Starting phenix.real_space_refine on Thu Sep 18 08:40:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cfv_45564/09_2025/9cfv_45564.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cfv_45564/09_2025/9cfv_45564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cfv_45564/09_2025/9cfv_45564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cfv_45564/09_2025/9cfv_45564.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cfv_45564/09_2025/9cfv_45564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cfv_45564/09_2025/9cfv_45564.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.040 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 92 5.16 5 C 9885 2.51 5 N 2679 2.21 5 O 2999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15664 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 2826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2826 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 Chain: "C" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2904 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 19, 'TRANS': 352} Chain: "D" Number of atoms: 2896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2896 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "P" Number of atoms: 5789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 5789 Classifications: {'peptide': 709} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 682} Chain: "R" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1165 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 145} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.82, per 1000 atoms: 0.24 Number of scatterers: 15664 At special positions: 0 Unit cell: (180.225, 136.17, 129.495, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 92 16.00 P 6 15.00 Mg 3 11.99 O 2999 8.00 N 2679 7.00 C 9885 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: 1.27 Conformation dependent library (CDL) restraints added in 676.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3662 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 26 sheets defined 55.9% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.039A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.906A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.545A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.707A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 285 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.535A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 55 through 62 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.128A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.590A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.596A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.586A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 288 through 295 removed outlier: 4.289A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 332 through 336 removed outlier: 4.447A pdb=" N LYS C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 353 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 366 through 368 No H-bonds generated for 'chain 'C' and resid 366 through 368' Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.697A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.149A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.538A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.776A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.774A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 260 removed outlier: 3.529A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.566A pdb=" N CYS D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.580A pdb=" N ARG D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 349 removed outlier: 3.600A pdb=" N ALA D 347 " --> pdb=" O GLY D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 353 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.043A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 19 Processing helix chain 'P' and resid 24 through 38 Processing helix chain 'P' and resid 58 through 61 removed outlier: 4.097A pdb=" N TYR P 61 " --> pdb=" O LEU P 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 58 through 61' Processing helix chain 'P' and resid 62 through 70 Processing helix chain 'P' and resid 80 through 95 Processing helix chain 'P' and resid 110 through 125 Processing helix chain 'P' and resid 128 through 142 removed outlier: 3.699A pdb=" N SER P 142 " --> pdb=" O ARG P 138 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 150 Processing helix chain 'P' and resid 188 through 193 removed outlier: 3.532A pdb=" N VAL P 193 " --> pdb=" O SER P 190 " (cutoff:3.500A) Processing helix chain 'P' and resid 203 through 212 Processing helix chain 'P' and resid 213 through 220 Processing helix chain 'P' and resid 225 through 228 Processing helix chain 'P' and resid 229 through 234 removed outlier: 3.789A pdb=" N VAL P 233 " --> pdb=" O TYR P 229 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS P 234 " --> pdb=" O LEU P 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 229 through 234' Processing helix chain 'P' and resid 244 through 259 removed outlier: 3.886A pdb=" N LYS P 254 " --> pdb=" O LYS P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 262 through 281 removed outlier: 3.628A pdb=" N ASN P 281 " --> pdb=" O LEU P 277 " (cutoff:3.500A) Processing helix chain 'P' and resid 296 through 307 removed outlier: 4.340A pdb=" N LEU P 300 " --> pdb=" O THR P 296 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR P 302 " --> pdb=" O ASN P 298 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ARG P 305 " --> pdb=" O LYS P 301 " (cutoff:3.500A) Processing helix chain 'P' and resid 310 through 318 Processing helix chain 'P' and resid 335 through 364 Processing helix chain 'P' and resid 397 through 430 Processing helix chain 'P' and resid 440 through 450 removed outlier: 4.387A pdb=" N ILE P 444 " --> pdb=" O ASN P 440 " (cutoff:3.500A) Processing helix chain 'P' and resid 454 through 465 Processing helix chain 'P' and resid 470 through 482 Processing helix chain 'P' and resid 497 through 501 removed outlier: 3.579A pdb=" N LYS P 500 " --> pdb=" O LYS P 497 " (cutoff:3.500A) Processing helix chain 'P' and resid 522 through 528 Processing helix chain 'P' and resid 532 through 540 Processing helix chain 'P' and resid 546 through 551 Processing helix chain 'P' and resid 552 through 558 removed outlier: 3.509A pdb=" N ASP P 558 " --> pdb=" O GLU P 555 " (cutoff:3.500A) Processing helix chain 'P' and resid 564 through 583 Processing helix chain 'P' and resid 603 through 614 removed outlier: 3.656A pdb=" N HIS P 609 " --> pdb=" O VAL P 605 " (cutoff:3.500A) Processing helix chain 'P' and resid 615 through 625 Processing helix chain 'P' and resid 633 through 641 removed outlier: 3.746A pdb=" N GLN P 638 " --> pdb=" O GLU P 634 " (cutoff:3.500A) Processing helix chain 'P' and resid 642 through 648 Proline residue: P 645 - end of helix Processing helix chain 'P' and resid 654 through 666 removed outlier: 3.797A pdb=" N ARG P 664 " --> pdb=" O ALA P 660 " (cutoff:3.500A) Processing helix chain 'P' and resid 684 through 719 removed outlier: 3.922A pdb=" N LEU P 688 " --> pdb=" O PHE P 684 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN P 700 " --> pdb=" O GLU P 696 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER P 701 " --> pdb=" O VAL P 697 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ARG P 716 " --> pdb=" O GLY P 712 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 22 removed outlier: 3.997A pdb=" N LEU R 19 " --> pdb=" O GLU R 15 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE R 20 " --> pdb=" O ALA R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 40 removed outlier: 3.593A pdb=" N LEU R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 57 removed outlier: 3.998A pdb=" N GLU R 55 " --> pdb=" O ASP R 51 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL R 56 " --> pdb=" O MET R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 77 Processing helix chain 'R' and resid 82 through 94 Processing helix chain 'R' and resid 103 through 112 Processing helix chain 'R' and resid 118 through 130 removed outlier: 3.959A pdb=" N GLU R 128 " --> pdb=" O GLU R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 147 Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.552A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.535A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.578A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB3, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'D' and resid 29 through 32 removed outlier: 4.914A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.581A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'P' and resid 42 through 45 removed outlier: 3.575A pdb=" N VAL P 48 " --> pdb=" O ILE P 45 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU P 49 " --> pdb=" O ARG P 589 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE P 591 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER P 51 " --> pdb=" O ILE P 591 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA P 100 " --> pdb=" O ALA P 586 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE P 588 " --> pdb=" O ALA P 100 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N MET P 102 " --> pdb=" O ILE P 588 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N CYS P 590 " --> pdb=" O MET P 102 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER P 104 " --> pdb=" O CYS P 590 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN P 99 " --> pdb=" O GLY P 383 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU P 385 " --> pdb=" O GLN P 99 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL P 101 " --> pdb=" O LEU P 385 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP P 172 " --> pdb=" O PRO P 177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 151 through 152 Processing sheet with id=AC3, first strand: chain 'P' and resid 284 through 286 Processing sheet with id=AC4, first strand: chain 'P' and resid 320 through 325 Processing sheet with id=AC5, first strand: chain 'P' and resid 488 through 490 Processing sheet with id=AC6, first strand: chain 'P' and resid 629 through 632 Processing sheet with id=AC7, first strand: chain 'R' and resid 27 through 29 Processing sheet with id=AC8, first strand: chain 'R' and resid 100 through 102 817 hydrogen bonds defined for protein. 