Starting phenix.real_space_refine on Sat Aug 8 03:06:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h67_34495/08_2026/8h67_34495.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h67_34495/08_2026/8h67_34495.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h67_34495/08_2026/8h67_34495.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h67_34495/08_2026/8h67_34495.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h67_34495/08_2026/8h67_34495.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h67_34495/08_2026/8h67_34495.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 58 5.49 5 S 76 5.16 5 C 16150 2.51 5 N 4382 2.21 5 O 4956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25622 Number of models: 1 Model: "" Number of chains: 15 Chain: "B" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 794 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 13, 'rna3p_pyr': 21} Link IDs: {'rna2p': 4, 'rna3p': 33} Chain: "C" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 229 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "D" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 182 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1664 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 189} Chain breaks: 1 Chain: "E" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2366 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain: "F" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2366 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain: "G" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2366 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain: "H" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2366 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain: "J" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2252 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 15, 'TRANS': 268} Chain breaks: 2 Chain: "K" Number of atoms: 1911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1911 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 13, 'TRANS': 227} Chain breaks: 4 Chain: "L" Number of atoms: 4051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 4051 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 17, 'TRANS': 478} Chain breaks: 4 Chain: "M" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 897 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain breaks: 1 Chain: "N" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 918 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "O" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 894 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 2, 'TRANS': 104} Chain: "I" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2366 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 283} Time building chain proxies: 5.77, per 1000 atoms: 0.23 Number of scatterers: 25622 At special positions: 0 Unit cell: (105.6, 121.44, 224.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 P 58 15.00 O 4956 8.00 N 4382 7.00 C 16150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.2 seconds 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5794 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 28 sheets defined 36.7% alpha, 6.8% beta 2 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 2.67 Creating SS restraints... Processing helix chain 'A' and resid 40 through 52 Processing helix chain 'A' and resid 105 through 111 removed outlier: 3.857A pdb=" N THR A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'E' and resid 45 through 60 removed outlier: 4.102A pdb=" N MET E 49 " --> pdb=" O SER E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 removed outlier: 3.732A pdb=" N PHE E 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 194 Processing helix chain 'E' and resid 236 through 249 Processing helix chain 'E' and resid 269 through 278 Processing helix chain 'E' and resid 286 through 300 removed outlier: 4.284A pdb=" N GLY E 300 " --> pdb=" O ASP E 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 60 removed outlier: 3.874A pdb=" N MET F 49 " --> pdb=" O SER F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 107 removed outlier: 3.559A pdb=" N MET F 107 " --> pdb=" O ALA F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 195 removed outlier: 4.123A pdb=" N TRP F 184 " --> pdb=" O ALA F 180 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS F 186 " --> pdb=" O PRO F 182 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU F 194 " --> pdb=" O GLN F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 235 removed outlier: 3.536A pdb=" N GLU F 234 " --> pdb=" O PHE F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 244 removed outlier: 3.708A pdb=" N THR F 244 " --> pdb=" O SER F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 267 removed outlier: 3.662A pdb=" N VAL F 265 " --> pdb=" O GLY F 261 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 278 removed outlier: 3.750A pdb=" N GLU F 277 " --> pdb=" O LYS F 273 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA F 278 " --> pdb=" O ALA F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 300 Processing helix chain 'G' and resid 47 through 60 removed outlier: 3.699A pdb=" N ASN G 51 " --> pdb=" O GLU G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 94 Processing helix chain 'G' and resid 180 through 195 removed outlier: 3.852A pdb=" N TRP G 184 " --> pdb=" O ALA G 180 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA G 193 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU G 194 " --> pdb=" O GLN G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 245 Processing helix chain 'G' and resid 262 through 267 removed outlier: 3.754A pdb=" N LYS G 267 " --> pdb=" O GLU G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 276 removed outlier: 3.727A pdb=" N LYS G 273 " --> pdb=" O ASP G 269 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA G 274 " --> pdb=" O GLN G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 300 removed outlier: 3.967A pdb=" N LEU G 290 " --> pdb=" O ASN G 286 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE G 291 " --> pdb=" O PRO G 287 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA G 292 " --> pdb=" O GLU G 288 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP G 293 " --> pdb=" O LYS G 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 60 removed outlier: 3.698A pdb=" N ASN H 51 " --> pdb=" O GLU H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 94 Processing helix chain 'H' and resid 180 through 195 removed outlier: 3.852A pdb=" N TRP H 184 " --> pdb=" O ALA H 180 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU H 194 " --> pdb=" O GLN H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 245 Processing helix chain 'H' and resid 262 through 267 removed outlier: 3.753A pdb=" N LYS H 267 " --> pdb=" O GLU H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 276 removed outlier: 3.727A pdb=" N LYS H 273 " --> pdb=" O ASP H 269 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA H 274 " --> pdb=" O GLN H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 300 removed outlier: 3.968A pdb=" N LEU H 290 " --> pdb=" O ASN H 286 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE H 291 " --> pdb=" O PRO H 287 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA H 292 " --> pdb=" O GLU H 288 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP H 293 " --> pdb=" O LYS H 289 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 60 removed outlier: 4.119A pdb=" N ASN J 51 " --> pdb=" O GLU J 47 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU J 55 " --> pdb=" O ASN J 51 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET J 56 " --> pdb=" O ALA J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 94 removed outlier: 3.823A pdb=" N PHE J 92 " --> pdb=" O PHE J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 107 removed outlier: 3.505A pdb=" N MET J 107 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 193 removed outlier: 4.196A pdb=" N ALA J 193 " --> pdb=" O LEU J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 245 Processing helix chain 'J' and resid 263 through 267 Processing helix chain 'J' and resid 269 through 278 removed outlier: 3.826A pdb=" N LYS J 273 " --> pdb=" O ASP J 269 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA J 274 " --> pdb=" O GLN J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 300 removed outlier: 3.552A pdb=" N GLY J 300 " --> pdb=" O ASP J 296 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 60 removed outlier: 4.110A pdb=" N ARG K 54 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU K 55 " --> pdb=" O ASN K 51 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET K 56 " --> pdb=" O ALA K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 