Starting phenix.real_space_refine on Mon Aug 25 05:25:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h67_34495/08_2025/8h67_34495.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h67_34495/08_2025/8h67_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8h67_34495/08_2025/8h67_34495.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h67_34495/08_2025/8h67_34495.map" model { file = "/net/cci-nas-00/data/ceres_data/8h67_34495/08_2025/8h67_34495.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h67_34495/08_2025/8h67_34495.cif" } 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-2.0-5787/lib/python3.9/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: 6.21, per 1000 atoms: 0.24 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: 2.56 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.2 microseconds 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: 3.11 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: 4.58 Time building geometry restraints manager: 3.28 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=" 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=" O3' C B 24 " pdb=" P A B 25 " ideal model delta sigma weight residual 1.607 1.567 0.040 1.50e-02 4.44e+03 7.19e+00 bond pdb=" O3' A B 25 " pdb=" P A B 26 " ideal model delta sigma weight residual 1.607 1.582 0.025 1.50e-02 4.44e+03 2.70e+00 bond pdb=" O5' A B 25 " pdb=" C5' A B 25 " ideal model delta sigma weight residual 1.424 1.447 -0.023 1.50e-02 4.44e+03 2.33e+00 bond pdb=" O5' U B 33 " pdb=" C5' U B 33 " ideal model delta sigma weight residual 1.420 1.443 -0.023 1.50e-02 4.44e+03 2.29e+00 ... (remaining 26314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 35013 1.96 - 3.93: 722 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: 3208 0.053 - 0.106: 554 0.106 - 0.160: 107 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.700 Find NCS groups from input model: 0.380 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 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= 0.139 Angle : 0.679 9.822 35877 Z= 0.359 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 aren 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 covalent geometry : bond 0.00274 (26319) covalent geometry : angle 0.67942 (35877) hydrogen bonds : bond 0.21431 ( 720) hydrogen bonds : angle 7.09864 ( 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 : 0.984 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: 0.8265 (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: 0.5927 (ptp) outliers start: 2 outliers final: 1 residues processed: 239 average time/residue: 0.1781 time to fit residues: 68.0137 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 : 1.032 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN E 286 ASN G 19 ASN H 19 ASN H 51 ASN ** K 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 422 GLN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.057159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.046539 restraints weight = 200456.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.047807 restraints weight = 121986.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.048674 restraints weight = 86160.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.049270 restraints weight = 67238.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.049686 restraints weight = 56189.413| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26319 Z= 0.165 Angle : 0.690 11.171 35877 Z= 0.351 Chirality : 0.043 0.230 3887 Planarity : 0.005 0.055 4474 Dihedral : 14.718 162.540 4140 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.26 % Favored : 88.47 % Rotamer: Outliers : 1.21 % Allowed : 11.21 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.44 (0.15), residues: 3002 helix: -0.06 (0.18), residues: 899 sheet: -1.53 (0.36), residues: 226 loop : -2.59 (0.13), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 66 TYR 0.029 0.002 TYR N 75 PHE 0.033 0.002 PHE F 291 TRP 0.025 0.001 TRP K 237 HIS 0.009 0.001 HIS G 164 Details of bonding type rmsd covalent geometry : bond 0.00359 (26319) covalent geometry : angle 0.69037 (35877) hydrogen bonds : bond 0.05227 ( 720) hydrogen bonds : angle 5.37298 ( 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 209 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 MET cc_start: 0.8744 (mpp) cc_final: 0.8253 (mpp) REVERT: E 124 MET cc_start: 0.8961 (ppp) cc_final: 0.8470 (ppp) REVERT: F 122 CYS cc_start: 0.8278 (t) cc_final: 0.8015 (t) REVERT: F 291 PHE cc_start: 0.9317 (t80) cc_final: 0.8895 (t80) REVERT: G 49 MET cc_start: 0.9394 (pmm) cc_final: 0.9099 (pmm) REVERT: G 279 MET cc_start: 0.4808 (ptt) cc_final: 0.3675 (pmm) REVERT: H 107 MET cc_start: 0.9298 (ppp) cc_final: 0.8863 (ppp) REVERT: H 124 MET cc_start: 0.8294 (ptm) cc_final: 0.7896 (ptm) REVERT: H 268 MET cc_start: 0.7744 (tmm) cc_final: 0.7140 (tmm) REVERT: H 279 MET cc_start: 0.5810 (ptp) cc_final: 0.5438 (ptp) REVERT: J 97 MET cc_start: 0.7449 (tpp) cc_final: 0.7155 (tpt) REVERT: J 124 MET cc_start: 0.8775 (pmm) cc_final: 0.8571 (pmm) REVERT: K 124 MET cc_start: 0.8610 (mmm) cc_final: 