2214 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.25 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4739 1.34 - 1.46: 3083 1.46 - 1.59: 8004 1.59 - 1.72: 2 1.72 - 1.84: 159 Bond restraints: 15987 Sorted by residual: bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.349 0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" C4 ADP D 401 " pdb=" C5 ADP D 401 " ideal model delta sigma weight residual 1.490 1.352 0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.352 0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" C5 ADP D 401 " pdb=" C6 ADP D 401 " ideal model delta sigma weight residual 1.490 1.385 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C5 ADP B 401 " pdb=" C6 ADP B 401 " ideal model delta sigma weight residual 1.490 1.388 0.102 2.00e-02 2.50e+03 2.59e+01 ... (remaining 15982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 18965 2.85 - 5.70: 2564 5.70 - 8.54: 92 8.54 - 11.39: 6 11.39 - 14.24: 5 Bond angle restraints: 21632 Sorted by residual: angle pdb=" CB HIS P 511 " pdb=" CG HIS P 511 " pdb=" CD2 HIS P 511 " ideal model delta sigma weight residual 131.20 123.71 7.49 1.30e+00 5.92e-01 3.32e+01 angle pdb=" C ILE P 362 " pdb=" N ASN P 363 " pdb=" CA ASN P 363 " ideal model delta sigma weight residual 120.28 127.73 -7.45 1.34e+00 5.57e-01 3.09e+01 angle pdb=" CA ASP R 65 " pdb=" CB ASP R 65 " pdb=" CG ASP R 65 " ideal model delta sigma weight residual 112.60 118.03 -5.43 1.00e+00 1.00e+00 2.95e+01 angle pdb=" CA PHE B 266 " pdb=" CB PHE B 266 " pdb=" CG PHE B 266 " ideal model delta sigma weight residual 113.80 118.98 -5.18 1.00e+00 1.00e+00 2.68e+01 angle pdb=" CA ASP P 98 " pdb=" CB ASP P 98 " pdb=" CG ASP P 98 " ideal model delta sigma weight residual 112.60 117.76 -5.16 1.00e+00 1.00e+00 2.66e+01 ... (remaining 21627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.40: 9197 24.40 - 48.79: 390 48.79 - 73.19: 62 73.19 - 97.59: 17 97.59 - 121.98: 4 Dihedral angle restraints: 9670 sinusoidal: 3974 harmonic: 5696 Sorted by residual: dihedral pdb=" C LYS P 483 " pdb=" N LYS P 483 " pdb=" CA LYS P 483 " pdb=" CB LYS P 483 " ideal model delta harmonic sigma weight residual -122.60 -138.02 15.42 0 2.50e+00 1.60e-01 3.80e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 61.99 -121.98 1 2.00e+01 2.50e-03 3.67e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 58.08 -118.07 1 2.00e+01 2.50e-03 3.53e+01 ... (remaining 9667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1854 0.108 - 0.215: 436 0.215 - 0.323: 84 0.323 - 0.431: 5 0.431 - 0.538: 1 Chirality restraints: 2380 Sorted by residual: chirality pdb=" CA LYS P 483 " pdb=" N LYS P 483 " pdb=" C LYS P 483 " pdb=" CB LYS P 483 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.24e+00 chirality pdb=" CA GLU D 167 " pdb=" N GLU D 167 " pdb=" C GLU D 167 " pdb=" CB GLU D 167 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CA PRO B 243 " pdb=" N PRO B 243 " pdb=" C PRO B 243 " pdb=" CB PRO B 243 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 2377 not shown) Planarity restraints: 2793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 340 " -0.295 2.00e-02 2.50e+03 1.48e-01 5.48e+02 pdb=" CG TRP D 340 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP D 340 " 0.117 2.00e-02 2.50e+03 pdb=" CD2 TRP D 340 " 0.112 2.00e-02 2.50e+03 pdb=" NE1 TRP D 340 " 0.069 2.00e-02 2.50e+03 pdb=" CE2 TRP D 340 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 340 " 0.191 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 340 " -0.171 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 340 " 0.090 2.00e-02 2.50e+03 pdb=" CH2 TRP D 340 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 340 " -0.220 2.00e-02 2.50e+03 1.15e-01 3.28e+02 pdb=" CG TRP C 340 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP C 340 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP C 340 " 0.150 2.00e-02 2.50e+03 pdb=" NE1 TRP C 340 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TRP C 340 " 0.057 2.00e-02 2.50e+03 pdb=" CE3 TRP C 340 " 0.151 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 340 " -0.092 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 340 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 340 " -0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 340 " -0.199 2.00e-02 2.50e+03 1.01e-01 2.55e+02 pdb=" CG TRP B 340 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP B 340 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP B 340 " 0.100 2.00e-02 2.50e+03 pdb=" NE1 TRP B 340 " 0.052 2.00e-02 2.50e+03 pdb=" CE2 TRP B 340 " 0.018 2.00e-02 2.50e+03 pdb=" CE3 TRP B 340 " 0.137 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 340 " -0.116 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 340 " 0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP B 340 " -0.111 2.00e-02 2.50e+03 ... (remaining 2790 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 5 2.46 - 3.07: 9418 3.07 - 3.68: 23748 3.68 - 4.29: 37257 4.29 - 4.90: 61850 Nonbonded interactions: 132278 Sorted by model distance: nonbonded pdb=" O3B ADP D 401 " pdb="MG MG D 402 " model vdw 1.853 2.170 nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 1.856 2.170 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 1.857 2.170 nonbonded pdb=" OD2 ASP B 11 " pdb="MG MG B 402 " model vdw 1.924 2.170 nonbonded pdb=" O1A ADP C 401 " pdb="MG MG C 402 " model vdw 1.960 2.170 ... (remaining 132273 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 'B' selection = (chain 'C' and (resid 4 through 39 or resid 50 through 402)) selection = (chain 'D' and (resid 4 through 39 or resid 50 through 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.720 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.230 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 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 : 0.012 0.141 15987 Z= 0.766 Angle : 1.865 14.240 21632 Z= 1.239 Chirality : 0.096 0.538 2380 Planarity : 0.018 0.219 2793 Dihedral : 14.558 121.983 6008 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 0.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.39 % Favored : 96.41 % Rotamer: Outliers : 2.20 % Allowed : 3.74 % Favored : 94.07 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.17), residues: 1949 helix: -1.86 (0.13), residues: 924 sheet: -0.29 (0.30), residues: 229 loop : -0.03 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG B 210 TYR 0.129 0.019 TYR P 438 PHE 0.074 0.013 PHE C 127 TRP 0.295 0.037 TRP D 340 HIS 0.015 0.004 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.01248 (15987) covalent geometry : angle 1.86450 (21632) hydrogen bonds : bond 0.17103 ( 811) hydrogen bonds : angle 7.59422 ( 2214) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 340 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 CYS cc_start: 0.8056 (m) cc_final: 0.7347 (t) REVERT: B 12 ASN cc_start: 0.7365 (m110) cc_final: 0.7073 (m110) REVERT: B 18 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7695 (mtmt) REVERT: B 28 ARG cc_start: 0.8285 (mtt180) cc_final: 0.7983 (mtt-85) REVERT: B 60 SER cc_start: 0.7131 (t) cc_final: 0.6907 (m) REVERT: B 68 LYS cc_start: 0.7708 (mttt) cc_final: 0.6288 (mtmt) REVERT: B 72 GLU cc_start: 0.7476 (tt0) cc_final: 0.6418 (mt-10) REVERT: B 91 TYR cc_start: 0.7036 (m-80) cc_final: 0.5880 (t80) REVERT: B 137 GLN cc_start: 0.8150 (mt0) cc_final: 0.7743 (mt0) REVERT: B 176 MET cc_start: 0.8234 (mmm) cc_final: 0.7865 (mtp) REVERT: B 206 ARG cc_start: 0.5757 (ttt180) cc_final: 0.5203 (ttm-80) REVERT: B 215 LYS cc_start: 0.6686 (mttp) cc_final: 0.6379 (mttt) REVERT: B 238 LYS cc_start: 0.5654 (mmtt) cc_final: 0.5424 (mmtm) REVERT: B 246 GLN cc_start: 0.5942 (mt0) cc_final: 0.5639 (mt0) REVERT: B 283 MET cc_start: 0.8286 (mmm) cc_final: 0.7736 (mmt) REVERT: B 287 ILE cc_start: 0.7580 (mt) cc_final: 0.7220 (tt) REVERT: B 326 LYS cc_start: 0.7300 (mmmt) cc_final: 0.6784 (mmtp) REVERT: B 328 LYS cc_start: 0.7472 (mmmt) cc_final: 0.6735 (mttt) REVERT: B 355 MET cc_start: 0.7774 (mtp) cc_final: 0.7364 (mtp) REVERT: B 364 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7180 (mm-30) REVERT: B 372 ARG cc_start: 0.6706 (mtt180) cc_final: 0.6425 (mtt-85) REVERT: C 12 ASN cc_start: 0.7739 (m110) cc_final: 0.6705 (p0) REVERT: C 44 MET cc_start: 0.2187 (mmm) cc_final: 0.1371 (mtp) REVERT: C 47 MET cc_start: 0.6679 (mtp) cc_final: 0.6284 (mtm) REVERT: C 50 LYS cc_start: 0.6882 (mmmm) cc_final: 0.6168 (mttt) REVERT: C 66 THR cc_start: 0.7922 (t) cc_final: 0.7706 (t) REVERT: C 72 GLU cc_start: 0.7183 (tt0) cc_final: 0.6574 (mt-10) REVERT: C 82 MET cc_start: 0.7646 (tpt) cc_final: 0.6866 (tpt) REVERT: C 95 ARG cc_start: 0.5425 (ttt90) cc_final: 0.4915 (mtp85) REVERT: C 99 GLU cc_start: 0.6437 (tt0) cc_final: 0.6184 (mp0) REVERT: C 113 LYS cc_start: 0.7519 (mttt) cc_final: 0.7260 (mtpt) REVERT: C 132 MET cc_start: 0.8287 (tmm) cc_final: 0.7937 (ppp) REVERT: C 162 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.8134 (m-40) REVERT: C 206 ARG cc_start: 0.6538 (ttt180) cc_final: 0.5940 (ttm-80) REVERT: C 248 ILE cc_start: 0.6936 (OUTLIER) cc_final: 0.6640 (mm) REVERT: C 250 ILE cc_start: 0.7329 (OUTLIER) cc_final: 0.7108 (tt) REVERT: C 286 ASP cc_start: 0.6136 (m-30) cc_final: 0.5825 (m-30) REVERT: C 289 ILE cc_start: 0.6574 (OUTLIER) cc_final: 0.6139 (pt) REVERT: C 290 ARG cc_start: 0.5301 (OUTLIER) cc_final: 0.4670 (mtt90) REVERT: C 292 ASP cc_start: 0.7153 (m-30) cc_final: 0.6921 (m-30) REVERT: C 325 MET cc_start: 0.6129 (mmt) cc_final: 0.5738 (mmp) REVERT: C 326 LYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6387 (mmpt) REVERT: C 336 LYS cc_start: 0.7207 (tttt) cc_final: 0.6807 (ttmt) REVERT: C 354 GLN cc_start: 0.7655 (mm-40) cc_final: 0.6865 (mp10) REVERT: C 355 MET cc_start: 0.7559 (mmm) cc_final: 0.6929 (mpp) REVERT: C 360 GLN cc_start: 0.7087 (tp40) cc_final: 0.6421 (pm20) REVERT: D 45 VAL cc_start: 0.8073 (t) cc_final: 0.7811 (t) REVERT: D 49 GLN cc_start: 0.6296 (mt0) cc_final: 0.5863 (mt0) REVERT: D 50 LYS cc_start: 0.7979 (mtpp) cc_final: 0.7441 (mtmt) REVERT: D 51 ASP cc_start: 0.8565 (m-30) cc_final: 0.7660 (p0) REVERT: D 57 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7233 (mm-30) REVERT: D 72 GLU cc_start: 0.6681 (tt0) cc_final: 0.5706 (mp0) REVERT: D 100 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7768 (mm-30) REVERT: D 117 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6635 (mt-10) REVERT: D 121 GLN cc_start: 0.7093 (tt0) cc_final: 0.6877 (tt0) REVERT: D 132 MET cc_start: 0.8245 (ppp) cc_final: 0.7330 (ppp) REVERT: D 155 SER cc_start: 0.8470 (m) cc_final: 0.8178 (t) REVERT: D 176 MET cc_start: 0.7265 (mtt) cc_final: 0.6929 (mmt) REVERT: D 206 ARG cc_start: 0.7248 (ttt180) cc_final: 0.6659 (ttm110) REVERT: D 225 ASN cc_start: 0.6838 (t0) cc_final: 0.6613 (m-40) REVERT: D 234 SER cc_start: 0.7901 (m) cc_final: 0.7392 (p) REVERT: D 246 GLN cc_start: 0.8607 (mt0) cc_final: 0.7925 (mt0) REVERT: D 284 LYS cc_start: 0.6818 (ttmt) cc_final: 0.6473 (tttm) REVERT: D 299 MET cc_start: 0.8987 (mtm) cc_final: 0.8643 (mtt) REVERT: D 305 MET cc_start: 0.8490 (mmm) cc_final: 0.8215 (mmm) REVERT: D 313 MET cc_start: 0.8175 (tpt) cc_final: 0.7788 (tpt) REVERT: D 325 MET cc_start: 0.6190 (mmt) cc_final: 0.5794 (mmp) REVERT: D 328 LYS cc_start: 0.7074 (mttt) cc_final: 0.6701 (mttp) REVERT: D 352 PHE cc_start: 0.4785 (m-80) cc_final: 0.3768 (m-80) REVERT: D 356 TRP cc_start: 0.4654 (m100) cc_final: 0.4248 (m-10) REVERT: D 360 GLN cc_start: 0.7080 (tp40) cc_final: 0.6682 (tp40) REVERT: D 364 GLU cc_start: 0.6681 (mt-10) cc_final: 0.6253 (mt-10) REVERT: D 372 ARG cc_start: 0.7462 (ttp-110) cc_final: 0.7257 (mtm110) REVERT: P 14 GLN cc_start: 0.6778 (pt0) cc_final: 0.6422 (mt0) REVERT: P 21 ASN cc_start: 0.7124 (p0) cc_final: 0.6619 (t0) REVERT: P 25 GLU cc_start: 0.7250 (tt0) cc_final: 0.6823 (tp30) REVERT: P 66 MET cc_start: 0.6172 (mtt) cc_final: 0.5938 (mtt) REVERT: P 102 MET cc_start: 0.8448 (mtp) cc_final: 0.8068 (mtm) REVERT: P 113 GLU cc_start: 0.6999 (tp30) cc_final: 0.6594 (mp0) REVERT: P 117 ARG cc_start: 0.6609 (mmt180) cc_final: 0.6140 (mmt-90) REVERT: P 120 GLN cc_start: 