94 removed outlier: 4.165A pdb=" N PHE K 92 " --> pdb=" O PHE K 88 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE K 94 " --> pdb=" O ASP K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 180 removed outlier: 3.527A pdb=" N ALA K 179 " --> pdb=" O LYS K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 195 removed outlier: 4.211A pdb=" N VAL K 185 " --> pdb=" O LYS K 181 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA K 187 " --> pdb=" O GLU K 183 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N GLN K 190 " --> pdb=" O LYS K 186 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA K 193 " --> pdb=" O LEU K 189 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU K 194 " --> pdb=" O GLN K 190 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU K 195 " --> pdb=" O ALA K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 271 through 279 removed outlier: 3.650A pdb=" N GLN K 275 " --> pdb=" O GLU K 271 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU K 276 " --> pdb=" O GLN K 272 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 299 removed outlier: 4.255A pdb=" N ALA K 292 " --> pdb=" O GLU K 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 18 No H-bonds generated for 'chain 'L' and resid 16 through 18' Processing helix chain 'L' and resid 20 through 38 removed outlier: 3.701A pdb=" N ARG L 24 " --> pdb=" O SER L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 51 Processing helix chain 'L' and resid 69 through 81 Processing helix chain 'L' and resid 126 through 132 removed outlier: 3.578A pdb=" N LEU L 129 " --> pdb=" O GLY L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 137 No H-bonds generated for 'chain 'L' and resid 135 through 137' Processing helix chain 'L' and resid 138 through 151 Processing helix chain 'L' and resid 155 through 158 Processing helix chain 'L' and resid 159 through 165 removed outlier: 3.557A pdb=" N ARG L 165 " --> pdb=" O PRO L 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 169 through 173 Processing helix chain 'L' and resid 177 through 189 removed outlier: 3.625A pdb=" N GLU L 181 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER L 182 " --> pdb=" O LYS L 178 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN L 189 " --> pdb=" O LYS L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 217 through 224 removed outlier: 3.653A pdb=" N LEU L 224 " --> pdb=" O TRP L 220 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 230 removed outlier: 5.429A pdb=" N ALA L 228 " --> pdb=" O HIS L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 273 Proline residue: L 268 - end of helix removed outlier: 3.566A pdb=" N SER L 272 " --> pdb=" O PRO L 268 " (cutoff:3.500A) Processing helix chain 'L' and resid 290 through 309 removed outlier: 4.157A pdb=" N GLY L 294 " --> pdb=" O VAL L 290 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA L 295 " --> pdb=" O PRO L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 318 Processing helix chain 'L' and resid 345 through 356 removed outlier: 3.832A pdb=" N VAL L 349 " --> pdb=" O ASN L 345 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA L 354 " --> pdb=" O ASP L 350 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE L 355 " --> pdb=" O ASP L 351 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS L 356 " --> pdb=" O TYR L 352 " (cutoff:3.500A) Processing helix chain 'L' and resid 364 through 373 removed outlier: 3.794A pdb=" N VAL L 373 " --> pdb=" O LEU L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 388 removed outlier: 3.639A pdb=" N ARG L 387 " --> pdb=" O TRP L 384 " (cutoff:3.500A) Processing helix chain 'L' and resid 390 through 400 removed outlier: 3.522A pdb=" N LEU L 397 " --> pdb=" O PHE L 393 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE L 400 " --> pdb=" O LEU L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 406 removed outlier: 3.910A pdb=" N LEU L 405 " --> pdb=" O PRO L 401 " (cutoff:3.500A) Processing helix chain 'L' and resid 409 through 423 removed outlier: 3.857A pdb=" N SER L 413 " --> pdb=" O ASN L 409 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP L 415 " --> pdb=" O TYR L 411 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA L 416 " --> pdb=" O PHE L 412 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR L 421 " --> pdb=" O ARG L 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 435 through 459 removed outlier: 3.713A pdb=" N VAL L 442 " --> pdb=" O TYR L 438 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR L 443 " --> pdb=" O ALA L 439 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS L 458 " --> pdb=" O LEU L 454 " (cutoff:3.500A) Processing helix chain 'L' and resid 461 through 468 removed outlier: 3.726A pdb=" N GLY L 467 " --> pdb=" O SER L 463 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN L 468 " --> pdb=" O LYS L 464 " (cutoff:3.500A) Processing helix chain 'L' and resid 471 through 492 removed outlier: 3.638A pdb=" N TYR L 475 " --> pdb=" O LEU L 471 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU L 485 " --> pdb=" O LYS L 481 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA L 486 " --> pdb=" O VAL L 482 " (cutoff:3.500A) Processing helix chain 'L' and resid 497 through 502 removed outlier: 3.790A pdb=" N ASP L 501 " --> pdb=" O GLN L 497 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR L 502 " --> pdb=" O ALA L 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 497 through 502' Processing helix chain 'L' and resid 502 through 507 removed outlier: 3.539A pdb=" N THR L 506 " --> pdb=" O TYR L 502 " (cutoff:3.500A) Processing helix chain 'L' and resid 519 through 527 removed outlier: 4.533A pdb=" N GLN L 525 " --> pdb=" O GLN L 521 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR L 527 " --> pdb=" O LEU L 523 " (cutoff:3.500A) Processing helix chain 'L' and resid 528 through 539 removed outlier: 3.848A pdb=" N SER L 539 " --> pdb=" O LEU L 535 " (cutoff:3.500A) Processing helix chain 'L' and resid 540 through 542 No H-bonds generated for 'chain 'L' and resid 540 through 542' Processing helix chain 'M' and resid 10 through 31 Processing helix chain 'M' and resid 34 through 41 removed outlier: 4.136A pdb=" N ASN M 41 " --> pdb=" O LYS M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 66 removed outlier: 3.879A pdb=" N GLU M 47 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA M 59 " --> pdb=" O VAL M 55 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG M 64 " --> pdb=" O PHE M 60 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG M 66 " --> pdb=" O ALA M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 72 removed outlier: 3.588A pdb=" N GLN M 70 " --> pdb=" O THR M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 80 Processing helix chain 'M' and resid 87 through 98 removed outlier: 4.000A pdb=" N ASP M 91 " --> pdb=" O ASP M 87 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN M 98 " --> pdb=" O GLN M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 115 removed outlier: 3.619A pdb=" N ARG M 104 " --> pdb=" O THR M 100 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU M 108 " --> pdb=" O ARG M 104 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU M 109 " --> pdb=" O SER M 105 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA M 110 " --> pdb=" O LEU M 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 31 Processing helix chain 'N' and resid 43 through 66 removed outlier: 3.865A pdb=" N ARG N 66 " --> pdb=" O ALA N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 69 through 76 Processing helix chain 'N' and resid 101 through 114 Processing helix chain 'O' and resid 10 through 31 removed outlier: 3.614A pdb=" N GLN O 20 " --> pdb=" O TYR O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 33 through 40 removed outlier: 3.813A pdb=" N LYS O 37 " --> pdb=" O GLN O 34 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS O 39 " --> pdb=" O SER O 36 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 64 removed outlier: 4.303A pdb=" N GLU O 45 " --> pdb=" O ASN O 41 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG O 46 " --> pdb=" O PRO O 42 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU O 47 " --> pdb=" O LYS O 43 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL O 56 " --> pdb=" O LYS O 52 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU O 58 " --> pdb=" O LYS O 54 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU O 61 " --> pdb=" O ASN O 57 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA O 62 " --> pdb=" O GLU O 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 81 removed outlier: 3.654A pdb=" N PHE O 72 " --> pdb=" O GLU O 68 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE O 76 " --> pdb=" O PHE O 72 