Starting phenix.real_space_refine on Sat May 24 14:31:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h67_34495/05_2025/8h67_34495.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h67_34495/05_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_34495/05_2025/8h67_34495.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h67_34495/05_2025/8h67_34495.map" model { file = "/net/cci-nas-00/data/ceres_data/8h67_34495/05_2025/8h67_34495.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h67_34495/05_2025/8h67_34495.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.93, per 1000 atoms: 0.54 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: 5.85 Conformation dependent library (CDL) restraints added in 2.8 seconds 6004 Ramachandran restraints generated. 3002 Oldfield, 0 Emsley, 3002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5794 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 28 sheets defined 36.7% alpha, 6.8% beta 2 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 6.84 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: 6.84 Time building geometry restraints manager: 6.89 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 1.040 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 53.740 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.100 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.330 ------------------------------------------------------------------------------- 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 : 19.90 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.012 0.001 TRP E 237 HIS 0.003 0.001 HIS E 164 PHE 0.044 0.001 PHE F 291 TYR 0.021 0.001 TYR O 75 ARG 0.011 0.000 ARG F 266 Details of bonding type rmsd hydrogen bonds : bond 0.21431 ( 720) hydrogen bonds : angle 7.09864 ( 1988) covalent geometry : bond 0.00274 (26319) covalent geometry : angle 0.67942 (35877) *********************** 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 : 3.078 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: 0.8346 (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: 0.8794 (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: 0.8643 (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: 0.5928 (ptp) outliers start: 2 outliers final: 1 residues processed: 239 average time/residue: 0.3602 time to fit residues: 137.2365 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 : 2.674 ------------------------------------------------------------------------------- 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 254 optimal weight: 10.0000 chunk 228 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 273 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN H 51 ASN ** K 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 208 ASN L 422 GLN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 ASN ** 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 = 0.3505 r_free = 0.3505 target = 0.055305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.044741 restraints weight = 201031.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.045973 restraints weight = 121677.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.046815 restraints weight = 85792.022| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26319 Z= 0.227 Angle : 0.747 12.934 35877 Z= 0.383 Chirality : 0.044 0.230 3887 Planarity : 0.005 0.058 4474 Dihedral : 14.915 166.739 4140 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.52 % Favored : 87.24 % Rotamer: Outliers : 1.56 % Allowed : 11.91 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.15), residues: 3002 helix: -0.07 (0.18), residues: 891 sheet: -1.67 (0.33), residues: 245 loop : -2.71 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 237 HIS 0.009 0.002 HIS G 164 PHE 0.031 0.002 PHE F 291 TYR 0.031 0.002 TYR N 75 ARG 0.012 0.001 ARG E 204 Details of bonding type rmsd hydrogen bonds : bond 0.05063 ( 720) hydrogen bonds : angle 5.42336 ( 1988) covalent geometry : bond 0.00489 (26319) covalent geometry : angle 0.74702 (35877) *********************** 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 211 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 MET cc_start: 0.8868 (mpp) cc_final: 0.8360 (mpp) REVERT: E 112 ARG cc_start: 0.6858 (ptt180) cc_final: 0.6607 (ptt180) REVERT: E 124 MET cc_start: 0.9092 (ppp) cc_final: 0.8586 (ppp) REVERT: F 124 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8502 (ttp) REVERT: F 291 PHE cc_start: 0.9330 (t80) cc_final: 0.8966 (t80) REVERT: G 49 MET cc_start: 0.9435 (pmm) cc_final: 0.9213 (pmm) REVERT: G 279 MET cc_start: 0.5470 (OUTLIER) cc_final: 0.4794 (pmm) REVERT: H 107 MET cc_start: 0.9411 (ppp) cc_final: 0.9025 (ppp) REVERT: H 124 MET cc_start: 0.8550 (ptm) cc_final: 0.8118 (ptm) REVERT: H 268 MET cc_start: 0.7733 (tmm) cc_final: 0.7113 (tmm) REVERT: J 97 MET cc_start: 0.7874 (tpp) cc_final: 0.7565 (tpp) REVERT: J 107 MET cc_start: 0.9172 (tpp) cc_final: 0.8941 (tpp) REVERT: J 124 MET cc_start: 0.8910 (pmm) cc_final: 0.8560 (pmm) REVERT: K 124 MET cc_start: 0.8752 (mmm) cc_final: 0.8228 (tmm) REVERT: L 365 ARG cc_start: 0.5355 (tmt170) cc_final: 0.5016 (tmt170) REVERT: L 390 TRP cc_start: 0.8673 (p-90) cc_final: 0.8456 (p-90) REVERT: N 75 TYR cc_start: 0.8322 (m-80) cc_final: 0.7878 (m-80) REVERT: O 72 PHE cc_start: 0.9297 (m-10) cc_final: 0.8851 (m-80) REVERT: O 99 ASP cc_start: 0.8379 (m-30) cc_final: 0.7949 (p0) REVERT: O 104 ARG cc_start: 0.8993 (mmt180) cc_final: 