0.8336 (mmm) REVERT: N 75 TYR cc_start: 0.8177 (m-80) cc_final: 0.7725 (m-80) REVERT: O 72 PHE cc_start: 0.9169 (m-10) cc_final: 0.8768 (m-80) REVERT: O 99 ASP cc_start: 0.8238 (m-30) cc_final: 0.7765 (p0) REVERT: O 104 ARG cc_start: 0.9046 (mmt180) cc_final: 0.8838 (mpt180) REVERT: I 119 ILE cc_start: 0.9217 (mm) cc_final: 0.8993 (mp) REVERT: I 279 MET cc_start: 0.6258 (ptp) cc_final: 0.5932 (ptp) outliers start: 31 outliers final: 25 residues processed: 194 average time/residue: 0.1692 time to fit residues: 53.7586 Evaluate side-chains 177 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 188 LEU Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 101 THR 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 J residue 167 PHE 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 269 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 32 optimal weight: 0.0170 chunk 122 optimal weight: 6.9990 chunk 86 optimal weight: 0.0670 chunk 72 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 273 optimal weight: 2.9990 overall best weight: 0.9558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN ** K 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 422 GLN ** 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 = 0.3574 r_free = 0.3574 target = 0.057932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.047110 restraints weight = 195715.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.048420 restraints weight = 118240.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.049283 restraints weight = 83416.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.049892 restraints weight = 65099.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.050322 restraints weight = 54422.712| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26319 Z= 0.120 Angle : 0.652 13.395 35877 Z= 0.326 Chirality : 0.042 0.242 3887 Planarity : 0.004 0.051 4474 Dihedral : 14.493 161.880 4140 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.03 % Favored : 89.77 % Rotamer: Outliers : 1.71 % Allowed : 13.78 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.15), residues: 3002 helix: -0.03 (0.18), residues: 908 sheet: -1.02 (0.34), residues: 242 loop : -2.63 (0.13), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 66 TYR 0.028 0.001 TYR E 133 PHE 0.025 0.001 PHE F 291 TRP 0.029 0.001 TRP I 237 HIS 0.008 0.001 HIS E 202 Details of bonding type rmsd covalent geometry : bond 0.00263 (26319) covalent geometry : angle 0.65246 (35877) hydrogen bonds : bond 0.04093 ( 720) hydrogen bonds : angle 5.02876 ( 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 212 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 0.780 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: 0.8916 (mpp) cc_final: 0.8346 (mpp) REVERT: E 124 MET cc_start: 0.8974 (ppp) cc_final: 0.8458 (ppp) REVERT: F 122 CYS cc_start: 0.8322 (t) cc_final: 0.8024 (t) REVERT: F 291 PHE cc_start: 0.9341 (t80) cc_final: 0.8977 (t80) REVERT: G 41 TYR cc_start: 0.6762 (p90) cc_final: 0.6486 (p90) REVERT: G 49 MET cc_start: 0.9398 (pmm) cc_final: 0.9116 (pmm) REVERT: G 279 MET cc_start: 0.4443 (ptt) cc_final: 0.3163 (pmm) REVERT: H 124 MET cc_start: 0.8364 (ptm) cc_final: 0.7925 (ptm) REVERT: H 268 MET cc_start: 0.7697 (tmm) cc_final: 0.7373 (tmm) REVERT: J 97 MET cc_start: 0.7303 (tpp) cc_final: 0.7062 (tpt) REVERT: J 124 MET cc_start: 0.8449 (pmm) cc_final: 0.8236 (pmm) REVERT: J 134 ASP cc_start: 0.8552 (m-30) cc_final: 0.7711 (p0) REVERT: K 124 MET cc_start: 0.8538 (mmm) cc_final: 0.8319 (mmm) REVERT: L 335 LYS cc_start: 0.9211 (mmmt) cc_final: 0.8916 (tppt) REVERT: N 75 TYR cc_start: 0.8312 (m-80) cc_final: 0.7894 (m-80) REVERT: O 64 ARG cc_start: 0.8666 (ptt-90) cc_final: 0.8237 (ptt-90) REVERT: O 72 PHE cc_start: 0.9135 (m-10) cc_final: 0.8557 (m-80) REVERT: O 76 PHE cc_start: 0.7966 (m-80) cc_final: 0.7577 (m-80) REVERT: O 81 TYR cc_start: 0.8325 (m-80) cc_final: 0.7992 (m-80) REVERT: O 99 ASP cc_start: 0.8239 (m-30) cc_final: 0.7828 (p0) REVERT: O 104 ARG cc_start: 0.8891 (mmt180) cc_final: 0.8579 (mmt-90) REVERT: I 119 ILE cc_start: 0.9188 (mm) cc_final: 0.8972 (mp) REVERT: I 279 MET cc_start: 0.6240 (ptp) cc_final: 0.5865 (ptp) outliers start: 44 outliers final: 24 residues processed: 198 average time/residue: 0.1688 time to fit residues: 54.7346 Evaluate side-chains 186 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 G residue 223 VAL Chi-restraints excluded: chain H residue 34 ILE 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 223 VAL 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 27 LEU 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 100 THR Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 247 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 41 optimal weight: 6.9990 chunk 227 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 11 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 149 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 292 optimal weight: 1.9990 chunk 271 optimal weight: 0.6980 chunk 280 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 ASN H 84 ASN ** K 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 208 ASN L 422 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.058333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.047570 restraints weight = 195812.