0.5756 (tt0) cc_final: 0.5016 (mm-40) REVERT: P 230 LEU cc_start: 0.8022 (mp) cc_final: 0.7606 (mt) REVERT: P 250 LYS cc_start: 0.6771 (mtmt) cc_final: 0.6562 (mppt) REVERT: P 253 ARG cc_start: 0.5991 (OUTLIER) cc_final: 0.5544 (mmm-85) REVERT: P 254 LYS cc_start: 0.6738 (ttmt) cc_final: 0.6383 (mppt) REVERT: P 298 ASN cc_start: 0.7273 (t0) cc_final: 0.6873 (m110) REVERT: P 323 ILE cc_start: 0.8303 (mt) cc_final: 0.7900 (mp) REVERT: P 331 LEU cc_start: 0.8619 (mt) cc_final: 0.8234 (mm) REVERT: P 337 GLU cc_start: 0.7044 (mp0) cc_final: 0.6708 (mp0) REVERT: P 427 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6677 (mt-10) REVERT: P 453 LYS cc_start: 0.7901 (ptpp) cc_final: 0.7493 (ptpp) REVERT: P 476 GLU cc_start: 0.7125 (tt0) cc_final: 0.6263 (tt0) REVERT: P 480 ASP cc_start: 0.7471 (t0) cc_final: 0.7125 (m-30) REVERT: P 492 LYS cc_start: 0.8174 (tttp) cc_final: 0.7533 (tptp) REVERT: P 500 LYS cc_start: 0.7545 (mptp) cc_final: 0.7330 (mttp) REVERT: P 525 ASP cc_start: 0.7676 (m-30) cc_final: 0.7020 (t70) REVERT: P 534 ASN cc_start: 0.6725 (t0) cc_final: 0.6427 (t0) REVERT: P 553 LYS cc_start: 0.7380 (mmtm) cc_final: 0.6963 (mppt) REVERT: P 563 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8119 (mt-10) REVERT: P 570 LYS cc_start: 0.7768 (tttt) cc_final: 0.7435 (tttm) REVERT: P 571 MET cc_start: 0.7611 (mmt) cc_final: 0.7221 (mpm) REVERT: P 598 GLN cc_start: 0.7544 (tt0) cc_final: 0.7088 (tm-30) REVERT: P 604 GLU cc_start: 0.7275 (tt0) cc_final: 0.6837 (tt0) outliers start: 37 outliers final: 8 residues processed: 369 average time/residue: 0.7693 time to fit residues: 307.5245 Evaluate side-chains 252 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain P residue 253 ARG Chi-restraints excluded: chain P residue 388 TYR Chi-restraints excluded: chain P residue 687 THR Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 91 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 0.0980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 HIS B 121 GLN D 280 ASN D 371 HIS P 39 ASN P 53 ASN P 293 GLN P 511 HIS ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.158345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.119649 restraints weight = 18164.489| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.03 r_work: 0.3212 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15987 Z= 0.155 Angle : 0.655 9.967 21632 Z= 0.336 Chirality : 0.045 0.209 2380 Planarity : 0.004 0.038 2793 Dihedral : 8.555 120.071 2222 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.05 % Favored : 97.90 % Rotamer: Outliers : 2.61 % Allowed : 9.55 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.19), residues: 1949 helix: 0.14 (0.16), residues: 923 sheet: -0.22 (0.31), residues: 249 loop : 0.75 (0.24), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 621 TYR 0.018 0.002 TYR P 44 PHE 0.017 0.002 PHE D 255 TRP 0.026 0.002 TRP D 340 HIS 0.006 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00351 (15987) covalent geometry : angle 0.65453 (21632) hydrogen bonds : bond 0.04135 ( 811) hydrogen bonds : angle 5.24877 ( 2214) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 262 time to evaluate : 0.613 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: B 28 ARG cc_start: 0.8476 (mtt180) cc_final: 0.8078 (mtt-85) REVERT: B 68 LYS cc_start: 0.8696 (mttt) cc_final: 0.7573 (mtmt) REVERT: B 82 MET cc_start: 0.8927 (tpt) cc_final: 0.8585 (tpt) REVERT: B 91 TYR cc_start: 0.7585 (m-80) cc_final: 0.6767 (t80) REVERT: B 121 GLN cc_start: 0.8117 (tt0) cc_final: 0.7907 (tt0) REVERT: B 176 MET cc_start: 0.8623 (mmm) cc_final: 0.8235 (mtp) REVERT: B 206 ARG cc_start: 0.8109 (ttt180) cc_final: 0.7555 (ttm-80) REVERT: B 225 ASN cc_start: 0.7725 (t0) cc_final: 0.7490 (m110) REVERT: B 246 GLN cc_start: 0.8974 (mt0) cc_final: 0.8721 (mt0) REVERT: B 248 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7804 (mp) REVERT: B 283 MET cc_start: 0.8846 (mmm) cc_final: 0.8410 (mmt) REVERT: B 326 LYS cc_start: 0.8138 (mmmt) cc_final: 0.7783 (mmtp) REVERT: B 328 LYS cc_start: 0.8294 (mmmt) cc_final: 0.7634 (mttp) REVERT: B 370 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8374 (m) REVERT: C 47 MET cc_start: 0.6775 (mtp) cc_final: 0.6329 (ttm) REVERT: C 50 LYS cc_start: 0.8213 (mmmm) cc_final: 0.7497 (mttt) REVERT: C 72 GLU cc_start: 0.7806 (tt0) cc_final: 0.7339 (mt-10) REVERT: C 82 MET cc_start: 0.8917 (tpt) cc_final: 0.8201 (tpt) REVERT: C 206 ARG cc_start: 0.7905 (ttt180) cc_final: 0.7304 (ttp-170) REVERT: C 211 ASP cc_start: 0.7914 (m-30) cc_final: 0.7668 (t70) REVERT: C 248 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7770 (mm) REVERT: C 286 ASP cc_start: 0.6871 (m-30) cc_final: 0.6640 (m-30) REVERT: C 290 ARG cc_start: 0.6283 (mtt180) cc_final: 0.5549 (mtt90) REVERT: C 323 SER cc_start: 0.8724 (p) cc_final: 0.8372 (t) REVERT: C 326 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7691 (tmtm) REVERT: C 328 LYS cc_start: 0.7819 (ttpt) cc_final: 0.7064 (tmtp) REVERT: C 336 LYS cc_start: 0.8095 (tttt) cc_final: 0.7776 (ttmp) REVERT: C 354 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7839 (mp-120) REVERT: C 355 MET cc_start: 0.8413 (mmm) cc_final: 0.8207 (mpp) REVERT: C 372 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7832 (mtp180) REVERT: D 43 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8788 (p) REVERT: D 50 LYS cc_start: 0.8376 (mtpp) cc_final: 0.8069 (mtmt) REVERT: D 51 ASP cc_start: 0.8578 (m-30) cc_final: 0.8099 (p0) REVERT: D 57 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7662 (mm-30) REVERT: D 72 GLU cc_start: 0.8155 (tt0) cc_final: 0.7583 (mp0) REVERT: D 100 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8070 (mm-30) REVERT: D 117 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8076 (mt-10) REVERT: D 206 ARG cc_start: 0.7743 (ttt180) cc_final: 0.7405 (ttm-80) REVERT: D 227 MET cc_start: 0.8618 (mmm) cc_final: 0.8184 (mmm) REVERT: D 276 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7858 (mt-10) REVERT: D 283 MET cc_start: 0.8967 (mmm) cc_final: 0.8529 (mmt) REVERT: D 299 MET cc_start: 0.9172 (mtm) cc_final: 0.8946 (mtt) REVERT: D 323 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8591 (t) REVERT: D 325 MET cc_start: 0.7232 (mmt) cc_final: 0.7004 (mmp) REVERT: D 326 LYS cc_start: 0.8613 (tppp) cc_final: 0.8274 (tppt) REVERT: D 352 PHE cc_start: 0.5539 (m-80) cc_final: 0.4336 (m-80) REVERT: D 356 TRP cc_start: 0.5327 (m100) cc_final: 0.4857 (m-10) REVERT: D 360 GLN cc_start: 0.7520 (tp40) cc_final: 0.7213 (tp40) REVERT: D 364 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6820 (mt-10) REVERT: P 14 GLN cc_start: 0.6987 (pt0) cc_final: 0.6454 (mt0) REVERT: P 21 ASN cc_start: 0.6442 (p0) cc_final: 0.6208 (t0) REVERT: P 102 MET cc_start: 0.8332 (mtp) cc_final: 0.7967 (mtm) REVERT: P 113 GLU cc_start: 0.7247 (tp30) cc_final: 0.6983 (mp0) REVERT: P 117 ARG cc_start: 0.6761 (mmt180) cc_final: 0.6467 (mmt-90) REVERT: P 120 GLN cc_start: 0.5883 (tt0) cc_final: 0.5434 (mt0) REVERT: P 124 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6964 (mt-10) REVERT: P 183 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7389 (tt) REVERT: P 224 ARG cc_start: 0.7243 (mtt90) cc_final: 0.6922 (mtt-85) REVERT: P 230 LEU cc_start: 0.8415 (mp) cc_final: 0.8107 (mt) REVERT: P 254 LYS cc_start: 0.7403 (ttmt) cc_final: 0.7001 (mppt) REVERT: P 298 ASN cc_start: 0.7480 (t0) cc_final: 0.6690 (m110) REVERT: P 337 GLU cc_start: 0.7183 (mp0) cc_final: 0.6785 (mp0) REVERT: P 399 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: P 427 GLU cc_start: 0.6733 (mt-10) cc_final: 0.6487 (mt-10) REVERT: P 472 LEU cc_start: 0.8279 (mt) cc_final: 0.7935 (mm) REVERT: P 476 GLU cc_start: 0.7116 (tt0) cc_final: 0.6660 (tt0) REVERT: P 480 ASP cc_start: 0.7707 (t0) cc_final: 0.7165 (m-30) REVERT: P 492 LYS cc_start: 0.8135 (tttp) cc_final: 0.7629 (tptp) REVERT: P 536 LYS cc_start: 0.7233 (mtmt) cc_final: 0.6806 (mtpt) REVERT: P 553 LYS cc_start: 0.7541 (mmtm) cc_final: 0.7170 (mmtm) REVERT: P 563 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8359 (mt-10) REVERT: P 584 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6915 (tt0) REVERT: P 598 GLN cc_start: 0.7582 (tt0) cc_final: 0.7139 (tm-30) REVERT: P 604 GLU cc_start: 0.7171 (tt0) cc_final: 0.6740 (tm-30) REVERT: P 675 MET cc_start: 0.8312 (mmt) cc_final: 0.7904 (mmm) REVERT: R 52 MET cc_start: 0.3043 (mtt) cc_final: 0.2019 (mtt) outliers start: 44 outliers final: 15 residues processed: 291 average time/residue: 0.7709 time to fit residues: 244.0010 Evaluate side-chains 246 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 183 LEU Chi-restraints excluded: chain P residue 312 THR Chi-restraints excluded: chain P residue 323 ILE Chi-restraints excluded: chain P residue 399 GLU Chi-restraints excluded: chain P residue 584 GLU Chi-restraints excluded: chain P residue 687 THR Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 64 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 159 optimal weight: 1.9990 chunk 192 optimal weight: 40.0000 chunk 138 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 ASN D 49 GLN D 121 GLN P 53 ASN P 196 ASN P 534 ASN R 42 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.153834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114150 restraints weight = 18336.802| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.94 r_work: 0.3151 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 15987 Z= 0.209 Angle : 0.659 9.976 21632 Z= 0.334 Chirality : 0.046 0.196 2380 Planarity : 0.005 0.052 2793 Dihedral : 7.957 130.814 2198 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.62 % Favored : 97.33 % Rotamer: Outliers : 2.97 % Allowed : 11.63 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.19), residues: 1949 helix: 0.46 (0.17), residues: 930 sheet: -0.14 (0.31), residues: 258 loop : 0.77 (0.24), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 601 TYR 0.016 0.002 TYR P 438 PHE 0.023 0.002 PHE R 17 TRP 0.020 0.002 TRP C 340 HIS 0.007 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00500 (15987) covalent geometry : angle 0.65949 (21632) hydrogen bonds : bond 0.04189 ( 811) hydrogen bonds : angle 5.09244 ( 2214) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8429 (mtt180) cc_final: 0.8031 (mtt-85) REVERT: B 68 LYS cc_start: 0.8759 (mttt) cc_final: 0.7570 (mtmm) REVERT: B 91 TYR cc_start: 0.7558 (m-80) cc_final: 0.6721 (t80) REVERT: B 206 ARG cc_start: 0.8113 (ttt180) cc_final: 0.7584 (ttm-80) REVERT: B 225 ASN cc_start: 0.7742 (t0) cc_final: 0.7525 (m110) REVERT: B 241 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: B 246 GLN cc_start: 0.8840 (mt0) cc_final: 0.8616 (mt0) REVERT: B 248 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7949 (mp) REVERT: B 283 MET cc_start: 0.8823 (mmm) cc_final: 0.8358 (mmt) REVERT: B 326 LYS cc_start: 0.8085 (mmmt) cc_final: 0.7653 (mmtp) REVERT: B 328 LYS cc_start: 0.8310 (mmmt) cc_final: 0.7651 (mttt) REVERT: C 47 MET cc_start: 0.6895 (mtp) cc_final: 0.6461 (ttm) REVERT: C 50 LYS cc_start: 0.8196 (mmmm) cc_final: 0.7469 (mttt) REVERT: C 68 LYS cc_start: 0.8848 (mttp) cc_final: 0.8381 (mtpp) REVERT: C 72 GLU cc_start: 0.7811 (tt0) cc_final: 0.7307 (mt-10) REVERT: C 82 MET cc_start: 0.8907 (tpt) cc_final: 0.8117 (tpt) REVERT: C 191 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8222 (ttmm) REVERT: C 206 ARG cc_start: 0.7745 (ttt180) cc_final: 0.7165 (ttm-80) REVERT: C 211 ASP cc_start: 0.7893 (m-30) cc_final: 0.7550 (t70) REVERT: C 248 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7742 (mm) REVERT: C 290 ARG cc_start: 0.6453 (mtt180) cc_final: 0.5618 (mtt90) REVERT: C 323 SER cc_start: 0.8688 (p) cc_final: 0.8291 (t) REVERT: C 326 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7739 (mmtt) REVERT: C 328 LYS cc_start: 0.8234 (ttpt) cc_final: 0.7250 (tttp) REVERT: C 336 LYS cc_start: 0.8196 (tttt) cc_final: 0.7896 (ttmt) REVERT: C 354 GLN cc_start: 0.8393 (mm-40) cc_final: 0.7829 (mp-120) REVERT: C 355 MET cc_start: 0.8446 (mmm) cc_final: 0.8189 (mpp) REVERT: D 50 LYS cc_start: 0.8380 (mtpp) cc_final: 0.8077 (mtmt) REVERT: D 51 ASP cc_start: 0.8550 (m-30) cc_final: 0.8070 (p0) REVERT: D 72 GLU cc_start: 0.8114 (tt0) cc_final: 0.7509 (mp0) REVERT: D 100 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7989 (mm-30) REVERT: D 107 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8811 (pt0) REVERT: D 122 ILE cc_start: 0.8244 (mm) cc_final: 0.7990 (mp) REVERT: D 206 ARG cc_start: 0.7580 (ttt180) cc_final: 0.7197 (ttp-170) REVERT: D 276 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7912 (mt-10) REVERT: D 299 MET cc_start: 0.9157 (mtm) cc_final: 0.8930 (mtt) REVERT: D 313 MET cc_start: 0.8673 (tpt) cc_final: 0.8400 (tpp) REVERT: D 323 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8548 (t) REVERT: D 325 MET cc_start: 0.7259 (mmt) cc_final: 0.6957 (mmp) REVERT: D 326 LYS cc_start: 0.8517 (tppp) cc_final: 0.8016 (mptt) REVERT: D 352 PHE cc_start: 0.5491 (m-80) cc_final: 0.4041 (m-80) REVERT: D 355 MET cc_start: 0.8600 (mmm) cc_final: 0.8350 (mmm) REVERT: D 356 TRP cc_start: 0.5425 (m100) cc_final: 0.4818 (m-10) REVERT: D 360 GLN cc_start: 0.7457 (tp40) cc_final: 0.6401 (pm20) REVERT: P 13 VAL cc_start: 0.5790 (m) cc_final: 0.5584 (m) REVERT: P 14 GLN cc_start: 0.7096 (pt0) cc_final: 0.6313 (mt0) REVERT: P 21 ASN cc_start: 0.6227 (p0) cc_final: 0.6022 (t0) REVERT: P 30 GLU cc_start: 0.6169 (tm-30) cc_final: 0.5633 (tp30) REVERT: P 66 MET cc_start: 0.5887 (mtt) cc_final: 0.5618 (mtt) REVERT: P 102 MET cc_start: 0.8388 (mtp) cc_final: 0.7964 (mtm) REVERT: P 104 SER cc_start: 0.7232 (t) cc_final: 0.6861 (p) REVERT: P 113 GLU cc_start: 0.7246 (tp30) cc_final: 0.6964 (mp0) REVERT: P 117 ARG cc_start: 0.6782 (mmt180) cc_final: 0.6390 (mmt-90) REVERT: P 120 GLN cc_start: 0.5859 (tt0) cc_final: 0.5480 (mm110) REVERT: P 183 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7510 (tt) REVERT: P 213 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.5940 (mp0) REVERT: P 230 LEU cc_start: 0.8432 (mp) cc_final: 0.8136 (mt) REVERT: P 254 LYS cc_start: 0.7511 (ttmt) cc_final: 0.6974 (mppt) REVERT: P 298 ASN cc_start: 0.7476 (t0) cc_final: 0.6650 (m110) REVERT: P 337 GLU cc_start: 0.7169 (mp0) cc_final: 0.6762 (mp0) REVERT: P 395 HIS cc_start: 0.7297 (m-70) cc_final: 0.6441 (t-90) REVERT: P 399 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6953 (pm20) REVERT: P 427 GLU cc_start: 0.6602 (mt-10) cc_final: 0.6375 (mt-10) REVERT: P 446 ASP cc_start: 0.7798 (m-30) cc_final: 0.7379 (m-30) REVERT: P 472 LEU cc_start: 0.8146 (mt) cc_final: 0.7877 (mm) REVERT: P 476 GLU cc_start: 0.7013 (tt0) cc_final: 0.6656 (tt0) REVERT: P 480 ASP cc_start: 0.7755 (t0) cc_final: 0.7283 (m-30) REVERT: P 492 LYS cc_start: 0.8160 (tttp) cc_final: 0.7588 (tptp) REVERT: P 536 LYS cc_start: 0.7200 (mtmt) cc_final: 0.6947 (mtpt) REVERT: P 553 LYS cc_start: 0.7764 (mmtm) cc_final: 0.7322 (mmtm) REVERT: P 584 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6785 (mt-10) REVERT: P 598 GLN cc_start: 0.7591 (tt0) cc_final: 0.7169 (tm-30) REVERT: P 604 GLU cc_start: 0.7145 (tt0) cc_final: 0.6630 (tm-30) REVERT: P 675 MET cc_start: 0.8294 (mmt) cc_final: 0.7929 (mmm) outliers start: 50 outliers final: 24 residues processed: 260 average time/residue: 0.7802 time to fit residues: 219.9050 Evaluate side-chains 247 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 161 SER Chi-restraints excluded: chain P residue 183 LEU Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain P residue 289 ASP Chi-restraints excluded: chain P residue 312 THR Chi-restraints excluded: chain P residue 379 THR Chi-restraints excluded: chain P residue 399 GLU Chi-restraints excluded: chain P residue 418 THR Chi-restraints excluded: chain P residue 515 GLU Chi-restraints excluded: chain P residue 584 GLU Chi-restraints excluded: chain P residue 687 THR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 145 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 27 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 120 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN C 162 ASN D 121 GLN P 534 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.153825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114172 restraints weight = 18256.974| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.92 r_work: 0.3142 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15987 Z= 0.193 Angle : 0.622 9.907 21632 Z= 0.313 Chirality : 0.045 0.187 2380 Planarity : 0.004 0.038 2793 Dihedral : 7.807 134.486 2197 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.21 % Favored : 97.69 % Rotamer: Outliers : 3.20 % Allowed : 12.40 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.19), residues: 1949 helix: 0.57 (0.17), residues: 943 sheet: -0.11 (0.31), residues: 252 loop : 0.73 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 335 TYR 0.023 0.002 TYR P 438 PHE 0.026 0.002 PHE P 173 TRP 0.019 0.002 TRP C 340 HIS 0.007 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00462 (15987) covalent geometry : angle 0.62195 (21632) hydrogen bonds : bond 0.03869 ( 811) hydrogen bonds : angle 4.99367 ( 2214) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 212 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8443 (mtt180) cc_final: 0.8043 (mtt-85) REVERT: B 68 LYS cc_start: 0.8843 (mttt) cc_final: 0.7638 (mtmm) REVERT: B 91 TYR cc_start: 0.7548 (m-80) cc_final: 0.6691 (t80) REVERT: B 129 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8310 (p) REVERT: B 176 MET cc_start: 0.8859 (mtp) cc_final: 0.8280 (mtp) REVERT: B 206 ARG cc_start: 0.8095 (ttt180) cc_final: 0.7566 (ttm-80) REVERT: B 246 GLN cc_start: 0.8875 (mt0) cc_final: 0.8665 (mt0) REVERT: B 248 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.8005 (mp) REVERT: B 252 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.8031 (t0) REVERT: B 283 MET cc_start: 0.8811 (mmm) cc_final: 0.8372 (mmt) REVERT: B 326 LYS cc_start: 0.8104 (mmmt) cc_final: 0.7660 (mmtp) REVERT: B 328 LYS cc_start: 0.8312 (mmmt) cc_final: 0.7694 (mtmm) REVERT: C 47 MET cc_start: 0.6962 (mtp) cc_final: 0.6433 (mtm) REVERT: C 50 LYS cc_start: 0.8196 (mmmm) cc_final: 0.7464 (mttt) REVERT: C 68 LYS cc_start: 0.8866 (mttp) cc_final: 0.8419 (mtpp) REVERT: C 72 GLU cc_start: 0.7768 (tt0) cc_final: 0.7301 (mt-10) REVERT: C 82 MET cc_start: 0.8945 (tpt) cc_final: 0.8144 (tpt) REVERT: C 162 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.8478 (m-40) REVERT: C 191 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8256 (ttmm) REVERT: C 206 ARG cc_start: 0.7810 (ttt180) cc_final: 0.7212 (ttm-80) REVERT: C 211 ASP cc_start: 0.7934 (m-30) cc_final: 0.7650 (t70) REVERT: C 290 ARG cc_start: 0.6468 (mtt180) cc_final: 0.5678 (mtt90) REVERT: C 323 SER cc_start: 0.8699 (p) cc_final: 0.8274 (t) REVERT: C 326 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7819 (mmtt) REVERT: C 336 LYS cc_start: 0.8307 (tttt) cc_final: 0.7992 (ttmt) REVERT: C 354 GLN cc_start: 0.8400 (mm-40) cc_final: 0.7849 (mp-120) REVERT: D 50 LYS cc_start: 0.8382 (mtpp) cc_final: 0.8084 (mtmt) REVERT: D 51 ASP cc_start: 0.8572 (m-30) cc_final: 0.7960 (p0) REVERT: D 72 GLU cc_start: 0.8118 (tt0) cc_final: 0.7507 (mp0) REVERT: D 122 ILE cc_start: 0.8227 (mm) cc_final: 0.7967 (mp) REVERT: D 132 MET cc_start: 0.8799 (ppp) cc_final: 0.8569 (ptm) REVERT: D 206 ARG cc_start: 0.7640 (ttt180) cc_final: 0.7343 (ttm110) REVERT: D 276 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7924 (mt-10) REVERT: D 299 MET cc_start: 0.9198 (mtm) cc_final: 0.8957 (mtt) REVERT: D 323 SER cc_start: 0.8873 (p) cc_final: 0.8571 (t) REVERT: D 325 MET cc_start: 0.7206 (mmt) cc_final: 0.6878 (mmp) REVERT: D 352 PHE cc_start: 0.5508 (m-80) cc_final: 0.4076 (m-80) REVERT: D 356 TRP cc_start: 0.5444 (m100) cc_final: 0.4876 (m-10) REVERT: D 360 GLN cc_start: 0.7321 (tp40) cc_final: 0.6440 (pm20) REVERT: P 13 VAL cc_start: 0.5822 (m) cc_final: 0.5541 (m) REVERT: P 14 GLN cc_start: 0.7165 (pt0) cc_final: 0.6234 (mt0) REVERT: P 30 GLU cc_start: 0.6160 (tm-30) cc_final: 0.5635 (tp30) REVERT: P 66 MET cc_start: 0.6069 (mtt) cc_final: 0.5585 (mtt) REVERT: P 102 MET cc_start: 0.8373 (mtp) cc_final: 0.7988 (mtm) REVERT: P 104 SER cc_start: 0.7257 (t) cc_final: 0.6876 (p) REVERT: P 113 GLU cc_start: 0.7264 (tp30) cc_final: 0.6983 (mp0) REVERT: P 117 ARG cc_start: 0.6883 (mmt180) cc_final: 0.6491 (mmt-90) REVERT: P 120 GLN cc_start: 0.6230 (tt0) cc_final: 0.5827 (mm110) REVERT: P 183 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7525 (tt) REVERT: P 213 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.5999 (mp0) REVERT: P 230 LEU cc_start: 0.8429 (mp) cc_final: 0.8127 (mt) REVERT: P 254 LYS cc_start: 0.7562 (ttmt) cc_final: 0.7040 (mppt) REVERT: P 298 ASN cc_start: 0.7131 (t0) cc_final: 0.6441 (m110) REVERT: P 337 GLU cc_start: 0.7142 (mp0) cc_final: 0.6748 (mp0) REVERT: P 395 HIS cc_start: 0.7326 (m-70) cc_final: 0.6397 (t-90) REVERT: P 399 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6890 (pm20) REVERT: P 427 GLU cc_start: 0.6602 (mt-10) cc_final: 0.6372 (mt-10) REVERT: P 446 ASP cc_start: 0.7919 (m-30) cc_final: 0.7418 (m-30) REVERT: P 472 LEU cc_start: 0.8188 (mt) cc_final: 0.7955 (mm) REVERT: P 476 GLU cc_start: 0.7031 (tt0) cc_final: 0.6675 (tt0) REVERT: P 480 ASP cc_start: 0.7724 (t0) cc_final: 0.7305 (m-30) REVERT: P 492 LYS cc_start: 0.8192 (tttp) cc_final: 0.7627 (tptp) REVERT: P 553 LYS cc_start: 0.7810 (mmtm) cc_final: 0.7292 (mmtm) REVERT: P 570 LYS cc_start: 0.7664 (tttt) cc_final: 0.7321 (tttm) REVERT: P 584 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6839 (mt-10) REVERT: P 598 GLN cc_start: 0.7597 (tt0) cc_final: 0.7199 (tm-30) REVERT: P 675 MET cc_start: 0.8271 (mmt) cc_final: 0.7879 (mmm) REVERT: R 83 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8125 (tp30) outliers start: 54 outliers final: 28 residues processed: 250 average time/residue: 0.7669 time to fit residues: 208.2585 Evaluate side-chains 241 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 161 SER Chi-restraints excluded: chain P residue 183 LEU Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain P residue 289 ASP Chi-restraints excluded: chain P residue 312 THR Chi-restraints excluded: chain P residue 323 ILE Chi-restraints excluded: chain P residue 379 THR Chi-restraints excluded: chain P residue 399 GLU Chi-restraints excluded: chain P residue 418 THR Chi-restraints excluded: chain P residue 515 GLU Chi-restraints excluded: chain P residue 584 GLU Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 