0.8737 (mmt-90) REVERT: I 119 ILE cc_start: 0.9281 (mm) cc_final: 0.9058 (mp) REVERT: I 279 MET cc_start: 0.6836 (ptp) cc_final: 0.6580 (ptp) outliers start: 40 outliers final: 28 residues processed: 195 average time/residue: 0.3626 time to fit residues: 115.0861 Evaluate side-chains 178 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 226 TYR Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 122 CYS Chi-restraints excluded: chain H residue 167 PHE Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 251 LEU 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 292 optimal weight: 7.9990 chunk 263 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 223 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 ASN ** 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 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.052356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.041939 restraints weight = 202515.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.043118 restraints weight = 121481.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.043913 restraints weight = 85429.193| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 26319 Z= 0.278 Angle : 0.816 15.535 35877 Z= 0.418 Chirality : 0.047 0.304 3887 Planarity : 0.006 0.119 4474 Dihedral : 15.132 167.576 4140 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.52 % Favored : 86.24 % Rotamer: Outliers : 3.08 % Allowed : 16.12 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.14), residues: 3002 helix: -0.22 (0.17), residues: 882 sheet: -2.01 (0.32), residues: 244 loop : -2.89 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP I 237 HIS 0.012 0.002 HIS E 202 PHE 0.035 0.002 PHE M 76 TYR 0.036 0.002 TYR E 138 ARG 0.011 0.001 ARG E 204 Details of bonding type rmsd hydrogen bonds : bond 0.05265 ( 720) hydrogen bonds : angle 5.54114 ( 1988) covalent geometry : bond 0.00600 (26319) covalent geometry : angle 0.81602 (35877) *********************** 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 228 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 149 time to evaluate : 2.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 MET cc_start: 0.8971 (mpp) cc_final: 0.8560 (mpp) REVERT: E 124 MET cc_start: 0.9170 (ppp) cc_final: 0.8717 (ppp) REVERT: E 171 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8569 (t80) REVERT: F 291 PHE cc_start: 0.9336 (t80) cc_final: 0.9010 (t80) REVERT: H 107 MET cc_start: 0.9402 (ppp) cc_final: 0.8999 (ppp) REVERT: H 124 MET cc_start: 0.8411 (ptm) cc_final: 0.8066 (ptm) REVERT: H 268 MET cc_start: 0.7710 (tmm) cc_final: 0.7345 (tmm) REVERT: J 97 MET cc_start: 0.8042 (tpp) cc_final: 0.7729 (tpp) REVERT: J 107 MET cc_start: 0.9254 (tpp) cc_final: 0.8911 (tpt) REVERT: J 134 ASP cc_start: 0.8469 (m-30) cc_final: 0.7858 (p0) REVERT: K 10 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7674 (tp) REVERT: K 94 PHE cc_start: 0.1390 (OUTLIER) cc_final: 0.0888 (m-80) REVERT: L 335 LYS cc_start: 0.9320 (mmmt) cc_final: 0.8760 (tppt) REVERT: L 390 TRP cc_start: 0.8579 (p-90) cc_final: 0.7972 (p-90) REVERT: M 91 ASP cc_start: 0.9442 (t0) cc_final: 0.9182 (p0) REVERT: N 75 TYR cc_start: 0.8436 (m-80) cc_final: 0.7964 (m-80) REVERT: O 72 PHE cc_start: 0.9308 (m-10) cc_final: 0.8957 (m-80) REVERT: O 76 PHE cc_start: 0.8039 (m-80) cc_final: 0.7673 (m-80) REVERT: O 94 GLN cc_start: 0.9169 (tm-30) cc_final: 0.8841 (tm-30) REVERT: O 99 ASP cc_start: 0.8429 (m-30) cc_final: 0.7998 (p0) REVERT: O 104 ARG cc_start: 0.9151 (mmt180) cc_final: 0.8772 (mpt180) REVERT: I 115 LYS cc_start: 0.7520 (mmmt) cc_final: 0.7136 (mmmt) REVERT: I 279 MET cc_start: 0.7160 (ptp) cc_final: 0.6695 (ptp) outliers start: 79 outliers final: 52 residues processed: 210 average time/residue: 0.3261 time to fit residues: 112.8279 Evaluate side-chains 193 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 138 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 171 PHE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 226 TYR Chi-restraints excluded: chain E residue 279 MET Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 41 TYR 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 215 VAL Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 122 CYS Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 167 PHE Chi-restraints excluded: chain H residue 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 J residue 226 TYR Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain O residue 11 TYR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 7 PHE Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 167 PHE Chi-restraints excluded: chain I residue 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 71 optimal weight: 0.9980 chunk 286 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 298 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 182 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** I 100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.054121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.043536 restraints weight = 198868.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.044813 restraints weight = 117172.