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL O 77 " --> pdb=" O ILE O 73 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU O 80 " --> pdb=" O PHE O 76 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR O 81 " --> pdb=" O VAL O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 84 through 91 removed outlier: 3.554A pdb=" N GLU O 88 " --> pdb=" O VAL O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 98 removed outlier: 4.357A pdb=" N LYS O 95 " --> pdb=" O ASP O 91 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 115 removed outlier: 3.647A pdb=" N ARG O 104 " --> pdb=" O THR O 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 60 removed outlier: 3.698A pdb=" N ASN I 51 " --> pdb=" O GLU I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 94 Processing helix chain 'I' and resid 180 through 195 removed outlier: 3.852A pdb=" N TRP I 184 " --> pdb=" O ALA I 180 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA I 193 " --> pdb=" O LEU I 189 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU I 194 " --> pdb=" O GLN I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 245 Processing helix chain 'I' and resid 262 through 267 removed outlier: 3.754A pdb=" N LYS I 267 " --> pdb=" O GLU I 263 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 276 removed outlier: 3.726A pdb=" N LYS I 273 " --> pdb=" O ASP I 269 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA I 274 " --> pdb=" O GLN I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 300 removed outlier: 3.967A pdb=" N LEU I 290 " --> pdb=" O ASN I 286 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE I 291 " --> pdb=" O PRO I 287 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA I 292 " --> pdb=" O GLU I 288 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP I 293 " --> pdb=" O LYS I 289 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 131 removed outlier: 3.657A pdb=" N LYS A 18 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU A 172 " --> pdb=" O LYS A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 136 removed outlier: 3.653A pdb=" N ALA A 77 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU A 76 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 90 Processing sheet with id=AA5, first strand: chain 'E' and resid 9 through 11 removed outlier: 3.503A pdb=" N GLN E 168 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL E 126 " --> pdb=" O GLN E 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 28 through 29 removed outlier: 4.009A pdb=" N SER E 29 " --> pdb=" O HIS E 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.959A pdb=" N LEU E 69 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA E 76 " --> pdb=" O LEU E 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 6 through 11 removed outlier: 4.014A pdb=" N LEU F 6 " --> pdb=" O LEU F 173 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 33 through 36 Processing sheet with id=AB1, first strand: chain 'G' and resid 121 through 122 removed outlier: 3.918A pdb=" N PHE G 7 " --> pdb=" O ARG G 217 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU G 11 " --> pdb=" O SER G 213 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N SER G 213 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP G 259 " --> pdb=" O ALA G 216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 15 through 17 removed outlier: 3.757A pdb=" N ALA G 15 " --> pdb=" O THR G 165 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 34 through 36 removed outlier: 7.366A pdb=" N ILE G 34 " --> pdb=" O TYR G 41 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR G 41 " --> pdb=" O ILE G 34 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 68 through 69 removed outlier: 3.601A pdb=" N LEU G 69 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA G 76 " --> pdb=" O LEU G 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'H' and resid 121 through 122 removed outlier: 3.918A pdb=" N PHE H 7 " --> pdb=" O ARG H 217 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU H 11 " --> pdb=" O SER H 213 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N SER H 213 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TRP H 259 " --> pdb=" O ALA H 216 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 15 through 17 removed outlier: 3.757A pdb=" N ALA H 15 " --> pdb=" O THR H 165 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 34 through 36 removed outlier: 7.366A pdb=" N ILE H 34 " --> pdb=" O TYR H 41 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR H 41 " --> pdb=" O ILE H 34 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 68 through 69 removed outlier: 3.601A pdb=" N LEU H 69 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA H 76 " --> pdb=" O LEU H 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'J' and resid 43 through 44 removed outlier: 3.647A pdb=" N ILE J 44 " --> pdb=" O ALA J 125 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA J 125 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE J 167 " --> pdb=" O THR J 12 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR J 12 " --> pdb=" O PHE J 167 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR J 9 " --> pdb=" O VAL J 215 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL J 215 " --> pdb=" O THR J 9 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 66 through 68 Processing sheet with id=AC2, first strand: chain 'L' and resid 9 through 14 Processing sheet with id=AC3, first strand: chain 'L' and resid 83 through 88 removed outlier: 3.570A pdb=" N ARG L 88 " --> pdb=" O TYR L 119 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR L 119 " --> pdb=" O ARG L 88 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 232 through 234 removed outlier: 4.346A pdb=" N GLY L 321 " --> pdb=" O ASP L 256 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL L 322 " --> pdb=" O TYR L 341 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYR L 341 " --> pdb=" O VAL L 322 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL L 324 " --> pdb=" O VAL L 339 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL L 339 " --> pdb=" O VAL L 324 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N HIS L 326 " --> pdb=" O HIS L 337 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 237 through 239 Processing sheet with id=AC6, first strand: chain 'L' and resid 278 through 279 Processing sheet with id=AC7, first strand: chain 'I' and resid 121 through 122 removed outlier: 3.918A pdb=" N PHE I 7 " --> pdb=" O ARG I 217 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LEU I 11 " --> pdb=" O SER I 213 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N SER I 213 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TRP I 259 " --> pdb=" O ALA I 216 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 15 through 17 removed outlier: 3.756A pdb=" N ALA I 15 " --> pdb=" O THR I 165 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 34 through 36 removed outlier: 7.366A pdb=" N ILE I 34 " --> pdb=" O TYR I 41 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR I 41 " --> pdb=" O ILE I 34 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 68 through 69 removed outlier: 3.601A pdb=" N LEU I 69 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA I 76 " --> pdb=" O LEU I 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 716 hydrogen bonds defined for protein. 1980 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4 hydrogen bonds 8 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 5.06 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7968 1.34 - 1.46: 4333 1.46 - 1.57: 13778 1.57 - 1.69: 112 1.69 - 1.81: 128 Bond restraints: 26319 Sorted by residual: bond pdb=" O3' C B 24 " pdb=" P A B 25 " ideal model delta sigma weight residual 1.607 1.567 0.040 1.20e-02 6.94e+03 1.12e+01 bond pdb=" C LYS F 181 " pdb=" N PRO F 182 " ideal model delta sigma weight residual 1.334 1.379 -0.044 1.51e-02 4.39e+03 8.61e+00 bond pdb=" N9 A B 14 " pdb=" C4 A B 14 " ideal model delta sigma weight residual 1.374 1.388 -0.014 6.00e-03 2.78e+04 5.25e+00 bond pdb=" O3' A B 25 " pdb=" P A B 26 " ideal model delta sigma weight residual 1.607 1.582 0.025 1.20e-02 6.94e+03 4.22e+00 bond pdb=" C1' G B 4 " pdb=" N9 G B 4 " ideal model delta sigma weight residual 1.483 1.459 0.024 1.50e-02 4.44e+03 2.59e+00 ... (remaining 26314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 34989 1.96 - 3.93: 746 3.93 - 5.89: 110 5.89 - 7.86: 25 7.86 - 9.82: 7 Bond angle restraints: 35877 Sorted by residual: angle pdb=" N GLN I 139 " pdb=" CA GLN I 139 " pdb=" C GLN I 139 " ideal model delta sigma weight residual 109.40 117.70 -8.30 1.63e+00 3.76e-01 2.59e+01 angle pdb=" N GLY A 104 " pdb=" CA GLY A 104 " pdb=" C GLY A 104 " ideal model delta sigma weight residual 