Starting phenix.real_space_refine on Thu Aug 6 14:14:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bc7_44426/08_2026/9bc7_44426.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bc7_44426/08_2026/9bc7_44426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bc7_44426/08_2026/9bc7_44426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bc7_44426/08_2026/9bc7_44426.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bc7_44426/08_2026/9bc7_44426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bc7_44426/08_2026/9bc7_44426.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 112 5.16 5 C 10248 2.51 5 N 2624 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15628 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3828 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 16, 'TRANS': 489} Chain breaks: 1 Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 6, 'PHE:plan': 2, 'GLU:plan': 14, 'ASP:plan': 15, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 173 Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 79 Unusual residues: {'PCW': 3} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-1': 2, 'PCW:plan-3': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 22 Restraints were copied for chains: B, C, D Time building chain proxies: 3.56, per 1000 atoms: 0.23 Number of scatterers: 15628 At special positions: 0 Unit cell: (115.838, 115.838, 127.747, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 112 16.00 P 4 15.00 O 2640 8.00 N 2624 7.00 C 10248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 710.8 milliseconds 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3856 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 8 sheets defined 72.0% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.964A pdb=" N PHE A 98 " --> pdb=" O MET A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 removed outlier: 3.557A pdb=" N LEU A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 129 removed outlier: 3.705A pdb=" N LYS A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 166 removed outlier: 3.712A pdb=" N GLY A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 172 through 194 removed outlier: 3.636A pdb=" N VAL A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 219 removed outlier: 3.574A pdb=" N MET A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 218 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 219 " --> pdb=" O MET A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 241 through 242 No H-bonds generated for 'chain 'A' and resid 241 through 242' Processing helix chain 'A' and resid 252 through 252 No H-bonds generated for 'chain 'A' and resid 252 through 252' Processing helix chain 'A' and resid 253 through 265 removed outlier: 4.163A pdb=" N VAL A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 290 removed outlier: 3.922A pdb=" N GLU A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 323 removed outlier: 3.738A pdb=" N GLY A 303 " --> pdb=" O PHE A 299 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 340 through 357 Processing helix chain 'A' and resid 368 through 401 removed outlier: 3.589A pdb=" N MET A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 421 removed outlier: 3.701A pdb=" N GLN A 413 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 415 " --> pdb=" O TYR A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 445 through 453 removed outlier: 4.032A pdb=" N ASN A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 452 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 465 Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 480 through 489 removed outlier: 3.504A pdb=" N ALA A 486 " --> pdb=" O ASN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 546 removed outlier: 4.239A pdb=" N LEU A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 576 removed outlier: 3.942A pdb=" N GLU A 575 " --> pdb=" O GLU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 594 removed outlier: 4.057A pdb=" N ARG A 580 " --> pdb=" O TYR A 576 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG A 581 " --> pdb=" O PRO A 577 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP A 589 " --> pdb=" O THR A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 606 removed outlier: 3.516A pdb=" N LEU A 602 " --> pdb=" O ASN A 598 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 107 through 115 removed outlier: 3.557A pdb=" N LEU B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 129 removed outlier: 3.705A pdb=" N LYS B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 166 removed outlier: 3.712A pdb=" N GLY B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 172 through 194 removed outlier: 3.635A pdb=" N VAL B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 219 removed outlier: 3.574A pdb=" N MET B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 218 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS B 219 " --> pdb=" O MET B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 241 through 242 No H-bonds generated for 'chain 'B' and resid 241 through 242' Processing helix chain 'B' and resid 252 through 252 No H-bonds generated for 'chain 'B' and resid 252 through 252' Processing helix chain 'B' and resid 253 through 265 removed outlier: 4.163A pdb=" N VAL B 257 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 269 Processing helix chain 'B' and resid 270 through 290 removed outlier: 3.922A pdb=" N GLU B 283 " --> pdb=" O HIS B 279 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 284 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP B 290 " --> pdb=" O HIS B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 323 removed outlier: 3.737A pdb=" N GLY B 303 " --> pdb=" O PHE B 299 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 368 through 401 removed outlier: 3.588A pdb=" N MET B 388 " --> pdb=" O THR B 384 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 421 removed outlier: 3.701A pdb=" N GLN B 413 " --> pdb=" O GLU B 409 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B 415 " --> pdb=" O TYR B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 440 Processing helix chain 'B' and resid 445 through 453 removed outlier: 4.031A pdb=" N ASN B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 452 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 453 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 465 Processing helix chain 'B' and resid 466 through 473 Processing helix chain 'B' and resid 480 through 489 removed outlier: 3.503A pdb=" N ALA B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 546 removed outlier: 4.239A pdb=" N LEU B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 576 removed outlier: 3.942A pdb=" N GLU B 575 " --> pdb=" O GLU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 594 removed outlier: 4.057A pdb=" N ARG B 580 " --> pdb=" O TYR B 576 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG B 581 " --> pdb=" O PRO B 577 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP B 589 " --> pdb=" O THR B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 606 removed outlier: 3.516A pdb=" N LEU B 602 " --> pdb=" O ASN B 598 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN B 606 " --> pdb=" O LEU B 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 100 Processing helix chain 'C' and resid 107 through 115 removed outlier: 3.557A pdb=" N LEU C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 129 removed outlier: 3.706A pdb=" N LYS C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 166 removed outlier: 3.712A pdb=" N GLY C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) Proline residue: C 161 - end of helix Processing helix chain 'C' and resid 172 through 194 removed outlier: 3.637A pdb=" N VAL C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 219 removed outlier: 3.574A pdb=" N MET C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 218 " --> pdb=" O LYS C 214 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS C 219 " --> pdb=" O MET C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 228 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 241 through 242 No H-bonds generated for 'chain 'C' and resid 241 through 242' Processing helix chain 'C' and resid 252 through 252 No H-bonds generated for 'chain 'C' and resid 252 through 252' Processing helix chain 'C' and resid 253 through 265 removed outlier: 4.163A pdb=" N VAL C 257 " --> pdb=" O ALA C 253 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 269 Processing helix chain 'C' and resid 270 through 290 removed outlier: 3.922A pdb=" N GLU C 283 " --> pdb=" O HIS C 279 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE C 284 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP C 290 " --> pdb=" O HIS C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 323 removed outlier: 3.738A pdb=" N GLY C 303 " --> pdb=" O PHE C 299 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE C 317 " --> pdb=" O GLY C 313 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 340 through 357 Processing