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.045646 restraints weight = 81416.900| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3150 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= 0.138 Angle : 0.686 15.109 35877 Z= 0.344 Chirality : 0.043 0.229 3887 Planarity : 0.004 0.053 4474 Dihedral : 14.731 164.440 4136 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.73 % Favored : 88.07 % Rotamer: Outliers : 2.69 % Allowed : 18.22 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.15), residues: 3002 helix: 0.06 (0.18), residues: 881 sheet: -1.58 (0.40), residues: 181 loop : -2.76 (0.13), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP I 237 HIS 0.011 0.001 HIS E 202 PHE 0.028 0.001 PHE M 76 TYR 0.020 0.001 TYR E 138 ARG 0.003 0.000 ARG A 57 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 720) hydrogen bonds : angle 5.13156 ( 1988) covalent geometry : bond 0.00303 (26319) covalent geometry : angle 0.68617 (35877) *********************** 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 218 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 149 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 MET cc_start: 0.9021 (mpp) cc_final: 0.8732 (mpp) REVERT: E 121 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.6901 (ttt180) REVERT: E 124 MET cc_start: 0.9093 (ppp) cc_final: 0.8547 (ppp) REVERT: E 139 GLN cc_start: 0.6275 (OUTLIER) cc_final: 0.4867 (mp-120) REVERT: F 291 PHE cc_start: 0.9270 (t80) cc_final: 0.8841 (t80) REVERT: G 268 MET cc_start: 0.8521 (tmm) cc_final: 0.7834 (tmm) REVERT: G 279 MET cc_start: 0.5212 (ptt) cc_final: 0.4430 (pmm) REVERT: H 124 MET cc_start: 0.8420 (ptm) cc_final: 0.8115 (ptm) REVERT: H 268 MET cc_start: 0.7715 (tmm) cc_final: 0.7413 (tmm) REVERT: H 279 MET cc_start: 0.5244 (ptt) cc_final: 0.5019 (ptt) REVERT: J 97 MET cc_start: 0.7842 (tpp) cc_final: 0.7510 (tpp) REVERT: J 107 MET cc_start: 0.9181 (tpp) cc_final: 0.8859 (tpp) REVERT: J 134 ASP cc_start: 0.8619 (m-30) cc_final: 0.7998 (p0) REVERT: K 124 MET cc_start: 0.8736 (mmm) cc_final: 0.8481 (mmm) REVERT: L 390 TRP cc_start: 0.8599 (p-90) cc_final: 0.8314 (p-90) REVERT: M 91 ASP cc_start: 0.9418 (t0) cc_final: 0.9013 (p0) REVERT: N 33 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6440 (pt) REVERT: N 75 TYR cc_start: 0.8281 (m-80) cc_final: 0.7925 (m-80) REVERT: O 72 PHE cc_start: 0.9218 (m-10) cc_final: 0.8886 (m-80) REVERT: O 76 PHE cc_start: 0.8072 (m-80) cc_final: 0.7713 (m-80) REVERT: O 104 ARG cc_start: 0.9134 (mmt180) cc_final: 0.8679 (mpt180) REVERT: I 49 MET cc_start: 0.9172 (mpp) cc_final: 0.8959 (mtm) REVERT: I 279 MET cc_start: 0.6893 (ptp) cc_final: 0.6606 (ptp) outliers start: 69 outliers final: 43 residues processed: 207 average time/residue: 0.3427 time to fit residues: 116.4796 Evaluate side-chains 191 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 2.776 ------------------------------------------------------------------------------- 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 121 ARG Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 171 PHE Chi-restraints excluded: chain E residue 226 TYR Chi-restraints excluded: chain E residue 279 MET Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 167 PHE 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 73 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 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 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 33 LEU Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain O residue 11 TYR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 7 PHE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 57 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 275 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 214 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 198 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 ASN L 422 GLN ** 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** ** I 19 ASN ** 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 = 0.3446 r_free = 0.3446 target = 0.053176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.042765 restraints weight = 200249.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.043977 restraints weight = 119642.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.044816 restraints weight = 83790.405| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26319 Z= 0.168 Angle : 0.702 14.240 35877 Z= 0.352 Chirality : 0.043 0.207 3887 Planarity : 0.005 0.053 4474 Dihedral : 14.731 167.121 4136 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.69 % Favored : 87.11 % Rotamer: Outliers : 3.62 % Allowed : 18.96 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.15), residues: 3002 helix: 0.03 (0.18), residues: 887 sheet: -1.47 (0.38), residues: 189 loop : -2.76 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP I 237 HIS 0.017 0.001 HIS E 202 PHE 0.028 0.002 PHE M 76 TYR 0.021 0.002 TYR E 138 ARG 0.004 0.000 ARG J 242 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 720) hydrogen bonds : angle 5.10841 ( 1988) covalent geometry : bond 0.00368 (26319) covalent geometry : angle 0.70219 (35877) *********************** 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 241 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 148 time to evaluate : 2.