Starting phenix.real_space_refine on Mon Jan 20 19:37:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bc7_44426/01_2025/9bc7_44426.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bc7_44426/01_2025/9bc7_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bc7_44426/01_2025/9bc7_44426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bc7_44426/01_2025/9bc7_44426.map" model { file = "/net/cci-nas-00/data/ceres_data/9bc7_44426/01_2025/9bc7_44426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bc7_44426/01_2025/9bc7_44426.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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, 'ASN:plan1': 2, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 6} 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: {'RNA': 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: C, B, D Time building chain proxies: 8.15, per 1000 atoms: 0.52 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: 3.71 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 1.59 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: 5.41 Time building geometry restraints manager: 4.30 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: 17404 2.27 - 4.54: 3907 4.54 - 6.80: 337 6.80 - 9.07: 48 9.07 - 11.34: 16 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: 9160 30.27 - 60.55: 204 60.55 - 90.82: 16 90.82 - 121.09: 4 121.09 - 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: 1764 0.095 - 0.191: 535 0.191 - 0.286: 105 0.286 - 0.381: 24 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.590 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 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= 0.973 Angle : 1.832 11.341 21712 Z= 1.222 Chirality : 0.098 0.476 2440 Planarity : 0.013 0.100 2716 Dihedral : 14.652 151.368 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (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 TRP 0.056 0.014 TRP B 311 HIS 0.010 0.004 HIS B 421 PHE 0.037 0.009 PHE D 141 TYR 0.100 0.018 TYR C 347 ARG 0.008 0.001 ARG B 549 *********************** 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 : 1.645 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: 0.7183 (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: 0.3152 time to fit residues: 208.4487 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 : 1.614 ------------------------------------------------------------------------------- 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 168 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3867 r_free = 0.3867 target = 0.166935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.137193 restraints weight = 17156.724| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.81 r_work: 0.3227 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16008 Z= 0.264 Angle : 0.694 11.363 21712 Z= 0.363 Chirality : 0.044 0.140 2440 Planarity : 0.004 0.033 2716 Dihedral : 14.198 148.306 2412 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.12 % Allowed : 7.06 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.18), residues: 2008 helix: 0.57 (0.14), residues: 1352 sheet: 2.04 (0.39), residues: 112 loop : -0.62 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 281 HIS 0.009 0.002 HIS D 355 PHE 0.015 0.002 PHE D 236 TYR 0.014 0.002 TYR C 576 ARG 0.005 0.001 ARG C 404 *********************** 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 393 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 348 time to evaluate : 1.807 Fit side-chains REVERT: A 117 GLN cc_start: 0.6233 (mt0) cc_final: 0.4930 (tp-100) REVERT: A 123 GLU cc_start: 0.6335 (tp30) cc_final: 