83 GLU Chi-restraints excluded: chain R residue 145 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 43 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 175 optimal weight: 0.5980 chunk 91 optimal weight: 0.0970 chunk 182 optimal weight: 0.0270 chunk 4 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 225 ASN C 162 ASN D 121 GLN P 53 ASN ** P 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 534 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.155645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.116401 restraints weight = 18258.838| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.88 r_work: 0.3180 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15987 Z= 0.128 Angle : 0.573 11.144 21632 Z= 0.285 Chirality : 0.042 0.175 2380 Planarity : 0.004 0.036 2793 Dihedral : 7.493 136.056 2194 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.46 % Favored : 97.49 % Rotamer: Outliers : 2.73 % Allowed : 14.12 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.19), residues: 1949 helix: 0.82 (0.17), residues: 941 sheet: -0.09 (0.32), residues: 242 loop : 0.81 (0.24), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 601 TYR 0.019 0.001 TYR P 438 PHE 0.015 0.001 PHE R 17 TRP 0.014 0.002 TRP C 340 HIS 0.008 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00293 (15987) covalent geometry : angle 0.57268 (21632) hydrogen bonds : bond 0.03398 ( 811) hydrogen bonds : angle 4.78173 ( 2214) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 213 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8385 (mtt180) cc_final: 0.8006 (mtt-85) REVERT: B 39 ARG cc_start: 0.7337 (ttp80) cc_final: 0.7107 (mtm180) REVERT: B 50 LYS cc_start: 0.8183 (mttt) cc_final: 0.7891 (mtpm) REVERT: B 68 LYS cc_start: 0.8822 (mttt) cc_final: 0.7613 (mtmm) REVERT: B 91 TYR cc_start: 0.7533 (m-80) cc_final: 0.6601 (t80) REVERT: B 129 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8220 (p) REVERT: B 176 MET cc_start: 0.8856 (mtp) cc_final: 0.8338 (mtp) REVERT: B 206 ARG cc_start: 0.8019 (ttt180) cc_final: 0.7532 (ttm-80) REVERT: B 246 GLN cc_start: 0.8742 (mt0) cc_final: 0.8522 (mt0) REVERT: B 283 MET cc_start: 0.8756 (mmm) cc_final: 0.8307 (mmt) REVERT: B 326 LYS cc_start: 0.8073 (mmmt) cc_final: 0.7734 (tttm) REVERT: B 328 LYS cc_start: 0.8315 (mmmt) cc_final: 0.7968 (mmmt) REVERT: C 50 LYS cc_start: 0.8156 (mmmm) cc_final: 0.7411 (mttt) REVERT: C 68 LYS cc_start: 0.8853 (mttp) cc_final: 0.8423 (mtpp) REVERT: C 72 GLU cc_start: 0.7842 (tt0) cc_final: 0.7335 (mt-10) REVERT: C 82 MET cc_start: 0.8936 (tpt) cc_final: 0.8436 (tpt) REVERT: C 95 ARG cc_start: 0.8472 (mtp85) cc_final: 0.8100 (mtt180) REVERT: C 162 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8434 (m110) REVERT: C 206 ARG cc_start: 0.7710 (ttt180) cc_final: 0.7224 (ttm-80) REVERT: C 211 ASP cc_start: 0.7875 (m-30) cc_final: 0.7567 (t70) REVERT: C 290 ARG cc_start: 0.6297 (mtt180) cc_final: 0.5557 (mtt90) REVERT: C 323 SER cc_start: 0.8656 (p) cc_final: 0.8209 (t) REVERT: C 326 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7744 (mmtt) REVERT: C 336 LYS cc_start: 0.8225 (tttt) cc_final: 0.7944 (ttmt) REVERT: C 354 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7813 (mp-120) REVERT: D 50 LYS cc_start: 0.8345 (mtpp) cc_final: 0.8038 (mtmt) REVERT: D 51 ASP cc_start: 0.8558 (m-30) cc_final: 0.7930 (p0) REVERT: D 72 GLU cc_start: 0.8141 (tt0) cc_final: 0.7429 (mp0) REVERT: D 107 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8666 (tt0) REVERT: D 122 ILE cc_start: 0.8195 (mm) cc_final: 0.7911 (mp) REVERT: D 132 MET cc_start: 0.8764 (ppp) cc_final: 0.8467 (ptm) REVERT: D 206 ARG cc_start: 0.7521 (ttt180) cc_final: 0.7295 (ttm110) REVERT: D 276 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7910 (mt-10) REVERT: D 299 MET cc_start: 0.9187 (mtm) cc_final: 0.8913 (mtt) REVERT: D 323 SER cc_start: 0.8894 (p) cc_final: 0.8566 (t) REVERT: D 325 MET cc_start: 0.7277 (mmt) cc_final: 0.7003 (mmp) REVERT: D 352 PHE cc_start: 0.5454 (m-80) cc_final: 0.3919 (m-80) REVERT: D 355 MET cc_start: 0.8666 (mmm) cc_final: 0.8360 (mmm) REVERT: D 356 TRP cc_start: 0.5294 (m100) cc_final: 0.4939 (m-10) REVERT: D 360 GLN cc_start: 0.7217 (tp40) cc_final: 0.6454 (pm20) REVERT: P 13 VAL cc_start: 0.5878 (m) cc_final: 0.5626 (m) REVERT: P 14 GLN cc_start: 0.6979 (pt0) cc_final: 0.6127 (mt0) REVERT: P 30 GLU cc_start: 0.6121 (tm-30) cc_final: 0.5604 (tp30) REVERT: P 66 MET cc_start: 0.5904 (mtt) cc_final: 0.5427 (mtt) REVERT: P 102 MET cc_start: 0.8372 (mtp) cc_final: 0.8052 (mtm) REVERT: P 104 SER cc_start: 0.7225 (t) cc_final: 0.6838 (p) REVERT: P 113 GLU cc_start: 0.7178 (tp30) cc_final: 0.6817 (mp0) REVERT: P 117 ARG cc_start: 0.6788 (mmt180) cc_final: 0.6361 (mmp80) REVERT: P 120 GLN cc_start: 0.6158 (tt0) cc_final: 0.5731 (mm-40) REVERT: P 156 ARG cc_start: 0.7166 (tpp80) cc_final: 0.6336 (ttm170) REVERT: P 183 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7512 (tt) REVERT: P 230 LEU cc_start: 0.8368 (mp) cc_final: 0.8072 (mt) REVERT: P 254 LYS cc_start: 0.7513 (ttmt) cc_final: 0.6990 (mppt) REVERT: P 298 ASN cc_start: 0.7048 (t0) cc_final: 0.6385 (m110) REVERT: P 316 GLU cc_start: 0.7970 (tt0) cc_final: 0.7755 (tt0) REVERT: P 337 GLU cc_start: 0.7091 (mp0) cc_final: 0.6705 (mp0) REVERT: P 395 HIS cc_start: 0.7245 (m-70) cc_final: 0.6296 (t-90) REVERT: P 399 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6946 (pm20) REVERT: P 427 GLU cc_start: 0.6540 (mt-10) cc_final: 0.6334 (mt-10) REVERT: P 446 ASP cc_start: 0.7725 (m-30) cc_final: 0.7151 (m-30) REVERT: P 476 GLU cc_start: 0.7001 (tt0) cc_final: 0.6631 (tt0) REVERT: P 480 ASP cc_start: 0.7692 (t0) cc_final: 0.7274 (m-30) REVERT: P 492 LYS cc_start: 0.8255 (tttp) cc_final: 0.7698 (tptp) REVERT: P 553 LYS cc_start: 0.7757 (mmtm) cc_final: 0.7296 (mmtm) REVERT: P 570 LYS cc_start: 0.7594 (tttt) cc_final: 0.7255 (tttp) REVERT: P 584 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6626 (mt-10) REVERT: P 598 GLN cc_start: 0.7601 (tt0) cc_final: 0.7210 (tm-30) REVERT: P 675 MET cc_start: 0.8243 (mmt) cc_final: 0.7844 (mmm) REVERT: P 688 LEU cc_start: 0.5291 (OUTLIER) cc_final: 0.4795 (tt) REVERT: P 691 THR cc_start: 0.4592 (m) cc_final: 0.4331 (p) REVERT: R 37 MET cc_start: 0.5312 (mtp) cc_final: 0.4937 (mtp) REVERT: R 83 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8126 (tp30) outliers start: 46 outliers final: 23 residues processed: 242 average time/residue: 0.7886 time to fit residues: 207.3083 Evaluate side-chains 236 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 183 LEU Chi-restraints excluded: chain P residue 289 ASP Chi-restraints excluded: chain P residue 312 THR Chi-restraints excluded: chain P residue 323 ILE Chi-restraints excluded: chain P residue 399 GLU Chi-restraints excluded: chain P residue 515 GLU Chi-restraints excluded: chain P residue 584 GLU Chi-restraints excluded: chain P residue 687 THR Chi-restraints excluded: chain P residue 688 LEU Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 83 GLU Chi-restraints excluded: chain R residue 145 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 57 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 191 optimal weight: 20.0000 chunk 123 optimal weight: 0.0970 chunk 40 optimal weight: 0.0170 chunk 115 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 147 optimal weight: 0.5980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN C 162 ASN D 41 GLN D 121 GLN P 440 ASN P 534 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.155732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.116482 restraints weight = 18190.478| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.92 r_work: 0.3183 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15987 Z= 0.134 Angle : 0.569 10.387 21632 Z= 0.281 Chirality : 0.042 0.173 2380 Planarity : 0.004 0.035 2793 Dihedral : 7.307 134.332 2192 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.41 % Favored : 97.54 % Rotamer: Outliers : 2.73 % Allowed : 14.42 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.19), residues: 1949 helix: 0.88 (0.17), residues: 947 sheet: -0.09 (0.32), residues: 242 loop : 0.86 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 601 TYR 0.017 0.001 TYR P 438 PHE 0.030 0.001 PHE P 173 TRP 0.015 0.002 TRP C 340 HIS 0.008 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00312 (15987) covalent geometry : angle 0.56853 (21632) hydrogen bonds : bond 0.03347 ( 811) hydrogen bonds : angle 4.71759 ( 2214) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 216 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8424 (mtt180) cc_final: 0.8038 (mtt-85) REVERT: B 39 ARG cc_start: 0.7382 (ttp80) cc_final: 0.7143 (mtm180) REVERT: B 50 LYS cc_start: 0.8201 (mttt) cc_final: 0.7930 (mtpm) REVERT: B 68 LYS cc_start: 0.8850 (mttt) cc_final: 0.7656 (mtmm) REVERT: B 91 TYR cc_start: 0.7545 (m-80) cc_final: 0.6616 (t80) REVERT: B 129 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8276 (p) REVERT: B 176 MET cc_start: 0.8848 (mtp) cc_final: 0.8355 (mtp) REVERT: B 206 ARG cc_start: 0.8038 (ttt180) cc_final: 0.7565 (ttm-80) REVERT: B 246 GLN cc_start: 0.8765 (mt0) cc_final: 0.8548 (mt0) REVERT: B 271 SER cc_start: 0.8473 (m) cc_final: 0.8247 (p) REVERT: B 283 MET cc_start: 0.8779 (mmm) cc_final: 0.8348 (mmt) REVERT: B 326 LYS cc_start: 0.8099 (mmmt) cc_final: 0.7750 (tttp) REVERT: B 328 LYS cc_start: 0.8291 (mmmt) cc_final: 0.7960 (mmmt) REVERT: C 50 LYS cc_start: 0.8171 (mmmm) cc_final: 0.7418 (mttt) REVERT: C 68 LYS cc_start: 0.8816 (mttp) cc_final: 0.8399 (mtpp) REVERT: C 72 GLU cc_start: 0.7854 (tt0) cc_final: 0.7304 (mt-10) REVERT: C 82 MET cc_start: 0.8978 (tpt) cc_final: 0.8500 (tpt) REVERT: C 95 ARG cc_start: 0.8492 (mtp85) cc_final: 0.8130 (mtt180) REVERT: C 162 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8434 (m-40) REVERT: C 206 ARG cc_start: 0.7722 (ttt180) cc_final: 0.7105 (ttm-80) REVERT: C 211 ASP cc_start: 0.7891 (m-30) cc_final: 0.7512 (t70) REVERT: C 287 ILE cc_start: 0.5090 (OUTLIER) cc_final: 0.4427 (tt) REVERT: C 290 ARG cc_start: 0.6295 (mtt180) cc_final: 0.5624 (mtt90) REVERT: C 323 SER cc_start: 0.8648 (p) cc_final: 0.8190 (t) REVERT: C 326 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7738 (mmtt) REVERT: C 336 LYS cc_start: 0.8276 (tttt) cc_final: 0.8001 (ttmt) REVERT: C 354 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7834 (mp-120) REVERT: D 50 LYS cc_start: 0.8296 (mtpp) cc_final: 0.7999 (mttt) REVERT: D 51 ASP cc_start: 0.8584 (m-30) cc_final: 0.7807 (p0) REVERT: D 57 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7672 (mt-10) REVERT: D 72 GLU cc_start: 0.8153 (tt0) cc_final: 0.7417 (mp0) REVERT: D 107 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8671 (tt0) REVERT: D 122 ILE cc_start: 0.8212 (mm) cc_final: 0.7942 (mp) REVERT: D 276 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7947 (mt-10) REVERT: D 299 MET cc_start: 0.9230 (mtm) cc_final: 0.8975 (mtt) REVERT: D 323 SER cc_start: 0.8885 (OUTLIER) cc_final: 0.8556 (t) REVERT: D 325 MET cc_start: 0.7288 (mmt) cc_final: 0.7020 (mmp) REVERT: D 352 PHE cc_start: 0.5489 (m-80) cc_final: 0.3934 (m-80) REVERT: D 355 MET cc_start: 0.8715 (mmm) cc_final: 0.8443 (mmm) REVERT: D 356 TRP cc_start: 