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 MET cc_start: 0.9019 (mpp) cc_final: 0.8705 (mpp) REVERT: E 121 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.6706 (ttt180) REVERT: E 124 MET cc_start: 0.9114 (ppp) cc_final: 0.8561 (ppp) REVERT: E 139 GLN cc_start: 0.6144 (OUTLIER) cc_final: 0.4729 (mp-120) REVERT: F 167 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7581 (p90) REVERT: F 291 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.8979 (t80) REVERT: G 268 MET cc_start: 0.8367 (tmm) cc_final: 0.7703 (tmm) REVERT: H 124 MET cc_start: 0.8253 (ptm) cc_final: 0.7895 (ptm) REVERT: H 173 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8882 (tt) REVERT: H 268 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7499 (tmm) REVERT: H 279 MET cc_start: 0.5908 (ptt) cc_final: 0.5633 (ptt) REVERT: J 97 MET cc_start: 0.7927 (tpp) cc_final: 0.7572 (tpp) REVERT: J 107 MET cc_start: 0.9126 (tpp) cc_final: 0.8797 (tpp) REVERT: J 134 ASP cc_start: 0.8641 (m-30) cc_final: 0.8046 (p0) REVERT: K 107 MET cc_start: 0.9233 (ptp) cc_final: 0.8875 (mmm) REVERT: K 124 MET cc_start: 0.8829 (mmm) cc_final: 0.8387 (mmm) REVERT: L 267 LEU cc_start: 0.9685 (tt) cc_final: 0.9251 (pp) REVERT: L 390 TRP cc_start: 0.8610 (p-90) cc_final: 0.8256 (p-90) REVERT: M 91 ASP cc_start: 0.9450 (t0) cc_final: 0.9027 (p0) REVERT: N 33 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.6454 (pt) REVERT: O 72 PHE cc_start: 0.9222 (m-10) cc_final: 0.8811 (m-80) REVERT: O 76 PHE cc_start: 0.8086 (m-80) cc_final: 0.7699 (m-80) REVERT: O 104 ARG cc_start: 0.9083 (mmt180) cc_final: 0.8873 (mmt180) REVERT: I 49 MET cc_start: 0.9165 (mpp) cc_final: 0.8953 (mtm) REVERT: I 279 MET cc_start: 0.7250 (ptp) cc_final: 0.6890 (ptp) outliers start: 93 outliers final: 58 residues processed: 223 average time/residue: 0.3340 time to fit residues: 122.9443 Evaluate side-chains 204 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 139 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 226 TYR Chi-restraints excluded: chain E residue 279 MET Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 167 PHE Chi-restraints excluded: chain F residue 198 VAL 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 215 VAL Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 122 CYS Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 167 PHE Chi-restraints excluded: chain H residue 173 LEU Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 268 MET Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 167 PHE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 226 TYR Chi-restraints excluded: chain J residue 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 101 THR Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain O residue 11 TYR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 7 PHE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 57 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 262 optimal weight: 6.9990 chunk 214 optimal weight: 7.9990 chunk 194 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 215 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN ** E 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 ASN ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN L 422 GLN N 98 GLN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN I 272 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.054932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.044389 restraints weight = 196379.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.045671 restraints weight = 116035.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.046519 restraints weight = 80893.208| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3489 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= 0.117 Angle : 0.681 14.984 35877 Z= 0.332 Chirality : 0.042 0.233 3887 Planarity : 0.004 0.052 4474 Dihedral : 14.497 162.766 4136 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.99 % Favored : 89.84 % Rotamer: Outliers : 2.76 % Allowed : 20.40 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.15), residues: 3002 helix: 0.07 (0.18), residues: 901 sheet: -1.22 (0.40), residues: 188 loop : -2.71 (0.13), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP G 237 HIS 0.005 0.001 HIS E 202 PHE 0.024 0.001 PHE E 94 TYR 0.015 0.001 TYR F 206 ARG 0.004 0.000 ARG L 531 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 720) hydrogen bonds : angle 4.87651 ( 1988) covalent geometry : bond 0.00256 (26319) covalent geometry : angle 0.68142 (35877) *********************** 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 231 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 160 time to evaluate : 2.723 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: 0.9002 (mpp) cc_final: 0.8512 (mpp) REVERT: E 121 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.6737 (ttt180) REVERT: E 124 MET cc_start: 0.9032 (ppp) cc_final: 0.8500 (ppp) REVERT: F 167 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7377 (p90) REVERT: F 291 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8808 (t80) REVERT: G 268 MET cc_start: 0.8306 (tmm) cc_final: 0.7599 (tmm) REVERT: H 124 MET cc_start: 0.8329 (ptm) cc_final: 0.8004 (ptm) REVERT: H 169 TYR cc_start: 0.7372 (t80) cc_final: 0.7078 (t80) REVERT: H 173 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8832 (tt) REVERT: H 268 MET cc_start: 0.7847 (tmm) cc_final: 0.7620 (tmm) REVERT: H 279 MET cc_start: 0.5722 (ptt) cc_final: 0.5475 (ptt) REVERT: J 97 MET cc_start: 0.7719 (tpp) cc_final: 0.7393 (tpp) REVERT: J 107 MET cc_start: 0.9065 (tpp) cc_final: 0.8819 (tpp) REVERT: J 131 TYR cc_start: 0.5937 (OUTLIER) cc_final: 0.2777 (m-80) REVERT: J 134 ASP cc_start: 0.8642 (m-30) cc_final: 0.7980 (p0) REVERT: K 107 MET cc_start: 0.9302 (ptp) cc_final: 0.8947 (mmm) REVERT: K 124 MET cc_start: 0.8777 (mmm) cc_final: 0.8474 (mmm) REVERT: L 