) REVERT: E 407 LYS cc_start: 0.7171 (pttp) cc_final: 0.6889 (ptmm) REVERT: F 817 ARG cc_start: 0.6961 (mtp180) cc_final: 0.6401 (mtp85) REVERT: G 167 MET cc_start: 0.8278 (ttm) cc_final: 0.7459 (mtp) REVERT: H 589 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6839 (mt-10) REVERT: H 613 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7085 (mt-10) REVERT: I 312 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7548 (tptt) REVERT: I 317 ASP cc_start: 0.7596 (m-30) cc_final: 0.7271 (m-30) REVERT: J 388 LYS cc_start: 0.7788 (mttt) cc_final: 0.7492 (mppt) REVERT: J 390 MET cc_start: 0.7876 (mmm) cc_final: 0.7561 (mmm) REVERT: J 395 ASP cc_start: 0.8367 (m-30) cc_final: 0.8061 (m-30) REVERT: J 437 MET cc_start: 0.7637 (mmm) cc_final: 0.7087 (mmt) REVERT: J 463 LYS cc_start: 0.7890 (mmmt) cc_final: 0.7456 (mmmt) REVERT: L 149 ASP cc_start: 0.7486 (p0) cc_final: 0.7177 (p0) REVERT: L 312 LYS cc_start: 0.7083 (mttt) cc_final: 0.6433 (tptt) REVERT: L 317 ASP cc_start: 0.7835 (m-30) cc_final: 0.7504 (m-30) REVERT: N 102 LYS cc_start: 0.8022 (mttt) cc_final: 0.7725 (mtpp) REVERT: N 104 TYR cc_start: 0.8984 (OUTLIER) cc_final: 0.7155 (m-80) REVERT: N 170 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8516 (mp10) REVERT: N 293 VAL cc_start: 0.7999 (t) cc_final: 0.7735 (t) REVERT: N 551 GLN cc_start: 0.8400 (mt0) cc_final: 0.8192 (mt0) REVERT: N 553 ILE cc_start: 0.8481 (tt) cc_final: 0.8054 (tp) REVERT: O 122 LYS cc_start: 0.6890 (tttt) cc_final: 0.6287 (tmtt) REVERT: O 196 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7627 (tt0) REVERT: O 215 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7284 (t0) REVERT: O 265 MET cc_start: 0.8069 (mtt) cc_final: 0.7452 (mtt) REVERT: Q 303 LYS cc_start: 0.8451 (mttt) cc_final: 0.8164 (mmtt) REVERT: R 97 LEU cc_start: 0.7940 (tt) cc_final: 0.7613 (tp) REVERT: R 234 MET cc_start: 0.8629 (mmm) cc_final: 0.7243 (mmm) REVERT: R 306 GLU cc_start: 0.6113 (mt-10) cc_final: 0.5778 (pt0) REVERT: S 218 ASN cc_start: 0.6618 (m-40) cc_final: 0.6185 (t0) outliers start: 73 outliers final: 42 residues processed: 458 average time/residue: 0.3804 time to fit residues: 268.6093 Evaluate side-chains 390 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 343 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 237 SER Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain J residue 452 THR Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 244 MET Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 170 GLN Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 321 GLN Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 357 GLN Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 215 ASP Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 264 MET Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 406 GLU Chi-restraints excluded: chain Q residue 268 ILE Chi-restraints excluded: chain Q residue 376 TRP Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain S residue 213 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 189 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 278 optimal weight: 1.9990 chunk 300 optimal weight: 20.0000 chunk 247 optimal weight: 3.9990 chunk 276 optimal weight: 0.0980 chunk 94 optimal weight: 4.9990 chunk 223 optimal weight: 0.0870 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 HIS ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 496 ASN H 506 GLN H 514 HIS K 430 GLN L 239 GLN M 4 GLN M 270 GLN M 378 GLN M 380 GLN O 97 HIS ** O 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 297 GLN R 123 GLN S 227 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25543 Z= 0.188 Angle : 0.535 13.019 34555 Z= 0.274 Chirality : 0.040 0.220 3971 Planarity : 0.004 0.070 4440 Dihedral : 4.903 53.932 3377 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.30 % Favored : 94.67 % Rotamer: Outliers : 2.45 % Allowed : 11.85 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.16), residues: 2946 helix: 2.11 (0.13), residues: 1523 sheet: -0.16 (0.36), residues: 193 loop : -2.06 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 273 HIS 0.008 0.001 HIS N 220 PHE 0.026 0.001 PHE R 83 TYR 0.012 0.001 TYR I 272 ARG 0.005 0.000 ARG M 456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 379 time to evaluate : 2.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 ARG cc_start: 0.7631 (ttt90) cc_final: 0.7173 (tmt170) REVERT: D 107 HIS cc_start: 0.7523 (t70) cc_final: 0.7168 (t-90) REVERT: E 329 ARG cc_start: 0.7617 (mtm110) cc_final: 0.6435 (mmt180) REVERT: E 387 GLU cc_start: 0.8474 (pt0) cc_final: 0.8159 (pt0) REVERT: E 407 LYS cc_start: 0.7280 (pttp) cc_final: 0.7011 (ptmm) REVERT: F 817 ARG cc_start: 0.6897 (mtp180) cc_final: 0.6400 (mtp85) REVERT: G 167 MET cc_start: 0.8194 (ttm) cc_final: 0.7741 (mtp) REVERT: H 589 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6756 (mt-10) REVERT: H 613 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7249 (mt-10) REVERT: I 90 ASP cc_start: 0.7666 (t0) cc_final: 0.7462 (t0) REVERT: I 312 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7550 (tptt) REVERT: I 317 ASP cc_start: 0.7691 (m-30) cc_final: 0.7371 (m-30) REVERT: I 329 MET cc_start: 0.8931 (mtp) cc_final: 0.8655 (mtm) REVERT: J 388 LYS cc_start: 0.7837 (mttt) cc_final: 0.7496 (mppt) REVERT: J 395 ASP cc_start: 0.8412 (m-30) cc_final: 0.8056 (m-30) REVERT: K 499 SER cc_start: 0.7837 (m) cc_final: 0.7109 (p) REVERT: K 501 GLN