112.51 119.68 -7.17 1.53e+00 4.27e-01 2.20e+01 angle pdb=" N LYS A 105 " pdb=" CA LYS A 105 " pdb=" C LYS A 105 " ideal model delta sigma weight residual 108.08 116.00 -7.92 1.69e+00 3.50e-01 2.20e+01 angle pdb=" N GLU I 23 " pdb=" CA GLU I 23 " pdb=" C GLU I 23 " ideal model delta sigma weight residual 112.24 106.35 5.89 1.28e+00 6.10e-01 2.12e+01 angle pdb=" C LYS A 105 " pdb=" CA LYS A 105 " pdb=" CB LYS A 105 " ideal model delta sigma weight residual 116.63 111.36 5.27 1.16e+00 7.43e-01 2.06e+01 ... (remaining 35872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.71: 15332 33.71 - 67.42: 485 67.42 - 101.14: 57 101.14 - 134.85: 2 134.85 - 168.56: 2 Dihedral angle restraints: 15878 sinusoidal: 6920 harmonic: 8958 Sorted by residual: dihedral pdb=" O4' U B 35 " pdb=" C1' U B 35 " pdb=" N1 U B 35 " pdb=" C2 U B 35 " ideal model delta sinusoidal sigma weight residual 200.00 43.71 156.29 1 1.50e+01 4.44e-03 8.17e+01 dihedral pdb=" CA ASN L 208 " pdb=" C ASN L 208 " pdb=" N ALA L 209 " pdb=" CA ALA L 209 " ideal model delta harmonic sigma weight residual 180.00 154.23 25.77 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA LYS F 181 " pdb=" C LYS F 181 " pdb=" N PRO F 182 " pdb=" CA PRO F 182 " ideal model delta harmonic sigma weight residual -180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 15875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3172 0.053 - 0.106: 578 0.106 - 0.160: 119 0.160 - 0.213: 16 0.213 - 0.266: 2 Chirality restraints: 3887 Sorted by residual: chirality pdb=" CA VAL A 100 " pdb=" N VAL A 100 " pdb=" C VAL A 100 " pdb=" CB VAL A 100 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA LYS A 105 " pdb=" N LYS A 105 " pdb=" C LYS A 105 " pdb=" CB LYS A 105 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA ARG E 242 " pdb=" N ARG E 242 " pdb=" C ARG E 242 " pdb=" CB ARG E 242 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.20e-01 ... (remaining 3884 not shown) Planarity restraints: 4474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 291 " -0.020 2.00e-02 2.50e+03 1.92e-02 6.44e+00 pdb=" CG PHE F 291 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE F 291 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE F 291 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE F 291 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 291 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE F 291 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 212 " -0.224 9.50e-02 1.11e+02 1.00e-01 6.21e+00 pdb=" NE ARG K 212 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG K 212 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG K 212 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG K 212 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 89 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.88e+00 pdb=" C ALA E 89 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA E 89 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP E 90 " 0.014 2.00e-02 2.50e+03 ... (remaining 4471 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 159 2.45 - 3.06: 17324 3.06 - 3.67: 40916 3.67 - 4.29: 54173 4.29 - 4.90: 86404 Nonbonded interactions: 198976 Sorted by model distance: nonbonded pdb=" N7 A B 25 " pdb=" OE2 GLU H 47 " model vdw 1.834 3.120 nonbonded pdb=" O2' G B 2 " pdb=" O4' A B 3 " model vdw 1.967 3.040 nonbonded pdb=" O5' A B 25 " pdb=" NH2 ARG H 68 " model vdw 2.003 3.120 nonbonded pdb=" CG2 VAL J 223 " pdb=" ND2 ASN I 196 " model vdw 2.008 3.540 nonbonded pdb=" OD2 ASP H 134 " pdb=" CD1 ILE I 34 " model vdw 2.024 3.460 ... (remaining 198971 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 'E' and (resid 3 through 21 or resid 28 through 148 or resid 157 through \ 300)) selection = (chain 'F' and (resid 3 through 21 or resid 28 through 148 or resid 157 through \ 300)) selection = (chain 'G' and (resid 3 through 21 or resid 28 through 148 or resid 157 through \ 300)) selection = (chain 'H' and (resid 3 through 21 or resid 28 through 148 or resid 157 through \ 300)) selection = (chain 'I' and (resid 3 through 21 or resid 28 through 148 or resid 157 through \ 300)) selection = chain 'J' } ncs_group { reference = (chain 'M' and resid 9 through 115) selection = (chain 'N' and (resid 9 through 82 or resid 86 through 115)) selection = (chain 'O' and (resid 9 through 82 or resid 86 through 115)) } 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 group one per residue 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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 25.720 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 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 : 0.003 0.044 26319 Z= 0.148 Angle : 0.681 9.822 35877 Z= 0.368 Chirality : 0.044 0.266 3887 Planarity : 0.004 0.100 4474 Dihedral : 16.400 168.561 10084 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.63 % Favored : 90.14 % Rotamer: Outliers : 0.08 % Allowed : 0.51 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.15), residues: 3002 helix: -0.31 (0.18), residues: 866 sheet: -1.84 (0.32), residues: 240 loop : -2.54 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 266 TYR 0.021 0.001 TYR O 75 PHE 0.044 0.001 PHE F 291 TRP 0.012 0.001 TRP E 237 HIS 0.003 0.001 HIS E 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (26319) covalent geometry : angle 0.68133 / 0.37 (35877) hydrogen bonds : bond 0.21431 / 21.97 ( 720) hydrogen bonds : angle 7.09864 / 9.31 ( 1988) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 237 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.4833 (pp30) cc_final: 0.4604 (pp30) REVERT: E 49 MET cc_start: 0.8770 (mpp) cc_final: 0.8345 (mpp) REVERT: E 124 MET cc_start: 0.8673 (ppp) cc_final: 0.8231 (ppp) REVERT: F 268 MET cc_start: 0.8070 (tpt) cc_final: 0.7594 (tmm) REVERT: F 291 PHE cc_start: 0.9162 (t80) cc_final: 0.8773 (t80) REVERT: G 49 MET cc_start: 0.9251 (pmm) cc_final: 0.8997 (pmm) REVERT: G 195 LEU cc_start: 0.9553 (tp) cc_final: 0.9323 (tp) REVERT: H 107 MET cc_start: 0.9408 (ppp) cc_final: 0.9139 (ppp) REVERT: H 169 TYR cc_start: 0.7100 (t80) cc_final: 0.6511 (t80) REVERT: H 268 MET cc_start: 0.7629 (tmm) cc_final: 0.7311 (ppp) REVERT: J 107 MET cc_start: 0.9274 (tpp) cc_final: 0.9006 (tpp) REVERT: J 124 MET cc_start: 0.8884 (pmm) cc_final: 0.8635 (pmm) REVERT: L 335 LYS cc_start: 0.9477 (mmpt) cc_final: 0.9158 (tppt) REVERT: L 390 TRP cc_start: 0.8610 (p-90) cc_final: 0.8359 (p-90) REVERT: N 75 TYR cc_start: 0.8266 (m-80) cc_final: 0.8062 (m-10) REVERT: O 72 PHE cc_start: 0.9276 (m-10) cc_final: 0.8747 (m-80) REVERT: I 119 ILE cc_start: 0.9183 (mm) cc_final: 0.8980 (mp) REVERT: I 279 MET cc_start: 0.6186 (ptp) cc_final: 0.5928 (ptp) outliers start: 2 outliers final: 1 residues processed: 239 average time/residue: 0.1748 time to fit residues: 67.4320 Evaluate side-chains 157 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 116 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 19 ASN E 65 ASN H 19 ASN ** K 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.057777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.047187 restraints weight = 199954.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.048469 restraints weight = 121945.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.049294 restraints weight = 86190.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.049902 restraints weight = 67435.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.050336 restraints weight = 56433.382| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26319 Z= 0.173 Angle : 0.709 11.294 35877 Z= 0.362 Chirality : 0.044 0.199 3887 Planarity : 0.005 0.064 4474 Dihedral : 14.737 164.554 4140 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.06 % Favored : 88.71 % Rotamer: Outliers : 1.09 % Allowed : 10.86 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.15), residues: 3002 helix: -0.09 (0.18), residues: 888 sheet: -1.46 (0.36), residues: 227 loop : -2.61 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 116 TYR 0.031 0.002 TYR O 81 PHE 0.031 0.002 PHE F 291 TRP 0.020 0.001 TRP I 237 HIS 0.011 0.001 HIS G 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (26319) covalent geometry : angle 0.70851 / 0.36 (35877) hydrogen bonds : bond 0.05748 / 5.95 ( 720) hydrogen bonds : angle 5.53257 / 7.18 ( 1988) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 MET cc_start: 0.8737 (mpp) cc_final: 0.8313 (mpp) REVERT: E 124 MET cc_start: 0.8974 (ppp) cc_final: 0.8521 (ppp) REVERT: F 49 MET cc_start: 0.8939 (mpp) cc_final: 0.8727 (mpp) REVERT: F 291 PHE cc_start: 0.9278 (t80) cc_final: 0.8864 (t80) REVERT: G 49 MET cc_start: 0.9370 (pmm) cc_final: 0.9092 (pmm) REVERT: H 97 MET cc_start: 0.4332 (OUTLIER) cc_final: 0.4040 (mmp) REVERT: H 107 MET cc_start: 0.9303 (ppp) cc_final: 0.8903 (ppp) REVERT: H 124 MET cc_start: 0.8266 (ptm) cc_final: 0.8017 (ptm) REVERT: H 268 MET cc_start: 0.7775 (tmm) cc_final: 0.7133 (tmm) REVERT: H 279 MET cc_start: 0.5520 (ptp) cc_final: 0.5196 (ptp) REVERT: K 124 MET cc_start: 0.8574 (mmm) cc_final: 0.8369 (mmm) REVERT: N 75 TYR cc_start: 0.8227 (m-80) cc_final: 0.7787 (m-80) REVERT: O 72 PHE cc_start: 0.9097 (m-10) cc_final: 0.8482 (m-80) REVERT: O 76 PHE cc_start: 0.7962 (m-80) cc_final: 0.7564 (m-80) REVERT: O 99 ASP cc_start: 0.8211 (m-30) cc_final: 0.7766 (p0) REVERT: I 119 ILE cc_start: 0.9188 (mm) cc_final: 0.8971 (mp) REVERT: I 279 MET cc_start: 0.6020 (ptp) cc_final: 0.5761 (ptp) outliers start: 28 outliers final: 21 residues processed: 189 average time/residue: 0.1677 time to fit residues: 52.3289 Evaluate side-chains 171 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 122 CYS Chi-restraints excluded: chain H residue 167 PHE Chi-restraints excluded: chain J residue 167 PHE Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain O residue 11 TYR Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 97 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 269 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 273 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 286 ASN G 19 ASN ** K 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 208 ASN L 422 GLN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 ASN ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.055216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.044667 restraints weight = 202534.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.045906 restraints weight = 122698.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.046713 restraints weight = 86375.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.047294 restraints weight = 67629.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.047687 restraints weight = 56599.129| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 26319 Z= 0.229 Angle : 0.743 16.231 35877 Z= 0.378 Chirality : 0.044 0.239 3887 Planarity : 0.005 0.087 4474 Dihedral : 14.761 166.466 4140 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.43 % Favored : 87.38 % Rotamer: Outliers : 2.26 % Allowed : 14.29 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.15), residues: 3002 helix: -0.10 (0.17), residues: 896 sheet: -1.74 (0.32), residues: 253 loop : -2.73 (0.13), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 242 TYR 0.027 0.002 TYR O 81 PHE 0.027 0.002 PHE F 291 TRP 0.032 0.002 TRP I 237 HIS 0.006 0.001 HIS E 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.23 (26319) covalent geometry : angle 0.74258 / 0.38 (35877) hydrogen bonds : bond 0.05068 / 5.23 ( 720) hydrogen bonds : angle 5.38533 / 6.92 ( 1988) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 160 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 MET cc_start: 0.8862 (mpp) cc_final: 0.8288 (mpp) REVERT: E 124 MET cc_start: 0.9074 (ppp) cc_final: 0.8592 (ppp) REVERT: F 49 MET cc_start: 0.8895 (mpp) cc_final: 0.8579 (mpp) REVERT: F 291 PHE cc_start: 0.9336 (t80) cc_final: 0.9008 (t80) REVERT: G 279 MET cc_start: 0.5760 (OUTLIER) cc_final: 0.3430 (pmm) REVERT: H 115 LYS cc_start: 0.7342 (mmmt) cc_final: 0.7138 (mmmt) REVERT: H 124 MET cc_start: 0.8432 (ptm) cc_final: 0.8060 (ptm) REVERT: H 268 MET cc_start: 0.7740 (tmm) cc_final: 0.7302 (tmm) REVERT: J 97 MET cc_start: 0.7601 (tpp) cc_final: 0.6760 (tpt) REVERT: K 124 MET cc_start: 0.8776 (mmm) cc_final: 0.8527 (mmm) REVERT: L 422 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8820 (pp30) REVERT: N 75 TYR cc_start: 0.8415 (m-80) cc_final: 0.7941 (m-80) REVERT: O 64 ARG cc_start: 0.8697 (ptt-90) cc_final: 0.8297 (ptt-90) REVERT: O 72 PHE cc_start: 0.9302 (m-10) cc_final: 0.8860 (m-80) REVERT: O 99 ASP cc_start: 0.8293 (m-30) cc_final: 0.7851 (p0) REVERT: I 119 ILE cc_start: 0.9258 (mm) cc_final: 0.9038 (mp) REVERT: I 279 MET cc_start: 0.6549 (ptp) cc_final: 0.6276 (ptp) outliers start: 58 outliers final: 38 residues processed: 199 average time/residue: 0.1648 time to fit residues: 54.2285 Evaluate side-chains 185 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 226 TYR Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 122 CYS Chi-restraints excluded: chain H residue 167 PHE Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain J residue 167 PHE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 422 GLN Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain N residue 81 TYR Chi-restraints excluded: chain O residue 11 TYR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 223 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 41 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 26 optimal weight: 0.0870 chunk 292 optimal weight: 3.9990 chunk 271 optimal weight: 1.9990 chunk 280 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 ASN ** K 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.056211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.045660 restraints weight = 199190.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.046919 restraints weight = 120471.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.047775 restraints weight = 84936.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.048366 restraints weight = 66060.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.048766 restraints weight = 55152.743| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26319 Z= 0.138 Angle : 0.675 14.510 35877 Z= 0.339 Chirality : 0.042 0.216 3887 Planarity : 0.004 0.051 4474 Dihedral : 14.614 163.569 4140 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.26 % Favored : 88.54 % Rotamer: Outliers : 1.91 % Allowed : 16.12 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.15), residues: 3002 helix: 0.01 (0.18), residues: 896 sheet: -1.43 (0.35), residues: 212 loop : -2.71 (0.13), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 66 TYR 0.022 0.002 TYR F 82 PHE 0.023 0.001 PHE M 76 TRP 0.030 0.001 TRP I 237 HIS 0.004 0.001 HIS F 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (26319) covalent geometry : angle 0.67545 / 0.34 (35877) hydrogen bonds : bond 0.04262 / 4.45 ( 720) hydrogen bonds : angle 5.18244 / 6.67 ( 1988) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 154 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 MET cc_start: 0.8864 (mpp) cc_final: 0.8245 (mpp) REVERT: E 124 MET cc_start: 0.9027 (ppp) cc_final: 0.8564 (ppp) REVERT: F 49 MET cc_start: 0.8878 (mpp) cc_final: 0.8580 (mpp) REVERT: F 291 PHE cc_start: 0.9327 (t80) cc_final: 0.9018 (t80) REVERT: G 49 MET cc_start: 0.9371 (pmm) cc_final: 0.9084 (pmm) REVERT: G 279 MET cc_start: 0.5259 (OUTLIER) cc_final: 0.3277 (pmm) REVERT: H 107 MET cc_start: 0.9289 (ppp) cc_final: 0.8950 (ppp) REVERT: H 124 MET cc_start: 0.8437 (ptm) cc_final: 0.8033 (ptm) REVERT: H 268 MET cc_start: 0.7745 (tmm) cc_final: 0.7391 (tmm) REVERT: J 124 MET cc_start: 0.8353 (pmm) cc_final: 0.7916 (pmm) REVERT: J 134 ASP cc_start: 0.8537 (m-30) cc_final: 0.7819 (p0) REVERT: K 124 MET cc_start: 0.8763 (mmm) cc_final: 0.8516 (mmm) REVERT: L 335 LYS cc_start: 0.9179 (mmmt) cc_final: 0.8884 (tppt) REVERT: N 75 TYR cc_start: 0.8286 (m-80) cc_final: 0.7883 (m-80) REVERT: O 64 ARG cc_start: 0.8679 (ptt-90) cc_final: 0.8290 (ptt-90) REVERT: O 72 PHE cc_start: 0.9232 (m-10) cc_final: 0.8638 (m-80) REVERT: O 76 PHE cc_start: 0.7976 (m-80) cc_final: 0.7602 (m-80) REVERT: O 99 ASP cc_start: 0.8248 (m-30) cc_final: 0.7815 (p0) REVERT: I 115 LYS cc_start: 0.6729 (mmmt) cc_final: 0.6379 (mmmt) REVERT: I 119 ILE cc_start: 0.9247 (mm) cc_final: 0.9030 (mp) REVERT: I 279 MET cc_start: 0.6071 (ptp) cc_final: 0.5798 (ptp) outliers start: 49 outliers final: 36 residues processed: 190 average time/residue: 0.1535 time to fit residues: 48.4062 Evaluate side-chains 184 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 122 CYS Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 167 PHE Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 167 PHE Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain O residue 11 TYR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 223 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 204 optimal weight: 0.0040 chunk 16 optimal weight: 8.9990 chunk 261 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 chunk 190 optimal weight: 20.0000 chunk 222 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 256 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 overall best weight: 1.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.055971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.045449 restraints weight = 198581.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.046698 restraints weight = 119585.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.047526 restraints weight = 84253.