helix chain 'C' and resid 368 through 401 removed outlier: 3.589A pdb=" N MET C 388 " --> pdb=" O THR C 384 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 421 removed outlier: 3.701A pdb=" N GLN C 413 " --> pdb=" O GLU C 409 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL C 414 " --> pdb=" O LYS C 410 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU C 415 " --> pdb=" O TYR C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 440 Processing helix chain 'C' and resid 445 through 453 removed outlier: 4.032A pdb=" N ASN C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 452 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 453 " --> pdb=" O ILE C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 465 Processing helix chain 'C' and resid 466 through 473 Processing helix chain 'C' and resid 480 through 489 removed outlier: 3.504A pdb=" N ALA C 486 " --> pdb=" O ASN C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 546 removed outlier: 4.239A pdb=" N LEU C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 576 removed outlier: 3.942A pdb=" N GLU C 575 " --> pdb=" O GLU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 594 removed outlier: 4.057A pdb=" N ARG C 580 " --> pdb=" O TYR C 576 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG C 581 " --> pdb=" O PRO C 577 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP C 589 " --> pdb=" O THR C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 606 removed outlier: 3.515A pdb=" N LEU C 602 " --> pdb=" O ASN C 598 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN C 606 " --> pdb=" O LEU C 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 107 through 115 removed outlier: 3.557A pdb=" N LEU D 111 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 129 removed outlier: 3.706A pdb=" N LYS D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 166 removed outlier: 3.712A pdb=" N GLY D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 172 through 194 removed outlier: 3.636A pdb=" N VAL D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 219 removed outlier: 3.573A pdb=" N MET D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 218 " --> pdb=" O LYS D 214 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS D 219 " --> pdb=" O MET D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 228 Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 241 through 242 No H-bonds generated for 'chain 'D' and resid 241 through 242' Processing helix chain 'D' and resid 252 through 252 No H-bonds generated for 'chain 'D' and resid 252 through 252' Processing helix chain 'D' and resid 253 through 265 removed outlier: 4.162A pdb=" N VAL D 257 " --> pdb=" O ALA D 253 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 265 " --> pdb=" O LYS D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 269 Processing helix chain 'D' and resid 270 through 290 removed outlier: 3.922A pdb=" N GLU D 283 " --> pdb=" O HIS D 279 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE D 284 " --> pdb=" O GLN D 280 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP D 290 " --> pdb=" O HIS D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 323 removed outlier: 3.738A pdb=" N GLY D 303 " --> pdb=" O PHE D 299 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE D 317 " --> pdb=" O GLY D 313 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 340 through 357 Processing helix chain 'D' and resid 368 through 401 removed outlier: 3.588A pdb=" N MET D 388 " --> pdb=" O THR D 384 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP D 401 " --> pdb=" O ILE D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 421 removed outlier: 3.700A pdb=" N GLN D 413 " --> pdb=" O GLU D 409 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 414 " --> pdb=" O LYS D 410 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU D 415 " --> pdb=" O TYR D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 440 Processing helix chain 'D' and resid 445 through 453 removed outlier: 4.032A pdb=" N ASN D 451 " --> pdb=" O GLU D 447 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU D 452 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 453 " --> pdb=" O ILE D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 465 Processing helix chain 'D' and resid 466 through 473 Processing helix chain 'D' and resid 480 through 489 removed outlier: 3.504A pdb=" N ALA D 486 " --> pdb=" O ASN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 546 removed outlier: 4.239A pdb=" N LEU D 543 " --> pdb=" O GLY D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 576 removed outlier: 3.942A pdb=" N GLU D 575 " --> pdb=" O GLU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 594 removed outlier: 4.057A pdb=" N ARG D 580 " --> pdb=" O TYR D 576 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG D 581 " --> pdb=" O PRO D 577 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP D 589 " --> pdb=" O THR D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 606 removed outlier: 3.516A pdb=" N LEU D 602 " --> pdb=" O ASN D 598 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN D 606 " --> pdb=" O LEU D 602 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.668A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.520A pdb=" N VAL A 553 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET A 530 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.668A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.521A pdb=" N VAL B 553 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET B 530 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.668A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.520A pdb=" N VAL C 553 " --> pdb=" O ILE C 502 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET C 530 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.668A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.520A pdb=" N VAL D 553 " --> pdb=" O ILE D 502 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET D 530 " --> pdb=" O VAL D 522 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2856 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: 2.66 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2376 1.29 - 1.42: 4488 1.42 - 1.55: 8931 1.55 - 1.68: 17 1.68 - 1.82: 196 Bond restraints: 16008 Sorted by residual: bond pdb=" C4 CMP D 704 " pdb=" C5 CMP D 704 " ideal model delta sigma weight residual 1.490 1.342 0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" C4 CMP B 704 " pdb=" C5 CMP B 704 " ideal model delta sigma weight residual 1.490 1.342 0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" C4 CMP A 704 " pdb=" C5 CMP A 704 " ideal model delta sigma weight residual 1.490 1.342 0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" C4 CMP C 704 " pdb=" C5 CMP C 704 " ideal model delta sigma weight residual 1.490 1.342 0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" CA ARG A 405 " pdb=" C ARG A 405 " ideal model delta sigma weight residual 1.524 1.439 0.085 1.26e-02 6.30e+03 4.54e+01 ... (remaining 16003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 17396 2.27 - 4.54: 3903 4.54 - 6.80: 337 6.80 - 9.07: 48 9.07 - 11.34: 28 Bond angle restraints: 21712 Sorted by residual: angle pdb=" N PHE D 143 " pdb=" CA PHE D 143 " pdb=" C PHE D 143 " ideal model delta sigma weight residual 111.36 117.74 -6.38 1.09e+00 8.42e-01 3.42e+01 angle pdb=" N PHE C 143 " pdb=" CA PHE C 143 " pdb=" C PHE C 143 " ideal model delta sigma weight residual 111.36 117.73 -6.37 1.09e+00 8.42e-01 3.42e+01 angle pdb=" N PHE A 143 " pdb=" CA PHE A 143 " pdb=" C PHE A 143 " ideal model delta sigma weight residual 111.36 117.73 -6.37 1.09e+00 8.42e-01 3.42e+01 angle pdb=" N PHE B 143 " pdb=" CA PHE B 143 " pdb=" C PHE B 143 " ideal model delta sigma weight residual 111.36 117.72 -6.36 1.09e+00 8.42e-01 3.41e+01 angle pdb=" N VAL C 508 " pdb=" CA VAL C 508 " pdb=" C VAL C 508 " ideal model delta sigma weight residual 108.27 116.06 -7.79 1.37e+00 5.33e-01 3.23e+01 ... (remaining 21707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.27: 9164 30.27 - 60.55: 204 60.55 - 90.82: 16 90.82 - 121.09: 0 121.09 - 151.37: 12 Dihedral angle restraints: 9396 sinusoidal: 3436 harmonic: 5960 Sorted by residual: dihedral pdb=" C5' CMP D 704 " pdb=" O5' CMP D 704 " pdb=" P CMP D 704 " pdb=" O1P CMP D 704 " ideal model delta sinusoidal sigma weight residual 60.00 -173.53 -126.47 1 2.00e+01 2.50e-03 3.83e+01 dihedral pdb=" C5' CMP A 704 " pdb=" O5' CMP A 704 " pdb=" P CMP A 704 " pdb=" O1P CMP A 704 " ideal model delta sinusoidal sigma weight residual 60.00 -173.56 -126.44 1 2.00e+01 2.50e-03 3.83e+01 dihedral pdb=" C5' CMP B 704 " pdb=" O5' CMP B 704 " pdb=" P CMP B 704 " pdb=" O1P CMP B 704 " ideal model delta sinusoidal sigma weight residual 60.00 -173.59 -126.41 1 2.00e+01 2.50e-03 3.82e+01 ... (remaining 9393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1763 0.095 - 0.191: 532 0.191 - 0.286: 105 0.286 - 0.381: 28 0.381 - 0.476: 12 Chirality restraints: 2440 Sorted by residual: chirality pdb=" CA ARG B 