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.048913 restraints weight = 117765.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.049790 restraints weight = 82527.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.050414 restraints weight = 64271.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.050856 restraints weight = 53548.964| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26319 Z= 0.114 Angle : 0.632 13.379 35877 Z= 0.315 Chirality : 0.041 0.199 3887 Planarity : 0.004 0.052 4474 Dihedral : 14.346 161.889 4136 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.06 % Favored : 89.74 % Rotamer: Outliers : 1.83 % Allowed : 15.84 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.15), residues: 3002 helix: 0.01 (0.18), residues: 908 sheet: -1.38 (0.35), residues: 233 loop : -2.60 (0.13), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 242 TYR 0.017 0.001 TYR A 116 PHE 0.022 0.001 PHE M 76 TRP 0.030 0.001 TRP I 237 HIS 0.003 0.001 HIS E 202 Details of bonding type rmsd covalent geometry : bond 0.00242 (26319) covalent geometry : angle 0.63155 (35877) hydrogen bonds : bond 0.03563 ( 720) hydrogen bonds : angle 4.83611 ( 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 223 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 MET cc_start: 0.8967 (mpp) cc_final: 0.8551 (mpp) REVERT: E 124 MET cc_start: 0.8976 (ppp) cc_final: 0.8423 (ppp) REVERT: F 291 PHE cc_start: 0.9355 (t80) cc_final: 0.8907 (t80) REVERT: G 49 MET cc_start: 0.9410 (pmm) cc_final: 0.9157 (pmm) REVERT: G 115 LYS cc_start: 0.7593 (tppt) cc_final: 0.6675 (tptt) REVERT: G 279 MET cc_start: 0.4426 (ptt) cc_final: 0.3277 (pmm) REVERT: H 107 MET cc_start: 0.9276 (ppp) cc_final: 0.8925 (ppp) REVERT: H 124 MET cc_start: 0.8363 (ptm) cc_final: 0.7932 (ptm) REVERT: H 268 MET cc_start: 0.7800 (tmm) cc_final: 0.7441 (tmm) REVERT: J 97 MET cc_start: 0.7271 (tpp) cc_final: 0.7031 (tpt) REVERT: J 124 MET cc_start: 0.8430 (pmm) cc_final: 0.8221 (pmm) REVERT: J 134 ASP cc_start: 0.8610 (m-30) cc_final: 0.7781 (p0) REVERT: K 124 MET cc_start: 0.8601 (mmm) cc_final: 0.8389 (mmm) REVERT: L 335 LYS cc_start: 0.9244 (mmmt) cc_final: 0.8788 (tppt) REVERT: M 91 ASP cc_start: 0.9314 (t0) cc_final: 0.8801 (p0) REVERT: N 46 ARG cc_start: 0.9463 (mmm160) cc_final: 0.8699 (tpt90) REVERT: N 75 TYR cc_start: 0.8294 (m-80) cc_final: 0.7913 (m-80) REVERT: O 72 PHE cc_start: 0.9101 (m-10) cc_final: 0.8522 (m-80) REVERT: O 76 PHE cc_start: 0.7979 (m-80) cc_final: 0.7556 (m-80) REVERT: O 94 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8414 (tm-30) REVERT: O 99 ASP cc_start: 0.8092 (m-30) cc_final: 0.7649 (p0) REVERT: O 104 ARG cc_start: 0.8992 (mmt180) cc_final: 0.8600 (mpt180) REVERT: I 119 ILE cc_start: 0.9161 (mm) cc_final: 0.8947 (mp) REVERT: I 279 MET cc_start: 0.5940 (ptp) cc_final: 0.5582 (ptp) outliers start: 47 outliers final: 29 residues processed: 209 average time/residue: 0.1701 time to fit residues: 58.0332 Evaluate side-chains 191 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 G residue 7 PHE Chi-restraints excluded: chain G residue 70 HIS 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 122 CYS 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 J residue 167 PHE Chi-restraints excluded: chain K residue 10 ILE 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 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 167 PHE 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: 3.9990 chunk 16 optimal weight: 8.9990 chunk 261 optimal weight: 0.9980 chunk 244 optimal weight: 0.7980 chunk 190 optimal weight: 10.0000 chunk 222 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 422 GLN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 ASN I 275 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.056281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.045568 restraints weight = 197362.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.046848 restraints weight = 118605.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.047724 restraints weight = 83472.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.048312 restraints weight = 64842.