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.048114 restraints weight = 65705.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.048532 restraints weight = 55037.460| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26319 Z= 0.135 Angle : 0.656 14.585 35877 Z= 0.331 Chirality : 0.042 0.218 3887 Planarity : 0.004 0.052 4474 Dihedral : 14.548 164.673 4140 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.46 % Favored : 88.37 % Rotamer: Outliers : 2.88 % Allowed : 16.70 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.15), residues: 3002 helix: 0.06 (0.18), residues: 896 sheet: -1.44 (0.35), residues: 224 loop : -2.66 (0.13), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 365 TYR 0.020 0.001 TYR E 138 PHE 0.022 0.001 PHE M 76 TRP 0.039 0.001 TRP I 237 HIS 0.004 0.001 HIS F 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (26319) covalent geometry : angle 0.65601 / 0.33 (35877) hydrogen bonds : bond 0.04014 / 4.21 ( 720) hydrogen bonds : angle 5.06394 / 6.52 ( 1988) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 153 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 MET cc_start: 0.8954 (mpp) cc_final: 0.8535 (mpp) REVERT: E 124 MET cc_start: 0.9039 (ppp) cc_final: 0.8546 (ppp) REVERT: E 251 LEU cc_start: 0.0098 (OUTLIER) cc_final: -0.1033 (mt) REVERT: F 49 MET cc_start: 0.8885 (mpp) cc_final: 0.8551 (mpp) REVERT: F 291 PHE cc_start: 0.9280 (t80) cc_final: 0.8947 (t80) REVERT: G 4 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8664 (mt) REVERT: G 49 MET cc_start: 0.9378 (pmm) cc_final: 0.9166 (pmm) REVERT: G 279 MET cc_start: 0.5345 (ptt) cc_final: 0.4292 (pmm) REVERT: H 4 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9055 (mt) REVERT: H 97 MET cc_start: 0.4719 (OUTLIER) cc_final: 0.3817 (mmp) REVERT: H 107 MET cc_start: 0.9293 (ppp) cc_final: 0.8922 (ppp) REVERT: H 124 MET cc_start: 0.8489 (ptm) cc_final: 0.8102 (ptm) REVERT: H 268 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7483 (tmm) REVERT: J 97 MET cc_start: 0.7242 (tpt) cc_final: 0.6160 (tpp) REVERT: J 124 MET cc_start: 0.8301 (pmm) cc_final: 0.7829 (pmm) REVERT: J 134 ASP cc_start: 0.8525 (m-30) cc_final: 0.7872 (p0) REVERT: K 124 MET cc_start: 0.8861 (mmm) cc_final: 0.8553 (mmm) REVERT: M 91 ASP cc_start: 0.9387 (t0) cc_final: 0.8887 (p0) REVERT: N 75 TYR cc_start: 0.8313 (m-80) cc_final: 0.7931 (m-80) REVERT: O 72 PHE cc_start: 0.9233 (m-10) cc_final: 0.8636 (m-80) REVERT: O 76 PHE cc_start: 0.8034 (m-80) cc_final: 0.7656 (m-80) REVERT: O 99 ASP cc_start: 0.8276 (m-30) cc_final: 0.7827 (p0) REVERT: I 115 LYS cc_start: 0.6883 (mmmt) cc_final: 0.6389 (mmmt) REVERT: I 119 ILE cc_start: 0.9251 (mm) cc_final: 0.9047 (mp) REVERT: I 279 MET cc_start: 0.6247 (ptp) cc_final: 0.5946 (ptp) outliers start: 74 outliers final: 54 residues processed: 209 average time/residue: 0.1582 time to fit residues: 55.0944 Evaluate side-chains 203 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 144 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 122 CYS Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 167 PHE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 268 MET Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 167 PHE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 391 TYR Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain O residue 11 TYR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 7 PHE Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 167 PHE Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 223 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 250 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 211 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.056347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.045601 restraints weight = 196932.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.046896 restraints weight = 118473.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.047771 restraints weight = 83090.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.048378 restraints weight = 64626.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.048786 restraints weight = 53885.520| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26319 Z= 0.123 Angle : 0.654 15.897 35877 Z= 0.325 Chirality : 0.041 0.184 3887 Planarity : 0.004 0.052 4474 Dihedral : 14.454 163.516 4136 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.93 % Favored : 88.91 % Rotamer: Outliers : 2.76 % Allowed : 17.79 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.15), residues: 3002 helix: 0.18 (0.18), residues: 882 sheet: -1.17 (0.39), residues: 188 loop : -2.61 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 242 TYR 0.018 0.001 TYR E 138 PHE 0.021 0.001 PHE M 76 TRP 0.041 0.001 TRP I 237 HIS 0.004 0.001 HIS E 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (26319) covalent geometry : angle 0.65381 / 0.32 (35877) hydrogen bonds : bond 0.03714 / 3.89 ( 720) hydrogen bonds : angle 4.97088 / 6.40 ( 1988) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 155 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 MET cc_start: 0.8954 (mpp) cc_final: 0.8521 (mpp) REVERT: E 124 MET cc_start: 0.9002 (ppp) cc_final: 0.8517 (ppp) REVERT: E 171 PHE cc_start: 0.8763 (t80) cc_final: 0.8432 (t80) REVERT: E 251 LEU cc_start: -0.0231 (OUTLIER) cc_final: -0.1475 (mt) REVERT: F 49 MET cc_start: 0.8864 (mpp) cc_final: 0.8470 (mpp) REVERT: F 291 PHE cc_start: 0.9284 (t80) cc_final: 0.8917 (t80) REVERT: G 4 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8681 (mt) REVERT: G 49 MET cc_start: 0.9411 (pmm) cc_final: 0.9157 (pmm) REVERT: G 279 MET cc_start: 0.5323 (ptt) cc_final: 0.4330 (pmm) REVERT: H 4 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9069 (mt) REVERT: H 124 MET cc_start: 0.8491 (ptm) cc_final: 0.8126 (ptm) REVERT: H 268 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7481 (tmm) REVERT: J 97 MET cc_start: 0.7203 (tpt) cc_final: 0.6394 (tpt) REVERT: J 124 MET cc_start: 0.8381 (pmm) cc_final: 0.7909 (pmm) REVERT: J 134 ASP cc_start: 0.8581 (m-30) cc_final: 0.7951 (p0) REVERT: K 10 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.7718 (tp) REVERT: K 124 MET cc_start: 0.8849 (mmm) cc_final: 0.8533 (mmm) REVERT: M 91 ASP cc_start: 0.9372 (t0) cc_final: 0.8887 (p0) REVERT: N 75 TYR cc_start: 0.8297 (m-80) cc_final: 0.7940 (m-80) REVERT: O 72 PHE cc_start: 0.9231 (m-10) cc_final: 0.8621 (m-80) REVERT: O 76 PHE cc_start: 0.8049 (m-80) cc_final: 0.7642 (m-80) REVERT: O 99 ASP cc_start: 0.8372 (m-30) cc_final: 0.7920 (p0) REVERT: I 279 MET cc_start: 0.6410 (ptp) cc_final: 0.6092 (ptp) outliers start: 71 outliers final: 51 residues processed: 211 average time/residue: 0.1535 time to fit residues: 54.8876 Evaluate side-chains 201 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 145 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 122 CYS Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 167 PHE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 268 MET Chi-restraints excluded: chain J residue 167 PHE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 391 TYR Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain O residue 11 TYR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 7 PHE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 167 PHE Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 223 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 159 optimal weight: 8.9990 chunk 208 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 195 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 0.4980 chunk 86 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 39 optimal weight: 0.0040 overall best weight: 1.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.055905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.045165 restraints weight = 197809.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.046457 restraints weight = 118597.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.047340 restraints weight = 83095.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.047907 restraints weight = 64536.