267 LEU cc_start: 0.9709 (tt) cc_final: 0.9299 (pp) REVERT: L 335 LYS cc_start: 0.9089 (mmmt) cc_final: 0.8491 (tppt) REVERT: L 390 TRP cc_start: 0.8575 (p-90) cc_final: 0.8261 (p-90) REVERT: M 91 ASP cc_start: 0.9436 (t0) cc_final: 0.8999 (p0) REVERT: O 72 PHE cc_start: 0.9192 (m-10) cc_final: 0.8843 (m-80) REVERT: O 76 PHE cc_start: 0.8061 (m-80) cc_final: 0.7662 (m-80) REVERT: I 49 MET cc_start: 0.9187 (mpp) cc_final: 0.8948 (mtm) REVERT: I 279 MET cc_start: 0.6838 (ptp) cc_final: 0.6568 (ptp) outliers start: 71 outliers final: 47 residues processed: 215 average time/residue: 0.3555 time to fit residues: 125.5217 Evaluate side-chains 205 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 2.676 ------------------------------------------------------------------------------- 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 26 GLU Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 279 MET Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 132 LYS 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 34 ILE 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 73 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 131 TYR Chi-restraints excluded: chain J residue 167 PHE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 10 ILE 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 61 LEU Chi-restraints excluded: chain O residue 81 TYR 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 167 PHE Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 223 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 123 optimal weight: 8.9990 chunk 211 optimal weight: 2.9990 chunk 294 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 266 optimal weight: 5.9990 chunk 219 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 277 optimal weight: 0.9980 chunk 255 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 ASN ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN ** L 422 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** ** I 19 ASN ** 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 = 0.3448 r_free = 0.3448 target = 0.053312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.042865 restraints weight = 200990.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.044096 restraints weight = 119936.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.044921 restraints weight = 84073.387| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26319 Z= 0.167 Angle : 0.708 14.426 35877 Z= 0.348 Chirality : 0.042 0.212 3887 Planarity : 0.005 0.053 4474 Dihedral : 14.601 166.479 4136 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.76 % Favored : 87.08 % Rotamer: Outliers : 3.50 % Allowed : 20.71 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.15), residues: 3002 helix: 0.16 (0.18), residues: 889 sheet: -1.25 (0.39), residues: 190 loop : -2.75 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP G 237 HIS 0.006 0.001 HIS A 96 PHE 0.031 0.001 PHE E 94 TYR 0.034 0.002 TYR A 116 ARG 0.004 0.000 ARG G 242 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 720) hydrogen bonds : angle 4.94617 ( 1988) covalent geometry : bond 0.00367 (26319) covalent geometry : angle 0.70757 (35877) *********************** 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 240 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 150 time to evaluate : 2.665 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: 0.9053 (mpp) cc_final: 0.8674 (mpp) REVERT: E 121 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.6640 (ttt180) REVERT: E 124 MET cc_start: 0.9118 (ppp) cc_final: 0.8603 (ppp) REVERT: E 139 GLN cc_start: 0.6137 (OUTLIER) cc_final: 0.4664 (mp-120) REVERT: F 167 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7563 (p90) REVERT: F 291 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.8946 (t80) REVERT: G 4 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8999 (mt) REVERT: G 268 MET cc_start: 0.8279 (tmm) cc_final: 0.7660 (tmm) REVERT: H 124 MET cc_start: 0.8298 (ptm) cc_final: 0.7915 (ptm) REVERT: H 173 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8978 (tt) REVERT: H 279 MET cc_start: 0.6163 (ptt) cc_final: 0.5955 (ptt) REVERT: J 97 MET cc_start: 0.7936 (tpp) cc_final: 0.7605 (tpp) REVERT: J 107 MET cc_start: 0.9087 (tpp) cc_final: 0.8852 (tpp) REVERT: J 131 TYR cc_start: 0.6225 (OUTLIER) cc_final: 0.2992 (m-80) REVERT: J 134 ASP cc_start: 0.8626 (m-30) cc_final: 0.8043 (p0) REVERT: K 94 PHE cc_start: 0.2000 (OUTLIER) cc_final: 0.1710 (m-80) REVERT: L 335 LYS cc_start: 0.9136 (mmmt) cc_final: 0.8518 (tppt) REVERT: L 390 TRP cc_start: 0.8567 (p-90) cc_final: 0.8249 (p-90) REVERT: M 91 ASP cc_start: 0.9482 (t0) cc_final: 0.9023 (p0) REVERT: O 72 PHE cc_start: 0.9237 (m-10) cc_final: 0.8829 (m-80) REVERT: O 76 PHE cc_start: 0.8084 (m-80) cc_final: 0.7661 (m-80) REVERT: O 104 ARG cc_start: 0.9073 (mmt180) cc_final: 0.8632 (mpt180) REVERT: I 279 MET cc_start: 0.7242 (ptp) cc_final: 0.6916 (ptp) outliers start: 90 outliers final: 63 residues processed: 223 average time/residue: 0.3242 time to fit residues: 119.2426 Evaluate side-chains 217 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 146 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 226 TYR Chi-restraints excluded: chain E residue 279 MET Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 131 TYR Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 167 PHE Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain G residue 