Starting phenix.real_space_refine on Sat May 17 08:16:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cfv_45564/05_2025/9cfv_45564.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cfv_45564/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cfv_45564/05_2025/9cfv_45564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cfv_45564/05_2025/9cfv_45564.map" model { file = "/net/cci-nas-00/data/ceres_data/9cfv_45564/05_2025/9cfv_45564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cfv_45564/05_2025/9cfv_45564.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.23, per 1000 atoms: 0.59 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: 3.93 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.05 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: 6.30 Time building geometry restraints manager: 4.56 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 374 or resid 401 through \ 402)) selection = (chain 'D' and (resid 4 through 39 or resid 50 through 374 or resid 401 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: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 37.330 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 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:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.180 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (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 TRP 0.295 0.037 TRP D 340 HIS 0.015 0.004 HIS C 275 PHE 0.074 0.013 PHE C 127 TYR 0.129 0.019 TYR P 438 ARG 0.015 0.002 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.17103 ( 811) hydrogen bonds : angle 7.59422 ( 2214) covalent geometry : bond 0.01248 (15987) covalent geometry : angle 1.86450 (21632) *********************** 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 : 1.654 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: 0.6706 (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: 0.5737 (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: 0.6420 (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: 0.8216 (mmm) 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: 0.6408 (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: 0.5937 (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: 0.5516 (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: 0.6676 (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: 1.5086 time to fit residues: 604.6057 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 : 1.633 ------------------------------------------------------------------------------- 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 163 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 99 optimal weight: 0.0470 chunk 78 optimal weight: 0.7980 chunk 152 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 113 optimal weight: 0.2980 chunk 176 optimal weight: 0.7980 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.157955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.119139 restraints weight = 18191.543| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.99 r_work: 0.3192 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15987 Z= 0.160 Angle : 0.662 9.953 21632 Z= 0.341 Chirality : 0.045 0.209 2380 Planarity : 0.004 0.039 2793 Dihedral : 8.587 120.244 2222 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.05 % Favored : 97.90 % Rotamer: Outliers : 2.67 % Allowed : 9.55 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.19), residues: 1949 helix: 0.09 (0.16), residues: 921 sheet: -0.21 (0.32), residues: 247 loop : 0.73 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 340 HIS 0.006 0.001 HIS C 161 PHE 0.018 0.002 PHE D 255 TYR 0.018 0.002 TYR P 44 ARG 0.005 0.001 ARG P 621 Details of bonding type rmsd hydrogen bonds : bond 0.04277 ( 811) hydrogen bonds : angle 5.28421 ( 2214) covalent geometry : bond 0.00362 (15987) covalent geometry : angle 0.66151 (21632) *********************** 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 305 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 260 time to evaluate : 1.782 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: 0.8483 (mtt180) cc_final: 0.8101 (mtt-85) REVERT: B 68 LYS cc_start: 0.8711 (mttt) cc_final: 0.7607 (mtmt) REVERT: B 82 MET cc_start: 0.8947 (tpt) cc_final: 0.8604 (tpt) REVERT: B 91 TYR cc_start: 0.7601 (m-80) cc_final: 0.6787 (t80) REVERT: B 121 GLN cc_start: 0.8137 (tt0) cc_final: 0.7927 (tt0) REVERT: B 206 ARG cc_start: 0.8109 (ttt180) cc_final: 0.7570 (ttm-80) REVERT: B 225 ASN cc_start: 0.7773 (t0) cc_final: 0.7527 (m110) REVERT: B 246 GLN cc_start: 0.9016 (mt0) cc_final: 0.8764 (mt0) REVERT: B 248 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7831 (mp) REVERT: B 283 MET cc_start: 0.8880 (mmm) cc_final: 0.8428 (mmt) REVERT: B 326 LYS cc_start: 0.8155 (mmmt) cc_final: 0.7814 (mmtp) REVERT: B 328 LYS cc_start: 0.8326 (mmmt) cc_final: 0.7682 (mttp) REVERT: C 47 MET cc_start: 0.6788 (mtp) cc_final: 0.6330 (ttm) REVERT: C 50 LYS cc_start: 0.8240 (mmmm) cc_final: 0.7536 (mttt) REVERT: C 72 GLU cc_start: 0.7820 (tt0) cc_final: 0.7366 (mt-10) REVERT: C 82 MET cc_start: 0.8940 (tpt) cc_final: 0.8227 (tpt) REVERT: C 206 ARG cc_start: 0.7934 (ttt180) cc_final: 0.7352 (ttp-170) REVERT: C 211 ASP cc_start: 0.7956 (m-30) cc_final: 0.7711 (t70) REVERT: C 248 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7796 (mm) REVERT: C 290 ARG cc_start: 0.6277 (mtt180) cc_final: 0.5542 (mtt90) REVERT: C 323 SER cc_start: 0.8736 (p) cc_final: 0.8384 (t) REVERT: C 326 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7724 (tmtm) REVERT: C 328 LYS cc_start: 0.7858 (ttpt) cc_final: 0.7154 (tmtp) REVERT: C 336 LYS cc_start: 0.8116 (tttt) cc_final: 0.7810 (ttmp) REVERT: C 354 GLN cc_start: 0.8403 (mm-40) cc_final: 0.7872 (mp-120) REVERT: C 355 MET cc_start: 0.8440 (mmm) cc_final: 0.8238 (mpp) REVERT: C 372 ARG cc_start: 0.8050 (mtt180) cc_final: 0.7838 (mtp180) REVERT: D 43 VAL cc_start: 0.9035 (OUTLIER) cc_final: 0.8801 (p) REVERT: D 50 LYS cc_start: 0.8388 (mtpp) cc_final: 0.8083 (mtmt) REVERT: D 51 ASP cc_start: 0.8579 (m-30) cc_final: 0.8109 (p0) REVERT: D 57 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7693 (mm-30) REVERT: D 72 GLU cc_start: 0.8166 (tt0) cc_final: 0.7612 (mp0) REVERT: D 100 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8089 (mm-30) REVERT: D 117 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8121 (mt-10) REVERT: D 206 ARG cc_start: 0.7743 (ttt180) cc_final: 0.7392 (ttm-80) REVERT: D 227 MET cc_start: 0.8607 (mmm) cc_final: 0.8182 (mmm) REVERT: D 234 SER cc_start: 0.8538 (m) cc_final: 0.8329 (p) REVERT: D 276 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7898 (mt-10) REVERT: D 299 MET cc_start: 0.9176 (mtm) cc_final: 0.8947 (mtt) REVERT: D 313 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8337 (tpp) REVERT: D 323 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8613 (t) REVERT: D 325 MET cc_start: 0.7254 (mmt) cc_final: 0.7033 (mmp) REVERT: D 326 LYS cc_start: 0.8631 (tppp) cc_final: 0.8289 (tppt) REVERT: D 352 PHE cc_start: 0.5569 (m-80) cc_final: 0.4351 (m-80) REVERT: D 356 TRP cc_start: 0.5358 (m100) cc_final: 0.4884 (m-10) REVERT: D 360 GLN cc_start: 0.7545 (tp40) cc_final: 0.7241 (tp40) REVERT: D 364 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6850 (mt-10) REVERT: P 14 GLN cc_start: 0.7006 (pt0) cc_final: 0.6458 (mt0) REVERT: P 21 ASN cc_start: 0.6493 (p0) cc_final: 0.6253 (t0) REVERT: P 102 MET cc_start: 0.8347 (mtp) cc_final: 0.7983 (mtm) REVERT: P 113 GLU cc_start: 0.7265 (tp30) cc_final: 0.7013 (mp0) REVERT: P 117 ARG cc_start: 0.6806 (mmt180) cc_final: 0.6441 (mmt-90) REVERT: P 120 GLN cc_start: 0.5922 (tt0) cc_final: 0.5577 (mm110) REVERT: P 183 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7424 (tt) REVERT: P 230 LEU cc_start: 0.8444 (mp) cc_final: 0.8136 (mt) REVERT: P 254 LYS cc_start: 0.7440 (ttmt) cc_final: 0.7038 (mppt) REVERT: P 298 ASN cc_start: 0.7496 (t0) cc_final: 0.6712 (m110) REVERT: P 337 GLU cc_start: 0.7218 (mp0) cc_final: 0.6820 (mp0) REVERT: P 394 GLN cc_start: 0.7511 (mp10) cc_final: 0.7299 (mp10) REVERT: P 399 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: P 427 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6495 (mt-10) REVERT: P 472 LEU cc_start: 0.8317 (mt) cc_final: 0.7969 (mm) REVERT: P 476 GLU cc_start: 0.7162 (tt0) cc_final: 0.6719 (tt0) REVERT: P 480 ASP cc_start: 0.7722 (t0) cc_final: 0.7213 (m-30) REVERT: P 492 LYS cc_start: 0.8171 (tttp) cc_final: 0.7671 (tptp) REVERT: P 536 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6869 (mtpt) REVERT: P 553 LYS cc_start: 0.7576 (mmtm) cc_final: 0.7209 (mmtm) REVERT: P 563 