438 " pdb=" N ARG B 438 " pdb=" C ARG B 438 " pdb=" CB ARG B 438 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" CA ARG D 438 " pdb=" N ARG D 438 " pdb=" C ARG D 438 " pdb=" CB ARG D 438 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" CA ARG A 438 " pdb=" N ARG A 438 " pdb=" C ARG A 438 " pdb=" CB ARG A 438 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.65e+00 ... (remaining 2437 not shown) Planarity restraints: 2716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 347 " 0.100 2.00e-02 2.50e+03 5.34e-02 5.71e+01 pdb=" CG TYR C 347 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR C 347 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR C 347 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR C 347 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR C 347 " -0.029 2.00e-02 2.50e+03 pdb=" CZ TYR C 347 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 347 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 347 " 0.100 2.00e-02 2.50e+03 5.33e-02 5.68e+01 pdb=" CG TYR A 347 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 347 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR A 347 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 TYR A 347 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 347 " -0.029 2.00e-02 2.50e+03 pdb=" CZ TYR A 347 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 347 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 347 " 0.100 2.00e-02 2.50e+03 5.33e-02 5.67e+01 pdb=" CG TYR D 347 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR D 347 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR D 347 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 TYR D 347 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR D 347 " -0.029 2.00e-02 2.50e+03 pdb=" CZ TYR D 347 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 347 " 0.077 2.00e-02 2.50e+03 ... (remaining 2713 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 652 2.75 - 3.29: 15715 3.29 - 3.82: 22632 3.82 - 4.36: 28903 4.36 - 4.90: 48617 Nonbonded interactions: 116519 Sorted by model distance: nonbonded pdb=" OD2 ASP B 401 " pdb=" CD ARG C 297 " model vdw 2.210 3.440 nonbonded pdb=" OD2 ASP A 401 " pdb=" CD ARG B 297 " model vdw 2.215 3.440 nonbonded pdb=" CD ARG A 297 " pdb=" OD2 ASP D 401 " model vdw 2.218 3.440 nonbonded pdb=" OD2 ASP C 401 " pdb=" CD ARG D 297 " model vdw 2.225 3.440 nonbonded pdb=" O ALA D 507 " pdb=" CD ARG D 548 " model vdw 2.459 3.440 ... (remaining 116514 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.810 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 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 : 0.015 0.148 16008 Z= 0.922 Angle : 1.847 11.341 21712 Z= 1.220 Chirality : 0.099 0.476 2440 Planarity : 0.013 0.100 2716 Dihedral : 14.305 151.368 5540 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.55 % Allowed : 1.59 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.16), residues: 2008 helix: -1.31 (0.12), residues: 1360 sheet: 2.25 (0.39), residues: 112 loop : -0.72 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 549 TYR 0.100 0.018 TYR C 347 PHE 0.037 0.009 PHE D 141 TRP 0.056 0.014 TRP B 311 HIS 0.010 0.004 HIS B 421 Details of bonding type rmsd/Z covalent geometry : bond 0.01491 / 0.92 (16008) covalent geometry : angle 1.84704 / 1.22 (21712) hydrogen bonds : bond 0.23508 / 15.62 ( 972) hydrogen bonds : angle 7.44036 / 5.52 ( 2856) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 461 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLN cc_start: 0.5760 (mt0) cc_final: 0.5377 (tt0) REVERT: A 140 ASP cc_start: 0.7275 (m-30) cc_final: 0.6849 (m-30) REVERT: A 144 TYR cc_start: 0.6543 (m-10) cc_final: 0.6300 (m-80) REVERT: A 281 TRP cc_start: 0.5863 (t60) cc_final: 0.5267 (t60) REVERT: A 343 LYS cc_start: 0.7182 (tppp) cc_final: 0.6462 (tptt) REVERT: A 347 TYR cc_start: 0.6922 (t80) cc_final: 0.5660 (t80) REVERT: A 351 LYS cc_start: 0.7230 (ttmm) cc_final: 0.6930 (tttm) REVERT: A 361 TYR cc_start: 0.6992 (OUTLIER) cc_final: 0.5454 (m-80) REVERT: A 367 VAL cc_start: 0.8659 (t) cc_final: 0.8366 (m) REVERT: A 426 ASP cc_start: 0.7430 (p0) cc_final: 0.7147 (t0) REVERT: A 430 LYS cc_start: 0.7146 (mtpt) cc_final: 0.6832 (mtpp) REVERT: A 433 ASP cc_start: 0.7663 (t70) cc_final: 0.7430 (t0) REVERT: A 451 ASN cc_start: 0.7767 (t0) cc_final: 0.7293 (m110) REVERT: A 494 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7231 (mt-10) REVERT: A 501 TYR cc_start: 0.8367 (m-80) cc_final: 0.8133 (m-80) REVERT: A 511 LYS cc_start: 0.7876 (mttt) cc_final: 0.7256 (mtmt) REVERT: A 554 ARG cc_start: 0.7700 (ttp-170) cc_final: 0.7409 (ttp-110) REVERT: B 117 GLN cc_start: 0.5683 (mt0) cc_final: 0.5282 (tt0) REVERT: B 123 GLU cc_start: 0.5935 (tp30) cc_final: 0.5557 (tp30) REVERT: B 140 ASP cc_start: 0.7183 (m-30) cc_final: 0.6771 (m-30) REVERT: B 144 TYR cc_start: 0.6603 (m-10) cc_final: 0.6365 (m-80) REVERT: B 281 TRP cc_start: 0.5878 (t60) cc_final: 0.5258 (t60) REVERT: B 343 LYS cc_start: 0.7188 (tppp) cc_final: 0.6465 (tptt) REVERT: B 347 TYR cc_start: 0.6864 (t80) cc_final: 0.5659 (t80) REVERT: B 361 TYR cc_start: 0.6993 (OUTLIER) cc_final: 0.5452 (m-80) REVERT: B 367 VAL cc_start: 0.8653 (t) cc_final: 0.8353 (m) REVERT: B 426 ASP cc_start: 0.7435 (p0) cc_final: 0.7141 (t0) REVERT: B 430 LYS cc_start: 0.7097 (mtpt) cc_final: 0.6791 (mtpp) REVERT: B 432 HIS cc_start: 0.7058 (t70) cc_final: 0.6855 (t70) REVERT: B 433 ASP cc_start: 0.7651 (t70) cc_final: 0.7404 (t0) REVERT: B 436 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7078 (mm-30) REVERT: B 451 ASN cc_start: 0.7761 (t0) cc_final: 0.7304 (m110) REVERT: B 494 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7102 (mt-10) REVERT: B 501 TYR cc_start: 0.8384 (m-80) cc_final: 0.8139 (m-80) REVERT: B 511 LYS cc_start: 0.7925 (mttt) cc_final: 0.7393 (mtmt) REVERT: B 554 ARG cc_start: 0.7722 (ttp-170) cc_final: 0.7425 (ttp-110) REVERT: C 117 GLN cc_start: 0.5694 (mt0) cc_final: 0.5287 (tt0) REVERT: C 123 GLU cc_start: 0.5951 (tp30) cc_final: 0.5574 (tp30) REVERT: C 140 ASP cc_start: 0.7199 (m-30) cc_final: 0.6770 (m-30) REVERT: C 144 TYR cc_start: 0.6574 (m-10) cc_final: 0.6330 (m-80) REVERT: C 281 TRP cc_start: 0.5887 (t60) cc_final: 0.5289 (t60) REVERT: C 343 LYS cc_start: 0.7180 (tppp) cc_final: 0.6462 (tptt) REVERT: C 347 TYR cc_start: 0.6866 (t80) cc_final: 0.5671 (t80) REVERT: C 361 TYR cc_start: 0.7048 (OUTLIER) cc_final: 0.5464 (m-80) REVERT: C 367 VAL cc_start: 0.8660 (t) cc_final: 0.8352 (m) REVERT: C 426 ASP cc_start: 0.7426 (p0) cc_final: 0.7149 (t0) REVERT: C 430 LYS cc_start: 0.7154 (mtpt) cc_final: 0.6809 (mtpp) REVERT: C 432 HIS cc_start: 0.6982 (t70) cc_final: 0.6728 (t70) REVERT: C 433 ASP cc_start: 0.7658 (t70) cc_final: 0.7405 (t0) REVERT: C 436 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7093 (mm-30) REVERT: C 451 ASN cc_start: 0.7753 (t0) cc_final: 0.7296 (m110) REVERT: C 494 GLU cc_start: 0.7747 (mt-10) cc_final: 0.6933 (mt-10) REVERT: C 501 TYR cc_start: 0.8388 (m-80) cc_final: 0.8142 (m-80) REVERT: C 511 LYS cc_start: 0.7903 (mttt) cc_final: 0.7379 (mtmt) REVERT: C 517 HIS cc_start: 0.6444 (t70) cc_final: 0.6219 (t70) REVERT: C 554 ARG cc_start: 0.7709 (ttp-170) cc_final: 0.7419 (ttp-110) REVERT: D 117 GLN cc_start: 0.5745 (mt0) cc_final: 0.5361 (tt0) REVERT: D 123 GLU cc_start: 0.5588 (tp30) cc_final: 0.5215 (tp30) REVERT: D 140 ASP cc_start: 0.7286 (m-30) cc_final: 0.6896 (m-30) REVERT: D 144 TYR cc_start: 0.6445 (m-10) cc_final: 0.6219 (m-80) REVERT: D 281 TRP cc_start: 0.5881 (t60) cc_final: 0.5258 (t60) REVERT: D 297 ARG cc_start: 0.4764 (mtp85) cc_final: 0.4461 (mtp85) REVERT: D 343 LYS cc_start: 0.7180 (tppp) cc_final: 0.6459 (tptt) REVERT: D 347 TYR cc_start: 0.6866 (t80) cc_final: 0.5664 (t80) REVERT: D 351 LYS cc_start: 0.7237 (ttmm) cc_final: 0.6943 (tttm) REVERT: D 353 MET cc_start: 0.7961 (ptp) cc_final: 0.7759 (ptm) REVERT: D 361 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.5583 (m-80) REVERT: D 367 VAL cc_start: 0.8644 (t) cc_final: 0.8339 (m) REVERT: D 426 ASP cc_start: 0.7391 (p0) cc_final: 0.7113 (t0) REVERT: D 430 LYS cc_start: 0.7155 (mtpt) cc_final: 0.6802 (mtpp) REVERT: D 432 HIS cc_start: 0.7107 (t70) cc_final: 0.6893 (t70) REVERT: D 433 ASP cc_start: 0.7669 (t70) cc_final: 0.7419 (t0) REVERT: D 436 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7097 (mm-30) REVERT: D 451 ASN cc_start: 0.7757 (t0) cc_final: 0.7290 (m110) REVERT: D 494 GLU cc_start: 0.7741 (mt-10) cc_final: 0.6934 (mt-10) REVERT: D 501 TYR cc_start: 0.8374 (m-80) cc_final: 0.8151 (m-80) REVERT: D 511 LYS cc_start: 0.7922 (mttt) cc_final: 0.7379 (mtmt) REVERT: D 554 ARG cc_start: 0.7715 (ttp-170) cc_final: 0.7416 (ttp-110) outliers start: 8 outliers final: 0 residues processed: 469 average time/residue: 0.1414 time to fit residues: 95.5607 Evaluate side-chains 354 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 350 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain D residue 361 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 HIS A 355 HIS A 440 GLN A 