0.5911 (tp30) REVERT: A 144 TYR cc_start: 0.7256 (m-10) cc_final: 0.6889 (m-10) REVERT: A 304 MET cc_start: 0.7845 (mmm) cc_final: 0.7638 (tpt) REVERT: A 343 LYS cc_start: 0.8121 (tppp) cc_final: 0.7720 (tptp) REVERT: A 404 ARG cc_start: 0.7801 (tpp80) cc_final: 0.7532 (tpp80) REVERT: A 409 GLU cc_start: 0.8035 (tt0) cc_final: 0.7796 (mt-10) REVERT: A 433 ASP cc_start: 0.8511 (t70) cc_final: 0.8306 (t0) REVERT: A 473 MET cc_start: 0.7542 (ttm) cc_final: 0.7215 (ttm) REVERT: A 517 HIS cc_start: 0.7574 (t-170) cc_final: 0.7065 (t-90) REVERT: A 588 ILE cc_start: 0.7983 (tp) cc_final: 0.7646 (pt) REVERT: B 117 GLN cc_start: 0.6193 (mt0) cc_final: 0.4881 (tp-100) REVERT: B 123 GLU cc_start: 0.6304 (tp30) cc_final: 0.5888 (tp30) REVERT: B 144 TYR cc_start: 0.7267 (m-10) cc_final: 0.6887 (m-10) REVERT: B 304 MET cc_start: 0.7838 (mmm) cc_final: 0.7635 (tpt) REVERT: B 343 LYS cc_start: 0.8116 (tppp) cc_final: 0.7719 (tptp) REVERT: B 404 ARG cc_start: 0.7815 (tpp80) cc_final: 0.7566 (tpp80) REVERT: B 409 GLU cc_start: 0.8033 (tt0) cc_final: 0.7801 (mt-10) REVERT: B 433 ASP cc_start: 0.8528 (t70) cc_final: 0.8294 (t0) REVERT: B 473 MET cc_start: 0.7549 (ttm) cc_final: 0.7233 (ttm) REVERT: B 502 ILE cc_start: 0.8505 (mt) cc_final: 0.8291 (mt) REVERT: B 517 HIS cc_start: 0.7564 (t-170) cc_final: 0.7050 (t-90) REVERT: B 588 ILE cc_start: 0.7970 (tp) cc_final: 0.7619 (pt) REVERT: C 117 GLN cc_start: 0.6154 (mt0) cc_final: 0.4863 (tp-100) REVERT: C 123 GLU cc_start: 0.6312 (tp30) cc_final: 0.5898 (tp30) REVERT: C 144 TYR cc_start: 0.7266 (m-10) cc_final: 0.6838 (m-10) REVERT: C 343 LYS cc_start: 0.8107 (tppp) cc_final: 0.7706 (tptp) REVERT: C 409 GLU cc_start: 0.8037 (tt0) cc_final: 0.7802 (mt-10) REVERT: C 433 ASP cc_start: 0.8514 (t70) cc_final: 0.8281 (t0) REVERT: C 473 MET cc_start: 0.7596 (ttm) cc_final: 0.7276 (ttm) REVERT: C 502 ILE cc_start: 0.8475 (mt) cc_final: 0.8271 (mt) REVERT: C 517 HIS cc_start: 0.7444 (t70) cc_final: 0.6966 (t-90) REVERT: C 588 ILE cc_start: 0.7965 (tp) cc_final: 0.7627 (pt) REVERT: D 117 GLN cc_start: 0.6214 (mt0) cc_final: 0.4907 (tp-100) REVERT: D 123 GLU cc_start: 0.6314 (tp30) cc_final: 0.5929 (tp30) REVERT: D 144 TYR cc_start: 0.7268 (m-10) cc_final: 0.6891 (m-10) REVERT: D 304 MET cc_start: 0.7854 (mmm) cc_final: 0.7644 (tpt) REVERT: D 343 LYS cc_start: 0.8116 (tppp) cc_final: 0.7716 (tptp) REVERT: D 353 MET cc_start: 0.9014 (ptp) cc_final: 0.8742 (ttp) REVERT: D 404 ARG cc_start: 0.7785 (tpp80) cc_final: 0.7512 (tpp80) REVERT: D 409 GLU cc_start: 0.8033 (tt0) cc_final: 0.7784 (mt-10) REVERT: D 433 ASP cc_start: 0.8544 (t70) cc_final: 0.8308 (t0) REVERT: D 473 MET cc_start: 0.7583 (ttm) cc_final: 0.7248 (ttm) REVERT: D 502 ILE cc_start: 0.8512 (mt) cc_final: 0.8300 (mt) REVERT: D 517 HIS cc_start: 0.7579 (t-170) cc_final: 0.7061 (t-90) REVERT: D 588 ILE cc_start: 0.7993 (tp) cc_final: 0.7657 (pt) outliers start: 45 outliers final: 20 residues processed: 368 average time/residue: 0.2816 time to fit residues: 152.1815 Evaluate side-chains 301 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 281 time to evaluate : 1.749 ------------------------------------------------------------------------------- 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 418 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 418 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 418 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 418 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 6 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 180 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 110 optimal