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.048737 restraints weight = 54322.759| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26319 Z= 0.142 Angle : 0.652 13.320 35877 Z= 0.327 Chirality : 0.041 0.228 3887 Planarity : 0.004 0.053 4474 Dihedral : 14.458 165.350 4136 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.29 % Favored : 88.51 % Rotamer: Outliers : 2.14 % Allowed : 16.47 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.15), residues: 3002 helix: 0.14 (0.18), residues: 900 sheet: -1.35 (0.35), residues: 226 loop : -2.67 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 366 TYR 0.029 0.001 TYR J 169 PHE 0.027 0.001 PHE M 76 TRP 0.033 0.001 TRP I 237 HIS 0.007 0.001 HIS E 202 Details of bonding type rmsd covalent geometry : bond 0.00315 (26319) covalent geometry : angle 0.65185 (35877) hydrogen bonds : bond 0.03672 ( 720) hydrogen bonds : angle 4.81097 ( 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 213 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 MET cc_start: 0.8970 (mpp) cc_final: 0.8552 (mpp) REVERT: E 124 MET cc_start: 0.9032 (ppp) cc_final: 0.8436 (ppp) REVERT: E 251 LEU cc_start: 0.0005 (OUTLIER) cc_final: -0.0976 (mt) REVERT: F 291 PHE cc_start: 0.9341 (t80) cc_final: 0.8843 (t80) REVERT: H 124 MET cc_start: 0.8572 (ptm) cc_final: 0.8226 (ptm) REVERT: H 268 MET cc_start: 0.7770 (tmm) cc_final: 0.7457 (tmm) REVERT: J 97 MET cc_start: 0.7778 (tpp) cc_final: 0.7506 (tpp) REVERT: J 124 MET cc_start: 0.8465 (pmm) cc_final: 0.8265 (pmm) REVERT: J 134 ASP cc_start: 0.8625 (m-30) cc_final: 0.7883 (p0) REVERT: K 10 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.7742 (tp) REVERT: K 124 MET cc_start: 0.8857 (mmm) cc_final: 0.8560 (mmm) REVERT: M 91 ASP cc_start: 0.9382 (t0) cc_final: 0.8910 (p0) REVERT: O 72 PHE cc_start: 0.9154 (m-10) cc_final: 0.8553 (m-80) REVERT: O 76 PHE cc_start: 0.8042 (m-80) cc_final: 0.7630 (m-80) REVERT: O 94 GLN cc_start: 0.9019 (tm-30) cc_final: 0.8745 (tm-30) REVERT: O 99 ASP cc_start: 0.8138 (m-30) cc_final: 0.7686 (p0) REVERT: O 104 ARG cc_start: 0.9074 (mmt180) cc_final: 0.8633 (mpt180) REVERT: I 49 MET cc_start: 0.9201 (mpp) cc_final: 0.8947 (mpp) REVERT: I 119 ILE cc_start: 0.9233 (mm) cc_final: 0.9013 (mp) REVERT: I 279 MET cc_start: 0.6108 (ptp) cc_final: 0.5858 (ptp) outliers start: 55 outliers final: 38 residues processed: 199 average time/residue: 0.1643 time to fit residues: 54.2258 Evaluate side-chains 191 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 251 LEU Chi-restraints excluded: chain F residue 124 MET 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 34 ILE Chi-restraints excluded: chain H residue 49 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 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 219 THR 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 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 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: 3.9990 chunk 56 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 211 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 208 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 142 optimal weight: 0.0010 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 422 GLN O 20 GLN I 275 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.057323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.046529 restraints weight = 194474.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.047874 restraints weight = 116400.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.048777 restraints weight = 81160.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.049412 restraints weight = 62777.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.049825 restraints weight = 52127.353| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26319 Z= 0.111 Angle : 0.633 13.986 35877 Z= 0.312 Chirality : 0.041 0.187 3887 Planarity : 0.004 0.053 4474 Dihedral : 14.326 163.454 4136 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.93 % Favored : 89.91 % Rotamer: Outliers : 2.30 % Allowed : 17.52 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.15), residues: 3002 helix: 0.18 (0.18), residues: 899 sheet: -1.00 (0.42), residues: 179 loop : -2.58 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 66 TYR 0.019 0.001 TYR M 81 PHE 0.022 0.001 PHE M 76 TRP 0.036 0.001 TRP I 237 HIS 0.004 0.001 HIS E 202 Details of bonding type rmsd covalent geometry : bond 0.00245 (26319) covalent geometry : angle 0.63282 (35877) hydrogen bonds : bond 0.03212 ( 720) hydrogen bonds : angle 4.68941 ( 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 225 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 166 time to evaluate : 1.066 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: 0.8980 (mpp) cc_final: 0.8504 (mpp) REVERT: E 124 MET cc_start: 0.8950 (ppp) cc_final: 0.8379 (ppp) REVERT: E 251 LEU cc_start: -0.0365 (OUTLIER) cc_final: -0.1206 (mt) REVERT: F 291 PHE cc_start: 0.9346 (t80) cc_final: 0.8801 (t80) REVERT: G 279 MET cc_start: 0.4388 (ptt) cc_final: 0.2833 (pmm) REVERT: H 124 MET cc_start: 0.8555 (ptm) cc_final: 0.8191 (ptm) REVERT: H 268 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7444 (tmm) REVERT: J 124 MET cc_start: 0.8449 (pmm) cc_final: 0.8181 (pmm) REVERT: J 134 ASP cc_start: 0.8543 (m-30) cc_final: 0.7858 (p0) REVERT: K 10 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.7601 (tp) REVERT: K 124 MET cc_start: 0.8773 (mmm) cc_final: 0.8514 (mmm) REVERT: M 91 ASP cc_start: 0.9352 (t0) cc_final: 0.8895 (p0) REVERT: N 46 ARG cc_start: 0.9466 (mmm160) cc_final: 0.8732 (tpt90) REVERT: O 72 PHE cc_start: 0.9125 (m-10) cc_final: 0.8516 (m-80) REVERT: O 76 PHE cc_start: 0.8015 (m-80) cc_final: 0.7612 (m-80) REVERT: O 81 TYR cc_start: 0.8526 (m-80) cc_final: 0.8316 (t80) REVERT: O 94 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8761 (tm-30) REVERT: O 99 ASP cc_start: 0.8007 (m-30) cc_final: 0.7541 (p0) REVERT: O 104 ARG cc_start: 0.9063 (mmt180) cc_final: 0.8620 (mpt180) REVERT: I 49 MET cc_start: 0.9183 (mpp) cc_final: 0.8921 (mpp) REVERT: I 119 ILE cc_start: 0.9222 (mm) cc_final: 0.9010 (mp) REVERT: I 279 MET cc_start: 0.6054 (ptp) cc_final: 0.5683 (ptp) outliers start: 59 outliers final: 43 residues processed: 209 average time/residue: 0.1606 time to fit residues: 55.6900 Evaluate side-chains 201 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 G residue 7 PHE Chi-restraints excluded: chain G residue 70 HIS 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 H residue 34 ILE Chi-restraints excluded: chain H residue 49 MET 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 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 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 527 THR Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain O residue 11 TYR Chi-restraints excluded: chain O residue 20 GLN 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 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 Chi-restraints excluded: chain I residue 247 ASP 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: 8.9990 chunk 98 optimal weight: 0.8980 chunk 195 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 chunk 244 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 188 GLN ** L 422 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** ** O 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 70 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 = 0.3492 r_free = 0.3492 target = 0.054860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.044118 restraints weight = 196260.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.045408 restraints weight = 116769.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.046286 restraints weight = 81400.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.046861 restraints weight = 63215.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.047292 restraints weight = 52878.152| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26319 Z= 0.188 Angle : 0.699 14.740 35877 Z= 0.347 Chirality : 0.042 0.192 3887 Planarity : 0.005 0.053 4474 Dihedral : 14.515 168.074 4136 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.26 % Favored : 87.57 % Rotamer: Outliers : 2.57 % Allowed : 18.76 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.37 (0.15), residues: 3002 helix: 0.17 (0.18), residues: 896 sheet: -1.33 (0.37), residues: 201 loop : -2.65 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 116 TYR 0.028 0.002 TYR J 169 PHE 0.026 0.002 PHE M 76 TRP 0.045 0.002 TRP G 237 HIS 0.005 0.001 HIS E 202 Details of bonding type rmsd covalent geometry : bond 0.00413 (26319) covalent geometry : angle 0.69915 (35877) hydrogen bonds : bond 0.03725 ( 720) hydrogen bonds : angle 4.85958 ( 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 227 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 161 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 MET cc_start: 0.9012 (mpp) cc_final: 0.8748 (mpp) REVERT: E 124 MET cc_start: 0.9090 (ppp) cc_final: 0.8513 (ppp) REVERT: E 251 LEU cc_start: -0.0251 (OUTLIER) cc_final: -0.1260 (mt) REVERT: F 291 PHE cc_start: 0.9381 (OUTLIER) cc_final: 0.8974 (t80) REVERT: G 268 MET cc_start: 0.8565 (tmm) cc_final: 0.8176 (tmm) REVERT: H 124 MET cc_start: 0.8347 (ptm) cc_final: 0.8010 (ptm) REVERT: H 173 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8930 (tt) REVERT: J 97 MET cc_start: 0.7469 (tpp) cc_final: 0.6426 (tpp) REVERT: J 124 MET cc_start: 0.8660 (pmm) cc_final: 0.8396 (pmm) REVERT: J 134 ASP cc_start: 0.8621 (m-30) cc_final: 0.7993 (p0) REVERT: K 10 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7508 (tp) REVERT: K 124 MET cc_start: 0.8860 (mmm) cc_final: 0.8527 (tpp) REVERT: L 365 ARG cc_start: 0.5883 (ttt180) cc_final: 0.5638 (ttt180) REVERT: M 91 ASP cc_start: 0.9385 (t0) cc_final: 0.8955 (p0) REVERT: O 72 PHE cc_start: 0.9233 (m-10) cc_final: 0.8602 (m-80) REVERT: O 76 PHE cc_start: 0.8000 (m-80) cc_final: 0.7533 (m-80) REVERT: O 94 GLN cc_start: 0.9200 (tm-30) cc_final: 0.8834 (tm-30) REVERT: O 99 ASP cc_start: 0.7932 (m-30) cc_final: 0.7556 (p0) REVERT: O 104 ARG cc_start: 0.9093 (mmt180) cc_final: 0.8878 (mmt180) REVERT: I 49 MET cc_start: 0.9199 (mpp) cc_final: 0.8958 (mpp) REVERT: I 279 MET cc_start: 0.6486 (ptp) cc_final: 0.6199 (ptp) outliers start: 66 outliers final: 48 residues processed: 210 average time/residue: 0.1564 time to fit residues: 54.7999 Evaluate side-chains 209 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 157 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 E residue 279 MET Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 291 PHE 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 H residue 34 ILE Chi-restraints excluded: chain H residue 49 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 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 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 527 THR Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain O residue 11 TYR 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 34 ILE Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 56 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 Chi-restraints excluded: chain I residue 247 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 150 optimal weight: 5.9990 chunk 229 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 266 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 GLN ** K 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 422 GLN ** N 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN ** O 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.054511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.043870 restraints weight = 198771.