482 ASN B 286 HIS B 355 HIS B 440 GLN B 482 ASN C 286 HIS C 355 HIS C 440 GLN C 482 ASN D 286 HIS D 355 HIS D 440 GLN D 482 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.168628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.139521 restraints weight = 17122.058| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.89 r_work: 0.3258 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16008 Z= 0.156 Angle : 0.701 11.363 21712 Z= 0.355 Chirality : 0.044 0.133 2440 Planarity : 0.004 0.031 2716 Dihedral : 12.623 138.623 2412 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.19 % Allowed : 6.79 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.18), residues: 2008 helix: 0.64 (0.14), residues: 1352 sheet: 2.16 (0.39), residues: 112 loop : -0.61 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 404 TYR 0.015 0.001 TYR C 576 PHE 0.015 0.001 PHE D 236 TRP 0.034 0.002 TRP C 281 HIS 0.011 0.002 HIS D 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (16008) covalent geometry : angle 0.70059 / 0.36 (21712) hydrogen bonds : bond 0.05813 / 3.95 ( 972) hydrogen bonds : angle 4.51014 / 3.34 ( 2856) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 353 time to evaluate : 0.510 Fit side-chains REVERT: A 117 GLN cc_start: 0.6149 (mt0) cc_final: 0.4929 (tp-100) REVERT: A 123 GLU cc_start: 0.6188 (tp30) cc_final: 0.5753 (tp30) REVERT: A 144 TYR cc_start: 0.6837 (m-10) cc_final: 0.6392 (m-10) REVERT: A 304 MET cc_start: 0.7576 (mmm) cc_final: 0.7338 (tpt) REVERT: A 343 LYS cc_start: 0.7889 (tppp) cc_final: 0.7565 (tptp) REVERT: A 347 TYR cc_start: 0.7682 (t80) cc_final: 0.7443 (t80) REVERT: A 367 VAL cc_start: 0.8929 (t) cc_final: 0.8727 (m) REVERT: A 404 ARG cc_start: 0.7660 (tpp80) cc_final: 0.7427 (tpp80) REVERT: A 502 ILE cc_start: 0.8370 (mt) cc_final: 0.8163 (mt) REVERT: A 517 HIS cc_start: 0.7349 (t-170) cc_final: 0.6887 (t-90) REVERT: A 530 MET cc_start: 0.6473 (OUTLIER) cc_final: 0.5979 (mtm) REVERT: A 576 TYR cc_start: 0.7300 (m-80) cc_final: 0.6993 (m-80) REVERT: A 588 ILE cc_start: 0.8010 (tp) cc_final: 0.7696 (pt) REVERT: B 117 GLN cc_start: 0.6123 (mt0) cc_final: 0.4897 (tp-100) REVERT: B 123 GLU cc_start: 0.6170 (tp30) cc_final: 0.5774 (tp30) REVERT: B 144 TYR cc_start: 0.6990 (m-10) cc_final: 0.6570 (m-10) REVERT: B 304 MET cc_start: 0.7576 (mmm) cc_final: 0.7345 (tpt) REVERT: B 343 LYS cc_start: 0.7936 (tppp) cc_final: 0.7578 (tptp) REVERT: B 347 TYR cc_start: 0.7711 (t80) cc_final: 0.7422 (t80) REVERT: B 367 VAL cc_start: 0.8934 (t) cc_final: 0.8717 (m) REVERT: B 404 ARG cc_start: 0.7614 (tpp80) cc_final: 0.7402 (tpp80) REVERT: B 473 MET cc_start: 0.7436 (ttm) cc_final: 0.7192 (ttm) REVERT: B 502 ILE cc_start: 0.8382 (mt) cc_final: 0.8161 (mt) REVERT: B 517 HIS cc_start: 0.7339 (t-170) cc_final: 0.6864 (t-90) REVERT: B 530 MET cc_start: 0.6481 (OUTLIER) cc_final: 0.6031 (mtm) REVERT: B 576 TYR cc_start: 0.7305 (m-80) cc_final: 0.6985 (m-80) REVERT: B 588 ILE cc_start: 0.7999 (tp) cc_final: 0.7676 (pt) REVERT: C 117 GLN cc_start: 0.6086 (mt0) cc_final: 0.4880 (tp-100) REVERT: C 123 GLU cc_start: 0.6281 (tp30) cc_final: 0.5890 (tp30) REVERT: C 144 TYR cc_start: 0.6991 (m-10) cc_final: 0.6565 (m-10) REVERT: C 304 MET cc_start: 0.7566 (mmm) cc_final: 0.7322 (tpt) REVERT: C 343 LYS cc_start: 0.7902 (tppp) cc_final: 0.7560 (tptp) REVERT: C 347 TYR cc_start: 0.7740 (t80) cc_final: 0.7509 (t80) REVERT: C 367 VAL cc_start: 0.8916 (t) cc_final: 0.8697 (m) REVERT: C 473 MET cc_start: 0.7457 (ttm) cc_final: 0.7214 (ttm) REVERT: C 502 ILE cc_start: 0.8371 (mt) cc_final: 0.8156 (mt) REVERT: C 517 HIS cc_start: 0.7207 (t70) cc_final: 0.6765 (t-90) REVERT: C 530 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.5998 (mtm) REVERT: C 588 ILE cc_start: 0.7982 (tp) cc_final: 0.7661 (pt) REVERT: D 117 GLN cc_start: 0.6111 (mt0) cc_final: 0.4925 (tp-100) REVERT: D 123 GLU cc_start: 0.6016 (tp30) cc_final: 0.5632 (tp30) REVERT: D 144 TYR cc_start: 0.6852 (m-10) cc_final: 0.6421 (m-10) REVERT: D 304 MET cc_start: 0.7580 (mmm) cc_final: 0.7341 (tpt) REVERT: D 343 LYS cc_start: 0.7909 (tppp) cc_final: 0.7550 (tptp) REVERT: D 347 TYR cc_start: 0.7688 (t80) cc_final: 0.7441 (t80) REVERT: D 367 VAL cc_start: 0.8941 (t) cc_final: 0.8729 (m) REVERT: D 404 ARG cc_start: 0.7593 (tpp80) cc_final: 0.7369 (tpp80) REVERT: D 502 ILE cc_start: 0.8397 (mt) cc_final: 0.8175 (mt) REVERT: D 517 HIS cc_start: 0.7366 (t-170) cc_final: 0.6869 (t-90) REVERT: D 530 MET cc_start: 0.6490 (OUTLIER) cc_final: 0.5999 (mtm) REVERT: D 576 TYR cc_start: 0.7324 (m-80) cc_final: 0.7000 (m-80) REVERT: D 588 ILE cc_start: 0.8009 (tp) cc_final: 0.7699 (pt) outliers start: 46 outliers final: 16 residues processed: 373 average time/residue: 0.1257 time to fit residues: 70.3108 Evaluate side-chains 312 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 292 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 530 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 74 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 118 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 GLN A 437 HIS A 440 GLN A 482 ASN B 398 GLN B 437 HIS B 440 GLN B 482 ASN C 136 HIS C 398 GLN C 437 HIS C 440 GLN C 482 ASN D 136 HIS D 398 GLN D 437 HIS D 440 GLN D 482 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.166290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.136934 restraints weight = 17614.508| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.81 r_work: 0.3212 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16008 Z= 0.136 Angle : 0.609 8.870 21712 Z= 0.299 Chirality : 0.042 0.137 2440 Planarity : 0.004 0.036 2716 Dihedral : 12.264 133.379 2412 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.32 % Allowed : 9.70 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.19), residues: 2008 helix: 1.07 (0.14), residues: 1392 sheet: 2.20 (0.40), residues: 112 loop : -0.65 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 554 TYR 0.013 0.001 TYR D 411 PHE 0.018 0.002 PHE D 143 TRP 0.014 0.002 TRP A 373 HIS 0.006 0.001 HIS A 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (16008) covalent geometry : angle 0.60946 / 0.30 (21712) hydrogen bonds : bond 0.04469 / 3.03 ( 972) hydrogen bonds : angle 3.99692 / 2.97 ( 2856) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 319 time to evaluate : 0.581 Fit side-chains REVERT: A 117 GLN cc_start: 0.6038 (mt0) cc_final: 0.4739 (tp-100) REVERT: A 123 GLU cc_start: 0.5969 (tp30) cc_final: 0.5580 (tp30) REVERT: A 144 TYR cc_start: 0.7055 (m-10) cc_final: 0.6828 (m-10) REVERT: A 259 PHE cc_start: 0.6925 (t80) cc_final: 0.6687 (t80) REVERT: A 304 MET cc_start: 0.7806 (mmm) cc_final: 0.7477 (tpt) REVERT: A 343 LYS cc_start: 0.8029 (tppp) cc_final: 0.7596 (tptp) REVERT: A 361 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: A 487 MET cc_start: 0.8003 (ttm) cc_final: 0.7653 (ttm) REVERT: A 517 HIS cc_start: 0.7555 (t-170) cc_final: 0.7006 (t-90) REVERT: A 530 MET cc_start: 0.6661 (OUTLIER) cc_final: 0.6299 (mtm) REVERT: A 588 ILE cc_start: 0.7992 (tp) cc_final: 0.7655 (mt) REVERT: B 117 GLN cc_start: 0.6151 (mt0) cc_final: 0.4801 (tp-100) REVERT: B 144 TYR cc_start: 0.7043 (m-10) cc_final: 0.6793 (m-10) REVERT: B 259 PHE cc_start: 0.6908 (t80) cc_final: 0.6674 (t80) REVERT: B 304 MET cc_start: 0.7790 (mmm) cc_final: 0.7466 (tpt) REVERT: B 343 LYS cc_start: 0.8054 (tppp) cc_final: 0.7620 (tptp) REVERT: B 361 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.7706 (m-80) REVERT: B 487 MET cc_start: 0.8004 (ttm) cc_final: 0.7640 (ttm) REVERT: B 517 HIS cc_start: 0.7617 (t-170) cc_final: 0.7036 (t-90) REVERT: B 530 MET cc_start: 0.6681 (OUTLIER) cc_final: 0.6322 (mtm) REVERT: B 588 ILE cc_start: 0.7958 (tp) cc_final: 0.7587 (mt) REVERT: C 117 GLN cc_start: 0.6082 (mt0) cc_final: 0.4735 (tp-100) REVERT: C 144 TYR cc_start: 0.7047 (m-10) cc_final: 0.6789 (m-10) REVERT: C 259 PHE cc_start: 0.6903 (t80) cc_final: 0.6692 (t80) REVERT: C 304 MET cc_start: 0.7772 (mmm) cc_final: 0.7448 (tpt) REVERT: C 343 LYS cc_start: 0.8035 (tppp) cc_final: 0.7600 (tptp) REVERT: C 361 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7645 (m-80) REVERT: C 487 MET cc_start: 0.8036 (ttm) cc_final: 0.7663 (ttm) REVERT: C 502 ILE cc_start: 0.8410 (mt) cc_final: 0.8198 (mt) REVERT: C 517 HIS cc_start: 0.7505 (t70) cc_final: 0.7025 (t-90) REVERT: C 530 MET cc_start: 0.6684 (OUTLIER) cc_final: 0.6314 (mtm) REVERT: C 541 ILE cc_start: 0.7638 (mm) cc_final: 0.7365 (mt) REVERT: C 588 ILE cc_start: 0.7921 (tp) cc_final: 0.7584 (mt) REVERT: D 117 GLN cc_start: 0.6007 (mt0) cc_final: 0.4674 (tp-100) REVERT: D 144 TYR cc_start: 0.7033 (m-10) cc_final: 0.6783 (m-10) REVERT: D 259 PHE cc_start: 0.6909 (t80) cc_final: 0.6694 (t80) REVERT: D 304 MET cc_start: 0.7803 (mmm) cc_final: 0.7464 (tpt) REVERT: D 343 LYS cc_start: 0.8044 (tppp) cc_final: 0.7613 (tptp) REVERT: D 361 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.7696 (m-80) REVERT: D 487 MET cc_start: 0.8024 (ttm) cc_final: 0.7658 (ttm) REVERT: D 517 HIS cc_start: 0.7617 (t-170) cc_final: 0.7049 (t-90) REVERT: D 