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8369 (mt-10) REVERT: P 584 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6905 (tt0) REVERT: P 598 GLN cc_start: 0.7605 (tt0) cc_final: 0.7169 (tm-30) REVERT: P 604 GLU cc_start: 0.7208 (tt0) cc_final: 0.6775 (tm-30) REVERT: P 675 MET cc_start: 0.8318 (mmt) cc_final: 0.7903 (mmm) REVERT: R 52 MET cc_start: 0.3004 (mtt) cc_final: 0.2021 (mtt) outliers start: 45 outliers final: 16 residues processed: 289 average time/residue: 1.4735 time to fit residues: 463.8749 Evaluate side-chains 245 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 1.607 ------------------------------------------------------------------------------- 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 313 MET 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 90 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 158 optimal weight: 0.0370 chunk 130 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.154048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.114384 restraints weight = 18085.186| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.98 r_work: 0.3142 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15987 Z= 0.195 Angle : 0.648 10.008 21632 Z= 0.328 Chirality : 0.046 0.197 2380 Planarity : 0.005 0.049 2793 Dihedral : 7.938 131.773 2198 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.62 % Favored : 97.33 % Rotamer: Outliers : 2.85 % Allowed : 11.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.19), residues: 1949 helix: 0.46 (0.17), residues: 934 sheet: -0.14 (0.31), residues: 248 loop : 0.77 (0.24), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 340 HIS 0.007 0.001 HIS C 161 PHE 0.016 0.002 PHE P 439 TYR 0.017 0.002 TYR P 438 ARG 0.005 0.001 ARG P 601 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 811) hydrogen bonds : angle 5.07259 ( 2214) covalent geometry : bond 0.00464 (15987) covalent geometry : angle 0.64797 (21632) *********************** 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 272 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 224 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8460 (mtt180) cc_final: 0.8045 (mtt-85) REVERT: B 68 LYS cc_start: 0.8774 (mttt) cc_final: 0.7590 (mtmm) REVERT: B 91 TYR cc_start: 0.7545 (m-80) cc_final: 0.6674 (t80) REVERT: B 176 MET cc_start: 0.8842 (mtp) cc_final: 0.8255 (mtp) REVERT: B 206 ARG cc_start: 0.8112 (ttt180) cc_final: 0.7569 (ttm-80) REVERT: B 225 ASN cc_start: 0.7751 (t0) cc_final: 0.7485 (m110) REVERT: B 241 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: B 246 GLN cc_start: 0.8853 (mt0) cc_final: 0.8633 (mt0) REVERT: B 248 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7963 (mp) REVERT: B 283 MET cc_start: 0.8792 (mmm) cc_final: 0.8344 (mmt) REVERT: B 326 LYS cc_start: 0.8110 (mmmt) cc_final: 0.7700 (mmtp) REVERT: B 328 LYS cc_start: 0.8339 (mmmt) cc_final: 0.7678 (mttt) REVERT: C 47 MET cc_start: 0.6941 (mtp) cc_final: 0.6537 (ttm) REVERT: C 50 LYS cc_start: 0.8204 (mmmm) cc_final: 0.7466 (mttt) REVERT: C 68 LYS cc_start: 0.8859 (mttp) cc_final: 0.8395 (mtpp) REVERT: C 72 GLU cc_start: 0.7853 (tt0) cc_final: 0.7322 (mt-10) REVERT: C 82 MET cc_start: 0.8914 (tpt) cc_final: 0.8115 (tpt) REVERT: C 191 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8237 (ttmm) REVERT: C 206 ARG cc_start: 0.7768 (ttt180) cc_final: 0.7182 (ttm-80) REVERT: C 211 ASP cc_start: 0.7918 (m-30) cc_final: 0.7624 (t70) REVERT: C 290 ARG cc_start: 0.6443 (mtt180) cc_final: 0.5621 (mtt90) REVERT: C 323 SER cc_start: 0.8685 (p) cc_final: 0.8285 (t) REVERT: C 326 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7749 (mmtt) REVERT: C 328 LYS cc_start: 0.8243 (ttpt) cc_final: 0.7270 (tttp) REVERT: C 336 LYS cc_start: 0.8205 (tttt) cc_final: 0.7907 (ttmt) REVERT: C 354 GLN cc_start: 0.8410 (mm-40) cc_final: 0.7839 (mp-120) REVERT: C 355 MET cc_start: 0.8456 (mmm) cc_final: 0.8206 (mpp) REVERT: D 50 LYS cc_start: 0.8377 (mtpp) cc_final: 0.8049 (mtmt) REVERT: D 51 ASP cc_start: 0.8573 (m-30) cc_final: 0.8080 (p0) REVERT: D 57 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7734 (mm-30) REVERT: D 72 GLU cc_start: 0.8129 (tt0) cc_final: 0.7509 (mp0) REVERT: D 100 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8099 (mm-30) REVERT: D 122 ILE cc_start: 0.8171 (mm) cc_final: 0.7892 (mp) REVERT: D 206 ARG cc_start: 0.7585 (ttt180) cc_final: 0.7194 (ttp-170) REVERT: D 276 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7921 (mt-10) REVERT: D 283 MET cc_start: 0.8990 (mmm) cc_final: 0.8635 (mmt) REVERT: D 299 MET cc_start: 0.9195 (mtm) cc_final: 0.8969 (mtt) REVERT: D 323 SER cc_start: 0.8860 (OUTLIER) cc_final: 0.8556 (t) REVERT: D 325 MET cc_start: 0.7257 (mmt) cc_final: 0.6965 (mmp) REVERT: D 326 LYS cc_start: 0.8534 (tppp) cc_final: 0.8041 (mptt) REVERT: D 352 PHE cc_start: 0.5481 (m-80) cc_final: 0.4049 (m-80) REVERT: D 355 MET cc_start: 0.8606 (mmm) cc_final: 0.8350 (mmm) REVERT: D 356 TRP cc_start: 0.5414 (m100) cc_final: 0.4825 (m-10) REVERT: D 360 GLN cc_start: 0.7460 (tp40) cc_final: 0.6396 (pm20) REVERT: P 13 VAL cc_start: 0.5776 (m) cc_final: 0.5569 (m) REVERT: P 14 GLN cc_start: 0.7101 (pt0) cc_final: 0.6286 (mt0) REVERT: P 21 ASN cc_start: 0.6192 (p0) cc_final: 0.5988 (t0) REVERT: P 30 GLU cc_start: 0.6174 (tm-30) cc_final: 0.5640 (tp30) REVERT: P 66 MET cc_start: 0.5875 (mtt) cc_final: 0.5655 (mtt) REVERT: P 102 MET cc_start: 0.8392 (mtp) cc_final: 0.7973 (mtm) REVERT: P 104 SER cc_start: 0.7234 (t) cc_final: 0.6868 (p) REVERT: P 113 GLU cc_start: 0.7258 (tp30) cc_final: 0.6968 (mp0) REVERT: P 117 ARG cc_start: 0.6788 (mmt180) cc_final: 0.6401 (mmt-90) REVERT: P 120 GLN cc_start: 0.5837 (tt0) cc_final: 0.5510 (mm110) REVERT: P 183 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7521 (tt) REVERT: P 213 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.5973 (mp0) REVERT: P 230 LEU cc_start: 0.8422 (mp) cc_final: 0.8130 (mt) REVERT: P 254 LYS cc_start: 0.7524 (ttmt) cc_final: 0.6986 (mppt) REVERT: P 298 ASN cc_start: 0.7475 (t0) cc_final: 0.6644 (m110) REVERT: P 337 GLU cc_start: 0.7197 (mp0) cc_final: 0.6796 (mp0) REVERT: P 395 HIS cc_start: 0.7437 (m-70) cc_final: 0.6472 (t-90) REVERT: P 399 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.6962 (pm20) REVERT: P 427 GLU cc_start: 0.6594 (mt-10) cc_final: 0.6360 (mt-10) REVERT: P 446 ASP cc_start: 0.7809 (m-30) cc_final: 0.7366 (m-30) REVERT: P 472 LEU cc_start: 0.8146 (mt) cc_final: 0.7880 (mm) REVERT: P 476 GLU cc_start: 0.7037 (tt0) cc_final: 0.6677 (tt0) REVERT: P 480 ASP cc_start: 0.7739 (t0) cc_final: 0.7278 (m-30) REVERT: P 492 LYS cc_start: 0.8167 (tttp) cc_final: 0.7588 (tptp) REVERT: P 536 LYS cc_start: 0.7162 (mtmt) cc_final: 0.6909 (mtpt) REVERT: P 553 LYS cc_start: 0.7755 (mmtm) cc_final: 0.7318 (mmtm) REVERT: P 584 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6802 (mt-10) REVERT: P 598 GLN cc_start: 0.7636 (tt0) cc_final: 0.7231 (tm-30) REVERT: P 604 GLU cc_start: 0.7143 (tt0) cc_final: 0.6623 (tm-30) REVERT: P 675 MET cc_start: 0.8299 (mmt) cc_final: 0.7919 (mmm) outliers start: 48 outliers final: 23 residues processed: 257 average time/residue: 1.5499 time to fit residues: 433.5042 Evaluate side-chains 242 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 1.842 ------------------------------------------------------------------------------- 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 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 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 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 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 129 optimal weight: 0.4980 chunk 121 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 100 optimal weight: 0.2980 chunk 157 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.153834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113902 restraints weight = 18211.475| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.90 r_work: 0.3156 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15987 Z= 0.189 Angle : 0.614 9.977 21632 Z= 0.309 Chirality : 0.045 0.186 2380 Planarity : 0.004 0.037 2793 Dihedral : 7.726 135.125 2195 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.26 % Favored : 97.69 % Rotamer: Outliers : 3.32 % Allowed : 12.