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.045134 restraints weight = 118276.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.045990 restraints weight = 82799.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.046577 restraints weight = 64481.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.046976 restraints weight = 53803.425| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26319 Z= 0.163 Angle : 0.702 15.156 35877 Z= 0.344 Chirality : 0.042 0.181 3887 Planarity : 0.004 0.051 4474 Dihedral : 14.524 168.420 4136 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.53 % Favored : 88.31 % Rotamer: Outliers : 2.72 % Allowed : 19.00 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.15), residues: 3002 helix: 0.06 (0.18), residues: 902 sheet: -1.17 (0.42), residues: 175 loop : -2.65 (0.13), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 116 TYR 0.021 0.001 TYR E 138 PHE 0.025 0.001 PHE M 76 TRP 0.048 0.002 TRP I 237 HIS 0.006 0.001 HIS E 202 Details of bonding type rmsd covalent geometry : bond 0.00359 (26319) covalent geometry : angle 0.70211 (35877) hydrogen bonds : bond 0.03552 ( 720) hydrogen bonds : angle 4.84793 ( 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 233 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 163 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 MET cc_start: 0.9014 (mpp) cc_final: 0.8717 (mpp) REVERT: E 124 MET cc_start: 0.9069 (ppp) cc_final: 0.8545 (ppp) REVERT: E 251 LEU cc_start: -0.0647 (OUTLIER) cc_final: -0.1598 (mt) REVERT: F 167 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7401 (p90) REVERT: F 291 PHE cc_start: 0.9328 (OUTLIER) cc_final: 0.8958 (t80) REVERT: G 115 LYS cc_start: 0.7626 (tppt) cc_final: 0.7107 (tptt) REVERT: G 268 MET cc_start: 0.8502 (tmm) cc_final: 0.7675 (tmm) REVERT: H 124 MET cc_start: 0.8344 (ptm) cc_final: 0.8018 (ptm) REVERT: H 139 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7600 (pp30) REVERT: H 173 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8866 (tt) REVERT: J 124 MET cc_start: 0.8672 (pmm) cc_final: 0.8367 (pmm) REVERT: J 134 ASP cc_start: 0.8566 (m-30) cc_final: 0.7953 (p0) REVERT: K 124 MET cc_start: 0.8861 (mmm) cc_final: 0.7375 (ptt) REVERT: M 91 ASP cc_start: 0.9401 (t0) cc_final: 0.8988 (p0) REVERT: O 72 PHE cc_start: 0.9211 (m-10) cc_final: 0.8575 (m-80) REVERT: O 76 PHE cc_start: 0.8008 (m-80) cc_final: 0.7544 (m-80) REVERT: O 94 GLN cc_start: 0.9254 (tm-30) cc_final: 0.8906 (tm-30) REVERT: O 99 ASP cc_start: 0.7956 (m-30) cc_final: 0.7550 (p0) REVERT: O 104 ARG cc_start: 0.9155 (mmt180) cc_final: 0.8906 (mmt180) REVERT: I 49 MET cc_start: 0.9221 (mpp) cc_final: 0.8952 (mpp) REVERT: I 279 MET cc_start: 0.6677 (ptp) cc_final: 0.6443 (ptp) outliers start: 70 outliers final: 48 residues processed: 219 average time/residue: 0.1515 time to fit residues: 55.4702 Evaluate side-chains 208 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 155 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 E residue 279 MET Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 167 PHE Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain G residue 70 HIS 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 H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE 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 139 GLN 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 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 291 PHE 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 27 LEU 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 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 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 Chi-restraints excluded: chain I residue 276 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 84 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 256 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 chunk 283 optimal weight: 0.1980 chunk 95 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.0470 overall best weight: 1.8484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 422 GLN ** N 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.054770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.044196 restraints weight = 199295.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.045484 restraints weight = 117829.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.046348 restraints weight = 82090.