530 MET cc_start: 0.6685 (OUTLIER) cc_final: 0.6315 (mtm) REVERT: D 588 ILE cc_start: 0.7985 (tp) cc_final: 0.7635 (mt) outliers start: 48 outliers final: 15 residues processed: 336 average time/residue: 0.1210 time to fit residues: 61.7550 Evaluate side-chains 282 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 259 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 530 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 69 optimal weight: 8.9990 chunk 127 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 152 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 chunk 166 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 158 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 HIS A 398 GLN A 432 HIS A 463 ASN A 517 HIS B 136 HIS B 432 HIS B 463 ASN B 517 HIS C 432 HIS C 463 ASN D 432 HIS D 463 ASN D 517 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.164915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.134524 restraints weight = 17613.754| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.95 r_work: 0.3190 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16008 Z= 0.132 Angle : 0.592 8.849 21712 Z= 0.286 Chirality : 0.041 0.137 2440 Planarity : 0.004 0.040 2716 Dihedral : 12.046 133.488 2412 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.60 % Allowed : 10.73 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.19), residues: 2008 helix: 1.30 (0.14), residues: 1392 sheet: 2.13 (0.41), residues: 112 loop : -0.82 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 404 TYR 0.016 0.001 TYR C 411 PHE 0.014 0.001 PHE A 143 TRP 0.012 0.002 TRP C 373 HIS 0.004 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (16008) covalent geometry : angle 0.59243 / 0.29 (21712) hydrogen bonds : bond 0.04169 / 2.83 ( 972) hydrogen bonds : angle 3.85440 / 2.86 ( 2856) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 272 time to evaluate : 0.606 Fit side-chains REVERT: A 117 GLN cc_start: 0.6197 (mt0) cc_final: 0.4853 (tp-100) REVERT: A 123 GLU cc_start: 0.5960 (tp30) cc_final: 0.5600 (tp30) REVERT: A 125 GLU cc_start: 0.6626 (tp30) cc_final: 0.6313 (tp30) REVERT: A 149 MET cc_start: 0.7731 (mmp) cc_final: 0.7335 (mmp) REVERT: A 153 MET cc_start: 0.7625 (ttm) cc_final: 0.7379 (mtt) REVERT: A 259 PHE cc_start: 0.6868 (t80) cc_final: 0.6631 (t80) REVERT: A 304 MET cc_start: 0.7860 (mmm) cc_final: 0.7507 (tpt) REVERT: A 361 TYR cc_start: 0.8304 (OUTLIER) cc_final: 0.7892 (m-80) REVERT: A 463 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.7992 (m-40) REVERT: A 473 MET cc_start: 0.6805 (OUTLIER) cc_final: 0.6112 (ttm) REVERT: A 487 MET cc_start: 0.8054 (ttm) cc_final: 0.7647 (ttm) REVERT: A 517 HIS cc_start: 0.7524 (t70) cc_final: 0.7146 (t-90) REVERT: A 530 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.6421 (mtm) REVERT: A 541 ILE cc_start: 0.7669 (mm) cc_final: 0.7371 (mt) REVERT: A 588 ILE cc_start: 0.7956 (tp) cc_final: 0.7605 (mt) REVERT: B 117 GLN cc_start: 0.6182 (mt0) cc_final: 0.4796 (tp-100) REVERT: B 125 GLU cc_start: 0.6663 (tp30) cc_final: 0.6378 (tp30) REVERT: B 144 TYR cc_start: 0.6967 (m-10) cc_final: 0.6752 (m-10) REVERT: B 149 MET cc_start: 0.7723 (mmp) cc_final: 0.7317 (mmp) REVERT: B 153 MET cc_start: 0.7624 (ttm) cc_final: 0.7374 (mtt) REVERT: B 259 PHE cc_start: 0.6869 (t80) cc_final: 0.6647 (t80) REVERT: B 304 MET cc_start: 0.7866 (mmm) cc_final: 0.7520 (tpt) REVERT: B 361 TYR cc_start: 0.8318 (OUTLIER) cc_final: 0.7891 (m-80) REVERT: B 463 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.7985 (m-40) REVERT: B 473 MET cc_start: 0.7229 (ttp) cc_final: 0.6580 (ttm) REVERT: B 487 MET cc_start: 0.8040 (ttm) cc_final: 0.7642 (ttm) REVERT: B 517 HIS cc_start: 0.7524 (t70) cc_final: 0.7299 (t-90) REVERT: B 530 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6431 (mtm) REVERT: B 541 ILE cc_start: 0.7686 (mm) cc_final: 0.7386 (mt) REVERT: B 588 ILE cc_start: 0.7951 (tp) cc_final: 0.7593 (mt) REVERT: C 117 GLN cc_start: 0.6180 (mt0) cc_final: 0.4757 (tp-100) REVERT: C 125 GLU cc_start: 0.6665 (tp30) cc_final: 0.6387 (tp30) REVERT: C 144 TYR cc_start: 0.6989 (m-10) cc_final: 0.6771 (m-10) REVERT: C 149 MET cc_start: 0.7732 (mmp) cc_final: 0.7334 (mmp) REVERT: C 153 MET cc_start: 0.7632 (ttm) cc_final: 0.7384 (mtt) REVERT: C 259 PHE cc_start: 0.6853 (t80) cc_final: 0.6647 (t80) REVERT: C 304 MET cc_start: 0.7845 (mmm) cc_final: 0.7495 (tpt) REVERT: C 361 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7833 (m-80) REVERT: C 463 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.7990 (m-40) REVERT: C 473 MET cc_start: 0.7246 (ttp) cc_final: 0.6595 (ttm) REVERT: C 487 MET cc_start: 0.8042 (ttm) cc_final: 0.7654 (ttm) REVERT: C 502 ILE cc_start: 0.8435 (mt) cc_final: 0.8218 (mt) REVERT: C 517 HIS cc_start: 0.7503 (t70) cc_final: 0.7279 (t-90) REVERT: C 530 MET cc_start: 0.6738 (OUTLIER) cc_final: 0.6427 (mtm) REVERT: C 588 ILE cc_start: 0.8024 (tp) cc_final: 0.7659 (mt) REVERT: D 117 GLN cc_start: 0.6157 (mt0) cc_final: 0.4779 (tp-100) REVERT: D 125 GLU cc_start: 0.6628 (tp30) cc_final: 0.6344 (tp30) REVERT: D 144 TYR cc_start: 0.6980 (m-10) cc_final: 0.6771 (m-10) REVERT: D 149 MET cc_start: 0.7729 (mmp) cc_final: 0.7339 (mmp) REVERT: D 153 MET cc_start: 0.7627 (ttm) cc_final: 0.7389 (mtt) REVERT: D 259 PHE cc_start: 0.6883 (t80) cc_final: 0.6681 (t80) REVERT: D 304 MET cc_start: 0.7870 (mmm) cc_final: 0.7519 (tpt) REVERT: D 361 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: D 398 GLN cc_start: 0.7998 (mt0) cc_final: 0.7595 (mt0) REVERT: D 463 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.8009 (m-40) REVERT: D 473 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.6098 (ttm) REVERT: D 487 MET cc_start: 0.8045 (ttm) cc_final: 0.7642 (ttm) REVERT: D 517 HIS cc_start: 0.7530 (t70) cc_final: 0.7307 (t-90) REVERT: D 530 MET cc_start: 0.6732 (OUTLIER) cc_final: 0.6427 (mtm) REVERT: D 541 ILE cc_start: 0.7682 (mm) cc_final: 0.7377 (mt) REVERT: D 588 ILE cc_start: 0.7951 (tp) cc_final: 0.7595 (mt) outliers start: 52 outliers final: 25 residues processed: 297 average time/residue: 0.1262 time to fit residues: 56.1340 Evaluate side-chains 298 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 259 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 281 TRP Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 281 TRP Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 281 TRP Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 463 ASN Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 530 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 150 optimal weight: 20.0000 chunk 136 optimal weight: 0.5980 chunk 156 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 122 optimal weight: 0.0970 chunk 138 optimal weight: 0.5980 chunk 194 optimal weight: 5.9990 chunk 175 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 GLN A 432 HIS A 440 GLN A 463 ASN B 156 ASN B 398 GLN B 432 HIS B 440 GLN B 463 ASN C 156 ASN C 398 GLN C 432 HIS C 440 GLN C 463 ASN D 432 HIS D 463 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.165725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.135387 restraints weight = 17614.450| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.95 r_work: 0.3196 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 16008 Z= 0.107 Angle : 0.556 8.738 21712 Z= 0.267 Chirality : 0.039 0.139 2440 Planarity : 0.003 0.040 2716 Dihedral : 11.825 133.180 2412 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.08 % Allowed : 12.26 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.19), residues: 2008 helix: 1.51 (0.14), residues: 1392 sheet: 2.11 (0.42), residues: 112 loop : -0.82 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 554 TYR 0.013 0.001 TYR A 411 PHE 0.012 0.001 PHE A 143 TRP 0.010 0.001 TRP C 373 HIS 0.003 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (16008) covalent geometry : angle 0.55592 / 0.27 (21712) hydrogen bonds : bond 0.03754 / 2.56 ( 972) hydrogen bonds : angle 3.72831 / 2.77 ( 2856) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 272 time to evaluate : 0.585 Fit side-chains REVERT: A 117 GLN cc_start: 0.6120 (mt0) cc_final: 0.4784 (tp-100) REVERT: A 124 GLN cc_start: 0.5718 (mt0) cc_final: 0.5383 (mt0) REVERT: A 125 GLU cc_start: 0.6568 (tp30) cc_final: 0.6282 (tp30) REVERT: A 149 MET cc_start: 0.7557 (mmp) cc_final: 0.7214 (mmp) REVERT: A 259 PHE cc_start: 0.6789 (t80) cc_final: 0.6542 (t80) REVERT: A 304 MET cc_start: 0.7647 (mmm) cc_final: 0.7350 (tpt) REVERT: A 361 TYR cc_start: 0.8197 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: A 473 MET cc_start: 0.6551 (OUTLIER) cc_final: 0.5969 (ttm) REVERT: A 517 HIS cc_start: 0.7273 (t70) cc_final: 0.7061 (t-90) REVERT: A 530 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.6404 (mtm) REVERT: A 541 ILE cc_start: 0.7638 (mm) cc_final: 0.7361 (mt) REVERT: A 588 ILE cc_start: 0.7876 (tp) cc_final: 0.7580 (pt) REVERT: B 117 GLN cc_start: 0.6061 (mt0) cc_final: 0.4724 (tp-100) REVERT: B 125 GLU cc_start: 0.6620 (tp30) cc_final: 0.6353 (tp30) REVERT: B 149 MET cc_start: 