0.5287 (m100) cc_final: 0.4982 (m-10) REVERT: D 360 GLN cc_start: 0.7242 (tp40) cc_final: 0.6467 (pm20) REVERT: P 13 VAL cc_start: 0.5754 (m) cc_final: 0.5491 (m) REVERT: P 14 GLN cc_start: 0.7005 (pt0) cc_final: 0.6148 (mt0) REVERT: P 24 SER cc_start: 0.8160 (t) cc_final: 0.7812 (t) REVERT: P 30 GLU cc_start: 0.6142 (tm-30) cc_final: 0.5623 (tp30) REVERT: P 66 MET cc_start: 0.5890 (mtt) cc_final: 0.5420 (mtt) REVERT: P 102 MET cc_start: 0.8385 (mtp) cc_final: 0.8056 (mtm) REVERT: P 104 SER cc_start: 0.7258 (t) cc_final: 0.6864 (p) REVERT: P 113 GLU cc_start: 0.7136 (tp30) cc_final: 0.6810 (mp0) REVERT: P 117 ARG cc_start: 0.6758 (mmt180) cc_final: 0.6393 (mmp80) REVERT: P 120 GLN cc_start: 0.6190 (tt0) cc_final: 0.5748 (mm-40) REVERT: P 156 ARG cc_start: 0.7402 (tpp80) cc_final: 0.6287 (ttm170) REVERT: P 183 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7607 (tt) REVERT: P 213 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.5931 (mp0) REVERT: P 230 LEU cc_start: 0.8375 (mp) cc_final: 0.8076 (mt) REVERT: P 254 LYS cc_start: 0.7481 (ttmt) cc_final: 0.6988 (mppt) REVERT: P 298 ASN cc_start: 0.7022 (t0) cc_final: 0.6345 (m110) REVERT: P 316 GLU cc_start: 0.7965 (tt0) cc_final: 0.7732 (tt0) REVERT: P 329 GLU cc_start: 0.8011 (pt0) cc_final: 0.7748 (mt-10) REVERT: P 337 GLU cc_start: 0.7198 (mp0) cc_final: 0.6819 (mp0) REVERT: P 395 HIS cc_start: 0.7251 (m-70) cc_final: 0.6293 (t-90) REVERT: P 399 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6995 (pm20) REVERT: P 408 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7286 (tp30) REVERT: P 427 GLU cc_start: 0.6520 (mt-10) cc_final: 0.6257 (mt-10) REVERT: P 446 ASP cc_start: 0.7709 (m-30) cc_final: 0.7148 (m-30) REVERT: P 476 GLU cc_start: 0.6990 (tt0) cc_final: 0.6609 (tt0) REVERT: P 480 ASP cc_start: 0.7703 (t0) cc_final: 0.7288 (m-30) REVERT: P 492 LYS cc_start: 0.8267 (tttp) cc_final: 0.7694 (tptp) REVERT: P 553 LYS cc_start: 0.7772 (mmtm) cc_final: 0.7287 (mmtm) REVERT: P 584 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6575 (mt-10) REVERT: P 598 GLN cc_start: 0.7566 (tt0) cc_final: 0.7180 (tm-30) REVERT: P 675 MET cc_start: 0.8245 (mmt) cc_final: 0.7825 (mmm) REVERT: R 37 MET cc_start: 0.5210 (mtp) cc_final: 0.4901 (mtp) outliers start: 46 outliers final: 22 residues processed: 249 average time/residue: 0.8045 time to fit residues: 217.3952 Evaluate side-chains 243 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 183 LEU Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain P residue 289 ASP Chi-restraints excluded: chain P residue 296 THR Chi-restraints excluded: chain P residue 312 THR Chi-restraints excluded: chain P residue 379 THR Chi-restraints excluded: chain P residue 399 GLU Chi-restraints excluded: chain P residue 515 GLU Chi-restraints excluded: chain P residue 584 GLU Chi-restraints excluded: chain R residue 64 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 59 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 113 optimal weight: 0.0770 chunk 185 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 225 ASN C 162 ASN D 41 GLN D 121 GLN P 53 ASN P 440 ASN P 534 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.153874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114087 restraints weight = 18159.259| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.90 r_work: 0.3135 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 15987 Z= 0.204 Angle : 0.626 9.987 21632 Z= 0.310 Chirality : 0.045 0.178 2380 Planarity : 0.004 0.043 2793 Dihedral : 7.433 133.387 2192 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.41 % Favored : 97.54 % Rotamer: Outliers : 3.15 % Allowed : 14.18 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.19), residues: 1949 helix: 0.77 (0.17), residues: 950 sheet: -0.05 (0.32), residues: 240 loop : 0.75 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 601 TYR 0.026 0.002 TYR P 640 PHE 0.013 0.002 PHE P 439 TRP 0.019 0.002 TRP C 340 HIS 0.007 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00490 (15987) covalent geometry : angle 0.62645 (21632) hydrogen bonds : bond 0.03713 ( 811) hydrogen bonds : angle 4.84922 ( 2214) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 212 time to evaluate : 0.657 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: B 28 ARG cc_start: 0.8479 (mtt180) cc_final: 0.8139 (mtt-85) REVERT: B 50 LYS cc_start: 0.8192 (mttt) cc_final: 0.7950 (mtpm) REVERT: B 68 LYS cc_start: 0.8861 (mttt) cc_final: 0.7927 (mtmp) REVERT: B 91 TYR cc_start: 0.7571 (m-80) cc_final: 0.6656 (t80) REVERT: B 129 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8259 (p) REVERT: B 176 MET cc_start: 0.8868 (mtp) cc_final: 0.8357 (mtp) REVERT: B 206 ARG cc_start: 0.8057 (ttt180) cc_final: 0.7611 (ttm-80) REVERT: B 241 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: B 246 GLN cc_start: 0.8844 (mt0) cc_final: 0.8618 (mt0) REVERT: B 283 MET cc_start: 0.8807 (mmm) cc_final: 0.8410 (mmt) REVERT: B 326 LYS cc_start: 0.8103 (mmmt) cc_final: 0.7642 (mmtp) REVERT: B 328 LYS cc_start: 0.8324 (mmmt) cc_final: 0.7738 (mppt) REVERT: C 44 MET cc_start: 0.8167 (mtm) cc_final: 0.7866 (mtt) REVERT: C 50 LYS cc_start: 0.8235 (mmmm) cc_final: 0.7521 (mttt) REVERT: C 68 LYS cc_start: 0.8839 (mttp) cc_final: 0.8429 (mtpp) REVERT: C 72 GLU cc_start: 0.7840 (tt0) cc_final: 0.7336 (mt-10) REVERT: C 82 MET cc_start: 0.8987 (tpt) cc_final: 0.8113 (tpt) REVERT: C 95 ARG cc_start: 0.8566 (mtp85) cc_final: 0.8200 (mtt180) REVERT: C 191 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8283 (ttmm) REVERT: C 206 ARG cc_start: 0.7764 (ttt180) cc_final: 0.7283 (ttm-80) REVERT: C 211 ASP cc_start: 0.7925 (m-30) cc_final: 0.7601 (t70) REVERT: C 287 ILE cc_start: 0.5229 (OUTLIER) cc_final: 0.4469 (tt) REVERT: C 290 ARG cc_start: 0.6454 (mtt180) cc_final: 0.5693 (mtt90) REVERT: C 323 SER cc_start: 0.8682 (p) cc_final: 0.8231 (t) REVERT: C 326 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7779 (mmtt) REVERT: C 336 LYS cc_start: 0.8288 (tttt) cc_final: 0.8031 (ttmt) REVERT: C 354 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7844 (mp-120) REVERT: D 50 LYS cc_start: 0.8351 (mtpp) cc_final: 0.8058 (mttt) REVERT: D 51 ASP cc_start: 0.8568 (m-30) cc_final: 0.7820 (p0) REVERT: D 72 GLU cc_start: 0.8164 (tt0) cc_final: 0.7434 (mp0) REVERT: D 107 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8725 (tt0) REVERT: D 122 ILE cc_start: 0.8298 (mm) cc_final: 0.8038 (mp) REVERT: D 276 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7962 (mt-10) REVERT: D 299 MET cc_start: 0.9283 (mtm) cc_final: 0.9033 (mtt) REVERT: D 323 SER cc_start: 0.8915 (OUTLIER) cc_final: 0.8580 (t) REVERT: D 325 MET cc_start: 0.7342 (mmt) cc_final: 0.7023 (mmp) REVERT: D 352 PHE cc_start: 0.5379 (m-80) cc_final: 0.3779 (m-80) REVERT: D 356 TRP cc_start: 0.5416 (m100) cc_final: 0.4946 (m-10) REVERT: D 360 GLN cc_start: 0.7185 (tp40) cc_final: 0.6473 (pm20) REVERT: P 13 VAL cc_start: 0.6019 (m) cc_final: 0.5738 (m) REVERT: P 14 GLN cc_start: 0.7166 (pt0) cc_final: 0.6245 (mt0) REVERT: P 18 LEU cc_start: 0.7716 (mt) cc_final: 0.7426 (mm) REVERT: P 24 SER cc_start: 0.8135 (t) cc_final: 0.7784 (t) REVERT: P 30 GLU cc_start: 0.6150 (tm-30) cc_final: 0.5650 (tp30) REVERT: P 66 MET cc_start: 0.6004 (mtt) cc_final: 0.5683 (mtt) REVERT: P 102 MET cc_start: 0.8441 (mtp) cc_final: 0.8133 (mtm) REVERT: P 104 SER cc_start: 0.7267 (t) cc_final: 0.6869 (p) REVERT: P 113 GLU cc_start: 0.7152 (tp30) cc_final: 0.6834 (mp0) REVERT: P 117 ARG cc_start: 0.6840 (mmt180) cc_final: 0.6518 (mmp80) REVERT: P 120 GLN cc_start: 0.6148 (tt0) cc_final: 0.5689 (mm-40) REVERT: P 156 ARG cc_start: 0.7444 (tpp80) cc_final: 0.6292 (ttm170) REVERT: P 183 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7547 (tt) REVERT: P 213 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.5990 (mp0) REVERT: P 215 GLU cc_start: 0.6106 (pm20) cc_final: 0.5799 (pm20) REVERT: P 230 LEU cc_start: 0.8410 (mp) cc_final: 0.8099 (mt) REVERT: P 254 LYS cc_start: 0.7499 (ttmt) cc_final: 0.7012 (mppt) REVERT: P 265 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6930 (mt-10) REVERT: P 298 ASN cc_start: 0.7014 (t0) cc_final: 0.6306 (m110) REVERT: P 329 GLU cc_start: 0.8034 (pt0) cc_final: 0.7215 (pt0) REVERT: P 337 GLU cc_start: 0.7154 (mp0) cc_final: 0.6774 (mp0) REVERT: P 395 HIS cc_start: 0.7265 (m-70) cc_final: 0.6325 (t-90) REVERT: P 399 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6911 (pm20) REVERT: P 446 ASP cc_start: 0.7732 (m-30) cc_final: 0.7174 (m-30) REVERT: P 476 GLU cc_start: 0.6990 (tt0) cc_final: 0.6598 (tt0) REVERT: P 480 ASP cc_start: 0.7736 (t0) cc_final: 0.7325 (m-30) REVERT: P 492 LYS cc_start: 0.8323 (tttp) cc_final: 0.7748 (tptp) REVERT: P 553 LYS cc_start: 0.7820 (mmtm) cc_final: 0.7327 (mmtm) REVERT: P 570 LYS cc_start: 0.7642 (tttt) cc_final: 0.7301 (tttm) REVERT: P 584 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6893 (mt-10) REVERT: P 598 GLN cc_start: 0.7686 (tt0) cc_final: 0.7336 (tt0) REVERT: P 602 PHE cc_start: 0.7413 (t80) cc_final: 0.7137 (t80) REVERT: P 675 MET cc_start: 0.8261 (mmt) cc_final: 0.7859 (mmm) REVERT: P 688 LEU cc_start: 0.5220 (tm) cc_final: 0.4895 (tt) REVERT: P 691 THR cc_start: 0.4528 (m) cc_final: 0.4312 (p) REVERT: R 37 MET cc_start: 0.5548 (mtp) cc_final: 0.5231 (mtp) outliers start: 53 outliers final: 32 residues processed: 248 average time/residue: 0.7525 time to fit residues: 203.3317 Evaluate side-chains 258 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 52 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 161 SER Chi-restraints excluded: chain P residue 168 ASP Chi-restraints excluded: chain P residue 183 LEU Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain P residue 263 GLU Chi-restraints excluded: chain P residue 289 ASP Chi-restraints excluded: chain P residue 296 THR Chi-restraints excluded: chain P residue 312 THR Chi-restraints excluded: chain P residue 323 ILE Chi-restraints excluded: chain P residue 379 THR Chi-restraints excluded: chain P residue 399 GLU Chi-restraints excluded: chain P residue 418 THR Chi-restraints excluded: chain P residue 515 GLU Chi-restraints excluded: chain P residue 584 GLU Chi-restraints excluded: chain P residue 687 THR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 145 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 85 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 129 optimal weight: 0.3980 chunk 70 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN D 41 GLN D 121 GLN P 440 ASN P 534 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.153637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113699 restraints weight = 18273.776| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.94 r_work: 0.3141 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 15987 Z= 0.204 Angle : 0.627 12.538 21632 Z= 0.310 Chirality : 0.045 0.219 2380 Planarity : 0.004 0.041 2793 Dihedral : 7.492 134.749 2192 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.57 % Favored : 97.38 % Rotamer: Outliers : 2.97 % Allowed : 14.18 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.19), residues: 1949 helix: 0.70 (0.17), residues: 957 sheet: -0.10 (0.31), residues: 240 loop : 0.68 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 