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.046949 restraints weight = 63529.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.047350 restraints weight = 52958.655| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26319 Z= 0.138 Angle : 0.711 15.347 35877 Z= 0.342 Chirality : 0.042 0.297 3887 Planarity : 0.004 0.053 4474 Dihedral : 14.466 168.273 4136 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.96 % Favored : 87.87 % Rotamer: Outliers : 2.49 % Allowed : 20.01 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.15), residues: 3002 helix: 0.07 (0.18), residues: 900 sheet: -1.16 (0.42), residues: 173 loop : -2.62 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 57 TYR 0.029 0.001 TYR J 169 PHE 0.023 0.001 PHE M 76 TRP 0.045 0.001 TRP G 237 HIS 0.003 0.001 HIS G 282 Details of bonding type rmsd covalent geometry : bond 0.00307 (26319) covalent geometry : angle 0.71117 (35877) hydrogen bonds : bond 0.03440 ( 720) hydrogen bonds : angle 4.82103 ( 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 225 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 161 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 MET cc_start: 0.8998 (mpp) cc_final: 0.8586 (mpp) REVERT: E 124 MET cc_start: 0.9025 (ppp) cc_final: 0.8468 (ppp) REVERT: E 251 LEU cc_start: -0.0742 (OUTLIER) cc_final: -0.1666 (mt) REVERT: F 167 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7417 (p90) REVERT: F 291 PHE cc_start: 0.9338 (OUTLIER) cc_final: 0.8929 (t80) REVERT: G 115 LYS cc_start: 0.7809 (tppt) cc_final: 0.7281 (tptt) REVERT: G 268 MET cc_start: 0.8521 (tmm) cc_final: 0.7854 (tmm) REVERT: H 49 MET cc_start: 0.9273 (mpp) cc_final: 0.8960 (pmm) REVERT: H 124 MET cc_start: 0.8355 (ptm) cc_final: 0.8032 (ptm) REVERT: H 169 TYR cc_start: 0.7403 (t80) cc_final: 0.7176 (t80) REVERT: H 173 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8863 (tt) REVERT: J 124 MET cc_start: 0.8683 (pmm) cc_final: 0.8350 (pmm) REVERT: J 134 ASP cc_start: 0.8700 (m-30) cc_final: 0.8086 (p0) REVERT: K 124 MET cc_start: 0.8799 (mmm) cc_final: 0.7324 (ptt) REVERT: L 267 LEU cc_start: 0.9739 (tt) cc_final: 0.9352 (pp) REVERT: L 365 ARG cc_start: 0.5737 (ttt180) cc_final: 0.5522 (ttt180) REVERT: M 91 ASP cc_start: 0.9405 (t0) cc_final: 0.8915 (p0) REVERT: O 72 PHE cc_start: 0.9208 (m-10) cc_final: 0.8637 (m-80) REVERT: O 76 PHE cc_start: 0.7988 (m-80) cc_final: 0.7546 (m-80) REVERT: O 94 GLN cc_start: 0.9251 (tm-30) cc_final: 0.8899 (tm-30) REVERT: O 99 ASP cc_start: 0.8015 (m-30) cc_final: 0.7616 (p0) REVERT: O 104 ARG cc_start: 0.9137 (mmt180) cc_final: 0.8933 (mpt180) REVERT: I 49 MET cc_start: 0.9209 (mpp) cc_final: 0.8879 (mpp) REVERT: I 115 LYS cc_start: 0.7203 (mmmt) cc_final: 0.6908 (mmmt) REVERT: I 279 MET cc_start: 0.6448 (ptp) cc_final: 0.6147 (ptp) outliers start: 64 outliers final: 51 residues processed: 212 average time/residue: 0.1624 time to fit residues: 57.1170 Evaluate side-chains 210 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 155 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 E residue 279 MET Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 167 PHE Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain G residue 7 PHE 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 H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE 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 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 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 76 PHE Chi-restraints excluded: chain O residue 81 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 34 ILE Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 75 LEU 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 Chi-restraints excluded: chain I residue 247 ASP Chi-restraints excluded: chain I residue 276 LEU 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: 0.7980 chunk 214 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 282 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 218 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 119 optimal weight: 0.0770 chunk 1 optimal weight: 10.0000 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 GLN L 422 GLN ** O 31 HIS ** 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 = 0.3522 r_free = 0.3522 target = 0.056019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.045368 restraints weight = 194286.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.046686 restraints weight = 114518.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.047597 restraints weight = 79392.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.048220 restraints weight = 61201.