0.7568 (mmp) cc_final: 0.7222 (mmp) REVERT: B 233 ASP cc_start: 0.7026 (p0) cc_final: 0.6825 (p0) REVERT: B 259 PHE cc_start: 0.6786 (t80) cc_final: 0.6541 (t80) REVERT: B 304 MET cc_start: 0.7638 (mmm) cc_final: 0.7339 (tpt) REVERT: B 361 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7856 (m-80) REVERT: B 473 MET cc_start: 0.6968 (ttp) cc_final: 0.6486 (ttm) REVERT: B 487 MET cc_start: 0.7904 (ttm) cc_final: 0.7480 (ttm) REVERT: B 517 HIS cc_start: 0.7284 (t70) cc_final: 0.7070 (t-90) REVERT: B 530 MET cc_start: 0.6626 (OUTLIER) cc_final: 0.6409 (mtm) REVERT: B 541 ILE cc_start: 0.7652 (mm) cc_final: 0.7373 (mt) REVERT: B 588 ILE cc_start: 0.7941 (tp) cc_final: 0.7574 (mt) REVERT: B 593 ARG cc_start: 0.7433 (ttm110) cc_final: 0.7063 (ttp-110) REVERT: C 125 GLU cc_start: 0.6606 (tp30) cc_final: 0.6333 (tp30) REVERT: C 144 TYR cc_start: 0.6768 (m-10) cc_final: 0.6563 (m-10) REVERT: C 259 PHE cc_start: 0.6786 (t80) cc_final: 0.6537 (t80) REVERT: C 304 MET cc_start: 0.7644 (mmm) cc_final: 0.7347 (tpt) REVERT: C 361 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.7715 (m-80) REVERT: C 473 MET cc_start: 0.7004 (ttp) cc_final: 0.6554 (ttm) REVERT: C 487 MET cc_start: 0.7905 (ttm) cc_final: 0.7464 (ttm) REVERT: C 502 ILE cc_start: 0.8319 (mt) cc_final: 0.8097 (mt) REVERT: C 517 HIS cc_start: 0.7272 (t70) cc_final: 0.7070 (t-90) REVERT: C 530 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.6411 (mtm) REVERT: C 588 ILE cc_start: 0.8006 (tp) cc_final: 0.7640 (pt) REVERT: C 593 ARG cc_start: 0.7430 (ttm110) cc_final: 0.7076 (ttp-110) REVERT: D 117 GLN cc_start: 0.6044 (mt0) cc_final: 0.4735 (tp-100) REVERT: D 125 GLU cc_start: 0.6573 (tp30) cc_final: 0.6299 (tp30) REVERT: D 144 TYR cc_start: 0.6832 (m-10) cc_final: 0.6598 (m-10) REVERT: D 236 PHE cc_start: 0.5570 (t80) cc_final: 0.5307 (t80) REVERT: D 259 PHE cc_start: 0.6786 (t80) cc_final: 0.6525 (t80) REVERT: D 304 MET cc_start: 0.7628 (mmm) cc_final: 0.7340 (tpt) REVERT: D 361 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.7766 (m-80) REVERT: D 473 MET cc_start: 0.6586 (OUTLIER) cc_final: 0.6014 (ttm) REVERT: D 517 HIS cc_start: 0.7277 (t70) cc_final: 0.7065 (t-90) REVERT: D 530 MET cc_start: 0.6618 (OUTLIER) cc_final: 0.6386 (mtm) REVERT: D 541 ILE cc_start: 0.7641 (mm) cc_final: 0.7357 (mt) REVERT: D 588 ILE cc_start: 0.7916 (tp) cc_final: 0.7601 (pt) outliers start: 30 outliers final: 12 residues processed: 283 average time/residue: 0.1199 time to fit residues: 51.8147 Evaluate side-chains 282 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 260 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 TRP Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 281 TRP Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 281 TRP Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 530 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 60 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 GLN A 463 ASN B 398 GLN B 463 ASN C 117 GLN C 398 GLN C 463 ASN D 463 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.163968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.132733 restraints weight = 17677.822| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.99 r_work: 0.3175 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16008 Z= 0.144 Angle : 0.591 8.817 21712 Z= 0.288 Chirality : 0.041 0.130 2440 Planarity : 0.004 0.041 2716 Dihedral : 11.822 134.403 2412 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.08 % Allowed : 12.81 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.19), residues: 2008 helix: 1.53 (0.14), residues: 1392 sheet: 2.08 (0.42), residues: 112 loop : -0.84 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 554 TYR 0.011 0.001 TYR C 411 PHE 0.011 0.001 PHE A 514 TRP 0.011 0.001 TRP D 373 HIS 0.005 0.001 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (16008) covalent geometry : angle 0.59072 / 0.29 (21712) hydrogen bonds : bond 0.04126 / 2.81 ( 972) hydrogen bonds : angle 3.79899 / 2.83 ( 2856) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 267 time to evaluate : 0.564 Fit side-chains REVERT: A 124 GLN cc_start: 0.6099 (mt0) cc_final: 0.5727 (mt0) REVERT: A 236 PHE cc_start: 0.5635 (t80) cc_final: 0.5425 (t80) REVERT: A 259 PHE cc_start: 0.6852 (t80) cc_final: 0.6349 (t80) REVERT: A 262 ILE cc_start: 0.8009 (mp) cc_final: 0.7543 (tt) REVERT: A 304 MET cc_start: 0.7698 (mmm) cc_final: 0.7265 (tpt) REVERT: A 473 MET cc_start: 0.6677 (OUTLIER) cc_final: 0.6074 (ttm) REVERT: A 517 HIS cc_start: 0.7271 (t70) cc_final: 0.7053 (t-90) REVERT: A 588 ILE cc_start: 0.7950 (tp) cc_final: 0.7643 (pt) REVERT: B 144 TYR cc_start: 0.6792 (m-10) cc_final: 0.6571 (m-10) REVERT: B 236 PHE cc_start: 0.5560 (t80) cc_final: 0.5310 (t80) REVERT: B 259 PHE cc_start: 0.6853 (t80) cc_final: 0.6528 (t80) REVERT: B 304 MET cc_start: 0.7704 (mmm) cc_final: 0.7274 (tpt) REVERT: B 473 MET cc_start: 0.7018 (ttp) cc_final: 0.6480 (ttm) REVERT: B 517 HIS cc_start: 0.7253 (t70) cc_final: 0.7032 (t-90) REVERT: B 588 ILE cc_start: 0.7940 (tp) cc_final: 0.7614 (pt) REVERT: B 593 ARG cc_start: 0.7466 (ttm110) cc_final: 0.7141 (ttp-110) REVERT: C 125 GLU cc_start: 0.6648 (tp30) cc_final: 0.6382 (tp30) REVERT: C 144 TYR cc_start: 0.6813 (m-10) cc_final: 0.6596 (m-10) REVERT: C 236 PHE cc_start: 0.5609 (t80) cc_final: 0.5390 (t80) REVERT: C 259 PHE cc_start: 0.6831 (t80) cc_final: 0.6509 (t80) REVERT: C 304 MET cc_start: 0.7681 (mmm) cc_final: 0.7249 (tpt) REVERT: C 473 MET cc_start: 0.7024 (ttp) cc_final: 0.6483 (ttm) REVERT: C 502 ILE cc_start: 0.8308 (mt) cc_final: 0.8079 (mt) REVERT: C 517 HIS cc_start: 0.7216 (t70) cc_final: 0.6985 (t-90) REVERT: C 588 ILE cc_start: 0.7974 (tp) cc_final: 0.7612 (pt) REVERT: C 593 ARG cc_start: 0.7462 (ttm110) cc_final: 0.7136 (ttp-110) REVERT: D 236 PHE cc_start: 0.5609 (t80) cc_final: 0.5387 (t80) REVERT: D 259 PHE cc_start: 0.6829 (t80) cc_final: 0.6502 (t80) REVERT: D 304 MET cc_start: 0.7716 (mmm) cc_final: 0.7286 (tpt) REVERT: D 473 MET cc_start: 0.6762 (OUTLIER) cc_final: 0.6184 (ttm) REVERT: D 517 HIS cc_start: 0.7264 (t70) cc_final: 0.7045 (t-90) REVERT: D 588 ILE cc_start: 0.7937 (tp) cc_final: 0.7624 (pt) outliers start: 30 outliers final: 20 residues processed: 272 average time/residue: 0.1053 time to fit residues: 44.0897 Evaluate side-chains 279 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 257 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 281 TRP Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 281 TRP Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 281 TRP Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 473 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 76 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 179 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 57 optimal weight: 0.0070 chunk 107 optimal weight: 0.6980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 GLN A 156 ASN A 398 GLN A 432 HIS B 117 GLN B 398 GLN B 432 HIS C 117 GLN C 398 GLN C 432 HIS D 117 GLN D 156 ASN D 432 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.166898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.136296 restraints weight = 17550.219| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.78 r_work: 0.3245 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16008 Z= 0.103 Angle : 0.547 8.557 21712 Z= 0.263 Chirality : 0.039 0.144 2440 Planarity : 0.003 0.041 2716 Dihedral : 11.410 133.530 2404 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.39 % Allowed : 13.71 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.19), residues: 2008 helix: 1.69 (0.14), residues: 1396 sheet: 2.28 (0.41), residues: 112 loop : -0.81 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 554 TYR 0.013 0.001 TYR D 411 PHE 0.011 0.001 PHE A 143 TRP 0.009 0.001 TRP D 373 HIS 0.003 0.001 HIS A 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (16008) covalent geometry : angle 0.54731 / 0.26 (21712) hydrogen bonds : bond 0.03444 / 2.33 ( 972) hydrogen bonds : angle 3.64936 / 2.72 ( 2856) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 275 time to evaluate : 0.630 Fit side-chains REVERT: A 117 GLN cc_start: 0.6173 (mt0) cc_final: 0.5758 (tt0) REVERT: A 124 GLN cc_start: 0.6177 (mt0) cc_final: 0.5851 (mt0) REVERT: A 149 MET cc_start: 0.7468 (mmp) cc_final: 0.7152 (mmp) REVERT: A 259 PHE cc_start: 0.6798 (t80) cc_final: 0.6290 (t80) REVERT: A 262 ILE cc_start: 0.8055 (mp) cc_final: 0.7585 (tt) REVERT: A 304 MET cc_start: 0.7785 (mmm) cc_final: 0.7516 (tpt) REVERT: A 404 ARG cc_start: 0.7698 (tpp80) cc_final: 0.7352 (tpp80) REVERT: A 517 HIS cc_start: 0.7502 (t70) cc_final: 0.7112 (t-90) REVERT: A 588 ILE cc_start: 0.7982 (tp) cc_final: 0.7633 (pt) REVERT: A 593 ARG cc_start: 0.7465 (ttm110) cc_final: 0.7228 (ttp-110) REVERT: B 123 GLU cc_start: 0.6151 (tp30) cc_final: 0.5869 (tp30) REVERT: B 149 MET cc_start: 0.7471 (mmp) cc_final: 0.7137 (mmp) REVERT: B 258 ARG cc_start: 0.6226 (mtm-85) cc_final: 0.5087 (ptm160) REVERT: B 259 PHE cc_start: 0.6763 (t80) cc_final: 0.6494 (t80) REVERT: B 262 ILE cc_start: 