49 MET 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 73 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 J residue 12 THR Chi-restraints excluded: chain J residue 131 TYR Chi-restraints excluded: chain J residue 167 PHE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 226 TYR Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 233 VAL 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 20 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 75 TYR 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 53 LEU Chi-restraints excluded: chain I residue 57 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 211 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 265 optimal weight: 10.0000 chunk 32 optimal weight: 0.4980 chunk 191 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 247 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 GLN ** L 422 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** ** O 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.051906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.041535 restraints weight = 202862.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.042747 restraints weight = 120421.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.043547 restraints weight = 84191.664| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 26319 Z= 0.210 Angle : 0.770 14.928 35877 Z= 0.380 Chirality : 0.044 0.290 3887 Planarity : 0.005 0.053 4474 Dihedral : 14.786 169.330 4136 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.19 % Favored : 86.64 % Rotamer: Outliers : 3.54 % Allowed : 21.29 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.15), residues: 3002 helix: 0.06 (0.18), residues: 883 sheet: -1.38 (0.41), residues: 172 loop : -2.80 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP I 237 HIS 0.008 0.001 HIS A 96 PHE 0.035 0.002 PHE E 94 TYR 0.036 0.002 TYR A 116 ARG 0.005 0.001 ARG G 242 Details of bonding type rmsd hydrogen bonds : bond 0.04058 ( 720) hydrogen bonds : angle 5.11928 ( 1988) covalent geometry : bond 0.00458 (26319) covalent geometry : angle 0.76963 (35877) *********************** 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 238 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 147 time to evaluate : 2.733 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: 0.9040 (mpp) cc_final: 0.8780 (mpp) REVERT: E 112 ARG cc_start: 0.6611 (ptt180) cc_final: 0.6407 (ptt90) REVERT: E 121 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.6718 (ttt180) REVERT: E 124 MET cc_start: 0.9166 (ppp) cc_final: 0.8624 (ppp) REVERT: E 139 GLN cc_start: 0.6249 (OUTLIER) cc_final: 0.4638 (mp-120) REVERT: F 167 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.7755 (p90) REVERT: F 202 HIS cc_start: 0.8519 (OUTLIER) cc_final: 0.8039 (t-90) REVERT: F 291 PHE cc_start: 0.9371 (OUTLIER) cc_final: 0.9036 (t80) REVERT: G 268 MET cc_start: 0.8255 (tmm) cc_final: 0.7666 (tmm) REVERT: H 124 MET cc_start: 0.8344 (ptm) cc_final: 0.7972 (ptm) REVERT: H 139 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7589 (pp30) REVERT: H 173 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9083 (tt) REVERT: J 107 MET cc_start: 0.9144 (tpp) cc_final: 0.8769 (tpp) REVERT: J 134 ASP cc_start: 0.8720 (m-30) cc_final: 0.8149 (p0) REVERT: J 221 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8415 (pttp) REVERT: K 124 MET cc_start: 0.8971 (mmm) cc_final: 0.8295 (tmm) REVERT: L 390 TRP cc_start: 0.8546 (p-90) cc_final: 0.7765 (p-90) REVERT: M 91 ASP cc_start: 0.9499 (t0) cc_final: 0.9233 (p0) REVERT: N 75 TYR cc_start: 0.8311 (m-10) cc_final: 0.7995 (m-80) REVERT: O 104 ARG cc_start: 0.9140 (mmt180) cc_final: 0.8517 (mpt180) REVERT: I 279 MET cc_start: 0.7326 (ptp) cc_final: 0.7061 (ptp) outliers start: 91 outliers final: 70 residues processed: 222 average time/residue: 0.3183 time to fit residues: 118.1485 Evaluate side-chains 216 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 138 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 226 TYR Chi-restraints excluded: chain E residue 279 MET Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 131 TYR Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 167 PHE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 202 HIS 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 39 GLN Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 165 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 7 PHE Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 122 CYS Chi-restraints excluded: chain H residue 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 H residue 290 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 131 TYR Chi-restraints excluded: chain J residue 167 PHE Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 226 TYR Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 269 ASP 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 L residue 27 LEU Chi-restraints excluded: chain L residue 233 VAL 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 20 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 75 TYR 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 53 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 117 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 184 optimal weight: 2.9990 chunk 268 optimal weight: 4.9990 chunk 208 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 260 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 chunk 257 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN L 422 GLN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3431 r_free = 0.3431 target = 0.052699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.042191 restraints weight = 199936.