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.048661 restraints weight = 50645.924| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26319 Z= 0.116 Angle : 0.709 15.704 35877 Z= 0.336 Chirality : 0.042 0.238 3887 Planarity : 0.004 0.053 4474 Dihedral : 14.292 165.524 4136 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.66 % Favored : 90.17 % Rotamer: Outliers : 2.06 % Allowed : 20.36 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.15), residues: 3002 helix: 0.11 (0.18), residues: 908 sheet: -0.99 (0.43), residues: 173 loop : -2.63 (0.13), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 66 TYR 0.023 0.001 TYR A 116 PHE 0.020 0.001 PHE M 92 TRP 0.040 0.001 TRP I 237 HIS 0.002 0.000 HIS E 202 Details of bonding type rmsd covalent geometry : bond 0.00255 (26319) covalent geometry : angle 0.70861 (35877) hydrogen bonds : bond 0.03183 ( 720) hydrogen bonds : angle 4.68626 ( 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 215 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 162 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 MET cc_start: 0.8976 (mpp) cc_final: 0.8563 (mpp) REVERT: E 124 MET cc_start: 0.8943 (ppp) cc_final: 0.8312 (ppp) REVERT: E 251 LEU cc_start: -0.0176 (OUTLIER) cc_final: -0.0872 (mt) REVERT: F 167 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7116 (p90) REVERT: F 291 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.8605 (t80) REVERT: G 115 LYS cc_start: 0.7800 (tppt) cc_final: 0.7249 (tptt) REVERT: G 268 MET cc_start: 0.8426 (tmm) cc_final: 0.7758 (tmm) REVERT: G 279 MET cc_start: 0.5160 (ptt) cc_final: 0.3664 (pmm) REVERT: H 107 MET cc_start: 0.9179 (ppp) cc_final: 0.8808 (ppp) REVERT: H 124 MET cc_start: 0.8324 (ptm) cc_final: 0.8017 (ptm) REVERT: H 139 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7522 (pp30) REVERT: H 173 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8886 (tt) REVERT: J 124 MET cc_start: 0.8635 (pmm) cc_final: 0.8290 (pmm) REVERT: J 134 ASP cc_start: 0.8667 (m-30) cc_final: 0.8027 (p0) REVERT: K 124 MET cc_start: 0.8807 (mmm) cc_final: 0.8509 (mmm) REVERT: K 237 TRP cc_start: 0.8203 (p-90) cc_final: 0.7858 (p-90) REVERT: L 267 LEU cc_start: 0.9710 (tt) cc_final: 0.9294 (pp) REVERT: M 91 ASP cc_start: 0.9344 (t0) cc_final: 0.8910 (p0) REVERT: O 72 PHE cc_start: 0.9179 (m-10) cc_final: 0.8615 (m-80) REVERT: O 76 PHE cc_start: 0.8114 (m-80) cc_final: 0.7585 (m-80) REVERT: O 99 ASP cc_start: 0.7872 (m-30) cc_final: 0.7506 (p0) REVERT: O 104 ARG cc_start: 0.9159 (mmt180) cc_final: 0.8893 (mpt180) REVERT: I 49 MET cc_start: 0.9209 (mpp) cc_final: 0.8853 (mpp) REVERT: I 279 MET cc_start: 0.6542 (ptp) cc_final: 0.6290 (ptp) outliers start: 53 outliers final: 44 residues processed: 205 average time/residue: 0.1671 time to fit residues: 56.5258 Evaluate side-chains 201 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 152 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 E residue 279 MET Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 167 PHE Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain G residue 70 HIS 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 H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE 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 139 GLN 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 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 246 THR Chi-restraints excluded: chain K residue 4 LEU 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 76 PHE 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 75 LEU 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 Chi-restraints excluded: chain I residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 230 optimal weight: 0.0970 chunk 33 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 279 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 250 optimal weight: 2.9990 chunk 77 optimal weight: 0.0770 chunk 248 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 overall best weight: 1.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 422 GLN ** O 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.056011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.045331 restraints weight = 193185.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.046653 restraints weight = 114178.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.047546 restraints weight = 79137.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.048161 restraints weight = 60978.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.048591 restraints weight = 50584.067| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.263 26319 Z= 0.185 Angle : 0.819 59.198 35877 Z= 0.428 Chirality : 0.044 0.749 3887 Planarity : 0.004 0.053 4474 Dihedral : 14.288 165.528 4136 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.89 % Favored : 89.94 % Rotamer: Outliers : 2.22 % Allowed : 20.47 % Favored : 77.31 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.15), residues: 3002 helix: 0.13 (0.18), residues: 902 sheet: -0.97 (0.43), residues: 173 loop : -2.62 (0.13), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 365 TYR 0.023 0.001 TYR A 116 PHE 0.058 0.001 PHE O 92 TRP 0.038 0.001 TRP G 237 HIS 0.002 0.000 HIS G 282 Details of bonding type rmsd covalent geometry : bond 0.00422 (26319) covalent geometry : angle 0.81880 (35877) hydrogen bonds : bond 0.03250 ( 720) hydrogen bonds : angle 4.68623 ( 1988) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4087.80 seconds wall clock time: 72 minutes 6.75 seconds (4326.75 seconds total)