0.7969 (mp) cc_final: 0.7655 (tt) REVERT: B 304 MET cc_start: 0.7798 (mmm) cc_final: 0.7540 (tpt) REVERT: B 404 ARG cc_start: 0.7695 (tpp80) cc_final: 0.7351 (tpp80) REVERT: B 473 MET cc_start: 0.7115 (ttp) cc_final: 0.6667 (ttm) REVERT: B 517 HIS cc_start: 0.7492 (t70) cc_final: 0.7274 (t-90) REVERT: B 588 ILE cc_start: 0.7984 (tp) cc_final: 0.7621 (pt) REVERT: B 593 ARG cc_start: 0.7359 (ttm110) cc_final: 0.7072 (ttp-110) REVERT: C 123 GLU cc_start: 0.6097 (tp30) cc_final: 0.5807 (tp30) REVERT: C 258 ARG cc_start: 0.6214 (mtm-85) cc_final: 0.5064 (ptm160) REVERT: C 259 PHE cc_start: 0.6755 (t80) cc_final: 0.6498 (t80) REVERT: C 262 ILE cc_start: 0.7914 (mp) cc_final: 0.7597 (tt) REVERT: C 304 MET cc_start: 0.7818 (mmm) cc_final: 0.7545 (tpt) REVERT: C 473 MET cc_start: 0.7085 (ttp) cc_final: 0.6642 (ttm) REVERT: C 502 ILE cc_start: 0.8359 (mt) cc_final: 0.8135 (mt) REVERT: C 517 HIS cc_start: 0.7496 (t70) cc_final: 0.7292 (t-90) REVERT: C 588 ILE cc_start: 0.8002 (tp) cc_final: 0.7635 (pt) REVERT: C 593 ARG cc_start: 0.7356 (ttm110) cc_final: 0.7064 (ttp-110) REVERT: D 123 GLU cc_start: 0.6101 (tp30) cc_final: 0.5808 (tp30) REVERT: D 258 ARG cc_start: 0.6217 (mtm-85) cc_final: 0.5074 (ptm160) REVERT: D 259 PHE cc_start: 0.6758 (t80) cc_final: 0.6499 (t80) REVERT: D 262 ILE cc_start: 0.7921 (mp) cc_final: 0.7597 (tt) REVERT: D 304 MET cc_start: 0.7810 (mmm) cc_final: 0.7531 (tpt) REVERT: D 404 ARG cc_start: 0.7716 (tpp80) cc_final: 0.7359 (tpp80) REVERT: D 517 HIS cc_start: 0.7506 (t70) cc_final: 0.7113 (t-90) REVERT: D 588 ILE cc_start: 0.7970 (tp) cc_final: 0.7605 (pt) REVERT: D 593 ARG cc_start: 0.7437 (ttm110) cc_final: 0.7203 (ttp-110) outliers start: 20 outliers final: 12 residues processed: 281 average time/residue: 0.1124 time to fit residues: 47.6789 Evaluate side-chains 277 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 265 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 281 TRP Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 281 TRP Chi-restraints excluded: chain C residue 285 PHE Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 281 TRP Chi-restraints excluded: chain D residue 445 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 21 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 99 optimal weight: 30.0000 chunk 72 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 65 optimal weight: 0.0870 chunk 103 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 117 GLN B 398 GLN C 117 GLN C 398 GLN D 117 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.167003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.134582 restraints weight = 17735.327| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.96 r_work: 0.3218 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16008 Z= 0.108 Angle : 0.548 8.601 21712 Z= 0.265 Chirality : 0.040 0.148 2440 Planarity : 0.003 0.041 2716 Dihedral : 11.301 134.167 2404 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.04 % Allowed : 14.89 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.19), residues: 2008 helix: 1.79 (0.14), residues: 1396 sheet: 2.40 (0.42), residues: 112 loop : -0.77 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 554 TYR 0.012 0.001 TYR A 411 PHE 0.011 0.001 PHE A 143 TRP 0.009 0.001 TRP C 373 HIS 0.006 0.001 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (16008) covalent geometry : angle 0.54830 / 0.27 (21712) hydrogen bonds : bond 0.03453 / 2.34 ( 972) hydrogen bonds : angle 3.63630 / 2.70 ( 2856) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 281 time to evaluate : 0.709 Fit side-chains REVERT: A 117 GLN cc_start: 0.6044 (mt0) cc_final: 0.5678 (tt0) REVERT: A 124 GLN cc_start: 0.6120 (mt0) cc_final: 0.5801 (mt0) REVERT: A 149 MET cc_start: 0.7452 (mmp) cc_final: 0.7088 (mmp) REVERT: A 258 ARG cc_start: 0.6280 (mtm-85) cc_final: 0.5092 (ptm160) REVERT: A 259 PHE cc_start: 0.6677 (t80) cc_final: 0.6341 (t80) REVERT: A 262 ILE cc_start: 0.8043 (mp) cc_final: 0.7609 (tt) REVERT: A 304 MET cc_start: 0.7626 (mmm) cc_final: 0.7329 (tpt) REVERT: A 404 ARG cc_start: 0.7639 (tpp80) cc_final: 0.7307 (tpp80) REVERT: A 473 MET cc_start: 0.6725 (OUTLIER) cc_final: 0.6343 (ttm) REVERT: A 517 HIS cc_start: 0.7250 (t70) cc_final: 0.6904 (t-90) REVERT: A 588 ILE cc_start: 0.7987 (tp) cc_final: 0.7637 (pt) REVERT: A 593 ARG cc_start: 0.7529 (ttm110) cc_final: 0.7310 (ttp-110) REVERT: B 117 GLN cc_start: 0.6177 (mt0) cc_final: 0.5827 (tt0) REVERT: B 123 GLU cc_start: 0.6091 (tp30) cc_final: 0.5843 (tp30) REVERT: B 149 MET cc_start: 0.7454 (mmp) cc_final: 0.7088 (mmp) REVERT: B 190 LEU cc_start: 0.6837 (tp) cc_final: 0.6598 (tp) REVERT: B 233 ASP cc_start: 0.7260 (p0) cc_final: 0.7051 (p0) REVERT: B 258 ARG cc_start: 0.6208 (mtm-85) cc_final: 0.5054 (ptm160) REVERT: B 259 PHE cc_start: 0.6647 (t80) cc_final: 0.6381 (t80) REVERT: B 262 ILE cc_start: 0.7918 (mp) cc_final: 0.7539 (tt) REVERT: B 304 MET cc_start: 0.7642 (mmm) cc_final: 0.7353 (tpt) REVERT: B 398 GLN cc_start: 0.7818 (mt0) cc_final: 0.7543 (mt0) REVERT: B 404 ARG cc_start: 0.7638 (tpp80) cc_final: 0.7306 (tpp80) REVERT: B 473 MET cc_start: 0.6984 (ttp) cc_final: 0.6637 (ttm) REVERT: B 517 HIS cc_start: 0.7279 (t70) cc_final: 0.6929 (t-90) REVERT: B 588 ILE cc_start: 0.7978 (tp) cc_final: 0.7619 (pt) REVERT: B 593 ARG cc_start: 0.7310 (ttm110) cc_final: 0.7039 (ttp-110) REVERT: C 117 GLN cc_start: 0.6062 (mt0) cc_final: 0.5699 (tt0) REVERT: C 123 GLU cc_start: 0.6046 (tp30) cc_final: 0.5791 (tp30) REVERT: C 258 ARG cc_start: 0.6201 (mtm-85) cc_final: 0.5050 (ptm160) REVERT: C 259 PHE cc_start: 0.6708 (t80) cc_final: 0.6435 (t80) REVERT: C 262 ILE cc_start: 0.7908 (mp) cc_final: 0.7535 (tt) REVERT: C 304 MET cc_start: 0.7651 (mmm) cc_final: 0.7352 (tpt) REVERT: C 398 GLN cc_start: 0.7871 (mt0) cc_final: 0.7393 (mt0) REVERT: C 404 ARG cc_start: 0.7672 (tpp80) cc_final: 0.7306 (tpp80) REVERT: C 473 MET cc_start: 0.6943 (ttp) cc_final: 0.6602 (ttm) REVERT: C 502 ILE cc_start: 0.8325 (mt) cc_final: 0.8112 (mt) REVERT: C 588 ILE cc_start: 0.7983 (tp) cc_final: 0.7627 (pt) REVERT: C 593 ARG cc_start: 0.7300 (ttm110) cc_final: 0.7029 (ttp-110) REVERT: D 117 GLN cc_start: 0.6224 (mt0) cc_final: 0.5900 (tt0) REVERT: D 123 GLU cc_start: 0.6078 (tp30) cc_final: 0.5831 (tp30) REVERT: D 258 ARG cc_start: 0.6217 (mtm-85) cc_final: 0.5069 (ptm160) REVERT: D 259 PHE cc_start: 0.6727 (t80) cc_final: 0.6453 (t80) REVERT: D 262 ILE cc_start: 0.7929 (mp) cc_final: 0.7552 (tt) REVERT: D 304 MET cc_start: 0.7634 (mmm) cc_final: 0.7332 (tpt) REVERT: D 404 ARG cc_start: 0.7642 (tpp80) cc_final: 0.7316 (tpp80) REVERT: D 473 MET cc_start: 0.6700 (ttp) cc_final: 0.6397 (ttm) REVERT: D 517 HIS cc_start: 0.7261 (t70) cc_final: 0.6910 (t-90) REVERT: D 588 ILE cc_start: 0.7976 (tp) cc_final: 0.7622 (pt) REVERT: D 593 ARG cc_start: 0.7515 (ttm110) cc_final: 0.7295 (ttp-110) outliers start: 15 outliers final: 12 residues processed: 282 average time/residue: 0.1292 time to fit residues: 54.7417 Evaluate side-chains 285 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 272 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 281 TRP Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 281 TRP Chi-restraints excluded: chain C residue 285 PHE Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 281 TRP Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 445 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 58 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 195 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 33 optimal weight: 0.0570 chunk 134 optimal weight: 0.0050 chunk 160 optimal weight: 9.9990 chunk 66 optimal weight: 0.1980 chunk 199 optimal weight: 30.0000 overall best weight: 1.0114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 HIS A 432 HIS B 432 HIS C 279 HIS C 432 HIS D 279 HIS D 432 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.165022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.133442 restraints weight = 17807.619| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.84 r_work: 0.3212 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16008 Z= 0.125 Angle : 0.566 8.650 21712 Z= 0.274 Chirality : 0.040 0.148 2440 Planarity : 0.004 0.042 2716 Dihedral : 11.296 134.741 2404 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.45 % Allowed : 13.43 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.19), residues: 2008 helix: 1.80 (0.14), residues: 1400 sheet: 2.43 (0.43), residues: 112 loop : -0.82 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 554 TYR 0.012 0.001 TYR A 411 PHE 0.011 0.001 PHE B 299 TRP 0.010 0.001 TRP A 373 HIS 0.002 0.001 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (16008) covalent geometry : angle 0.56555 / 0.27 (21712) hydrogen bonds : bond 0.03765 / 2.56 ( 972) hydrogen bonds : angle 3.64955 / 2.71 ( 2856) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 267 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLN cc_start: 0.6179 (mt0) cc_final: 0.5804 (tt0) REVERT: A 149 MET cc_start: 0.7578 (mmp) cc_final: 0.7156 (mmp) REVERT: A 