cc_start: 0.7029 (mt0) cc_final: 0.6739 (mt0) REVERT: L 66 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7201 (mt-10) REVERT: L 149 ASP cc_start: 0.7345 (p0) cc_final: 0.6722 (p0) REVERT: L 312 LYS cc_start: 0.7074 (mttt) cc_final: 0.6450 (tptt) REVERT: L 317 ASP cc_start: 0.7874 (m-30) cc_final: 0.7595 (m-30) REVERT: M 445 GLN cc_start: 0.7857 (pt0) cc_final: 0.7302 (pp30) REVERT: N 102 LYS cc_start: 0.7987 (mttt) cc_final: 0.7749 (mtpp) REVERT: N 104 TYR cc_start: 0.9162 (OUTLIER) cc_final: 0.7550 (m-80) REVERT: N 170 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8458 (mp10) REVERT: N 293 VAL cc_start: 0.8024 (t) cc_final: 0.7787 (t) REVERT: N 553 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8109 (tp) REVERT: O 80 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.7227 (t80) REVERT: O 122 LYS cc_start: 0.7052 (tttt) cc_final: 0.6412 (tmtt) REVERT: O 129 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7533 (pt0) REVERT: O 405 ASP cc_start: 0.7819 (p0) cc_final: 0.7296 (p0) REVERT: Q 303 LYS cc_start: 0.8514 (mttt) cc_final: 0.8178 (mmtt) REVERT: Q 341 LYS cc_start: 0.7558 (tttp) cc_final: 0.7314 (tptt) REVERT: R 97 LEU cc_start: 0.8049 (tt) cc_final: 0.7810 (tp) REVERT: R 234 MET cc_start: 0.8736 (mmm) cc_final: 0.7345 (mmm) REVERT: R 306 GLU cc_start: 0.6111 (mt-10) cc_final: 0.5769 (pt0) REVERT: S 218 ASN cc_start: 0.6646 (m-40) cc_final: 0.6228 (t0) outliers start: 68 outliers final: 45 residues processed: 421 average time/residue: 0.3831 time to fit residues: 247.8684 Evaluate side-chains 383 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 333 time to evaluate : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 530 LYS Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 237 SER Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain J residue 452 THR Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 244 MET Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 170 GLN Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 553 ILE Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 80 PHE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain Q residue 268 ILE Chi-restraints excluded: chain Q residue 344 VAL Chi-restraints excluded: chain Q residue 376 TRP Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain S residue 198 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 0.7980 chunk 209 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 132 optimal weight: 0.0670 chunk 186 optimal weight: 1.9990 chunk 279 optimal weight: 10.0000 chunk 295 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 264 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 HIS ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 GLN F 855 ASN H 506 GLN H 512 GLN H 601 HIS I 60 GLN J 394 ASN K 430 GLN N 551 GLN O 97 HIS O 196 GLN O 225 ASN O 484 ASN ** Q 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 227 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25543 Z= 0.164 Angle : 0.509 12.289 34555 Z= 0.261 Chirality : 0.039 0.207 3971 Planarity : 0.004 0.069 4440 Dihedral : 4.750 59.852 3377 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 2.67 % Allowed : 12.00 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.16), residues: 2946 helix: 2.39 (0.13), residues: 1524 sheet: -0.01 (0.37), residues: 195 loop : -1.86 (0.16), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 273 HIS 0.005 0.001 HIS N 220 PHE 0.018 0.001 PHE R 83 TYR 0.020 0.001 TYR E 410 ARG 0.004 0.000 ARG M 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 370 time to evaluate : 2.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 GLU cc_start: 0.7894 (tp30) cc_final: 0.7638 (tp30) REVERT: C 48 ARG cc_start: 0.7499 (ttt90) cc_final: 0.7043 (tmt170) REVERT: C 64 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: D 6 MET cc_start: 0.3577 (tpp) cc_final: 0.3293 (mmp) REVERT: D 23 GLN cc_start: 0.7882 (mp10) cc_final: 0.7613 (mp10) REVERT: D 107 HIS cc_start: 0.7591 (t70) cc_final: 0.7240 (t-90) REVERT: E 329 ARG cc_start: 0.7595 (mtm110) cc_final: 0.6488 (mmt180) REVERT: E 420 ARG cc_start: 0.7345 (mtp180) cc_final: 0.6807 (ttp80) REVERT: F 817 ARG cc_start: 0.6837 (mtp180) cc_final: 0.6428 (mtp85) REVERT: G 167 MET cc_start: 0.8155 (ttm) cc_final: 0.7868 (mtp) REVERT: H 446 LYS cc_start: 0.8571 (ttpt) cc_final: 0.8261 (ptpt) REVERT: H 531 GLU cc_start: 0.7963 (mp0) cc_final: 0.7555 (tp30) REVERT: H 613 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7399 (mt-10) REVERT: I 63 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7863 (mm-40) REVERT: I 90 ASP cc_start: 0.7700 (t0) cc_final: 0.7430 (t0) REVERT: I 183 PHE cc_start: 0.7410 (t80) cc_final: 0.6518 (p90) REVERT: I 191 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8591 (pp) REVERT: I 312 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7298 (pttt) REVERT: I 317 ASP cc_start: 0.7711 (m-30) cc_final: 0.7434 (m-30) REVERT: I 352 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7550 (tp30) REVERT: J 388 LYS cc_start: 0.7873 (mttt) cc_final: 0.7508 (mppt) REVERT: J 395 ASP cc_start: 0.8342 (m-30) cc_final: 0.7964 (m-30) REVERT: J 463 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7693 (mttm) REVERT: K 499 SER cc_start: 0.7906 (m) cc_final: 0.7174 (p) REVERT: K 501 GLN cc_start: 0.6924 (mt0) cc_final: 0.6697 (mt0) REVERT: L 66 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6723 (mt-10) REVERT: L 148 MET cc_start: 0.8220 (mtp) cc_final: 0.7983 (mtp) REVERT: L 149 ASP cc_start: 0.7248 (p0) cc_final: 0.6704 (p0) REVERT: L 312 LYS cc_start: 0.7107 (mttt) cc_final: 0.6368 (tptt) REVERT: L 317 ASP cc_start: 0.7898 (m-30) cc_final: 0.7671 (m-30) REVERT: M 445 GLN cc_start: 0.7723 (pt0) cc_final: 0.7306 (pp30) REVERT: M 468 ARG cc_start: 0.7177 (mmm-85) cc_final: 0.6247 (mpt180) REVERT: N 28 MET cc_start: 0.4812 (tmm) cc_final: 0.4560 (tmm) REVERT: N 104 TYR cc_start: 0.9217 (OUTLIER) cc_final: 0.7634 (m-80) REVERT: N 170 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8519 (mp10) REVERT: N 293 VAL cc_start: 0.7999 (t) cc_final: 0.7765 (t) REVERT: N 310 ASP cc_start: 0.8089 (m-30) cc_final: 0.7803 (m-30) REVERT: N 553 ILE cc_start: 0.8535 (tt) cc_final: 0.8114 (tp) REVERT: O 29 HIS cc_start: 0.7379 (OUTLIER) cc_final: 0.6834 (m90) REVERT: O 48 TYR cc_start: 0.6470 (t80) cc_final: 0.5903 (t80) REVERT: O 122 LYS cc_start: 0.7047 (tttt) cc_final: 0.6398 (tmtt) REVERT: O 129 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7516 (pt0) REVERT: O 202 MET cc_start: 0.7058 (pmm) cc_final: 0.6352 (pmm) REVERT: O 215 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7382 (t0) REVERT: O 406 GLU cc_start: 0.7949 (mp0) cc_final: 0.7733 (mp0) REVERT: Q 303 LYS cc_start: 0.8574 (mttt) cc_final: 0.8107 (mmtt) REVERT: R 50 ARG cc_start: 0.7044 (ttt90) cc_final: 0.6763 (mtp-110) REVERT: R 259 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7796 (pt0) REVERT: R 306 GLU cc_start: 0.6102 (mt-10) cc_final: 0.5766 (pt0) REVERT: S 218 ASN cc_start: 0.6549 (m-40) cc_final: 0.6126 (t0) outliers start: 74 outliers final: 48 residues processed: 417 average time/residue: 0.3834 time to fit residues: 244.1442 Evaluate side-chains 391 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 334 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 530 LYS Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 237 SER Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain I residue 352 GLU Chi-restraints excluded: chain J residue 486 LEU Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 244 MET Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 170 GLN Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 512 ASN Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 29 HIS Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 215 ASP Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain S residue 211 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 220 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 252 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 151 optimal weight: 50.0000 chunk 265 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 HIS ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 855 ASN G 180 HIS H 506 GLN H 601 HIS J 394 ASN ** M 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 HIS O 234 GLN ** O 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 480 GLN ** Q 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN ** R 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 227 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 25543 Z= 0.370 Angle : 0.637 15.756 34555 Z= 0.326 Chirality : 0.043 0.259 3971 Planarity : 0.004 0.078 4440 Dihedral : 5.074 56.265 3375 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.48 % Favored : 93.45 % Rotamer: Outliers : 3.17 % Allowed : 12.86 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.16), residues: 2946 helix: 2.09 (0.13), residues: 1527 sheet: 0.04 (0.37), residues: 184 loop : -1.91 (0.16), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP O 273 HIS 0.007 0.001 HIS N 220 PHE 0.022 0.002 PHE O 476 TYR 0.025 0.002 TYR M 17 ARG 0.006 0.001 ARG Q 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 364 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 GLU cc_start: 0.7907 (tp30) cc_final: 0.7669 (tp30) REVERT: C 48 ARG cc_start: 0.7568 (ttt90) cc_final: 0.7060 (tmt170) REVERT: C 63 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7587 (mm-30) REVERT: D 107 HIS cc_start: 0.7640 (t70) cc_final: 0.7337 (t-90) REVERT: E 329 ARG cc_start: 0.7708 (mtm110) cc_final: 0.6476 (mmt180) REVERT: E 420 ARG cc_start: 0.7613 (mtp180) cc_final: 0.7198 (ttp80) REVERT: F 817 ARG cc_start: 0.6927 (mtp180) cc_final: 0.6149 (mtp85) REVERT: G 176 GLU cc_start: 0.3436 (OUTLIER) cc_final: 0.2492 (tt0) REVERT: H 531 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7564 (tp30) REVERT: H 613 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7486 (mt-10) REVERT: I 183 PHE cc_start: 0.7474 (t80) cc_final: 0.6597 (p90) REVERT: I 191 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8610 (pp) REVERT: I 192 ASP cc_start: 0.7575 (t0) cc_final: 0.7292 (t0) REVERT: I 239 GLN cc_start: 0.8038 (mp10) cc_final: 0.7829 (mp10) REVERT: J 388 LYS cc_start: 0.7966 (mttt) cc_final: 0.7509 (mppt) REVERT: K 430 GLN cc_start: 0.7638 (mt0) cc_final: 0.7418 (mt0) REVERT: K 499 SER cc_start: 0.7912 (OUTLIER) cc_final: 0.7042 (p) REVERT: K 501 GLN cc_start: 0.7219 (mt0) cc_final: 0.6974 (mt0) REVERT: L 66 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6812 (mt-10) REVERT: L 149 ASP cc_start: 0.7605 (p0) cc_final: 0.6690 (p0) REVERT: M 445 GLN cc_start: 0.8001 (pt0) cc_final: 0.7637 (pp30) REVERT: M 468 ARG cc_start: 0.7367 (mmm-85) cc_final: 0.6573 (mpt180) REVERT: N 321 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.7143 (mt0) REVERT: N 331 GLU cc_start: 0.8068 (pm20) cc_final: 