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.048353 restraints weight = 54063.454| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26319 Z= 0.132 Angle : 0.660 14.493 35877 Z= 0.328 Chirality : 0.041 0.179 3887 Planarity : 0.004 0.052 4474 Dihedral : 14.448 163.881 4136 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.63 % Favored : 88.21 % Rotamer: Outliers : 2.76 % Allowed : 18.65 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.15), residues: 3002 helix: 0.18 (0.18), residues: 882 sheet: -1.19 (0.42), residues: 173 loop : -2.59 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 242 TYR 0.029 0.001 TYR J 169 PHE 0.021 0.001 PHE M 76 TRP 0.042 0.001 TRP I 237 HIS 0.003 0.001 HIS F 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (26319) covalent geometry : angle 0.66030 / 0.33 (35877) hydrogen bonds : bond 0.03734 / 3.90 ( 720) hydrogen bonds : angle 4.93495 / 6.35 ( 1988) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 149 time to evaluate : 0.957 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: E 49 MET cc_start: 0.8956 (mpp) cc_final: 0.8521 (mpp) REVERT: E 124 MET cc_start: 0.9032 (ppp) cc_final: 0.8499 (ppp) REVERT: E 251 LEU cc_start: -0.0273 (OUTLIER) cc_final: -0.1302 (mt) REVERT: F 49 MET cc_start: 0.8871 (mpp) cc_final: 0.8471 (mpp) REVERT: F 291 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.8881 (t80) REVERT: G 4 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8659 (mt) REVERT: G 268 MET cc_start: 0.8509 (tmm) cc_final: 0.8067 (tmm) REVERT: H 124 MET cc_start: 0.8393 (ptm) cc_final: 0.8070 (ptm) REVERT: H 173 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8876 (tt) REVERT: H 268 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7495 (tmm) REVERT: J 97 MET cc_start: 0.7235 (tpt) cc_final: 0.6305 (tpt) REVERT: J 124 MET cc_start: 0.8445 (pmm) cc_final: 0.7958 (pmm) REVERT: J 134 ASP cc_start: 0.8547 (m-30) cc_final: 0.7831 (p0) REVERT: K 10 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7496 (tp) REVERT: K 124 MET cc_start: 0.8837 (mmm) cc_final: 0.8490 (tpp) REVERT: M 91 ASP cc_start: 0.9385 (t0) cc_final: 0.8914 (p0) REVERT: O 72 PHE cc_start: 0.9236 (m-10) cc_final: 0.8612 (m-80) REVERT: O 76 PHE cc_start: 0.8010 (m-80) cc_final: 0.7607 (m-80) REVERT: O 99 ASP cc_start: 0.8400 (m-30) cc_final: 0.7942 (p0) REVERT: I 56 MET cc_start: 0.9169 (mmm) cc_final: 0.8937 (mtm) REVERT: I 279 MET cc_start: 0.6334 (ptp) cc_final: 0.6086 (ptp) outliers start: 71 outliers final: 51 residues processed: 203 average time/residue: 0.1492 time to fit residues: 51.5116 Evaluate side-chains 203 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 146 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 122 CYS Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 167 PHE Chi-restraints excluded: chain H residue 173 LEU Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 268 MET Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 167 PHE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 391 TYR Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain O residue 11 TYR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 7 PHE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 167 PHE Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 223 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 150 optimal weight: 6.9990 chunk 229 optimal weight: 7.9990 chunk 9 optimal weight: 0.5980 chunk 142 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 198 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 188 GLN L 422 GLN ** N 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.053714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.043153 restraints weight = 200902.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.044359 restraints weight = 121030.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.045176 restraints weight = 85466.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.045755 restraints weight = 66875.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.046142 restraints weight = 55982.129| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 26319 Z= 0.227 Angle : 0.756 13.578 35877 Z= 0.377 Chirality : 0.044 0.215 3887 Planarity : 0.005 0.054 4474 Dihedral : 14.642 165.603 4136 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.19 % Favored : 86.64 % Rotamer: Outliers : 2.96 % Allowed : 18.80 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.15), residues: 3002 helix: 0.08 (0.18), residues: 895 sheet: -1.54 (0.37), residues: 201 loop : -2.75 (0.13), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 159 TYR 0.027 0.002 TYR E 138 PHE 0.027 0.002 PHE E 94 TRP 0.051 0.002 TRP I 237 HIS 0.006 0.001 HIS G 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 (26319) covalent geometry : angle 0.75625 / 0.38 (35877) hydrogen bonds : bond 0.04270 / 4.42 ( 720) hydrogen bonds : angle 5.11260 / 6.54 ( 1988) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 146 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 MET cc_start: 0.9060 (mpp) cc_final: 0.8784 (mpp) REVERT: E 124 MET cc_start: 0.9110 (ppp) cc_final: 0.8526 (ppp) REVERT: E 251 LEU cc_start: -0.0143 (OUTLIER) cc_final: -0.1415 (mt) REVERT: F 49 MET cc_start: 0.8953 (mpp) cc_final: 0.8564 (mpp) REVERT: F 291 PHE cc_start: 0.9364 (OUTLIER) cc_final: 0.8995 (t80) REVERT: G 4 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8910 (mt) REVERT: G 49 MET cc_start: 0.9450 (pmm) cc_final: 0.9194 (pmm) REVERT: G 268 MET cc_start: 0.8540 (tmm) cc_final: 0.7787 (tmm) REVERT: G 279 MET cc_start: 0.5784 (OUTLIER) cc_final: 0.3424 (pmm) REVERT: H 124 MET cc_start: 0.8503 (ptm) cc_final: 0.8168 (ptm) REVERT: H 173 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8885 (tt) REVERT: H 268 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7479 (tmm) REVERT: J 124 MET cc_start: 0.8510 (pmm) cc_final: 0.8194 (pmm) REVERT: J 134 ASP cc_start: 0.8563 (m-30) cc_final: 0.7995 (p0) REVERT: K 10 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7547 (tp) REVERT: K 56 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7788 (tpt) REVERT: K 124 MET cc_start: 0.8854 (mmm) cc_final: 0.8525 (tpp) REVERT: L 422 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8659 (pp30) REVERT: M 91 ASP cc_start: 0.9425 (t0) cc_final: 0.8973 (p0) REVERT: N 75 TYR cc_start: 0.8365 (m-10) cc_final: 0.8007 (m-80) REVERT: O 72 PHE cc_start: 0.9253 (m-10) cc_final: 0.8862 (m-80) REVERT: O 76 PHE cc_start: 0.7998 (m-80) cc_final: 0.7542 (m-80) REVERT: O 99 ASP cc_start: 0.8397 (m-30) cc_final: 0.7943 (p0) REVERT: I 115 LYS cc_start: 0.7369 (mmmt) cc_final: 0.6655 (mmmt) REVERT: I 279 MET cc_start: 0.6860 (ptp) cc_final: 0.6575 (ptp) outliers start: 76 outliers final: 60 residues processed: 202 average time/residue: 0.1452 time to fit residues: 50.1339 Evaluate side-chains 215 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 146 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 226 TYR Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 167 PHE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 122 CYS Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 167 PHE Chi-restraints excluded: chain H residue 173 LEU Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 268 MET Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 167 PHE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 226 TYR Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 56 MET Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 391 TYR Chi-restraints excluded: chain L residue 422 GLN Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain O residue 11 TYR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 75 TYR Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 7 PHE Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 167 PHE Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 223 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 84 optimal weight: 0.0040 chunk 130 optimal weight: 2.9990 chunk 256 optimal weight: 7.9990 chunk 199 optimal weight: 9.9990 chunk 283 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 75 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN I 275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.054768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.044165 restraints weight = 198082.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.045439 restraints weight = 117404.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.046301 restraints weight = 81950.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.046847 restraints weight = 63765.