258 ARG cc_start: 0.6337 (mtm-85) cc_final: 0.5095 (ptm160) REVERT: A 259 PHE cc_start: 0.6668 (t80) cc_final: 0.6337 (t80) REVERT: A 262 ILE cc_start: 0.8101 (mt) cc_final: 0.7676 (tt) REVERT: A 304 MET cc_start: 0.7846 (mmm) cc_final: 0.7590 (tpt) REVERT: A 473 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6383 (ttm) REVERT: A 517 HIS cc_start: 0.7520 (t70) cc_final: 0.7138 (t-90) REVERT: A 588 ILE cc_start: 0.7969 (tp) cc_final: 0.7617 (pt) REVERT: A 593 ARG cc_start: 0.7596 (ttm110) cc_final: 0.7375 (ttp-110) REVERT: B 117 GLN cc_start: 0.6291 (mt0) cc_final: 0.5929 (tt0) REVERT: B 123 GLU cc_start: 0.6140 (tp30) cc_final: 0.5895 (tp30) REVERT: B 149 MET cc_start: 0.7616 (mmp) cc_final: 0.7174 (mmp) REVERT: B 233 ASP cc_start: 0.7156 (p0) cc_final: 0.6942 (p0) REVERT: B 258 ARG cc_start: 0.6225 (mtm-85) cc_final: 0.5028 (ptm160) REVERT: B 259 PHE cc_start: 0.6784 (t80) cc_final: 0.6511 (t80) REVERT: B 262 ILE cc_start: 0.8045 (mp) cc_final: 0.7669 (tt) REVERT: B 304 MET cc_start: 0.7855 (mmm) cc_final: 0.7602 (tpt) REVERT: B 473 MET cc_start: 0.7135 (ttp) cc_final: 0.6699 (ttm) REVERT: B 517 HIS cc_start: 0.7525 (t70) cc_final: 0.7144 (t-90) REVERT: B 588 ILE cc_start: 0.7995 (tp) cc_final: 0.7641 (pt) REVERT: B 593 ARG cc_start: 0.7455 (ttm110) cc_final: 0.7180 (ttp-110) REVERT: C 117 GLN cc_start: 0.6076 (mt0) cc_final: 0.5724 (tt0) REVERT: C 123 GLU cc_start: 0.6135 (tp30) cc_final: 0.5894 (tp30) REVERT: C 258 ARG cc_start: 0.6268 (mtm-85) cc_final: 0.5061 (ptm160) REVERT: C 259 PHE cc_start: 0.6795 (t80) cc_final: 0.6510 (t80) REVERT: C 262 ILE cc_start: 0.8028 (mp) cc_final: 0.7651 (tt) REVERT: C 304 MET cc_start: 0.7858 (mmm) cc_final: 0.7601 (tpt) REVERT: C 404 ARG cc_start: 0.7773 (tpp80) cc_final: 0.7361 (tpp80) REVERT: C 473 MET cc_start: 0.7132 (ttp) cc_final: 0.6706 (ttm) REVERT: C 502 ILE cc_start: 0.8459 (mt) cc_final: 0.8256 (mt) REVERT: C 588 ILE cc_start: 0.8028 (tp) cc_final: 0.7671 (pt) REVERT: C 593 ARG cc_start: 0.7401 (ttm110) cc_final: 0.7127 (ttp-110) REVERT: D 117 GLN cc_start: 0.6389 (mt0) cc_final: 0.6010 (tt0) REVERT: D 123 GLU cc_start: 0.6146 (tp30) cc_final: 0.5909 (tp30) REVERT: D 258 ARG cc_start: 0.6282 (mtm-85) cc_final: 0.5076 (ptm160) REVERT: D 259 PHE cc_start: 0.6799 (t80) cc_final: 0.6534 (t80) REVERT: D 262 ILE cc_start: 0.8029 (mp) cc_final: 0.7651 (tt) REVERT: D 304 MET cc_start: 0.7867 (mmm) cc_final: 0.7602 (tpt) REVERT: D 473 MET cc_start: 0.6771 (OUTLIER) cc_final: 0.6373 (ttm) REVERT: D 517 HIS cc_start: 0.7514 (t70) cc_final: 0.7128 (t-90) REVERT: D 554 ARG cc_start: 0.8252 (ttp-110) cc_final: 0.8041 (ttp-110) REVERT: D 588 ILE cc_start: 0.8008 (tp) cc_final: 0.7653 (pt) REVERT: D 593 ARG cc_start: 0.7590 (ttm110) cc_final: 0.7372 (ttp-110) outliers start: 21 outliers final: 16 residues processed: 272 average time/residue: 0.1300 time to fit residues: 52.7130 Evaluate side-chains 282 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 264 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 281 TRP Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 281 TRP Chi-restraints excluded: chain C residue 285 PHE Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 281 TRP Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 473 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 152 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 146 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 chunk 21 optimal weight: 0.3980 chunk 105 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 398 GLN C 398 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.165756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.134807 restraints weight = 17725.580| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.84 r_work: 0.3219 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16008 Z= 0.117 Angle : 0.559 8.604 21712 Z= 0.272 Chirality : 0.040 0.143 2440 Planarity : 0.003 0.042 2716 Dihedral : 11.081 134.377 2404 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.39 % Allowed : 13.71 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.19), residues: 2008 helix: 1.84 (0.14), residues: 1400 sheet: 2.43 (0.43), residues: 112 loop : -0.82 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 554 TYR 0.010 0.001 TYR D 347 PHE 0.011 0.001 PHE A 143 TRP 0.010 0.001 TRP A 373 HIS 0.006 0.001 HIS C 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (16008) covalent geometry : angle 0.55890 / 0.27 (21712) hydrogen bonds : bond 0.03582 / 2.43 ( 972) hydrogen bonds : angle 3.62112 / 2.69 ( 2856) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 262 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLN cc_start: 0.6179 (mt0) cc_final: 0.5803 (tt0) REVERT: A 149 MET cc_start: 0.7573 (mmp) cc_final: 0.7186 (mmp) REVERT: A 258 ARG cc_start: 0.6284 (mtm-85) cc_final: 0.5010 (ptm160) REVERT: A 259 PHE cc_start: 0.6776 (t80) cc_final: 0.6452 (t80) REVERT: A 262 ILE cc_start: 0.8106 (mt) cc_final: 0.7691 (tt) REVERT: A 304 MET cc_start: 0.7820 (mmm) cc_final: 0.7558 (tpt) REVERT: A 473 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6377 (ttm) REVERT: A 517 HIS cc_start: 0.7492 (t70) cc_final: 0.7099 (t-90) REVERT: A 588 ILE cc_start: 0.7989 (tp) cc_final: 0.7632 (pt) REVERT: A 593 ARG cc_start: 0.7590 (ttm110) cc_final: 0.7374 (ttp-110) REVERT: B 117 GLN cc_start: 0.6300 (mt0) cc_final: 0.5944 (tt0) REVERT: B 123 GLU cc_start: 0.6032 (tp30) cc_final: 0.5813 (tp30) REVERT: B 149 MET cc_start: 0.7581 (mmp) cc_final: 0.7173 (mmp) REVERT: B 258 ARG cc_start: 0.6215 (mtm-85) cc_final: 0.5014 (ptm160) REVERT: B 259 PHE cc_start: 0.6757 (t80) cc_final: 0.6484 (t80) REVERT: B 262 ILE cc_start: 0.8033 (mp) cc_final: 0.7651 (tt) REVERT: B 304 MET cc_start: 0.7834 (mmm) cc_final: 0.7578 (tpt) REVERT: B 473 MET cc_start: 0.7088 (ttp) cc_final: 0.6652 (ttm) REVERT: B 517 HIS cc_start: 0.7473 (t70) cc_final: 0.7081 (t-90) REVERT: B 588 ILE cc_start: 0.7981 (tp) cc_final: 0.7619 (pt) REVERT: B 593 ARG cc_start: 0.7482 (ttm110) cc_final: 0.7216 (ttp-110) REVERT: C 117 GLN cc_start: 0.6106 (mt0) cc_final: 0.5745 (tt0) REVERT: C 258 ARG cc_start: 0.6220 (mtm-85) cc_final: 0.5019 (ptm160) REVERT: C 259 PHE cc_start: 0.6764 (t80) cc_final: 0.6501 (t80) REVERT: C 262 ILE cc_start: 0.8042 (mp) cc_final: 0.7662 (tt) REVERT: C 304 MET cc_start: 0.7827 (mmm) cc_final: 0.7558 (tpt) REVERT: C 404 ARG cc_start: 0.7740 (tpp80) cc_final: 0.7369 (tpp80) REVERT: C 473 MET cc_start: 0.7078 (ttp) cc_final: 0.6647 (ttm) REVERT: C 588 ILE cc_start: 0.8016 (tp) cc_final: 0.7659 (pt) REVERT: C 593 ARG cc_start: 0.7438 (ttm110) cc_final: 0.7170 (ttp-110) REVERT: D 117 GLN cc_start: 0.6388 (mt0) cc_final: 0.6024 (tt0) REVERT: D 258 ARG cc_start: 0.6225 (mtm-85) cc_final: 0.5022 (ptm160) REVERT: D 259 PHE cc_start: 0.6761 (t80) cc_final: 0.6499 (t80) REVERT: D 262 ILE cc_start: 0.8044 (mp) cc_final: 0.7663 (tt) REVERT: D 304 MET cc_start: 0.7832 (mmm) cc_final: 0.7560 (tpt) REVERT: D 473 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6329 (ttm) REVERT: D 517 HIS cc_start: 0.7471 (t70) cc_final: 0.7077 (t-90) REVERT: D 554 ARG cc_start: 0.8238 (ttp-110) cc_final: 0.8033 (ttp-110) REVERT: D 588 ILE cc_start: 0.7991 (tp) cc_final: 0.7631 (pt) REVERT: D 593 ARG cc_start: 0.7582 (ttm110) cc_final: 0.7367 (ttp-110) outliers start: 20 outliers final: 16 residues processed: 266 average time/residue: 0.1266 time to fit residues: 49.7885 Evaluate side-chains 278 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 260 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 281 TRP Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 281 TRP Chi-restraints excluded: chain C residue 285 PHE Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 281 TRP Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 473 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 78 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 199 optimal weight: 30.0000 chunk 100 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.163195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.132094 restraints weight = 17739.600| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.90 r_work: 0.3177 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16008 Z= 0.157 Angle : 0.605 8.669 21712 Z= 0.297 Chirality : 0.042 0.143 2440 Planarity : 0.004 0.043 2716 Dihedral : 11.197 136.095 2404 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.45 % Allowed : 13.85 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.19), residues: 2008 helix: 1.76 (0.14), residues: 1400 sheet: 2.20 (0.43), residues: 112 loop : -0.85 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 554 TYR 0.013 0.002 TYR B 347 PHE 0.013 0.001 PHE B 186 TRP 0.009 0.001 TRP A 373 HIS 0.004 0.001 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (16008) covalent geometry : angle 0.60469 / 0.30 (21712) hydrogen bonds : bond 0.04214 / 2.86 ( 972) hydrogen bonds : angle 3.70363 / 2.74 ( 2856) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3940.54 seconds wall clock time: 68 minutes 9.14 seconds (4089.14 seconds total)