0.7768 (pm20) REVERT: N 553 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8417 (tp) REVERT: O 48 TYR cc_start: 0.6489 (t80) cc_final: 0.6063 (t80) REVERT: O 122 LYS cc_start: 0.6762 (tttt) cc_final: 0.6162 (tmtt) REVERT: O 129 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7538 (pt0) REVERT: O 406 GLU cc_start: 0.7784 (mp0) cc_final: 0.7582 (mp0) REVERT: Q 303 LYS cc_start: 0.8603 (mttt) cc_final: 0.8104 (mmtt) REVERT: R 50 ARG cc_start: 0.7432 (ttt90) cc_final: 0.7093 (mtp-110) REVERT: R 229 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7681 (t0) REVERT: R 259 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.7989 (pt0) REVERT: R 306 GLU cc_start: 0.6424 (mt-10) cc_final: 0.6137 (pt0) REVERT: S 218 ASN cc_start: 0.6611 (m-40) cc_final: 0.6152 (t0) outliers start: 88 outliers final: 59 residues processed: 421 average time/residue: 0.3795 time to fit residues: 245.6212 Evaluate side-chains 398 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 331 time to evaluate : 3.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain F residue 798 ILE Chi-restraints excluded: chain F residue 800 ASN Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 527 THR Chi-restraints excluded: chain H residue 531 GLU Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain J residue 452 THR Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 474 SER Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 499 SER Chi-restraints excluded: chain K residue 504 SER Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 321 GLN Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 357 GLN Chi-restraints excluded: chain N residue 512 ASN Chi-restraints excluded: chain N residue 553 ILE Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 176 ILE Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 207 THR Chi-restraints excluded: chain Q residue 344 VAL Chi-restraints excluded: chain Q residue 376 TRP Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 229 ASP Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain S residue 211 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 1.9990 chunk 266 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 173 optimal weight: 0.3980 chunk 73 optimal weight: 0.3980 chunk 296 optimal weight: 9.9990 chunk 245 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 506 GLN J 394 ASN O 97 HIS ** Q 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25543 Z= 0.193 Angle : 0.540 15.210 34555 Z= 0.277 Chirality : 0.040 0.237 3971 Planarity : 0.004 0.075 4440 Dihedral : 4.646 51.006 3370 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.30 % Favored : 94.67 % Rotamer: Outliers : 2.63 % Allowed : 14.37 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.16), residues: 2946 helix: 2.36 (0.13), residues: 1529 sheet: 0.17 (0.37), residues: 186 loop : -1.78 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP O 273 HIS 0.006 0.001 HIS N 220 PHE 0.023 0.001 PHE O 109 TYR 0.013 0.001 TYR I 272 ARG 0.003 0.000 ARG Q 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 368 time to evaluate : 3.162 Fit side-chains REVERT: C 38 GLU cc_start: 0.7916 (tp30) cc_final: 0.7616 (tp30) REVERT: C 48 ARG cc_start: 0.7552 (ttt90) cc_final: 0.7112 (tmt170) REVERT: C 63 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7563 (mm-30) REVERT: D 107 HIS cc_start: 0.7627 (t70) cc_final: 0.7328 (t-90) REVERT: D 116 LYS cc_start: 0.7942 (ttpt) cc_final: 0.7682 (ttmt) REVERT: E 329 ARG cc_start: 0.7523 (mtm110) cc_final: 0.6213 (mmt180) REVERT: F 817 ARG cc_start: 0.6951 (mtp180) cc_final: 0.6101 (mtp85) REVERT: H 446 LYS cc_start: 0.8710 (ttpt) cc_final: 0.8434 (ptpt) REVERT: H 531 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7580 (tp30) REVERT: H 613 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7332 (mt-10) REVERT: I 183 PHE cc_start: 0.7403 (t80) cc_final: 0.6556 (p90) REVERT: I 191 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8563 (pp) REVERT: I 312 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7149 (pttt) REVERT: I 365 ARG cc_start: 0.7982 (ttp80) cc_final: 0.7749 (ttp80) REVERT: J 388 LYS cc_start: 0.7809 (mttt) cc_final: 0.7396 (mppt) REVERT: J 395 ASP cc_start: 0.8156 (m-30) cc_final: 0.7823 (m-30) REVERT: K 468 MET cc_start: 0.6989 (tmm) cc_final: 0.6772 (tmm) REVERT: K 499 SER cc_start: 0.7840 (m) cc_final: 0.7056 (p) REVERT: L 66 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6717 (mt-10) REVERT: L 149 ASP cc_start: 0.7454 (p0) cc_final: 0.6592 (p0) REVERT: M 445 GLN cc_start: 0.7886 (pt0) cc_final: 0.7579 (pp30) REVERT: N 28 MET cc_start: 0.4064 (tmm) cc_final: 0.3241 (tmm) REVERT: N 310 ASP cc_start: 0.8146 (m-30) cc_final: 0.7851 (m-30) REVERT: N 331 GLU cc_start: 0.7974 (pm20) cc_final: 0.7675 (pm20) REVERT: N 553 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8103 (tp) REVERT: O 48 TYR cc_start: 0.6451 (t80) cc_final: 0.6011 (t80) REVERT: O 122 LYS cc_start: 0.6738 (tttt) cc_final: 0.6148 (tmtt) REVERT: O 129 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7475 (pt0) REVERT: O 421 ASP cc_start: 0.7515 (t70) cc_final: 0.7301 (t0) REVERT: Q 265 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7980 (mp) REVERT: Q 303 LYS cc_start: 0.8606 (mttt) cc_final: 0.8109 (mmtt) REVERT: R 50 ARG cc_start: 0.7286 (ttt90) cc_final: 0.6925 (mtp-110) REVERT: R 83 PHE cc_start: 0.8904 (m-80) cc_final: 0.8467 (m-80) REVERT: R 259 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7858 (pt0) REVERT: S 218 ASN cc_start: 0.6599 (m-40) cc_final: 0.6171 (t0) outliers start: 73 outliers final: 50 residues processed: 415 average time/residue: 0.3761 time to fit residues: 241.5711 Evaluate side-chains 397 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 341 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain F residue 873 LYS Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 531 GLU Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain I residue 352 GLU Chi-restraints excluded: chain J residue 452 THR Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 357 GLN Chi-restraints excluded: chain N residue 553 ILE Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain Q residue 207 THR Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain Q residue 376 TRP Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain S residue 211 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 216 optimal weight: 0.9980 chunk 167 optimal weight: 6.9990 chunk 249 optimal weight: 8.9990 chunk 165 optimal weight: 0.0980 chunk 294 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 HIS ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 506 GLN J 394 ASN K 430 GLN ** N 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 HIS O 234 GLN O 484 ASN ** Q 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 264 ASN S 227 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25543 Z= 0.173 Angle : 0.520 14.076 34555 Z= 0.267 Chirality : 0.039 0.222 3971 Planarity : 0.004 0.072 4440 Dihedral : 4.482 50.142 3370 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.77 % Favored : 94.20 % Rotamer: Outliers : 2.59 % Allowed : 14.70 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.16), residues: 2946 helix: 2.53 (0.13), residues: 1521 sheet: 0.06 (0.36), residues: 198 loop : -1.70 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 273 HIS 0.007 0.001 HIS R 68 PHE 0.013 0.001 PHE I 85 TYR 0.013 0.001 TYR L 272 ARG 0.003 0.000 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 369 time to evaluate : 3.169 Fit side-chains revert: symmetry clash REVERT: C 38 GLU cc_start: 0.7970 (tp30) cc_final: 0.7635 (tp30) REVERT: C 48 ARG cc_start: 0.7583 (ttt90) cc_final: 0.7171 (tmt170) REVERT: C 63 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7548 (mm-30) REVERT: D 107 HIS cc_start: 0.7634 (t70) cc_final: 0.7338 (t-90) REVERT: D 116 LYS cc_start: 0.7968 (ttpt) cc_final: 0.7688 (ttmt) REVERT: E 329 ARG cc_start: 0.7510 (mtm110) cc_final: 0.6199 (mmt180) REVERT: E 397 LYS cc_start: 0.8876 (mtpp) cc_final: 0.8388 (pttt) REVERT: F 817 ARG cc_start: 0.6920 (mtp180) cc_final: 0.6056 (mtp85) REVERT: H 446 LYS cc_start: 0.8690 (ttpt) cc_final: 0.8437 (ptpt) REVERT: H 531 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7606 (tp30) REVERT: H 613 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7348 (mt-10) REVERT: I 183 PHE cc_start: 0.7387 (t80) cc_final: 0.6303 (p90) REVERT: I 192 ASP cc_start: 0.7396 (t0) cc_final: 0.7140 (t0) REVERT: I 193 THR cc_start: 0.8025 (t) cc_final: 0.7549 (t) REVERT: J 388 LYS cc_start: 0.7619 (mttt) cc_final: 0.7276 (mppt) REVERT: K 468 MET cc_start: 0.6975 (tmm) cc_final: 0.6761 (tmm) REVERT: K 499 SER cc_start: 0.7855 (m) cc_final: 0.7067 (p) REVERT: L 66 GLU cc_start: 0.6636 (mt-10) cc_final: 0.6372 (mt-10) REVERT: L 149 ASP cc_start: 0.7468 (p0) cc_final: 0.6614 (p0) REVERT: L 362 ASN cc_start: 0.8690 (m-40) cc_final: 0.8452 (m-40) REVERT: M 445 GLN cc_start: 0.7752 (pt0) cc_final: 0.7450 (pp30) REVERT: N 28 MET cc_start: 0.3686 (tmm) cc_final: 0.3084 (tmm) REVERT: N 310 ASP cc_start: 0.8134 (m-30) cc_final: 0.7821 (m-30) REVERT: N 553 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8071 (tp) REVERT: O 33 GLU cc_start: 0.5244 (mm-30) cc_final: 0.4899 (mm-30) REVERT: O 48 TYR cc_start: 0.5956 (t80) cc_final: 0.5530 (t80) REVERT: O 122 LYS cc_start: 0.6581 (tttt) cc_final: 0.6102 (tmtt) REVERT: O 129 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7486 (pt0) REVERT: O 406 GLU cc_start: 0.7537 (mp0) cc_final: 0.7138 (mp0) REVERT: O 491 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7485 (ttt-90) REVERT: Q 303 LYS cc_start: 0.8658 (mttt) cc_final: 0.8152 (mmtt) REVERT: R 50 ARG cc_start: 0.7313 (ttt90) cc_final: 0.6954 (mtp85) REVERT: R 83 PHE cc_start: 0.8881 (m-80) cc_final: 0.8468 (m-80) REVERT: R 229 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7892 (t0) REVERT: R 259 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7823 (pt0) REVERT: R 261 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8660 (tp) REVERT: S 199 MET cc_start: 0.8581 (ptp) cc_final: 0.8304 (pmm) REVERT: S 218 ASN cc_start: 0.6583 (m-40) cc_final: 0.6162 (t0) outliers start: 72 outliers final: 54 residues processed: 410 average time/residue: 0.3720 time to fit residues: 236.3511 Evaluate side-chains 408 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 348 time to evaluate : 3.