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.047272 restraints weight = 53755.634| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26319 Z= 0.134 Angle : 0.703 15.165 35877 Z= 0.345 Chirality : 0.042 0.215 3887 Planarity : 0.004 0.052 4474 Dihedral : 14.504 163.431 4136 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.29 % Favored : 88.54 % Rotamer: Outliers : 2.45 % Allowed : 19.62 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.15), residues: 3002 helix: 0.20 (0.18), residues: 880 sheet: -1.27 (0.41), residues: 173 loop : -2.65 (0.13), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 242 TYR 0.021 0.001 TYR M 81 PHE 0.024 0.001 PHE M 76 TRP 0.047 0.001 TRP I 237 HIS 0.005 0.001 HIS E 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (26319) covalent geometry : angle 0.70317 / 0.34 (35877) hydrogen bonds : bond 0.03745 / 3.90 ( 720) hydrogen bonds : angle 4.95859 / 6.42 ( 1988) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 150 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 MET cc_start: 0.8980 (mpp) cc_final: 0.8684 (mpp) REVERT: E 124 MET cc_start: 0.9023 (ppp) cc_final: 0.8485 (ppp) REVERT: E 251 LEU cc_start: -0.0220 (OUTLIER) cc_final: -0.1291 (mt) REVERT: F 49 MET cc_start: 0.8897 (mpp) cc_final: 0.8520 (mpp) REVERT: F 291 PHE cc_start: 0.9342 (OUTLIER) cc_final: 0.8956 (t80) REVERT: G 4 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8879 (mt) REVERT: G 49 MET cc_start: 0.9393 (pmm) cc_final: 0.9114 (pmm) REVERT: G 268 MET cc_start: 0.8488 (tmm) cc_final: 0.7817 (tmm) REVERT: H 97 MET cc_start: 0.7573 (ptt) cc_final: 0.5994 (mmp) REVERT: H 124 MET cc_start: 0.8446 (ptm) cc_final: 0.8117 (ptm) REVERT: H 173 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8812 (tt) REVERT: H 268 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7495 (tmm) REVERT: J 97 MET cc_start: 0.6793 (tpt) cc_final: 0.5816 (tpt) REVERT: J 124 MET cc_start: 0.8473 (pmm) cc_final: 0.8066 (pmm) REVERT: J 134 ASP cc_start: 0.8538 (m-30) cc_final: 0.7842 (p0) REVERT: K 10 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7467 (tp) REVERT: K 124 MET cc_start: 0.8807 (mmm) cc_final: 0.8448 (tpp) REVERT: K 190 GLN cc_start: 0.9209 (pm20) cc_final: 0.8954 (pm20) REVERT: L 267 LEU cc_start: 0.9676 (tt) cc_final: 0.9296 (pp) REVERT: M 91 ASP cc_start: 0.9391 (t0) cc_final: 0.8946 (p0) REVERT: N 75 TYR cc_start: 0.8302 (m-10) cc_final: 0.7936 (m-80) REVERT: O 72 PHE cc_start: 0.9242 (m-10) cc_final: 0.8696 (m-80) REVERT: O 76 PHE cc_start: 0.7993 (m-80) cc_final: 0.7572 (m-80) REVERT: O 99 ASP cc_start: 0.8267 (m-30) cc_final: 0.7773 (p0) REVERT: I 56 MET cc_start: 0.9147 (mmm) cc_final: 0.8891 (mtm) REVERT: I 115 LYS cc_start: 0.7279 (mmmt) cc_final: 0.6621 (mmmt) REVERT: I 279 MET cc_start: 0.6619 (ptp) cc_final: 0.6345 (ptp) outliers start: 63 outliers final: 53 residues processed: 200 average time/residue: 0.1465 time to fit residues: 49.1301 Evaluate side-chains 203 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 144 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 122 CYS Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 167 PHE Chi-restraints excluded: chain H residue 173 LEU Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 268 MET Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 167 PHE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 226 TYR Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 391 TYR Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain O residue 11 TYR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 7 PHE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 167 PHE Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 41 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 282 optimal weight: 0.5980 chunk 158 optimal weight: 20.0000 chunk 218 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 1 optimal weight: 20.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 151 ASN ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 GLN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.055749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.045107 restraints weight = 196476.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.046403 restraints weight = 116781.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.047283 restraints weight = 81628.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.047881 restraints weight = 63366.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.048305 restraints weight = 52937.901| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26319 Z= 0.118 Angle : 0.702 15.647 35877 Z= 0.340 Chirality : 0.042 0.208 3887 Planarity : 0.004 0.053 4474 Dihedral : 14.354 162.282 4136 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.93 % Favored : 88.91 % Rotamer: Outliers : 2.41 % Allowed : 19.85 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.15), residues: 3002 helix: 0.15 (0.18), residues: 889 sheet: -1.03 (0.42), residues: 173 loop : -2.62 (0.13), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 104 TYR 0.020 0.001 TYR M 81 PHE 0.021 0.001 PHE M 76 TRP 0.050 0.001 TRP G 237 HIS 0.004 0.001 HIS E 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (26319) covalent geometry : angle 0.70217 / 0.34 (35877) hydrogen bonds : bond 0.03443 / 3.61 ( 720) hydrogen bonds : angle 4.86860 / 6.29 ( 1988) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 152 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 MET cc_start: 0.8951 (mpp) cc_final: 0.8516 (mpp) REVERT: E 124 MET cc_start: 0.8974 (ppp) cc_final: 0.8405 (ppp) REVERT: E 251 LEU cc_start: -0.0607 (OUTLIER) cc_final: -0.1566 (mt) REVERT: F 49 MET cc_start: 0.8876 (mpp) cc_final: 0.8463 (mpp) REVERT: F 291 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8679 (t80) REVERT: G 4 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8837 (mt) REVERT: G 49 MET cc_start: 0.9383 (pmm) cc_final: 0.9091 (pmm) REVERT: G 237 TRP cc_start: 0.6760 (t60) cc_final: 0.6515 (t60) REVERT: G 268 MET cc_start: 0.8473 (tmm) cc_final: 0.7690 (tmm) REVERT: H 97 MET cc_start: 0.7409 (ptt) cc_final: 0.5808 (mmp) REVERT: H 124 MET cc_start: 0.8453 (ptm) cc_final: 0.8120 (ptm) REVERT: H 173 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8860 (tt) REVERT: H 268 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7591 (tmm) REVERT: J 97 MET cc_start: 0.6778 (tpt) cc_final: 0.5773 (tpt) REVERT: J 124 MET cc_start: 0.8460 (pmm) cc_final: 0.8018 (pmm) REVERT: J 134 ASP cc_start: 0.8539 (m-30) cc_final: 0.7858 (p0) REVERT: K 10 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7448 (tp) REVERT: K 124 MET cc_start: 0.8796 (mmm) cc_final: 0.8484 (mmm) REVERT: K 190 GLN cc_start: 0.9225 (pm20) cc_final: 0.8956 (pm20) REVERT: M 91 ASP cc_start: 0.9373 (t0) cc_final: 0.8941 (p0) REVERT: O 72 PHE cc_start: 0.9163 (m-10) cc_final: 0.8598 (m-80) REVERT: O 76 PHE cc_start: 0.7998 (m-80) cc_final: 0.7577 (m-80) REVERT: O 99 ASP cc_start: 0.8196 (m-30) cc_final: 0.7720 (p0) REVERT: O 101 ASP cc_start: 0.8963 (t70) cc_final: 0.8679 (p0) REVERT: O 104 ARG cc_start: 0.8997 (mmt180) cc_final: 0.8563 (mpt180) REVERT: I 56 MET cc_start: 0.9194 (mmm) cc_final: 0.8918 (mtm) REVERT: I 279 MET cc_start: 0.6312 (ptp) cc_final: 0.5976 (ptp) outliers start: 62 outliers final: 50 residues processed: 200 average time/residue: 0.1437 time to fit residues: 48.2841 Evaluate side-chains 204 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 148 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 122 CYS Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 167 PHE Chi-restraints excluded: chain H residue 173 LEU Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 268 MET Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 167 PHE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 226 TYR Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 391 TYR Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 7 PHE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 167 PHE Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 230 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 279 optimal weight: 0.6980 chunk 181 optimal weight: 5.9990 chunk 250 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 248 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 275 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.055091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.044453 restraints weight = 196825.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.045738 restraints weight = 116827.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.046601 restraints weight = 81559.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.047204 restraints weight = 63235.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.047588 restraints weight = 52863.973| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26319 Z= 0.139 Angle : 0.700 15.873 35877 Z= 0.342 Chirality : 0.042 0.198 3887 Planarity : 0.004 0.053 4474 Dihedral : 14.363 162.762 4136 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.19 % Favored : 88.64 % Rotamer: Outliers : 2.34 % Allowed : 20.01 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.15), residues: 3002 helix: 0.10 (0.18), residues: 900 sheet: -1.11 (0.42), residues: 173 loop : -2.63 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 242 TYR 0.025 0.001 TYR J 169 PHE 0.022 0.001 PHE M 76 TRP 0.046 0.001 TRP I 237 HIS 0.003 0.001 HIS G 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (26319) covalent geometry : angle 0.69988 / 0.34 (35877) hydrogen bonds : bond 0.03596 / 3.74 ( 720) hydrogen bonds : angle 4.85895 / 6.28 ( 1988) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3861.73 seconds wall clock time: 68 minutes 2.29 seconds (4082.29 seconds total)