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.043467 restraints weight = 117213.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.044296 restraints weight = 81147.268| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26319 Z= 0.153 Angle : 0.737 15.368 35877 Z= 0.357 Chirality : 0.043 0.195 3887 Planarity : 0.004 0.053 4474 Dihedral : 14.663 166.805 4136 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.29 % Favored : 87.54 % Rotamer: Outliers : 3.27 % Allowed : 22.27 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.15), residues: 3002 helix: 0.07 (0.18), residues: 889 sheet: -1.30 (0.42), residues: 169 loop : -2.75 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP I 237 HIS 0.007 0.001 HIS A 96 PHE 0.027 0.001 PHE E 94 TYR 0.029 0.001 TYR A 116 ARG 0.004 0.000 ARG A 57 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 720) hydrogen bonds : angle 4.95453 ( 1988) covalent geometry : bond 0.00339 (26319) covalent geometry : angle 0.73650 (35877) *********************** 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 232 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 148 time to evaluate : 2.730 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: 0.8994 (mpp) cc_final: 0.8707 (mpp) REVERT: E 121 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.6596 (ttt180) REVERT: E 124 MET cc_start: 0.9097 (ppp) cc_final: 0.8499 (ppp) REVERT: E 139 GLN cc_start: 0.6211 (OUTLIER) cc_final: 0.5186 (mt0) REVERT: F 167 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7661 (p90) REVERT: F 291 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.8989 (t80) REVERT: G 268 MET cc_start: 0.8168 (tmm) cc_final: 0.7606 (tmm) REVERT: H 124 MET cc_start: 0.8347 (ptm) cc_final: 0.7966 (ptm) REVERT: H 139 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7741 (pp30) REVERT: H 173 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9046 (tt) REVERT: J 97 MET cc_start: 0.7797 (mmm) cc_final: 0.7517 (tpp) REVERT: J 107 MET cc_start: 0.9103 (tpp) cc_final: 0.8873 (tpp) REVERT: J 131 TYR cc_start: 0.5963 (OUTLIER) cc_final: 0.2919 (m-80) REVERT: J 134 ASP cc_start: 0.8753 (m-30) cc_final: 0.8177 (p0) REVERT: K 124 MET cc_start: 0.8889 (mmm) cc_final: 0.8213 (tmm) REVERT: L 267 LEU cc_start: 0.9714 (tt) cc_final: 0.9339 (pp) REVERT: L 390 TRP cc_start: 0.8584 (p-90) cc_final: 0.8084 (p-90) REVERT: M 91 ASP cc_start: 0.9492 (t0) cc_final: 0.9241 (p0) REVERT: N 75 TYR cc_start: 0.8316 (m-10) cc_final: 0.7989 (m-80) REVERT: O 72 PHE cc_start: 0.9122 (m-80) cc_final: 0.8812 (m-80) REVERT: I 279 MET cc_start: 0.7250 (ptp) cc_final: 0.7042 (ptp) outliers start: 84 outliers final: 72 residues processed: 217 average time/residue: 0.3307 time to fit residues: 119.3071 Evaluate side-chains 218 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 139 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 226 TYR Chi-restraints excluded: chain E residue 279 MET Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 131 TYR Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 167 PHE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 198 VAL 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 39 GLN Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 159 HIS Chi-restraints excluded: chain G residue 165 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 7 PHE Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 122 CYS Chi-restraints excluded: chain H residue 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 H residue 290 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 131 TYR Chi-restraints excluded: chain J residue 167 PHE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 226 TYR Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 269 ASP 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 L residue 27 LEU Chi-restraints excluded: chain L residue 233 VAL 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 20 GLN Chi-restraints excluded: chain O residue 61 LEU 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 53 LEU Chi-restraints excluded: chain I residue 57 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 Chi-restraints excluded: chain I residue 290 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 295 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 chunk 299 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 113 optimal weight: 0.0770 chunk 278 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 102 optimal weight: 0.1980 chunk 187 optimal weight: 0.0000 chunk 89 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 overall best weight: 1.6546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.053137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.042835 restraints weight = 200383.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.044073 restraints weight = 118294.