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.19), residues: 1949 helix: 0.61 (0.17), residues: 938 sheet: -0.10 (0.32), residues: 252 loop : 0.74 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 340 HIS 0.007 0.001 HIS C 161 PHE 0.025 0.002 PHE P 173 TYR 0.026 0.002 TYR P 438 ARG 0.004 0.000 ARG D 335 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 811) hydrogen bonds : angle 4.95221 ( 2214) covalent geometry : bond 0.00449 (15987) covalent geometry : angle 0.61422 (21632) *********************** 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: 56 poor density : 210 time to evaluate : 1.588 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: 0.8422 (mtt180) cc_final: 0.8041 (mtt-85) REVERT: B 68 LYS cc_start: 0.8844 (mttt) cc_final: 0.7907 (mtmp) REVERT: B 91 TYR cc_start: 0.7564 (m-80) cc_final: 0.6630 (t80) REVERT: B 129 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8301 (p) REVERT: B 176 MET cc_start: 0.8902 (mtp) cc_final: 0.8343 (mtp) REVERT: B 206 ARG cc_start: 0.8078 (ttt180) cc_final: 0.7551 (ttm-80) REVERT: B 225 ASN cc_start: 0.7761 (t0) cc_final: 0.7544 (m110) REVERT: B 283 MET cc_start: 0.8804 (mmm) cc_final: 0.8364 (mmt) REVERT: B 326 LYS cc_start: 0.8103 (mmmt) cc_final: 0.7622 (mmtp) REVERT: B 328 LYS cc_start: 0.8325 (mmmt) cc_final: 0.7703 (mtmt) REVERT: C 47 MET cc_start: 0.6948 (mtp) cc_final: 0.6434 (mtm) REVERT: C 50 LYS cc_start: 0.8183 (mmmm) cc_final: 0.7440 (mttt) REVERT: C 68 LYS cc_start: 0.8885 (mttp) cc_final: 0.8449 (mtpp) REVERT: C 72 GLU cc_start: 0.7811 (tt0) cc_final: 0.7322 (mt-10) REVERT: C 82 MET cc_start: 0.8932 (tpt) cc_final: 0.8122 (tpt) REVERT: C 162 ASN cc_start: 0.8959 (OUTLIER) cc_final: 0.8482 (m-40) REVERT: C 191 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8248 (ttmm) REVERT: C 206 ARG cc_start: 0.7801 (ttt180) cc_final: 0.7198 (ttm-80) REVERT: C 211 ASP cc_start: 0.7914 (m-30) cc_final: 0.7626 (t70) REVERT: C 290 ARG cc_start: 0.6402 (mtt180) cc_final: 0.5589 (mtt90) REVERT: C 323 SER cc_start: 0.8696 (p) cc_final: 0.8268 (t) REVERT: C 326 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7766 (mmtt) REVERT: C 336 LYS cc_start: 0.8238 (tttt) cc_final: 0.7943 (ttmt) REVERT: C 354 GLN cc_start: 0.8391 (mm-40) cc_final: 0.7833 (mp-120) REVERT: C 355 MET cc_start: 0.8525 (mmm) cc_final: 0.8279 (mpp) REVERT: D 50 LYS cc_start: 0.8362 (mtpp) cc_final: 0.8070 (mtmt) REVERT: D 51 ASP cc_start: 0.8557 (m-30) cc_final: 0.7943 (p0) REVERT: D 57 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7645 (mm-30) REVERT: D 72 GLU cc_start: 0.8111 (tt0) cc_final: 0.7489 (mp0) REVERT: D 100 GLU cc_start: 0.8218 (mt-10) cc_final: 0.8015 (mm-30) REVERT: D 107 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8658 (tt0) REVERT: D 122 ILE cc_start: 0.8230 (mm) cc_final: 0.7973 (mp) REVERT: D 132 MET cc_start: 0.8822 (ppp) cc_final: 0.8553 (ptm) REVERT: D 206 ARG cc_start: 0.7587 (ttt180) cc_final: 0.7307 (ttm110) REVERT: D 276 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7922 (mt-10) REVERT: D 283 MET cc_start: 0.8977 (mmm) cc_final: 0.8616 (mmt) REVERT: D 299 MET cc_start: 0.9198 (mtm) cc_final: 0.8957 (mtt) REVERT: D 323 SER cc_start: 0.8796 (p) cc_final: 0.8470 (t) REVERT: D 325 MET cc_start: 0.7308 (mmt) cc_final: 0.6988 (mmp) REVERT: D 352 PHE cc_start: 0.5519 (m-80) cc_final: 0.4054 (m-80) REVERT: D 356 TRP cc_start: 0.5417 (m100) cc_final: 0.4865 (m-10) REVERT: D 360 GLN cc_start: 0.7285 (tp40) cc_final: 0.6459 (pm20) REVERT: P 13 VAL cc_start: 0.5842 (m) cc_final: 0.5577 (m) REVERT: P 14 GLN cc_start: 0.7152 (pt0) cc_final: 0.6233 (mt0) REVERT: P 30 GLU cc_start: 0.6151 (tm-30) cc_final: 0.5628 (tp30) REVERT: P 66 MET cc_start: 0.6094 (mtt) cc_final: 0.5531 (mtt) REVERT: P 102 MET cc_start: 0.8419 (mtp) cc_final: 0.8029 (mtm) REVERT: P 104 SER cc_start: 0.7256 (t) cc_final: 0.6873 (p) REVERT: P 113 GLU cc_start: 0.7249 (tp30) cc_final: 0.6979 (mp0) REVERT: P 117 ARG cc_start: 0.6881 (mmt180) cc_final: 0.6498 (mmt-90) REVERT: P 120 GLN cc_start: 0.6197 (tt0) cc_final: 0.5731 (mm-40) REVERT: P 183 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7517 (tt) REVERT: P 199 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7561 (mt-10) REVERT: P 213 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.5980 (mp0) REVERT: P 230 LEU cc_start: 0.8414 (mp) cc_final: 0.8113 (mt) REVERT: P 254 LYS cc_start: 0.7557 (ttmt) cc_final: 0.7030 (mppt) REVERT: P 265 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6963 (mt-10) REVERT: P 298 ASN cc_start: 0.7119 (t0) cc_final: 0.6427 (m110) REVERT: P 337 GLU cc_start: 0.7145 (mp0) cc_final: 0.6756 (mp0) REVERT: P 395 HIS cc_start: 0.7382 (m-70) cc_final: 0.6468 (t-90) REVERT: P 399 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6958 (pm20) REVERT: P 427 GLU cc_start: 0.6595 (mt-10) cc_final: 0.6369 (mt-10) REVERT: P 446 ASP cc_start: 0.8055 (m-30) cc_final: 0.7533 (m-30) REVERT: P 472 LEU cc_start: 0.8175 (mt) cc_final: 0.7964 (mm) REVERT: P 476 GLU cc_start: 0.7009 (tt0) cc_final: 0.6653 (tt0) REVERT: P 480 ASP cc_start: 0.7721 (t0) cc_final: 0.7299 (m-30) REVERT: P 492 LYS cc_start: 0.8250 (tttp) cc_final: 0.7695 (tptp) REVERT: P 553 LYS cc_start: 0.7798 (mmtm) cc_final: 0.7287 (mmtm) REVERT: P 570 LYS cc_start: 0.7634 (tttt) cc_final: 0.7289 (tttm) REVERT: P 584 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6821 (mt-10) REVERT: P 598 GLN cc_start: 0.7617 (tt0) cc_final: 0.7213 (tm-30) REVERT: P 604 GLU cc_start: 0.6819 (tt0) cc_final: 0.6616 (tm-30) REVERT: P 675 MET cc_start: 0.8260 (mmt) cc_final: 0.7856 (mmm) REVERT: R 83 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8164 (tp30) outliers start: 56 outliers final: 25 residues processed: 248 average time/residue: 1.4733 time to fit residues: 398.3520 Evaluate side-chains 238 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 1.786 ------------------------------------------------------------------------------- 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 191 LYS Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 232 SER 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 351 THR Chi-restraints excluded: chain D residue 370 VAL 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 199 GLU 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 1 MET 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 135 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 184 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN D 121 GLN P 53 ASN P 181 HIS ** P 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 534 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.153592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113773 restraints weight = 18292.995| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.93 r_work: 0.3134 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 15987 Z= 0.197 Angle : 0.621 11.156 21632 Z= 0.310 Chirality : 0.045 0.180 2380 Planarity : 0.004 0.040 2793 Dihedral : 7.616 136.349 2192 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.57 % Favored : 97.38 % Rotamer: Outliers : 3.38 % Allowed : 13.00 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.19), residues: 1949 helix: 0.68 (0.17), residues: 940 sheet: -0.11 (0.32), residues: 242 loop : 0.66 (0.24), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 340 HIS 0.010 0.001 HIS C 161 PHE 0.013 0.002 PHE B 127 TYR 0.019 0.002 TYR P 438 ARG 0.006 0.000 ARG P 601 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 811) hydrogen bonds : angle 4.91965 ( 2214) covalent geometry : bond 0.00474 (15987) covalent geometry : angle 0.62097 (21632) *********************** 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 270 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 213 time to evaluate : 1.812 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: 0.8496 (mtt180) cc_final: 0.8134 (mtt-85) REVERT: B 50 LYS cc_start: 0.8227 (mttt) cc_final: 0.7939 (mtpm) REVERT: B 68 LYS cc_start: 0.8858 (mttt) cc_final: 0.7918 (mtmp) REVERT: B 91 TYR cc_start: 0.7568 (m-80) cc_final: 0.6652 (t80) REVERT: B 129 VAL cc_start: 0.8677 (OUTLIER) cc_final: 0.8323 (p) REVERT: B 176 MET cc_start: 0.8963 (mtp) cc_final: 0.8491 (mtp) REVERT: B 206 ARG cc_start: 0.8090 (ttt180) cc_final: 0.7634 (ttm-80) REVERT: B 283 MET cc_start: 0.8835 (mmm) cc_final: 0.8389 (mmt) REVERT: B 326 LYS cc_start: 0.8119 (mmmt) cc_final: 0.7645 (mmtp) REVERT: B 328 LYS cc_start: 0.8332 (mmmt) cc_final: 0.7741 (mppt) REVERT: C 50 LYS cc_start: 0.8206 (mmmm) cc_final: 0.7489 (mttt) REVERT: C 57 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7780 (tt0) REVERT: C 68 LYS cc_start: 0.8830 (mttp) cc_final: 0.8406 (mtpp) REVERT: C 72 GLU cc_start: 0.7787 (tt0) cc_final: 0.7314 (mt-10) REVERT: C 82 MET cc_start: 0.8965 (tpt) cc_final: 0.8127 (tpt) REVERT: C 95 ARG cc_start: 0.8565 (mtp85) cc_final: 0.8200 (mtt180) REVERT: C 162 ASN cc_start: 0.8779 (OUTLIER) cc_final: 0.8508 (m110) REVERT: C 191 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8275 (ttmm) REVERT: C 206 ARG cc_start: 0.7793 (ttt180) cc_final: 0.7183 (ttm-80) REVERT: C 211 ASP cc_start: 0.7942 (m-30) cc_final: 0.7595 (t70) REVERT: C 290 ARG cc_start: 0.6465 (mtt180) cc_final: 0.5630 (mtt90) REVERT: C 323 SER cc_start: 0.8701 (p) cc_final: 0.8268 (t) REVERT: C 326 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7767 (mmtt) REVERT: C 336 LYS cc_start: 0.8280 (tttt) cc_final: 0.7997 (ttmt) REVERT: C 354 GLN cc_start: 0.8401 (mm-40) cc_final: 0.7843 (mp-120) REVERT: C 355 MET cc_start: 0.8502 (mmm) cc_final: 0.8245 (mpp) REVERT: D 50 LYS cc_start: 0.8359 (mtpp) cc_final: 0.8079 (mtmt) REVERT: D 51 ASP cc_start: 0.8554 (m-30) cc_final: 0.7944 (p0) REVERT: D 57 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7544 (mt-10) REVERT: D 72 GLU cc_start: 0.8132 (tt0) cc_final: 0.7504 (mp0) REVERT: D 100 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7941 (mm-30) REVERT: D 107 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8611 (tt0) REVERT: D 122 ILE cc_start: 0.8220 (mm) cc_final: 0.7959 (mp) REVERT: D 132 MET cc_start: 0.8837 (ppp) cc_final: 0.8570 (ptm) REVERT: D 206 ARG cc_start: 0.7629 (ttt180) cc_final: 0.7358 (ttm110) REVERT: D 276 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7951 (mt-10) REVERT: D 283 MET cc_start: 0.8992 (mmm) cc_final: 0.8623 (mmt) REVERT: D 299 MET cc_start: 0.9261 (mtm) cc_final: 0.9021 (mtt) REVERT: D 323 SER cc_start: 0.8804 (OUTLIER) cc_final: 0.8477 (t) REVERT: D 325 MET cc_start: 0.7338 (mmt) cc_final: 0.7057 (mmp) REVERT: D 352 PHE cc_start: 0.5431 (m-80) cc_final: 0.4135 (m-80) REVERT: D 356 TRP cc_start: 0.5457 (m100) cc_final: 0.4908 (m-10) REVERT: D 360 GLN cc_start: 0.7269 (tp40) cc_final: 0.6492 (pm20) REVERT: P 13 VAL cc_start: 0.5984 (m) cc_final: 0.5703 (m) REVERT: P 14 GLN cc_start: 0.7172 (pt0) cc_final: 0.6239 (mt0) REVERT: P 30 GLU cc_start: 0.6146 (tm-30) cc_final: 0.5640 (tp30) REVERT: P 66 MET cc_start: 0.6024 (mtt) cc_final: 0.5659 (mtt) REVERT: P 97 ARG cc_start: 0.6335 (OUTLIER) cc_final: 0.5977 (ttt180) REVERT: P 102 MET cc_start: 0.8486 (mtp) cc_final: 0.8110 (mtm) REVERT: P 104 SER cc_start: 0.7244 (t) cc_final: 0.6857 (p) REVERT: P 113 GLU cc_start: 0.7246 (tp30) cc_final: 0.6964 (mp0) REVERT: P 117 ARG cc_start: 0.6873 (mmt180) cc_final: 0.6447 (mmt-90) REVERT: P 120 GLN cc_start: 0.6097 (tt0) cc_final: 0.5625 (mm-40) REVERT: P 156 ARG cc_start: 0.7428 (tpp80) cc_final: 0.6319 (ttm170) REVERT: P 183 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7527 (tt) REVERT: P 213 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.6010 (mp0) REVERT: P 215 GLU cc_start: 0.6102 (pm20) cc_final: 0.5821 (pm20) REVERT: P 230 LEU cc_start: 0.8426 (mp) cc_final: 0.8116 (mt) REVERT: P 254 LYS cc_start: 0.7578 (ttmt) cc_final: 0.7053 (mppt) REVERT: P 265 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6895 (mt-10) REVERT: P 298 ASN cc_start: 0.7112 (t0) cc_final: 0.6415 (m110) REVERT: P 337 GLU cc_start: 0.7150 (mp0) cc_final: 0.6770 (mp0) REVERT: P 395 HIS cc_start: 0.7396 (m-70) cc_final: 0.6483 (t-90) REVERT: P 399 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6943 (pm20) REVERT: P 427 GLU cc_start: 0.6586 (mt-10) cc_final: 0.6365 (mt-10) REVERT: P 446 ASP cc_start: 0.7776 (m-30) cc_final: 0.7233 (m-30) REVERT: P 476 GLU cc_start: 0.7033 (tt0) cc_final: 0.6666 (tt0) REVERT: P 480 ASP cc_start: 0.7742 (t0) cc_final: 0.7317 (m-30) REVERT: P 492 LYS cc_start: 0.8296 (tttp) cc_final: 0.7719 (tptp) REVERT: P 553 LYS cc_start: 0.7815 (mmtm) cc_final: 0.7334 (mmtm) REVERT: P 570 LYS cc_start: 0.7633 (tttt) cc_final: 0.7296 (tttm) REVERT: P 584 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6880 (mt-10) REVERT: P 598 GLN cc_start: 0.7625 (tt0) cc_final: 0.7204 (tm-30) REVERT: P 675 MET cc_start: 0.8260 (mmt) cc_final: 0.7859 (mmm) REVERT: P 688 LEU cc_start: 0.5372 (OUTLIER) cc_final: 0.5169 (tm) REVERT: R 37 MET cc_start: 0.6080 (mtp) cc_final: 0.5788 (mtp) REVERT: R 83 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8143 (tp30) outliers start: 57 outliers final: 32 residues processed: 250 average time/residue: 1.4723 time to fit residues: 401.3392 Evaluate side-chains 252 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 206 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 248 ILE 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 57 GLU 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 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 77 VAL Chi-restraints excluded: chain P residue 97 ARG 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 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 688 LEU Chi-restraints excluded: chain R residue 1 MET 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 187 optimal weight: 40.0000 chunk 6 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 180 optimal weight: 40.0000 chunk 182 optimal weight: 50.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN C 162 ASN D 121 GLN ** P 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 534 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.152101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112014 restraints weight = 18307.582| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.02 r_work: 0.3125 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 15987 Z= 0.268 Angle : 0.673 10.605 21632 Z= 0.335 Chirality : 0.048 0.205 2380 Planarity : 0.005 0.057 2793 Dihedral : 7.774 136.902 2192 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.77 % Favored : 97.18 % Rotamer: Outliers : 4.09 % Allowed : 12.82 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.19), residues: 1949 helix: 0.55 (0.17), residues: 940 sheet: -0.19 (0.31), residues: 246 loop : 0.57 (0.24), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 340 HIS 0.007 0.001 HIS C 161 PHE 0.029 0.002 PHE P 173 TYR 0.019 0.002 TYR P 438 ARG 0.005 0.001 ARG P 601 Details of bonding type rmsd hydrogen bonds : bond 0.04130 ( 811) hydrogen bonds : angle 5.04657 ( 2214) covalent geometry : bond 0.00651 (15987) covalent geometry : angle 0.67295 (21632) *********************** 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 286 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 217 time to evaluate : 1.868 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: 0.8499 (mtt180) cc_final: 0.8163 (mtt-85) REVERT: B 50 LYS cc_start: 0.8254 (mttt) cc_final: 0.7977 (mtpm) REVERT: B 68 LYS cc_start: 0.8877 (mttt) cc_final: 0.7905 (mtmp) REVERT: B 91 TYR cc_start: 0.7498 (m-80) cc_final: 0.6431 (t80) REVERT: B 129 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8295 (p) REVERT: B 176 MET cc_start: 0.8976 (mtp) cc_final: 0.8515 (mtp) REVERT: B 206 ARG cc_start: 0.8078 (ttt180) cc_final: 0.7621 (ttm-80) REVERT: B 283 MET cc_start: 0.8871 (mmm) cc_final: 0.8432 (mmt) REVERT: B 326 LYS cc_start: 0.8108 (mmmt) cc_final: 0.7638 (mmtp) REVERT: B 328 LYS cc_start: 0.8248 (mmmt) cc_final: 0.7637 (mppt) REVERT: C 50 LYS cc_start: 0.8213 (mmmm) cc_final: 0.7511 (mttt) REVERT: C 57 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7541 (tt0) REVERT: C 68 LYS cc_start: 0.8820 (mttp) cc_final: 0.8393 (mtpp) REVERT: C 72 GLU cc_start: 0.7977 (tt0) cc_final: 0.7353 (mt-10) REVERT: C 82 MET cc_start: 0.8978 (tpt) cc_final: 0.8166 (tpt) REVERT: C 95 ARG cc_start: 0.8593 (mtp85) cc_final: 0.8230 (mtt180) REVERT: C 206 ARG cc_start: 0.7785 (ttt180) cc_final: 0.7163 (ttm-80) REVERT: C 211 ASP cc_start: 0.7983 (m-30) cc_final: 0.7658 (t70) REVERT: C 287 ILE cc_start: 0.5424 (OUTLIER) cc_final: 0.4604 (tt) REVERT: C 290 ARG cc_start: 0.6590 (mtt180) cc_final: 0.5744 (mtt90) REVERT: C 323 SER cc_start: 0.8698 (p) cc_final: 0.8272 (t) REVERT: C 326 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7743 (mmtt) REVERT: C 336 LYS cc_start: 0.8296 (tttt) cc_final: 0.8013 (ttmt) REVERT: C 354 GLN cc_start: 0.8409 (mm-40) cc_final: 0.7849 (mp-120) REVERT: C 355 MET cc_start: 0.8574 (mmm) cc_final: 0.8258 (mpp) REVERT: D 50 LYS cc_start: 0.8352 (mtpp) cc_final: 0.8061 (mttt) REVERT: D 51 ASP cc_start: 0.8612 (m-30) cc_final: 0.7970 (p0) REVERT: D 57 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7552 (mt-10) REVERT: D 72 GLU cc_start: 0.8132 (tt0) cc_final: 0.7510 (mp0) REVERT: D 100 GLU cc_start: 0.8214 (mt-10) cc_final: 0.8003 (mm-30) REVERT: D 122 ILE cc_start: 0.8051 (mm) cc_final: 0.7792 (mp) REVERT: D 132 MET cc_start: 0.8798 (ppp) cc_final: 0.8535 (ptm) REVERT: D 176 MET cc_start: 0.9054 (mmt) cc_final: 0.8761 (mmt) REVERT: D 206 ARG cc_start: 0.7647 (ttt180) cc_final: 0.7394 (ttm110) REVERT: D 276 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7910 (mt-10) REVERT: D 283 MET cc_start: 0.8994 (mmm) cc_final: 0.8677 (mmt) REVERT: D 289 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8480 (pt) REVERT: D 299 MET cc_start: 0.9295 (mtm) cc_final: 0.9057 (mtt) REVERT: D 323 SER cc_start: 0.8874 (OUTLIER) cc_final: 0.8578 (t) REVERT: D 325 MET cc_start: 0.7277 (mmt) cc_final: 0.6940 (mmp) REVERT: D 352 PHE cc_start: 0.5306 (m-80) cc_final: 0.3887 (m-80) REVERT: D 356 TRP cc_start: 0.5543 (m100) cc_final: 0.4945 (m-10) REVERT: D 360 GLN cc_start: 0.7178 (tp40) cc_final: 0.6455 (pm20) REVERT: P 13 VAL cc_start: 0.6127 (m) cc_final: 0.5837 (m) REVERT: P 14 GLN cc_start: 0.7325 (pt0) cc_final: 0.6227 (mt0) REVERT: P 18 LEU cc_start: 0.7713 (mt) cc_final: 0.7353 (mm) REVERT: P 24 SER cc_start: 0.8191 (t) cc_final: 0.7871 (t) REVERT: P 30 GLU cc_start: 0.6173 (tm-30) cc_final: 0.5685 (tp30) REVERT: P 66 MET cc_start: 0.6099 (mtt) cc_final: 0.5664 (mtt) REVERT: P 97 ARG cc_start: 0.6367 (OUTLIER) cc_final: 0.6051 (ttt180) REVERT: P 102 MET cc_start: 0.8450 (mtp) cc_final: 0.8120 (mtm) REVERT: P 104 SER cc_start: 0.7247 (t) cc_final: 0.6853 (p) REVERT: P 113 GLU cc_start: 0.7226 (tp30) cc_final: 0.6977 (mp0) REVERT: P 117 ARG cc_start: 0.6895 (mmt180) cc_final: 0.6479 (mmt-90) REVERT: P 120 GLN cc_start: 0.5841 (tt0) cc_final: 0.5343 (mm-40) REVERT: P 156 ARG cc_start: 0.7458 (tpp80) cc_final: 0.6342 (ttm170) REVERT: P 183 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7533 (tt) REVERT: P 199 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7613 (mt-10) REVERT: P 213 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.5999 (mp0) REVERT: P 215 GLU cc_start: 0.6187 (pm20) cc_final: 0.5835 (pm20) REVERT: P 230 LEU cc_start: 0.8449 (mp) cc_final: 0.8075 (mt) REVERT: P 254 LYS cc_start: 0.7546 (ttmt) cc_final: 0.7030 (mppt) REVERT: P 265 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6912 (mt-10) REVERT: P 298 ASN cc_start: 0.7412 (t0) cc_final: 0.6648 (m110) REVERT: P 329 GLU cc_start: 0.8125 (pt0) cc_final: 0.7332 (pt0) REVERT: P 337 GLU cc_start: 0.7166 (mp0) cc_final: 0.6794 (mp0) REVERT: P 394 GLN cc_start: 0.7655 (mp10) cc_final: 0.7267 (mp10) REVERT: P 395 HIS cc_start: 0.7386 (m-70) cc_final: 0.6472 (t-90) REVERT: P 399 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6974 (pm20) REVERT: P 427 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6496 (mt-10) REVERT: P 446 ASP cc_start: 0.7739 (m-30) cc_final: 0.7150 (m-30) REVERT: P 476 GLU cc_start: 0.7055 (tt0) cc_final: 0.6705 (tt0) REVERT: P 480 ASP cc_start: 0.7626 (t0) cc_final: 0.7182 (m-30) REVERT: P 492 LYS cc_start: 0.8302 (tttp) cc_final: 0.7678 (tptp) REVERT: P 553 LYS cc_start: 0.7819 (mmtm) cc_final: 0.7274 (mmtm) REVERT: P 570 LYS cc_start: 0.7673 (tttt) cc_final: 0.7324 (tttm) REVERT: P 584 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6877 (mt-10) REVERT: P 598 GLN cc_start: 0.7571 (tt0) cc_final: 0.7288 (tt0) REVERT: P 602 PHE cc_start: 0.7396 (t80) cc_final: 0.7169 (t80) REVERT: P 675 MET cc_start: 0.8281 (mmt) cc_final: 0.8034 (mmt) REVERT: R 37 MET cc_start: 0.5555 (mtp) cc_final: 0.5208 (mtp) outliers start: 69 outliers final: 35 residues processed: 263 average time/residue: 1.5049 time to fit residues: 433.0367 Evaluate side-chains 256 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 1.632 ------------------------------------------------------------------------------- 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 57 GLU 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 248 ILE Chi-restraints excluded: chain D residue 289 ILE 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 97 ARG 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 199 GLU 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 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 1 MET Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 145 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 0.0980 chunk 107 optimal weight: 0.6980 chunk 30 optimal weight: 0.0980 chunk 47 optimal weight: 0.5980 chunk 89 optimal weight: 0.2980 chunk 117 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 193 optimal weight: 40.0000 chunk 99 optimal weight: 0.1980 overall best weight: 0.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN D 121 GLN D 162 ASN 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 = 0.3781 r_free = 0.3781 target = 0.155643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116402 restraints weight = 18309.758| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.02 r_work: 0.3181 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3225 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= 0.120 Angle : 0.578 13.075 21632 Z= 0.283 Chirality : 0.042 0.175 2380 Planarity : 0.004 0.036 2793 Dihedral : 7.411 141.002 2192 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.36 % Favored : 97.59 % Rotamer: Outliers : 2.26 % Allowed : 14.72 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.19), residues: 1949 helix: 0.82 (0.17), residues: 954 sheet: -0.08 (0.32), residues: 238 loop : 0.69 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.004 0.001 HIS C 161 PHE 0.015 0.001 PHE R 17 TYR 0.017 0.001 TYR P 438 ARG 0.005 0.000 ARG P 608 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 811) hydrogen bonds : angle 4.75476 ( 2214) covalent geometry : bond 0.00272 (15987) covalent geometry : angle 0.57792 (21632) *********************** 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 254 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8460 (mtt180) cc_final: 0.8113 (mtt-85) REVERT: B 50 LYS cc_start: 0.8159 (mttt) cc_final: 0.7939 (mtpm) REVERT: B 68 LYS cc_start: 0.8848 (mttt) cc_final: 0.7905 (mtmp) REVERT: B 91 TYR cc_start: 0.7452 (m-80) cc_final: 0.6406 (t80) REVERT: B 176 MET cc_start: 0.8894 (mtp) cc_final: 0.8535 (mtp) REVERT: B 206 ARG cc_start: 0.8002 (ttt180) cc_final: 0.7558 (ttm-80) REVERT: B 267 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7771 (pt) REVERT: B 283 MET cc_start: 0.8739 (mmm) cc_final: 0.8321 (mmt) REVERT: B 328 LYS cc_start: 0.8241 (mmmt) cc_final: 0.7975 (mmmt) REVERT: C 50 LYS cc_start: 0.8185 (mmmm) cc_final: 0.7455 (mttt) REVERT: C 68 LYS cc_start: 0.8823 (mttp) cc_final: 0.8434 (mtpp) REVERT: C 72 GLU cc_start: 0.7792 (tt0) cc_final: 0.7350 (mt-10) REVERT: C 82 MET cc_start: 0.8961 (tpt) cc_final: 0.8511 (tpt) REVERT: C 95 ARG cc_start: 0.8557 (mtp85) cc_final: 0.8203 (mtt180) REVERT: C 125 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7652 (mm-30) REVERT: C 128 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8305 (m-40) REVERT: C 206 ARG cc_start: 0.7683 (ttt180) cc_final: 0.7061 (ttm-80) REVERT: C 211 ASP cc_start: 0.7899 (m-30) cc_final: 0.7522 (t70) REVERT: C 290 ARG cc_start: 0.6315 (mtt180) cc_final: 0.5615 (mtt90) REVERT: C 323 SER cc_start: 0.8652 (p) cc_final: 0.8199 (t) REVERT: C 326 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7732 (mmtt) REVERT: C 336 LYS cc_start: 0.8270 (tttt) cc_final: 0.8019 (ttmt) REVERT: C 354 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7829 (mp-120) REVERT: C 355 MET cc_start: 0.8528 (mmm) cc_final: 0.8248 (mpp) REVERT: D 50 LYS cc_start: 0.8288 (mtpp) cc_final: 0.8009 (mttt) REVERT: D 51 ASP cc_start: 0.8565 (m-30) cc_final: 0.7834 (p0) REVERT: D 57 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7519 (mt-10) REVERT: D 72 GLU cc_start: 0.8126 (tt0) cc_final: 0.7486 (mp0) REVERT: D 100 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7924 (mm-30) REVERT: D 107 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8703 (tt0) REVERT: D 122 ILE cc_start: 0.8279 (mm) cc_final: 0.8017 (mp) REVERT: D 132 MET cc_start: 0.8725 (ppp) cc_final: 0.8513 (ptm) REVERT: D 176 MET cc_start: 0.9054 (mmt) cc_final: 0.8791 (mmt) REVERT: D 276 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7921 (mt-10) REVERT: D 299 MET cc_start: 0.9268 (mtm) cc_final: 0.8986 (mtt) REVERT: D 323 SER cc_start: 0.8776 (p) cc_final: 0.8448 (t) REVERT: D 325 MET cc_start: 0.7332 (mmt) cc_final: 0.7041 (mmp) REVERT: D 352 PHE cc_start: 0.5313 (m-80) cc_final: 0.3632 (m-80) REVERT: D 355 MET cc_start: 0.8754 (mmm) cc_final: 0.8484 (mmm) REVERT: D 356 TRP cc_start: 0.5367 (m100) cc_final: 0.4989 (m-10) REVERT: D 360 GLN cc_start: 0.7136 (tp40) cc_final: 0.6444 (pm20) REVERT: P 13 VAL cc_start: 0.6026 (m) cc_final: 0.5734 (m) REVERT: P 14 GLN cc_start: 0.7053 (pt0) cc_final: 0.6214 (mt0) REVERT: P 18 LEU cc_start: 0.7458 (mt) cc_final: 0.7150 (mm) REVERT: P 24 SER cc_start: 0.8251 (t) cc_final: 0.7896 (t) REVERT: P 30 GLU cc_start: 0.6110 (tm-30) cc_final: 0.5597 (tp30) REVERT: P 66 MET cc_start: 0.5944 (mtt) cc_final: 0.5589 (mtt) REVERT: P 102 MET cc_start: 0.8382 (mtp) cc_final: 0.8168 (mtm) REVERT: P 104 SER cc_start: 0.7253 (t) cc_final: 0.6862 (p) REVERT: P 113 GLU cc_start: 0.7184 (tp30) cc_final: 0.6848 (mp0) REVERT: P 120 GLN cc_start: 0.6127 (tt0) cc_final: 0.5627 (mm-40) REVERT: P 156 ARG cc_start: 0.7395 (tpp80) cc_final: 0.6307 (ttm170) REVERT: P 183 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7573 (tt) REVERT: P 215 GLU cc_start: 0.6085 (pm20) cc_final: 0.5730 (pm20) REVERT: P 230 LEU cc_start: 0.8391 (mp) cc_final: 0.8090 (mt) REVERT: P 254 LYS cc_start: 0.7510 (ttmt) cc_final: 0.7008 (mppt) REVERT: P 298 ASN cc_start: 0.7205 (t0) cc_final: 0.6520 (m110) REVERT: P 316 GLU cc_start: 0.8027 (tt0) cc_final: 0.7642 (tt0) REVERT: P 329 GLU cc_start: 0.7996 (pt0) cc_final: 0.7776 (mt-10) REVERT: P 337 GLU cc_start: 0.7123 (mp0) cc_final: 0.6757 (mp0) REVERT: P 394 GLN cc_start: 0.7648 (mp10) cc_final: 0.7228 (mp10) REVERT: P 395 HIS cc_start: 0.7393 (m-70) cc_final: 0.6480 (t-90) REVERT: P 399 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6974 (pm20) REVERT: P 427 GLU cc_start: 0.6507 (mt-10) cc_final: 0.6293 (mt-10) REVERT: P 446 ASP cc_start: 0.7631 (m-30) cc_final: 0.7043 (m-30) REVERT: P 476 GLU cc_start: 0.6960 (tt0) cc_final: 0.6574 (tt0) REVERT: P 480 ASP cc_start: 0.7719 (t0) cc_final: 0.7319 (m-30) REVERT: P 492 LYS cc_start: 0.8326 (tttp) cc_final: 0.7690 (tptp) REVERT: P 553 LYS cc_start: 0.7811 (mmtm) cc_final: 0.7311 (mmtm) REVERT: P 570 LYS cc_start: 0.7637 (tttt) cc_final: 0.7291 (tttp) REVERT: P 584 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6685 (mt-10) REVERT: P 598 GLN cc_start: 0.7549 (tt0) cc_final: 0.7298 (tt0) REVERT: P 602 PHE cc_start: 0.7366 (t80) cc_final: 0.7133 (t80) REVERT: P 608 ARG cc_start: 0.7857 (ttm110) cc_final: 0.7572 (ttm110) REVERT: P 675 MET cc_start: 0.8227 (mmt) cc_final: 0.7798 (mmm) REVERT: P 688 LEU cc_start: 0.5042 (tm) cc_final: 0.4688 (tt) REVERT: P 691 THR cc_start: 0.4570 (m) cc_final: 0.4366 (p) REVERT: R 37 MET cc_start: 0.5487 (mtp) cc_final: 0.5196 (mtp) outliers start: 38 outliers final: 21 residues processed: 241 average time/residue: 1.5357 time to fit residues: 402.3350 Evaluate side-chains 235 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 267 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 128 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 99 GLU Chi-restraints excluded: chain D residue 107 GLU 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 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 380 THR 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 1 MET 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 60 optimal weight: 0.9980 chunk 175 optimal weight: 0.0040 chunk 110 optimal weight: 0.7980 chunk 101 optimal weight: 0.2980 chunk 183 optimal weight: 20.0000 chunk 144 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN D 121 GLN P 440 ASN P 534 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.154787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.115423 restraints weight = 18176.982| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.89 r_work: 0.3151 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15987 Z= 0.160 Angle : 0.605 13.507 21632 Z= 0.298 Chirality : 0.044 0.227 2380 Planarity : 0.004 0.036 2793 Dihedral : 7.370 137.293 2192 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.43 % Rotamer: Outliers : 2.26 % Allowed : 14.72 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.19), residues: 1949 helix: 0.86 (0.17), residues: 950 sheet: -0.12 (0.31), residues: 248 loop : 0.73 (0.24), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 340 HIS 0.005 0.001 HIS B 161 PHE 0.028 0.001 PHE P 173 TYR 0.031 0.001 TYR P 640 ARG 0.005 0.000 ARG P 608 Details of bonding type rmsd hydrogen bonds : bond 0.03439 ( 811) hydrogen bonds : angle 4.76456 ( 2214) covalent geometry : bond 0.00380 (15987) covalent geometry : angle 0.60538 (21632) *********************** 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 248 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 1.792 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: 0.8467 (mtt180) cc_final: 0.8126 (mtt-85) REVERT: B 50 LYS cc_start: 0.8209 (mttt) cc_final: 0.7972 (mtpm) REVERT: B 68 LYS cc_start: 0.8858 (mttt) cc_final: 0.7646 (mtmm) REVERT: B 91 TYR cc_start: 0.7460 (m-80) cc_final: 0.6386 (t80) REVERT: B 129 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8254 (p) REVERT: B 176 MET cc_start: 0.8908 (mtp) cc_final: 0.8558 (mtp) REVERT: B 206 ARG cc_start: 0.8027 (ttt180) cc_final: 0.7593 (ttm-80) REVERT: B 283 MET cc_start: 0.8792 (mmm) cc_final: 0.8369 (mmt) REVERT: B 328 LYS cc_start: 0.8249 (mmmt) cc_final: 0.7966 (mmmt) REVERT: C 50 LYS cc_start: 0.8215 (mmmm) cc_final: 0.7479 (mttt) REVERT: C 68 LYS cc_start: 0.8827 (mttp) cc_final: 0.8369 (mtpp) REVERT: C 72 GLU cc_start: 0.8045 (tt0) cc_final: 0.7378 (mt-10) REVERT: C 82 MET cc_start: 0.8971 (tpt) cc_final: 0.8489 (tpt) REVERT: C 95 ARG cc_start: 0.8572 (mtp85) cc_final: 0.8208 (mtt180) REVERT: C 125 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7717 (mm-30) REVERT: C 206 ARG cc_start: 0.7723 (ttt180) cc_final: 0.7130 (ttm-80) REVERT: C 211 ASP cc_start: 0.7911 (m-30) cc_final: 0.7584 (t70) REVERT: C 287 ILE cc_start: 0.5207 (OUTLIER) cc_final: 0.4472 (tt) REVERT: C 290 ARG cc_start: 0.6414 (mtt180) cc_final: 0.5707 (mtt90) REVERT: C 323 SER cc_start: 0.8669 (p) cc_final: 0.8213 (t) REVERT: C 326 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7748 (mmtt) REVERT: C 336 LYS cc_start: 0.8171 (tttt) cc_final: 0.7925 (ttmt) REVERT: C 354 GLN cc_start: 0.8406 (mm-40) cc_final: 0.7837 (mp-120) REVERT: C 355 MET cc_start: 0.8552 (mmm) cc_final: 0.8268 (mpp) REVERT: D 50 LYS cc_start: 0.8289 (mtpp) cc_final: 0.8018 (mtmt) REVERT: D 51 ASP cc_start: 0.8576 (m-30) cc_final: 0.7842 (p0) REVERT: D 57 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7529 (mt-10) REVERT: D 72 GLU cc_start: 0.8123 (tt0) cc_final: 0.7433 (mp0) REVERT: D 100 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7877 (mm-30) REVERT: D 107 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8620 (tt0) REVERT: D 122 ILE cc_start: 0.8281 (mm) cc_final: 0.8017 (mp) REVERT: D 132 MET cc_start: 0.8747 (ppp) cc_final: 0.8537 (ptm) REVERT: D 176 MET cc_start: 0.9047 (mmt) cc_final: 0.8776 (mmt) REVERT: D 276 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7935 (mt-10) REVERT: D 299 MET cc_start: 0.9265 (mtm) cc_final: 0.8985 (mtt) REVERT: D 323 SER cc_start: 0.8895 (p) cc_final: 0.8572 (t) REVERT: D 325 MET cc_start: 0.7355 (mmt) cc_final: 0.7059 (mmp) REVERT: D 352 PHE cc_start: 0.5363 (m-80) cc_final: 0.3759 (m-80) REVERT: D 356 TRP cc_start: 0.5405 (m100) cc_final: 0.5006 (m-10) REVERT: D 360 GLN cc_start: 0.7073 (tp40) cc_final: 0.6424 (pm20) REVERT: P 13 VAL cc_start: 0.6076 (m) cc_final: 0.5786 (m) REVERT: P 14 GLN cc_start: 0.7181 (pt0) cc_final: 0.6295 (mt0) REVERT: P 18 LEU cc_start: 0.7445 (mt) cc_final: 0.7143 (mm) REVERT: P 24 SER cc_start: 0.8279 (t) cc_final: 0.7917 (t) REVERT: P 30 GLU cc_start: 0.6128 (tm-30) cc_final: 0.5767 (tp30) REVERT: P 66 MET cc_start: 0.5898 (mtt) cc_final: 0.5494 (mtt) REVERT: P 102 MET cc_start: 0.8391 (mtp) cc_final: 0.8105 (mtm) REVERT: P 113 GLU cc_start: 0.7128 (tp30) cc_final: 0.6893 (mp0) REVERT: P 117 ARG cc_start: 0.6832 (mmt180) cc_final: 0.6426 (mmt-90) REVERT: P 120 GLN cc_start: 0.6463 (tt0) cc_final: 0.5714 (mm-40) REVERT: P 156 ARG cc_start: 0.7404 (tpp80) cc_final: 0.6313 (ttm170) REVERT: P 183 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7657 (tt) REVERT: P 215 GLU cc_start: 0.5996 (pm20) cc_final: 0.5649 (pm20) REVERT: P 230 LEU cc_start: 0.8381 (mp) cc_final: 0.8068 (mt) REVERT: P 254 LYS cc_start: 0.7526 (ttmt) cc_final: 0.7031 (mppt) REVERT: P 265 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6887 (mt-10) REVERT: P 298 ASN cc_start: 0.7226 (t0) cc_final: 0.6538 (m110) REVERT: P 329 GLU cc_start: 0.8023 (pt0) cc_final: 0.7751 (mt-10) REVERT: P 337 GLU cc_start: 0.7143 (mp0) cc_final: 0.6768 (mp0) REVERT: P 394 GLN cc_start: 0.7664 (mp10) cc_final: 0.7226 (mp10) REVERT: P 395 HIS cc_start: 0.7413 (m-70) cc_final: 0.6479 (t70) REVERT: P 399 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6997 (pm20) REVERT: P 427 GLU cc_start: 0.6484 (mt-10) cc_final: 0.6257 (mt-10) REVERT: P 446 ASP cc_start: 0.7758 (m-30) cc_final: 0.7168 (m-30) REVERT: P 476 GLU cc_start: 0.6988 (tt0) cc_final: 0.6573 (tt0) REVERT: P 480 ASP cc_start: 0.7732 (t0) cc_final: 0.7334 (m-30) REVERT: P 492 LYS cc_start: 0.8309 (tttp) cc_final: 