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain F residue 811 LEU Chi-restraints excluded: chain F residue 873 LYS Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 530 LYS Chi-restraints excluded: chain H residue 531 GLU Chi-restraints excluded: chain H residue 588 THR Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain J residue 452 THR Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 147 CYS Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 357 GLN Chi-restraints excluded: chain N residue 553 ILE Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain O residue 491 ARG Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 229 ASP Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain S residue 211 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 200 optimal weight: 0.1980 chunk 145 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 231 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 HIS ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 506 GLN I 78 HIS I 255 HIS J 394 ASN K 402 GLN K 430 GLN K 501 GLN ** M 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 HIS Q 352 HIS S 227 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25543 Z= 0.201 Angle : 0.549 18.852 34555 Z= 0.277 Chirality : 0.040 0.215 3971 Planarity : 0.004 0.072 4440 Dihedral : 4.495 47.935 3370 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 2.59 % Allowed : 15.02 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.16), residues: 2946 helix: 2.55 (0.13), residues: 1522 sheet: 0.07 (0.37), residues: 189 loop : -1.64 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 273 HIS 0.005 0.001 HIS N 220 PHE 0.028 0.001 PHE O 109 TYR 0.013 0.001 TYR O 117 ARG 0.004 0.000 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 352 time to evaluate : 3.245 Fit side-chains revert: symmetry clash REVERT: C 38 GLU cc_start: 0.7954 (tp30) cc_final: 0.7617 (tp30) REVERT: C 48 ARG cc_start: 0.7587 (ttt90) cc_final: 0.7168 (tmt170) REVERT: C 63 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7671 (mm-30) REVERT: D 107 HIS cc_start: 0.7643 (t70) cc_final: 0.7339 (t-90) REVERT: D 116 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7664 (ttmt) REVERT: E 329 ARG cc_start: 0.7530 (mtm110) cc_final: 0.6197 (mmt180) REVERT: E 397 LYS cc_start: 0.8784 (mtpp) cc_final: 0.8548 (ptmt) REVERT: F 817 ARG cc_start: 0.6906 (mtp180) cc_final: 0.6033 (mtp85) REVERT: H 446 LYS cc_start: 0.8675 (ttpt) cc_final: 0.8421 (ptpt) REVERT: H 531 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7617 (tp30) REVERT: H 613 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7142 (mt-10) REVERT: I 183 PHE cc_start: 0.7385 (t80) cc_final: 0.6286 (p90) REVERT: I 191 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8572 (pp) REVERT: I 192 ASP cc_start: 0.7463 (t0) cc_final: 0.7179 (t0) REVERT: I 193 THR cc_start: 0.8074 (t) cc_final: 0.7639 (t) REVERT: J 388 LYS cc_start: 0.7629 (mttt) cc_final: 0.7270 (mppt) REVERT: J 395 ASP cc_start: 0.8160 (m-30) cc_final: 0.7818 (m-30) REVERT: J 493 LYS cc_start: 0.7002 (mtmm) cc_final: 0.6799 (pttp) REVERT: K 468 MET cc_start: 0.7071 (tmm) cc_final: 0.6836 (tmm) REVERT: K 499 SER cc_start: 0.7838 (m) cc_final: 0.7079 (p) REVERT: L 66 GLU cc_start: 0.6632 (mt-10) cc_final: 0.6373 (mt-10) REVERT: L 149 ASP cc_start: 0.7484 (p0) cc_final: 0.6619 (p0) REVERT: L 362 ASN cc_start: 0.8674 (m-40) cc_final: 0.8419 (m-40) REVERT: M 445 GLN cc_start: 0.7769 (pt0) cc_final: 0.7481 (pp30) REVERT: N 104 TYR cc_start: 0.9236 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: N 310 ASP cc_start: 0.8144 (m-30) cc_final: 0.7837 (m-30) REVERT: N 553 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8073 (tp) REVERT: O 33 GLU cc_start: 0.5224 (mm-30) cc_final: 0.4918 (mm-30) REVERT: O 48 TYR cc_start: 0.5929 (t80) cc_final: 0.5462 (t80) REVERT: O 109 PHE cc_start: 0.8153 (t80) cc_final: 0.7878 (t80) REVERT: O 122 LYS cc_start: 0.6541 (tttt) cc_final: 0.6052 (tmtt) REVERT: O 129 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7495 (pt0) REVERT: O 406 GLU cc_start: 0.7645 (mp0) cc_final: 0.7180 (mp0) REVERT: Q 303 LYS cc_start: 0.8667 (mttt) cc_final: 0.8159 (mmtt) REVERT: R 50 ARG cc_start: 0.7347 (ttt90) cc_final: 0.7042 (mtp85) REVERT: R 83 PHE cc_start: 0.8832 (m-80) cc_final: 0.8602 (m-80) REVERT: R 229 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.7926 (t0) REVERT: R 259 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7860 (pt0) REVERT: R 261 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8670 (tp) REVERT: S 198 LEU cc_start: 0.8654 (tt) cc_final: 0.8370 (tt) REVERT: S 218 ASN cc_start: 0.6768 (m-40) cc_final: 0.6151 (t0) outliers start: 72 outliers final: 56 residues processed: 400 average time/residue: 0.4119 time to fit residues: 256.8301 Evaluate side-chains 402 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 339 time to evaluate : 2.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain F residue 811 LEU Chi-restraints excluded: chain F residue 873 LYS Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 531 GLU Chi-restraints excluded: chain H residue 588 THR Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain J residue 452 THR Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 474 SER Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain N residue 147 CYS Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 357 GLN Chi-restraints excluded: chain N residue 553 ILE Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 80 PHE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 207 THR Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 229 ASP Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain S residue 211 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 274 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 215 optimal weight: 0.0370 chunk 84 optimal weight: 0.7980 chunk 248 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 