601 TYR 0.023 0.002 TYR P 640 PHE 0.028 0.002 PHE P 173 TRP 0.019 0.002 TRP C 340 HIS 0.006 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00492 (15987) covalent geometry : angle 0.62709 (21632) hydrogen bonds : bond 0.03691 ( 811) hydrogen bonds : angle 4.89360 ( 2214) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 213 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8461 (mtt180) cc_final: 0.8117 (mtt-85) REVERT: B 50 LYS cc_start: 0.8200 (mttt) cc_final: 0.7947 (mtpm) REVERT: B 68 LYS cc_start: 0.8851 (mttt) cc_final: 0.7882 (mtmp) REVERT: B 91 TYR cc_start: 0.7445 (m-80) cc_final: 0.6390 (t80) REVERT: B 129 VAL cc_start: 0.8578 (OUTLIER) cc_final: 0.8253 (p) REVERT: B 176 MET cc_start: 0.8945 (mtp) cc_final: 0.8464 (mtp) REVERT: B 206 ARG cc_start: 0.8026 (ttt180) cc_final: 0.7565 (ttm-80) REVERT: B 246 GLN cc_start: 0.8807 (mt0) cc_final: 0.8563 (mt0) REVERT: B 283 MET cc_start: 0.8789 (mmm) cc_final: 0.8373 (mmt) REVERT: B 326 LYS cc_start: 0.8057 (mmmt) cc_final: 0.7582 (mmtp) REVERT: B 328 LYS cc_start: 0.8212 (mmmt) cc_final: 0.7623 (mppt) REVERT: C 44 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8111 (mtt) REVERT: C 47 MET cc_start: 0.7013 (mtp) cc_final: 0.6720 (mtp) REVERT: C 50 LYS cc_start: 0.8200 (mmmm) cc_final: 0.7448 (mttt) REVERT: C 68 LYS cc_start: 0.8818 (mttp) cc_final: 0.8339 (mtpp) REVERT: C 72 GLU cc_start: 0.7816 (tt0) cc_final: 0.7308 (mt-10) REVERT: C 82 MET cc_start: 0.8943 (tpt) cc_final: 0.8074 (tpt) REVERT: C 95 ARG cc_start: 0.8554 (mtp85) cc_final: 0.8200 (mtt180) REVERT: C 125 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7661 (mm-30) REVERT: C 191 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8253 (ttmm) REVERT: C 206 ARG cc_start: 0.7732 (ttt180) cc_final: 0.7127 (ttm-80) REVERT: C 211 ASP cc_start: 0.7912 (m-30) cc_final: 0.7555 (t70) REVERT: C 287 ILE cc_start: 0.5236 (OUTLIER) cc_final: 0.4501 (tt) REVERT: C 290 ARG cc_start: 0.6453 (mtt180) cc_final: 0.5676 (mtt90) REVERT: C 323 SER cc_start: 0.8662 (p) cc_final: 0.8213 (t) REVERT: C 326 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7710 (mmtt) REVERT: C 336 LYS cc_start: 0.8267 (tttt) cc_final: 0.7988 (ttmt) REVERT: C 354 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7815 (mp-120) REVERT: D 50 LYS cc_start: 0.8318 (mtpp) cc_final: 0.8026 (mttt) REVERT: D 51 ASP cc_start: 0.8542 (m-30) cc_final: 0.7931 (p0) REVERT: D 72 GLU cc_start: 0.8143 (tt0) cc_final: 0.7387 (mp0) REVERT: D 107 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8716 (tt0) REVERT: D 122 ILE cc_start: 0.8253 (mm) cc_final: 0.7988 (mp) REVERT: D 276 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7868 (mt-10) REVERT: D 299 MET cc_start: 0.9279 (mtm) cc_final: 0.9015 (mtt) REVERT: D 323 SER cc_start: 0.8893 (OUTLIER) cc_final: 0.8565 (t) REVERT: D 325 MET cc_start: 0.7330 (mmt) cc_final: 0.7013 (mmp) REVERT: D 352 PHE cc_start: 0.5206 (m-80) cc_final: 0.3796 (m-80) REVERT: D 356 TRP cc_start: 0.5441 (m100) cc_final: 0.4893 (m-10) REVERT: D 360 GLN cc_start: 0.7074 (tp40) cc_final: 0.6400 (pm20) REVERT: P 13 VAL cc_start: 0.6071 (m) cc_final: 0.5782 (m) REVERT: P 14 GLN cc_start: 0.7282 (pt0) cc_final: 0.6191 (mt0) REVERT: P 18 LEU cc_start: 0.7374 (mt) cc_final: 0.7077 (mm) REVERT: P 24 SER cc_start: 0.8127 (t) cc_final: 0.7772 (t) REVERT: P 30 GLU cc_start: 0.6126 (tm-30) cc_final: 0.5631 (tp30) REVERT: P 66 MET cc_start: 0.5961 (mtt) cc_final: 0.5620 (mtt) REVERT: P 86 ASP cc_start: 0.6859 (t70) cc_final: 0.6648 (m-30) REVERT: P 102 MET cc_start: 0.8440 (mtp) cc_final: 0.8126 (mtm) REVERT: P 104 SER cc_start: 0.7247 (t) cc_final: 0.6837 (p) REVERT: P 113 GLU cc_start: 0.7238 (tp30) cc_final: 0.6949 (mp0) REVERT: P 117 ARG cc_start: 0.6818 (mmt180) cc_final: 0.6415 (mmt-90) REVERT: P 120 GLN cc_start: 0.5783 (tt0) cc_final: 0.5299 (mm-40) REVERT: P 156 ARG cc_start: 0.7477 (tpp80) cc_final: 0.6333 (ttm170) REVERT: P 183 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7567 (tt) REVERT: P 213 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.5946 (mp0) REVERT: P 215 GLU cc_start: 0.6008 (pm20) cc_final: 0.5699 (pm20) REVERT: P 230 LEU cc_start: 0.8357 (mp) cc_final: 0.8039 (mt) REVERT: P 254 LYS cc_start: 0.7365 (ttmt) cc_final: 0.6882 (mppt) REVERT: P 265 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6971 (mt-10) REVERT: P 298 ASN cc_start: 0.7234 (t0) cc_final: 0.6540 (m110) REVERT: P 329 GLU cc_start: 0.8041 (pt0) cc_final: 0.7208 (pt0) REVERT: P 337 GLU cc_start: 0.7126 (mp0) cc_final: 0.6748 (mp0) REVERT: P 395 HIS cc_start: 0.7299 (m-70) cc_final: 0.6375 (t-90) REVERT: P 399 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6887 (pm20) REVERT: P 446 ASP cc_start: 0.7699 (m-30) cc_final: 0.7103 (m-30) REVERT: P 476 GLU cc_start: 0.6965 (tt0) cc_final: 0.6569 (tt0) REVERT: P 480 ASP cc_start: 0.7596 (t0) cc_final: 0.7161 (m-30) REVERT: P 492 LYS cc_start: 0.8307 (tttp) cc_final: 0.7661 (tptp) REVERT: P 553 LYS cc_start: 0.7831 (mmtm) cc_final: 0.7311 (mmtm) REVERT: P 570 LYS cc_start: 0.7608 (tttt) cc_final: 0.7254 (tttm) REVERT: P 584 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6848 (mt-10) REVERT: P 602 PHE cc_start: 0.7517 (t80) cc_final: 0.7189 (t80) REVERT: P 675 MET cc_start: 0.8266 (mmt) cc_final: 0.7851 (mmm) REVERT: P 688 LEU cc_start: 0.5343 (tm) cc_final: 0.4924 (tt) REVERT: P 691 THR cc_start: 0.4516 (m) cc_final: 0.4313 (p) REVERT: R 37 MET cc_start: 0.5321 (mtp) cc_final: 0.4965 (mtp) outliers start: 50 outliers final: 28 residues processed: 247 average time/residue: 0.7552 time to fit residues: 202.9330 Evaluate side-chains 246 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 52 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 161 SER Chi-restraints excluded: chain P residue 168 ASP Chi-restraints excluded: chain P residue 183 LEU Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain P residue 289 ASP Chi-restraints excluded: chain P residue 296 THR Chi-restraints excluded: chain P residue 312 THR Chi-restraints excluded: chain P residue 379 THR Chi-restraints excluded: chain P residue 399 GLU Chi-restraints excluded: chain P residue 515 GLU Chi-restraints excluded: chain P residue 584 GLU Chi-restraints excluded: chain P residue 687 THR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 145 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 171 optimal weight: 0.7980 chunk 103 optimal weight: 0.3980 chunk 156 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 225 ASN D 41 GLN D 121 GLN P 440 ASN P 534 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.154333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.114499 restraints weight = 18303.970| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.00 r_work: 0.3156 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 15987 Z= 0.174 Angle : 0.615 13.238 21632 Z= 0.302 Chirality : 0.044 0.190 2380 Planarity : 0.004 0.036 2793 Dihedral : 7.438 136.254 2192 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.43 % Rotamer: Outliers : 2.67 % Allowed : 14.84 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.19), residues: 1949 helix: 0.79 (0.17), residues: 953 sheet: -0.05 (0.31), residues: 240 loop : 0.67 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 601 TYR 0.026 0.001 TYR P 640 PHE 0.020 0.001 PHE R 17 TRP 0.017 0.002 TRP C 340 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00415 (15987) covalent geometry : angle 0.61469 (21632) hydrogen bonds : bond 0.03505 ( 811) hydrogen bonds : angle 4.81648 ( 2214) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 212 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8448 (mtt180) cc_final: 0.8108 (mtt-85) REVERT: B 50 LYS cc_start: 0.8169 (mttt) cc_final: 0.7932 (mtpm) REVERT: B 68 LYS cc_start: 0.8859 (mttt) cc_final: 0.7902 (mtmp) REVERT: B 91 TYR cc_start: 0.7458 (m-80) cc_final: 0.6407 (t80) REVERT: B 129 VAL cc_start: 0.8600 (OUTLIER) cc_final: 0.8260 (p) REVERT: B 176 MET cc_start: 0.8940 (mtp) cc_final: 0.8504 (mtp) REVERT: B 206 ARG cc_start: 0.8012 (ttt180) cc_final: 0.7560 (ttm-80) REVERT: B 246 GLN cc_start: 0.8799 (mt0) cc_final: 0.8558 (mt0) REVERT: B 283 MET cc_start: 0.8776 (mmm) cc_final: 0.8348 (mmt) REVERT: B 326 LYS cc_start: 0.8050 (mmmt) cc_final: 0.7584 (mmtp) REVERT: B 328 LYS cc_start: 0.8254 (mmmt) cc_final: 0.7728 (mppt) REVERT: C 44 MET cc_start: 0.8321 (mtm) cc_final: 0.8082 (mtt) REVERT: C 50 LYS cc_start: 0.8204 (mmmm) cc_final: 0.7452 (mttt) REVERT: C 68 LYS cc_start: 0.8814 (mttp) cc_final: 0.8348 (mtpp) REVERT: C 72 GLU cc_start: 0.7923 (tt0) cc_final: 0.7307 (mt-10) REVERT: C 82 MET cc_start: 0.8946 (tpt) cc_final: 0.8404 (tpt) REVERT: C 95 ARG cc_start: 0.8547 (mtp85) cc_final: 0.8199 (mtt180) REVERT: C 125 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7671 (mm-30) REVERT: C 191 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.7713 (tttm) REVERT: C 206 ARG cc_start: 0.7694 (ttt180) cc_final: 0.7212 (ttm-80) REVERT: C 211 ASP cc_start: 0.7921 (m-30) cc_final: 0.7611 (t70) REVERT: C 287 ILE cc_start: 0.5203 (OUTLIER) cc_final: 0.4512 (tt) REVERT: C 290 ARG cc_start: 0.6397 (mtt180) cc_final: 0.5683 (mtt90) REVERT: C 323 SER cc_start: 0.8655 (p) cc_final: 0.8199 (t) REVERT: C 326 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7718 (mmtt) REVERT: C 336 LYS cc_start: 0.8191 (tttt) cc_final: 0.7928 (ttmt) REVERT: C 354 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7823 (mp-120) REVERT: D 50 LYS cc_start: 0.8305 (mtpp) cc_final: 0.8023 (mtmt) REVERT: D 51 ASP cc_start: 0.8545 (m-30) cc_final: 0.7933 (p0) REVERT: D 57 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7677 (mt-10) REVERT: D 72 GLU cc_start: 0.8109 (tt0) cc_final: 0.7412 (mp0) REVERT: D 107 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8742 (tt0) REVERT: D 122 ILE cc_start: 0.8207 (mm) cc_final: 0.7941 (mp) REVERT: D 132 MET cc_start: 0.8851 (ppp) cc_final: 0.8622 (ptm) REVERT: D 176 MET cc_start: 0.9040 (mmt) cc_final: 0.8794 (mmt) REVERT: D 276 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7924 (mt-10) REVERT: D 299 MET cc_start: 0.9268 (mtm) cc_final: 0.8982 (mtt) REVERT: D 323 SER cc_start: 0.8890 (OUTLIER) cc_final: 0.8563 (t) REVERT: D 325 MET cc_start: 0.7331 (mmt) cc_final: 0.7035 (mmp) REVERT: D 352 PHE cc_start: 0.5179 (m-80) cc_final: 0.3773 (m-80) REVERT: D 356 TRP cc_start: 0.5402 (m100) cc_final: 0.4921 (m-10) REVERT: D 360 GLN cc_start: 0.7040 (tp40) cc_final: 0.6399 (pm20) REVERT: P 13 VAL cc_start: 0.6094 (m) cc_final: 0.5804 (m) REVERT: P 14 GLN cc_start: 0.7190 (pt0) cc_final: 0.6295 (mt0) REVERT: P 18 LEU cc_start: 0.7299 (mt) cc_final: 0.7014 (mm) REVERT: P 24 SER cc_start: 0.8186 (t) cc_final: 0.7831 (t) REVERT: P 30 GLU cc_start: 0.6121 (tm-30) cc_final: 0.5767 (tp30) REVERT: P 32 LEU cc_start: 0.5806 (mt) cc_final: 0.5583 (tp) REVERT: P 66 MET cc_start: 0.5919 (mtt) cc_final: 0.5586 (mtt) REVERT: P 86 ASP cc_start: 0.6840 (t70) cc_final: 0.6620 (m-30) REVERT: P 102 MET cc_start: 0.8362 (mtp) cc_final: 0.8046 (mtm) REVERT: P 104 SER cc_start: 0.7251 (t) cc_final: 0.6844 (p) REVERT: P 113 GLU cc_start: 0.7177 (tp30) cc_final: 0.6925 (mp0) REVERT: P 117 ARG cc_start: 0.6832 (mmt180) cc_final: 0.6402 (mmt-90) REVERT: P 120 GLN cc_start: 0.5811 (tt0) cc_final: 0.5318 (mm-40) REVERT: P 156 ARG cc_start: 0.7463 (tpp80) cc_final: 0.6319 (ttm170) REVERT: P 183 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7625 (tt) REVERT: P 213 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.5932 (mp0) REVERT: P 215 GLU cc_start: 0.5965 (pm20) cc_final: 0.5647 (pm20) REVERT: P 230 LEU cc_start: 0.8372 (mp) cc_final: 0.8066 (mt) REVERT: P 254 LYS cc_start: 0.7478 (ttmt) cc_final: 0.6986 (mppt) REVERT: P 265 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6956 (mt-10) REVERT: P 298 ASN cc_start: 0.7217 (t0) cc_final: 0.6530 (m110) REVERT: P 316 GLU cc_start: 0.7946 (tt0) cc_final: 0.7615 (tt0) REVERT: P 323 ILE cc_start: 0.8214 (mt) cc_final: 0.7576 (mp) REVERT: P 329 GLU cc_start: 0.8015 (pt0) cc_final: 0.7274 (pt0) REVERT: P 337 GLU cc_start: 0.7122 (mp0) cc_final: 0.6744 (mp0) REVERT: P 395 HIS cc_start: 0.7317 (m-70) cc_final: 0.6369 (t-90) REVERT: P 399 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6988 (pm20) REVERT: P 446 ASP cc_start: 0.7685 (m-30) cc_final: 0.7120 (m-30) REVERT: P 468 GLU cc_start: 0.7397 (tp30) cc_final: 0.7135 (tp30) REVERT: P 476 GLU cc_start: 0.6960 (tt0) cc_final: 0.6544 (tt0) REVERT: P 480 ASP cc_start: 0.7699 (t0) cc_final: 0.7292 (m-30) REVERT: P 492 LYS cc_start: 0.8310 (tttp) cc_final: 0.7660 (tptp) REVERT: P 553 LYS cc_start: 0.7821 (mmtm) cc_final: 0.7300 (mmtm) REVERT: P 570 LYS cc_start: 0.7617 (tttt) cc_final: 0.7263 (tttm) REVERT: P 602 PHE cc_start: 0.7506 (t80) cc_final: 0.7229 (t80) REVERT: P 675 MET cc_start: 0.8264 (mmt) cc_final: 0.7836 (mmm) REVERT: P 688 LEU cc_start: 0.5382 (tm) cc_final: 0.4947 (tt) REVERT: R 37 MET cc_start: 0.5409 (mtp) cc_final: 0.5120 (mtp) outliers start: 45 outliers final: 29 residues processed: 243 average time/residue: 0.7569 time to fit residues: 200.3831 Evaluate side-chains 245 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 52 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 161 SER Chi-restraints excluded: chain P residue 168 ASP Chi-restraints excluded: chain P residue 183 LEU Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain P residue 289 ASP Chi-restraints excluded: chain P residue 296 THR Chi-restraints excluded: chain P residue 312 THR Chi-restraints excluded: chain P residue 379 THR Chi-restraints excluded: chain P residue 380 THR Chi-restraints excluded: chain P residue 399 GLU Chi-restraints excluded: chain P residue 515 GLU Chi-restraints excluded: chain P residue 687 THR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 145 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 1 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 152 optimal weight: 0.4980 chunk 149 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 225 ASN D 41 GLN D 121 GLN P 181 HIS P 440 ASN P 534 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.153462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113317 restraints weight = 18208.968| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.05 r_work: 0.3134 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 15987 Z= 0.232 Angle : 0.661 13.265 21632 Z= 0.325 Chirality : 0.047 0.243 2380 Planarity : 0.005 0.049 2793 Dihedral : 7.584 135.811 2192 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.72 % Favored : 97.23 % Rotamer: Outliers : 2.79 % Allowed : 14.90 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.19), residues: 1949 helix: 0.70 (0.17), residues: 946 sheet: -0.10 (0.31), residues: 240 loop : 0.59 (0.24), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 601 TYR 0.020 0.002 TYR P 640 PHE 0.027 0.002 PHE P 173 TRP 0.021 0.002 TRP C 340 HIS 0.007 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00562 (15987) covalent geometry : angle 0.66073 (21632) hydrogen bonds : bond 0.03842 ( 811) hydrogen bonds : angle 4.94399 ( 2214) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 203 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8460 (mtt180) cc_final: 0.8101 (mtt-85) REVERT: B 50 LYS cc_start: 0.8205 (mttt) cc_final: 0.7937 (mtpm) REVERT: B 68 LYS cc_start: 0.8836 (mttt) cc_final: 0.7825 (mtmp) REVERT: B 91 TYR cc_start: 0.7405 (m-80) cc_final: 0.6278 (t80) REVERT: B 129 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8213 (p) REVERT: B 206 ARG cc_start: 0.7972 (ttt180) cc_final: 0.7496 (ttm-80) REVERT: B 246 GLN cc_start: 0.8757 (mt0) cc_final: 0.8509 (mt0) REVERT: B 283 MET cc_start: 0.8760 (mmm) cc_final: 0.8334 (mmt) REVERT: B 326 LYS cc_start: 0.8025 (mmmt) cc_final: 0.7545 (mmtp) REVERT: B 328 LYS cc_start: 0.8220 (mmmt) cc_final: 0.7601 (mtmm) REVERT: C 44 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8137 (mtt) REVERT: C 50 LYS cc_start: 0.8147 (mmmm) cc_final: 0.7372 (mttt) REVERT: C 68 LYS cc_start: 0.8754 (mttp) cc_final: 0.8244 (mtpp) REVERT: C 72 GLU cc_start: 0.7919 (tt0) cc_final: 0.7227 (mt-10) REVERT: C 82 MET cc_start: 0.8876 (tpt) cc_final: 0.8056 (tpt) REVERT: C 95 ARG cc_start: 0.8519 (mtp85) cc_final: 0.8156 (mtt180) REVERT: C 125 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7548 (mm-30) REVERT: C 191 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8189 (ttmm) REVERT: C 206 ARG cc_start: 0.7672 (ttt180) cc_final: 0.7054 (ttm-80) REVERT: C 211 ASP cc_start: 0.7858 (m-30) cc_final: 0.7503 (t70) REVERT: C 287 ILE cc_start: 0.5374 (OUTLIER) cc_final: 0.4065 (tt) REVERT: C 290 ARG cc_start: 0.6414 (mtt180) cc_final: 0.5642 (mtt90) REVERT: C 323 SER cc_start: 0.8636 (p) cc_final: 0.8190 (t) REVERT: C 326 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7688 (mmtt) REVERT: C 336 LYS cc_start: 0.8245 (tttt) cc_final: 0.7976 (ttmt) REVERT: C 354 GLN cc_start: 0.8356 (mm-40) cc_final: 0.7773 (mp-120) REVERT: D 50 LYS cc_start: 0.8269 (mtpp) cc_final: 0.7980 (mtmt) REVERT: D 51 ASP cc_start: 0.8537 (m-30) cc_final: 0.7850 (p0) REVERT: D 72 GLU cc_start: 0.8058 (tt0) cc_final: 0.7317 (mp0) REVERT: D 107 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8730 (tt0) REVERT: D 132 MET cc_start: 0.8747 (ppp) cc_final: 0.8536 (ptm) REVERT: D 176 MET cc_start: 0.9028 (mmt) cc_final: 0.8780 (mmt) REVERT: D 276 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7815 (mt-10) REVERT: D 299 MET cc_start: 0.9275 (mtm) cc_final: 0.8997 (mtt) REVERT: D 323 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8513 (t) REVERT: D 325 MET cc_start: 0.7297 (mmt) cc_final: 0.6961 (mmp) REVERT: D 352 PHE cc_start: 0.5229 (m-80) cc_final: 0.3814 (m-80) REVERT: D 356 TRP cc_start: 0.5412 (m100) cc_final: 0.4873 (m-10) REVERT: D 360 GLN cc_start: 0.6895 (tp40) cc_final: 0.6321 (pm20) REVERT: P 13 VAL cc_start: 0.6068 (m) cc_final: 0.5775 (m) REVERT: P 14 GLN cc_start: 0.7222 (pt0) cc_final: 0.6145 (mt0) REVERT: P 18 LEU cc_start: 0.7207 (mt) cc_final: 0.6901 (mm) REVERT: P 24 SER cc_start: 0.8176 (t) cc_final: 0.7810 (t) REVERT: P 30 GLU cc_start: 0.6075 (tm-30) cc_final: 0.5593 (tp30) REVERT: P 66 MET cc_start: 0.5922 (mtt) cc_final: 0.5425 (mtt) REVERT: P 86 ASP cc_start: 0.6764 (t70) cc_final: 0.6500 (m-30) REVERT: P 102 MET cc_start: 0.8412 (mtp) cc_final: 0.8090 (mtm) REVERT: P 104 SER cc_start: 0.7198 (t) cc_final: 0.6772 (p) REVERT: P 113 GLU cc_start: 0.7123 (tp30) cc_final: 0.6873 (mp0) REVERT: P 117 ARG cc_start: 0.6759 (mmt180) cc_final: 0.6372 (mmt-90) REVERT: P 120 GLN cc_start: 0.5715 (tt0) cc_final: 0.5217 (mm-40) REVERT: P 156 ARG cc_start: 0.7511 (tpp80) cc_final: 0.6373 (ttm170) REVERT: P 183 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7515 (tt) REVERT: P 213 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.5876 (mp0) REVERT: P 215 GLU cc_start: 0.6043 (pm20) cc_final: 0.5695 (pm20) REVERT: P 230 LEU cc_start: 0.8295 (mp) cc_final: 0.7960 (mt) REVERT: P 254 LYS cc_start: 0.7412 (ttmt) cc_final: 0.6907 (mppt) REVERT: P 265 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6943 (mt-10) REVERT: P 323 ILE cc_start: 0.8132 (mt) cc_final: 0.7491 (mp) REVERT: P 329 GLU cc_start: 0.8020 (pt0) cc_final: 0.7274 (pt0) REVERT: P 337 GLU cc_start: 0.7063 (mp0) cc_final: 0.6682 (mp0) REVERT: P 395 HIS cc_start: 0.7264 (m-70) cc_final: 0.6272 (t70) REVERT: P 399 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6818 (pm20) REVERT: P 446 ASP cc_start: 0.7631 (m-30) cc_final: 0.7020 (m-30) REVERT: P 476 GLU cc_start: 0.6903 (tt0) cc_final: 0.6476 (tt0) REVERT: P 480 ASP cc_start: 0.7528 (t0) cc_final: 0.7063 (m-30) REVERT: P 492 LYS cc_start: 0.8068 (tttp) cc_final: 0.7597 (tptp) REVERT: P 553 LYS cc_start: 0.7744 (mmtm) cc_final: 0.7179 (mmtm) REVERT: P 570 LYS cc_start: 0.7507 (tttt) cc_final: 0.7154 (tttm) REVERT: P 602 PHE cc_start: 0.7354 (t80) cc_final: 0.7025 (t80) REVERT: P 650 MET cc_start: 0.8251 (mpp) cc_final: 0.8036 (mmp) REVERT: P 675 MET cc_start: 0.8305 (mmt) cc_final: 0.7852 (mmm) REVERT: P 688 LEU cc_start: 0.4875 (tm) cc_final: 0.4652 (tt) REVERT: R 37 MET cc_start: 0.5403 (mtp) cc_final: 0.5149 (mtp) outliers start: 47 outliers final: 29 residues processed: 238 average time/residue: 0.7561 time to fit residues: 195.9637 Evaluate side-chains 236 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 52 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 161 SER Chi-restraints excluded: chain P residue 168 ASP Chi-restraints excluded: chain P residue 183 LEU Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain P residue 289 ASP Chi-restraints excluded: chain P residue 296 THR Chi-restraints excluded: chain P residue 312 THR Chi-restraints excluded: chain P residue 379 THR Chi-restraints excluded: chain P residue 380 THR Chi-restraints excluded: chain P residue 399 GLU Chi-restraints excluded: chain P residue 515 GLU Chi-restraints excluded: chain P residue 687 THR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 145 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 85 optimal weight: 0.4980 chunk 183 optimal weight: 20.0000 chunk 181 optimal weight: 9.9990 chunk 54 optimal weight: 0.2980 chunk 89 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 157 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 225 ASN D 41 GLN D 121 GLN P 440 ASN P 534 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.154534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114813 restraints weight = 18142.375| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.92 r_work: 0.3168 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 15987 Z= 0.159 Angle : 0.605 13.672 21632 Z= 0.296 Chirality : 0.044 0.202 2380 Planarity : 0.004 0.035 2793 Dihedral : 7.436 137.545 2192 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.43 % Rotamer: Outliers : 2.31 % Allowed : 15.43 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.19), residues: 1949 helix: 0.82 (0.17), residues: 953 sheet: -0.11 (0.30), residues: 250 loop : 0.67 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 601 TYR 0.022 0.001 TYR P 640 PHE 0.017 0.001 PHE R 17 TRP 0.016 0.002 TRP C 340 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00377 (15987) covalent geometry : angle 0.60545 (21632) hydrogen bonds : bond 0.03410 ( 811) hydrogen bonds : angle 4.79600 ( 2214) =============================================================================== Job complete usr+sys time: 7508.80 seconds wall clock time: 128 minutes 30.52 seconds (7710.52 seconds total)