0.7688 (tptp) REVERT: P 553 LYS cc_start: 0.7825 (mmtm) cc_final: 0.7339 (mmtm) REVERT: P 570 LYS cc_start: 0.7641 (tttt) cc_final: 0.7292 (tttm) REVERT: P 584 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6629 (mt-10) REVERT: P 598 GLN cc_start: 0.7564 (tt0) cc_final: 0.7310 (tt0) REVERT: P 602 PHE cc_start: 0.7443 (t80) cc_final: 0.7144 (t80) REVERT: P 608 ARG cc_start: 0.7898 (ttm110) cc_final: 0.7610 (ttm110) REVERT: P 675 MET cc_start: 0.8254 (mmt) cc_final: 0.7823 (mmm) REVERT: P 688 LEU cc_start: 0.5219 (tm) cc_final: 0.4918 (tt) REVERT: R 37 MET cc_start: 0.5531 (mtp) cc_final: 0.5233 (mtp) outliers start: 38 outliers final: 22 residues processed: 236 average time/residue: 1.5535 time to fit residues: 398.5298 Evaluate side-chains 232 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 1.761 ------------------------------------------------------------------------------- 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 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 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 72 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 379 THR Chi-restraints excluded: chain P residue 380 THR 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 1 MET 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 132 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 120 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 4 optimal weight: 0.3980 chunk 98 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN D 121 GLN P 440 ASN P 534 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.115560 restraints weight = 18188.564| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.92 r_work: 0.3189 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15987 Z= 0.153 Angle : 0.602 13.278 21632 Z= 0.294 Chirality : 0.044 0.194 2380 Planarity : 0.004 0.037 2793 Dihedral : 7.292 135.986 2192 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.43 % Rotamer: Outliers : 2.14 % Allowed : 15.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.19), residues: 1949 helix: 0.85 (0.17), residues: 954 sheet: -0.05 (0.30), residues: 248 loop : 0.76 (0.24), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 340 HIS 0.005 0.001 HIS D 161 PHE 0.013 0.001 PHE C 255 TYR 0.015 0.001 TYR P 640 ARG 0.005 0.000 ARG P 608 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 811) hydrogen bonds : angle 4.73683 ( 2214) covalent geometry : bond 0.00362 (15987) covalent geometry : angle 0.60216 (21632) *********************** 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 248 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 212 time to evaluate : 1.751 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: 0.8456 (mtt180) cc_final: 0.8117 (mtt-85) REVERT: B 50 LYS cc_start: 0.8157 (mttt) cc_final: 0.7924 (mtpm) REVERT: B 68 LYS cc_start: 0.8850 (mttt) cc_final: 0.7625 (mtmm) REVERT: B 91 TYR cc_start: 0.7451 (m-80) cc_final: 0.6367 (t80) REVERT: B 129 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8227 (p) REVERT: B 176 MET cc_start: 0.8886 (mtp) cc_final: 0.8522 (mtp) REVERT: B 206 ARG cc_start: 0.8011 (ttt180) cc_final: 0.7565 (ttm-80) REVERT: B 283 MET cc_start: 0.8751 (mmm) cc_final: 0.8372 (mmt) REVERT: B 326 LYS cc_start: 0.8735 (tmtm) cc_final: 0.8164 (tttm) REVERT: B 328 LYS cc_start: 0.8282 (mmmt) cc_final: 0.7768 (mtpt) REVERT: C 50 LYS cc_start: 0.8182 (mmmm) cc_final: 0.7442 (mttt) REVERT: C 68 LYS cc_start: 0.8818 (mttp) cc_final: 0.8358 (mtpp) REVERT: C 72 GLU cc_start: 0.8103 (tt0) cc_final: 0.7390 (mt-10) REVERT: C 82 MET cc_start: 0.8932 (tpt) cc_final: 0.8437 (tpt) REVERT: C 95 ARG cc_start: 0.8556 (mtp85) cc_final: 0.8205 (mtt180) REVERT: C 125 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7701 (mm-30) REVERT: C 128 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8305 (m-40) REVERT: C 206 ARG cc_start: 0.7684 (ttt180) cc_final: 0.7205 (ttm-80) REVERT: C 211 ASP cc_start: 0.7886 (m-30) cc_final: 0.7506 (t70) REVERT: C 287 ILE cc_start: 0.5155 (OUTLIER) cc_final: 0.4465 (tt) REVERT: C 290 ARG cc_start: 0.6350 (mtt180) cc_final: 0.5691 (mtt90) REVERT: C 323 SER cc_start: 0.8653 (p) cc_final: 0.8195 (t) REVERT: C 326 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7733 (mmtt) REVERT: C 336 LYS cc_start: 0.8192 (tttt) cc_final: 0.7941 (ttmt) REVERT: C 354 GLN cc_start: 0.8390 (mm-40) cc_final: 0.7822 (mp-120) REVERT: C 355 MET cc_start: 0.8549 (mmm) cc_final: 0.8254 (mpp) REVERT: D 50 LYS cc_start: 0.8267 (mtpp) cc_final: 0.7997 (mtmt) REVERT: D 51 ASP cc_start: 0.8561 (m-30) cc_final: 0.7813 (p0) REVERT: D 57 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7491 (mt-10) REVERT: D 72 GLU cc_start: 0.8121 (tt0) cc_final: 0.7413 (mp0) REVERT: D 100 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7863 (mm-30) REVERT: D 107 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8630 (tt0) REVERT: D 122 ILE cc_start: 0.8265 (mm) cc_final: 0.8000 (mp) REVERT: D 132 MET cc_start: 0.8729 (ppp) cc_final: 0.8506 (ptm) REVERT: D 176 MET cc_start: 0.9041 (mmt) cc_final: 0.8780 (mmt) REVERT: D 276 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7907 (mt-10) REVERT: D 323 SER cc_start: 0.8883 (OUTLIER) cc_final: 0.8549 (t) REVERT: D 325 MET cc_start: 0.7331 (mmt) cc_final: 0.7042 (mmp) REVERT: D 352 PHE cc_start: 0.5352 (m-80) cc_final: 0.3730 (m-80) REVERT: D 356 TRP cc_start: 0.5346 (m100) cc_final: 0.5046 (m-10) REVERT: D 360 GLN cc_start: 0.7035 (tp40) cc_final: 0.6412 (pm20) REVERT: P 13 VAL cc_start: 0.6060 (m) cc_final: 0.5773 (m) REVERT: P 14 GLN cc_start: 0.7184 (pt0) cc_final: 0.6292 (mt0) REVERT: P 18 LEU cc_start: 0.7671 (mt) cc_final: 0.7380 (mm) REVERT: P 24 SER cc_start: 0.8268 (t) cc_final: 0.7906 (t) REVERT: P 30 GLU cc_start: 0.6109 (tm-30) cc_final: 0.5854 (tp30) REVERT: P 66 MET cc_start: 0.5937 (mtt) cc_final: 0.5540 (mtt) REVERT: P 102 MET cc_start: 0.8384 (mtp) cc_final: 0.8139 (mtm) REVERT: P 113 GLU cc_start: 0.7134 (tp30) cc_final: 0.6884 (mp0) REVERT: P 117 ARG cc_start: 0.6814 (mmt180) cc_final: 0.6372 (mmt-90) REVERT: P 120 GLN cc_start: 0.6198 (tt0) cc_final: 0.5556 (mm-40) REVERT: P 156 ARG cc_start: 0.7400 (tpp80) cc_final: 0.6295 (ttm170) REVERT: P 183 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7666 (tt) REVERT: P 215 GLU cc_start: 0.6101 (pm20) cc_final: 0.5727 (pm20) REVERT: P 230 LEU cc_start: 0.8358 (mp) cc_final: 0.8048 (mt) REVERT: P 254 LYS cc_start: 0.7538 (ttmt) cc_final: 0.7005 (mppt) REVERT: P 265 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6904 (mt-10) REVERT: P 298 ASN cc_start: 0.7195 (t0) cc_final: 0.6522 (m110) REVERT: P 329 GLU cc_start: 0.8066 (pt0) cc_final: 0.7822 (mt-10) REVERT: P 337 GLU cc_start: 0.7113 (mp0) cc_final: 0.6733 (mp0) REVERT: P 394 GLN cc_start: 0.7661 (mp10) cc_final: 0.7216 (mp10) REVERT: P 395 HIS cc_start: 0.7412 (m-70) cc_final: 0.6462 (t70) REVERT: P 399 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6958 (pm20) REVERT: P 427 GLU cc_start: 0.6548 (mt-10) cc_final: 0.6334 (mt-10) REVERT: P 446 ASP cc_start: 0.7570 (m-30) cc_final: 0.6947 (m-30) REVERT: P 476 GLU cc_start: 0.6955 (tt0) cc_final: 0.6542 (tt0) REVERT: P 480 ASP cc_start: 0.7711 (t0) cc_final: 0.7317 (m-30) REVERT: P 492 LYS cc_start: 0.8306 (tttp) cc_final: 0.7673 (tptp) REVERT: P 553 LYS cc_start: 0.7810 (mmtm) cc_final: 0.7339 (mmtm) REVERT: P 570 LYS cc_start: 0.7605 (tttt) cc_final: 0.7255 (tttp) REVERT: P 584 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6544 (mt-10) REVERT: P 598 GLN cc_start: 0.7560 (tt0) cc_final: 0.7310 (tt0) REVERT: P 602 PHE cc_start: 0.7440 (t80) cc_final: 0.7146 (t80) REVERT: P 608 ARG cc_start: 0.7898 (ttm110) cc_final: 0.7595 (ttm110) REVERT: P 675 MET cc_start: 0.8327 (mmt) cc_final: 0.7861 (mmm) REVERT: R 37 MET cc_start: 0.5430 (mtp) cc_final: 0.5159 (mtp) outliers start: 36 outliers final: 22 residues processed: 236 average time/residue: 1.5222 time to fit residues: 394.5746 Evaluate side-chains 234 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 1.765 ------------------------------------------------------------------------------- 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 128 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 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 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 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 584 GLU Chi-restraints excluded: chain P residue 687 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 64 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 173 optimal weight: 0.4980 chunk 152 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 chunk 