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.044904 restraints weight = 82157.842| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26319 Z= 0.137 Angle : 0.738 15.610 35877 Z= 0.356 Chirality : 0.043 0.211 3887 Planarity : 0.004 0.053 4474 Dihedral : 14.597 165.651 4136 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.66 % Favored : 88.17 % Rotamer: Outliers : 3.04 % Allowed : 22.65 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.15), residues: 3002 helix: 0.10 (0.18), residues: 883 sheet: -1.37 (0.39), residues: 196 loop : -2.76 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP I 237 HIS 0.007 0.001 HIS A 96 PHE 0.025 0.001 PHE E 94 TYR 0.028 0.001 TYR A 116 ARG 0.004 0.000 ARG O 85 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 720) hydrogen bonds : angle 4.88991 ( 1988) covalent geometry : bond 0.00305 (26319) covalent geometry : angle 0.73771 (35877) ********************** 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 225 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 147 time to evaluate : 3.101 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: 0.9000 (mpp) cc_final: 0.8700 (mpp) REVERT: E 121 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.6507 (ttt180) REVERT: E 124 MET cc_start: 0.9025 (ppp) cc_final: 0.8500 (ppp) REVERT: E 139 GLN cc_start: 0.6381 (OUTLIER) cc_final: 0.5168 (mt0) REVERT: F 167 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7624 (p90) REVERT: F 202 HIS cc_start: 0.8619 (OUTLIER) cc_final: 0.7979 (t-90) REVERT: F 291 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8785 (t80) REVERT: G 268 MET cc_start: 0.8163 (tmm) cc_final: 0.7644 (tmm) REVERT: H 124 MET cc_start: 0.8335 (ptm) cc_final: 0.7966 (ptm) REVERT: H 139 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7678 (pp30) REVERT: H 173 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9026 (tt) REVERT: J 97 MET cc_start: 0.7827 (mmm) cc_final: 0.7538 (tpp) REVERT: J 107 MET cc_start: 0.9017 (tpp) cc_final: 0.8781 (tpp) REVERT: J 131 TYR cc_start: 0.6174 (OUTLIER) cc_final: 0.2848 (m-80) REVERT: J 134 ASP cc_start: 0.8735 (m-30) cc_final: 0.8142 (p0) REVERT: K 107 MET cc_start: 0.8888 (ptp) cc_final: 0.8634 (pmm) REVERT: K 124 MET cc_start: 0.8871 (mmm) cc_final: 0.8482 (mmm) REVERT: L 267 LEU cc_start: 0.9713 (tt) cc_final: 0.9341 (pp) REVERT: L 365 ARG cc_start: 0.5143 (tmt170) cc_final: 0.4793 (tmt170) REVERT: L 390 TRP cc_start: 0.8550 (p-90) cc_final: 0.8208 (p-90) REVERT: M 91 ASP cc_start: 0.9482 (t0) cc_final: 0.9236 (p0) REVERT: N 75 TYR cc_start: 0.8294 (m-10) cc_final: 0.7974 (m-80) REVERT: O 72 PHE cc_start: 0.9138 (m-80) cc_final: 0.8824 (m-80) REVERT: O 104 ARG cc_start: 0.9106 (mpt180) cc_final: 0.8756 (mpt180) outliers start: 78 outliers final: 66 residues processed: 211 average time/residue: 0.3658 time to fit residues: 128.6775 Evaluate side-chains 216 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 142 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 226 TYR Chi-restraints excluded: chain E residue 279 MET Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 131 TYR Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 167 PHE Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 202 HIS 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 49 MET Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 159 HIS Chi-restraints excluded: chain G residue 165 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 7 PHE Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 122 CYS Chi-restraints excluded: chain H residue 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 H residue 290 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 131 TYR Chi-restraints excluded: chain J residue 167 PHE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 226 TYR Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 269 ASP 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 L residue 27 LEU Chi-restraints excluded: chain L residue 233 VAL 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 20 GLN Chi-restraints excluded: chain O residue 61 LEU 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 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 290 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 152 optimal weight: 4.9990 chunk 215 optimal weight: 0.0170 chunk 149 optimal weight: 10.0000 chunk 223 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 277 optimal weight: 0.9990 chunk 198 optimal weight: 5.9990 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.053162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.042852 restraints weight = 200837.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.044078 restraints weight = 118459.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.044904 restraints weight = 82459.619| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4366 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= 0.141 Angle : 0.737 15.891 35877 Z= 0.355 Chirality : 0.043 0.195 3887 Planarity : 0.004 0.053 4474 Dihedral : 14.571 165.303 4136 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.96 % Favored : 87.87 % Rotamer: Outliers : 3.04 % Allowed : 22.85 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.15), residues: 3002 helix: 0.07 (0.18), residues: 884 sheet: -1.36 (0.38), residues: 196 loop : -2.75 (0.13), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP I 237 HIS 0.007 0.001 HIS A 96 PHE 0.025 0.001 PHE E 94 TYR 0.030 0.001 TYR A 116 ARG 0.009 0.000 ARG I 242 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 720) hydrogen bonds : angle 4.86015 ( 1988) covalent geometry : bond 0.00316 (26319) covalent geometry : angle 0.73692 (35877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6855.58 seconds wall clock time: 121 minutes 56.60 seconds (7316.60 seconds total)