chunk 273 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 23 GLN D 122 HIS ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 506 GLN J 394 ASN K 430 GLN K 501 GLN ** N 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 HIS ** O 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 352 HIS S 227 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25543 Z= 0.192 Angle : 0.544 17.288 34555 Z= 0.274 Chirality : 0.039 0.219 3971 Planarity : 0.004 0.071 4440 Dihedral : 4.399 47.426 3368 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.60 % Favored : 94.37 % Rotamer: Outliers : 2.67 % Allowed : 14.99 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.16), residues: 2946 helix: 2.59 (0.13), residues: 1520 sheet: 0.15 (0.37), residues: 189 loop : -1.62 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 273 HIS 0.005 0.001 HIS N 220 PHE 0.024 0.001 PHE O 109 TYR 0.014 0.001 TYR N 257 ARG 0.003 0.000 ARG Q 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 347 time to evaluate : 3.034 Fit side-chains revert: symmetry clash REVERT: C 38 GLU cc_start: 0.7953 (tp30) cc_final: 0.7621 (tp30) REVERT: C 48 ARG cc_start: 0.7549 (ttt90) cc_final: 0.7121 (tmt170) REVERT: C 63 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7540 (mm-30) REVERT: D 107 HIS cc_start: 0.7637 (t70) cc_final: 0.7337 (t-90) REVERT: D 116 LYS cc_start: 0.8027 (ttpt) cc_final: 0.7735 (ttmt) REVERT: E 397 LYS cc_start: 0.8898 (mtpp) cc_final: 0.8690 (mtpp) REVERT: F 817 ARG cc_start: 0.6934 (mtp180) cc_final: 0.6115 (mtp85) REVERT: H 531 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7610 (tp30) REVERT: H 613 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7149 (mt-10) REVERT: I 183 PHE cc_start: 0.7343 (t80) cc_final: 0.6241 (p90) REVERT: I 191 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8560 (pp) REVERT: I 192 ASP cc_start: 0.7481 (t0) cc_final: 0.7189 (t0) REVERT: I 193 THR cc_start: 0.8120 (t) cc_final: 0.7632 (t) REVERT: J 388 LYS cc_start: 0.7621 (mttt) cc_final: 0.7255 (mppt) REVERT: J 463 LYS cc_start: 0.7952 (mmmt) cc_final: 0.7709 (mttm) REVERT: K 468 MET cc_start: 0.7070 (tmm) cc_final: 0.6852 (tmm) REVERT: K 499 SER cc_start: 0.7661 (m) cc_final: 0.6821 (p) REVERT: L 66 GLU cc_start: 0.6636 (mt-10) cc_final: 0.6377 (mt-10) REVERT: L 362 ASN cc_start: 0.8607 (m-40) cc_final: 0.8352 (m-40) REVERT: M 445 GLN cc_start: 0.7759 (pt0) cc_final: 0.7475 (pp30) REVERT: N 310 ASP cc_start: 0.8136 (m-30) cc_final: 0.7821 (m-30) REVERT: N 553 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8069 (tp) REVERT: O 48 TYR cc_start: 0.5954 (t80) cc_final: 0.5479 (t80) REVERT: O 122 LYS cc_start: 0.6547 (tttt) cc_final: 0.6055 (tmtt) REVERT: O 129 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7489 (pt0) REVERT: O 406 GLU cc_start: 0.7863 (mp0) cc_final: 0.7478 (mp0) REVERT: Q 272 GLU cc_start: 0.7235 (pm20) cc_final: 0.7017 (pm20) REVERT: Q 303 LYS cc_start: 0.8682 (mttt) cc_final: 0.8174 (mmtt) REVERT: Q 338 LYS cc_start: 0.7713 (ttmt) cc_final: 0.7488 (tptt) REVERT: R 50 ARG cc_start: 0.7360 (ttt90) cc_final: 0.7032 (mtp85) REVERT: R 83 PHE cc_start: 0.8851 (m-80) cc_final: 0.8616 (m-80) REVERT: R 229 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.7936 (t0) REVERT: R 259 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7849 (pt0) REVERT: R 261 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8676 (tp) REVERT: S 198 LEU cc_start: 0.8598 (tt) cc_final: 0.8348 (tt) REVERT: S 199 MET cc_start: 0.8611 (ptp) cc_final: 0.8327 (pmm) REVERT: S 218 ASN cc_start: 0.6762 (m-40) cc_final: 0.6151 (t0) outliers start: 74 outliers final: 56 residues processed: 395 average time/residue: 0.3712 time to fit residues: 228.6548 Evaluate side-chains 400 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 338 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain F residue 873 LYS Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 531 GLU Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain J residue 452 THR Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 474 SER Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 501 GLN Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 147 CYS Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 357 GLN Chi-restraints excluded: chain N residue 553 ILE Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 80 PHE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 176 ILE Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 207 THR Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain Q residue 376 TRP Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 229 ASP Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain S residue 211 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 0.8980 chunk 177 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 chunk 304 optimal weight: 10.0000 chunk 280 optimal weight: 5.9990 chunk 242 optimal weight: 0.6980 chunk 25 optimal weight: 0.0670 chunk 187 optimal weight: 0.9980 chunk 148 optimal weight: 0.0670 chunk 192 optimal weight: 0.9980 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 HIS E 331 ASN H 506 GLN K 394 ASN K 430 GLN ** N 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 HIS O 196 GLN ** O 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 352 HIS S 227 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25543 Z= 0.152 Angle : 0.527 17.398 34555 Z= 0.267 Chirality : 0.039 0.219 3971 Planarity : 0.004 0.069 4440 Dihedral : 4.299 45.472 3368 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.23 % Favored : 94.74 % Rotamer: Outliers : 2.13 % Allowed : 15.45 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.16), residues: 2946 helix: 2.69 (0.13), residues: 1520 sheet: 0.23 (0.38), residues: 191 loop : -1.55 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 273 HIS 0.005 0.001 HIS N 220 PHE 0.026 0.001 PHE N 29 TYR 0.013 0.001 TYR I 136 ARG 0.003 0.000 ARG D 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 349 time to evaluate : 3.008 Fit side-chains revert: symmetry clash REVERT: C 38 GLU cc_start: 0.7961 (tp30) cc_final: 0.7622 (tp30) REVERT: C 48 ARG cc_start: 0.7516 (ttt90) cc_final: 0.7113 (tmt170) REVERT: C 63 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7616 (mm-30) REVERT: D 107 HIS cc_start: 0.7627 (t70) cc_final: 0.7328 (t-90) REVERT: D 116 LYS cc_start: 0.8045 (ttpt) cc_final: 0.7810 (ttmt) REVERT: F 817 ARG cc_start: 0.6936 (mtp180) cc_final: 0.5944 (mtp85) REVERT: H 531 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7719 (tp30) REVERT: H 613 GLU cc_start: 0.7606 (mt-10) cc_final: 0.6910 (mm-30) REVERT: I 183 PHE cc_start: 0.7262 (t80) cc_final: 0.6190 (p90) REVERT: I 191 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8557 (pp) REVERT: I 192 ASP cc_start: 0.7427 (t0) cc_final: 0.7128 (t0) REVERT: I 193 THR cc_start: 0.8040 (t) cc_final: 0.7598 (t) REVERT: J 388 LYS cc_start: 0.7635 (mttt) cc_final: 0.7160 (mppt) REVERT: K 468 MET cc_start: 0.7065 (tmm) cc_final: 0.6849 (tmm) REVERT: K 499 SER cc_start: 0.7627 (m) cc_final: 0.6765 (p) REVERT: L 66 GLU cc_start: 0.6598 (mt-10) cc_final: 0.6342 (mt-10) REVERT: M 445 GLN cc_start: 0.7737 (pt0) cc_final: 0.7444 (pp30) REVERT: N 73 LYS cc_start: 0.8659 (mtpt) cc_final: 0.8397 (mtmt) REVERT: N 293 VAL cc_start: 0.8090 (t) cc_final: 0.7712 (t) REVERT: N 310 ASP cc_start: 0.8104 (m-30) cc_final: 0.7794 (m-30) REVERT: N 553 ILE cc_start: 0.8487 (tt) cc_final: 0.8066 (tp) REVERT: O 48 TYR cc_start: 0.5961 (t80) cc_final: 0.5480 (t80) REVERT: O 122 LYS cc_start: 0.6531 (tttt) cc_final: 0.6039 (tmtt) REVERT: O 129 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7461 (pt0) REVERT: O 215 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7543 (m-30) REVERT: O 406 GLU cc_start: 0.7978 (mp0) cc_final: 0.7563 (mp0) REVERT: Q 245 MET cc_start: 0.6892 (mmm) cc_final: 0.6541 (mmt) REVERT: Q 272 GLU cc_start: 0.7206 (pm20) cc_final: 0.6997 (pm20) REVERT: Q 303 LYS cc_start: 0.8686 (mttt) cc_final: 0.8174 (mmtt) REVERT: Q 338 LYS cc_start: 0.7742 (ttmt) cc_final: 0.7521 (tptt) REVERT: R 50 ARG cc_start: 0.7346 (ttt90) cc_final: 0.7020 (mtp85) REVERT: R 229 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7891 (t0) REVERT: R 259 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7812 (pt0) REVERT: R 261 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8646 (tp) REVERT: S 198 LEU cc_start: 0.8569 (tt) cc_final: 0.8356 (tt) REVERT: S 199 MET cc_start: 0.8595 (ptp) cc_final: 0.8312 (pmm) REVERT: S 218 ASN cc_start: 0.6745 (m-40) cc_final: 0.6156 (t0) outliers start: 59 outliers final: 46 residues processed: 388 average time/residue: 0.3718 time to fit residues: 226.1674 Evaluate side-chains 387 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 335 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain F residue 811 LEU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 531 GLU Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 147 CYS Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 80 PHE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 176 ILE Chi-restraints excluded: chain O residue 215 ASP Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 207 THR Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 229 ASP Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain S residue 211 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 223 optimal weight: 0.0570 chunk 35 optimal weight: 0.0060 chunk 67 optimal weight: 3.9990 chunk 243 optimal weight: 0.4980 chunk 101 optimal weight: 8.9990 chunk 249 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 213 optimal weight: 0.9990 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 23 GLN D 122 HIS H 506 GLN K 394 ASN K 430 GLN K 478 GLN K 501 GLN ** N 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 HIS O 196 GLN ** O 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 352 HIS S 227 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.158476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.114362 restraints weight = 36455.054| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.40 r_work: 0.3214 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25543 Z= 0.150 Angle : 0.524 17.017 34555 Z= 0.265 Chirality : 0.039 0.219 3971 Planarity : 0.004 0.066 4440 Dihedral : 4.198 45.375 3366 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.30 % Favored : 94.67 % Rotamer: Outliers : 2.05 % Allowed : 15.74 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.16), residues: 2946 helix: 2.71 (0.13), residues: 1522 sheet: 0.26 (0.37), residues: 192 loop : -1.49 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 319 HIS 0.005 0.001 HIS N 220 PHE 0.046 0.001 PHE R 83 TYR 0.017 0.001 TYR H 455 ARG 0.004 0.000 ARG N 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6495.87 seconds wall clock time: 115 minutes 36.83 seconds (6936.83 seconds total)