161 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 193 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 126 optimal weight: 0.0980 chunk 66 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN D 121 GLN P 440 ASN P 534 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.154509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.114579 restraints weight = 18314.322| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.98 r_work: 0.3157 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 15987 Z= 0.171 Angle : 0.618 13.436 21632 Z= 0.302 Chirality : 0.044 0.209 2380 Planarity : 0.004 0.066 2793 Dihedral : 7.321 134.163 2192 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.72 % Favored : 97.23 % Rotamer: Outliers : 1.96 % Allowed : 15.43 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.19), residues: 1949 helix: 0.85 (0.17), residues: 954 sheet: -0.03 (0.30), residues: 248 loop : 0.71 (0.24), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 340 HIS 0.005 0.001 HIS D 161 PHE 0.027 0.002 PHE P 173 TYR 0.019 0.001 TYR P 640 ARG 0.006 0.000 ARG P 624 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 811) hydrogen bonds : angle 4.77163 ( 2214) covalent geometry : bond 0.00408 (15987) covalent geometry : angle 0.61820 (21632) ********************** 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 236 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 1.637 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: 0.8464 (mtt180) cc_final: 0.8102 (mtt-85) REVERT: B 50 LYS cc_start: 0.8173 (mttt) cc_final: 0.7948 (mtpm) REVERT: B 68 LYS cc_start: 0.8860 (mttt) cc_final: 0.7882 (mtmp) REVERT: B 91 TYR cc_start: 0.7454 (m-80) cc_final: 0.6355 (t80) REVERT: B 129 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8234 (p) REVERT: B 176 MET cc_start: 0.8904 (mtp) cc_final: 0.8532 (mtp) REVERT: B 206 ARG cc_start: 0.8027 (ttt180) cc_final: 0.7577 (ttm-80) REVERT: B 283 MET cc_start: 0.8769 (mmm) cc_final: 0.8388 (mmt) REVERT: B 326 LYS cc_start: 0.8705 (tmtm) cc_final: 0.8106 (tttm) REVERT: B 328 LYS cc_start: 0.8292 (mmmt) cc_final: 0.7721 (ttpt) REVERT: C 50 LYS cc_start: 0.8195 (mmmm) cc_final: 0.7453 (mttt) REVERT: C 68 LYS cc_start: 0.8821 (mttp) cc_final: 0.8362 (mtpp) REVERT: C 72 GLU cc_start: 0.8111 (tt0) cc_final: 0.7389 (mt-10) REVERT: C 82 MET cc_start: 0.8937 (tpt) cc_final: 0.8404 (tpt) REVERT: C 95 ARG cc_start: 0.8567 (mtp85) cc_final: 0.8213 (mtt180) REVERT: C 125 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7683 (mm-30) REVERT: C 128 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8302 (m-40) REVERT: C 206 ARG cc_start: 0.7693 (ttt180) cc_final: 0.7094 (ttm-80) REVERT: C 211 ASP cc_start: 0.7898 (m-30) cc_final: 0.7519 (t70) REVERT: C 287 ILE cc_start: 0.5367 (OUTLIER) cc_final: 0.4709 (tt) REVERT: C 290 ARG cc_start: 0.6182 (mtt180) cc_final: 0.5481 (mtt90) REVERT: C 323 SER cc_start: 0.8663 (p) cc_final: 0.8206 (t) REVERT: C 326 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7748 (mmtt) REVERT: C 354 GLN cc_start: 0.8398 (mm-40) cc_final: 0.7826 (mp-120) REVERT: C 355 MET cc_start: 0.8564 (mmm) cc_final: 0.8253 (mpp) REVERT: D 50 LYS cc_start: 0.8258 (mtpp) cc_final: 0.7996 (mtmt) REVERT: D 51 ASP cc_start: 0.8564 (m-30) cc_final: 0.7808 (p0) REVERT: D 57 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7496 (mt-10) REVERT: D 72 GLU cc_start: 0.8115 (tt0) cc_final: 0.7392 (mp0) REVERT: D 100 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7866 (mm-30) REVERT: D 107 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8622 (tt0) REVERT: D 122 ILE cc_start: 0.8248 (mm) cc_final: 0.7976 (mp) REVERT: D 132 MET cc_start: 0.8721 (ppp) cc_final: 0.8508 (ptm) REVERT: D 176 MET cc_start: 0.9040 (mmt) cc_final: 0.8776 (mmt) REVERT: D 276 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7931 (mt-10) REVERT: D 323 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.8534 (t) REVERT: D 325 MET cc_start: 0.7329 (mmt) cc_final: 0.7038 (mmp) REVERT: D 352 PHE cc_start: 0.5201 (m-80) cc_final: 0.3769 (m-80) REVERT: D 356 TRP cc_start: 0.5401 (m100) cc_final: 0.4984 (m-10) REVERT: D 360 GLN cc_start: 0.6935 (tp40) cc_final: 0.6398 (pm20) REVERT: P 13 VAL cc_start: 0.6071 (m) cc_final: 0.5779 (m) REVERT: P 14 GLN cc_start: 0.7205 (pt0) cc_final: 0.6285 (mt0) REVERT: P 18 LEU cc_start: 0.7677 (mt) cc_final: 0.7364 (mm) REVERT: P 24 SER cc_start: 0.8256 (t) cc_final: 0.7890 (t) REVERT: P 30 GLU cc_start: 0.6098 (tm-30) cc_final: 0.5733 (tp30) REVERT: P 66 MET cc_start: 0.6108 (mtt) cc_final: 0.5735 (mtt) REVERT: P 102 MET cc_start: 0.8403 (mtp) cc_final: 0.8155 (mtm) REVERT: P 113 GLU cc_start: 0.7135 (tp30) cc_final: 0.6771 (mp0) REVERT: P 120 GLN cc_start: 0.6229 (tt0) cc_final: 0.5598 (mm-40) REVERT: P 156 ARG cc_start: 0.7465 (tpp80) cc_final: 0.6356 (ttm170) REVERT: P 183 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7656 (tt) REVERT: P 215 GLU cc_start: 0.6096 (pm20) cc_final: 0.5718 (pm20) REVERT: P 230 LEU cc_start: 0.8361 (mp) cc_final: 0.8052 (mt) REVERT: P 254 LYS cc_start: 0.7541 (ttmt) cc_final: 0.7008 (mppt) REVERT: P 298 ASN cc_start: 0.7236 (t0) cc_final: 0.6504 (m110) REVERT: P 323 ILE cc_start: 0.8184 (mt) cc_final: 0.7477 (mp) REVERT: P 329 GLU cc_start: 0.7869 (pt0) cc_final: 0.7581 (mt-10) REVERT: P 337 GLU cc_start: 0.7123 (mp0) cc_final: 0.6744 (mp0) REVERT: P 394 GLN cc_start: 0.7680 (mp10) cc_final: 0.7217 (mp10) REVERT: P 395 HIS cc_start: 0.7418 (m-70) cc_final: 0.6452 (t70) REVERT: P 399 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6974 (pm20) REVERT: P 427 GLU cc_start: 0.6528 (mt-10) cc_final: 0.6280 (mt-10) REVERT: P 446 ASP cc_start: 0.7564 (m-30) cc_final: 0.6934 (m-30) REVERT: P 476 GLU cc_start: 0.6950 (tt0) cc_final: 0.6551 (tt0) REVERT: P 480 ASP cc_start: 0.7604 (t0) cc_final: 0.7222 (m-30) REVERT: P 492 LYS cc_start: 0.8204 (tttp) cc_final: 0.7728 (tptp) REVERT: P 553 LYS cc_start: 0.7818 (mmtm) cc_final: 0.7320 (mmtm) REVERT: P 570 LYS cc_start: 0.7609 (tttt) cc_final: 0.7253 (tttm) REVERT: P 584 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6578 (mt-10) REVERT: P 598 GLN cc_start: 0.7575 (tt0) cc_final: 0.7313 (tt0) REVERT: P 602 PHE cc_start: 0.7441 (t80) cc_final: 0.7131 (t80) REVERT: P 608 ARG cc_start: 0.7893 (ttm110) cc_final: 0.7583 (ttm110) REVERT: P 650 MET cc_start: 0.8214 (mpp) cc_final: 0.7988 (mmp) REVERT: P 675 MET cc_start: 0.8351 (mmt) cc_final: 0.7889 (mmm) REVERT: R 37 MET cc_start: 0.5401 (mtp) cc_final: 0.5162 (mtp) outliers start: 33 outliers final: 22 residues processed: 227 average time/residue: 1.4924 time to fit residues: 368.8241 Evaluate side-chains 231 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 1.729 ------------------------------------------------------------------------------- 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 128 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 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 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 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 584 GLU Chi-restraints excluded: chain P residue 687 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 64 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 34 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 48 optimal weight: 0.0770 chunk 11 optimal weight: 0.1980 chunk 149 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN D 121 GLN P 440 ASN P 534 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.155720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116492 restraints weight = 18191.112| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.87 r_work: 0.3184 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15987 Z= 0.135 Angle : 0.589 14.119 21632 Z= 0.287 Chirality : 0.043 0.201 2380 Planarity : 0.004 0.047 2793 Dihedral : 7.161 132.165 2192 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.43 % Rotamer: Outliers : 1.72 % Allowed : 15.55 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 1949 helix: 0.96 (0.17), residues: 952 sheet: -0.01 (0.30), residues: 249 loop : 0.74 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 340 HIS 0.004 0.001 HIS D 161 PHE 0.014 0.001 PHE R 17 TYR 0.018 0.001 TYR P 640 ARG 0.004 0.000 ARG P 608 Details of bonding type rmsd hydrogen bonds : bond 0.03214 ( 811) hydrogen bonds : angle 4.66866 ( 2214) covalent geometry : bond 0.00316 (15987) covalent geometry : angle 0.58912 (21632) =============================================================================== Job complete usr+sys time: 14810.42 seconds wall clock time: 256 minutes 53.49 seconds (15413.49 seconds total)