weight: 0.3980 chunk 153 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN A 440 GLN A 463 ASN A 482 ASN B 398 GLN B 440 GLN B 463 ASN B 482 ASN C 398 GLN C 440 GLN C 463 ASN C 482 ASN D 398 GLN D 440 GLN D 463 ASN D 482 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.165501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.135949 restraints weight = 17276.986| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.82 r_work: 0.3204 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16008 Z= 0.212 Angle : 0.579 7.967 21712 Z= 0.302 Chirality : 0.041 0.127 2440 Planarity : 0.004 0.038 2716 Dihedral : 14.074 150.401 2412 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.84 % Allowed : 10.32 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 2008 helix: 1.06 (0.14), residues: 1360 sheet: 2.20 (0.40), residues: 112 loop : -0.71 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 373 HIS 0.005 0.001 HIS A 432 PHE 0.016 0.002 PHE A 143 TYR 0.013 0.002 TYR D 411 ARG 0.003 0.000 ARG C 405 *********************** 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 328 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 287 time to evaluate : 1.604 Fit side-chains REVERT: A 117 GLN cc_start: 0.6070 (mt0) cc_final: 0.4734 (tp-100) REVERT: A 123 GLU cc_start: 0.6352 (tp30) cc_final: 0.5927 (tp30) REVERT: A 144 TYR cc_start: 0.7005 (m-10) cc_final: 0.6739 (m-10) REVERT: A 259 PHE cc_start: 0.6892 (t80) cc_final: 0.6634 (t80) REVERT: A 304 MET cc_start: 0.7825 (mmm) cc_final: 0.7486 (tpt) REVERT: A 343 LYS cc_start: 0.8069 (tppp) cc_final: 0.7603 (tptp) REVERT: A 361 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.7696 (m-80) REVERT: A 433 ASP cc_start: 0.8594 (t70) cc_final: 0.8344 (t0) REVERT: A 463 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.7940 (m-40) REVERT: A 517 HIS cc_start: 0.7535 (t-170) cc_final: 0.6969 (t-90) REVERT: A 588 ILE cc_start: 0.7921 (tp) cc_final: 0.7586 (mt) REVERT: B 117 GLN cc_start: 0.6079 (mt0) cc_final: 0.4750 (tp-100) REVERT: B 123 GLU cc_start: 0.6000 (tp30) cc_final: 0.5602 (tp30) REVERT: B 144 TYR cc_start: 0.7018 (m-10) cc_final: 0.6697 (m-10) REVERT: B 259 PHE cc_start: 0.6887 (t80) cc_final: 0.6660 (t80) REVERT: B 304 MET cc_start: 0.7820 (mmm) cc_final: 0.7489 (tpt) REVERT: B 343 LYS cc_start: 0.8107 (tppp) cc_final: 0.7636 (tptp) REVERT: B 361 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: B 433 ASP cc_start: 0.8587 (t70) cc_final: 0.8337 (t0) REVERT: B 463 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7910 (m-40) REVERT: B 502 ILE cc_start: 0.8441 (mt) cc_final: 0.8216 (mt) REVERT: B 517 HIS cc_start: 0.7593 (t-170) cc_final: 0.7020 (t-90) REVERT: B 588 ILE cc_start: 0.7983 (tp) cc_final: 0.7644 (mt) REVERT: C 117 GLN cc_start: 0.6035 (mt0) cc_final: 0.4693 (tp-100) REVERT: C 123 GLU cc_start: 0.5992 (tp30) cc_final: 0.5602 (tp30) REVERT: C 144 TYR cc_start: 0.7018 (m-10) cc_final: 0.6694 (m-10) REVERT: C 259 PHE cc_start: 0.6868 (t80) cc_final: 0.6636 (t80) REVERT: C 343 LYS cc_start: 0.8079 (tppp) cc_final: 0.7610 (tptp) REVERT: C 361 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7628 (m-80) REVERT: C 433 ASP cc_start: 0.8576 (t70) cc_final: 0.8322 (t0) REVERT: C 463 ASN cc_start: 0.8245 (OUTLIER) cc_final: 0.7946 (m-40) REVERT: C 502 ILE cc_start: 0.8443 (mt) cc_final: 0.8221 (mt) REVERT: C 517 HIS cc_start: 0.7489 (t70) cc_final: 0.7007 (t-90) REVERT: C 541 ILE cc_start: 0.7637 (mm) cc_final: 0.7373 (mt) REVERT: C 588 ILE cc_start: 0.7979 (tp) cc_final: 0.7637 (mt) REVERT: D 117 GLN cc_start: 0.6050 (mt0) cc_final: 0.4707 (tp-100) REVERT: D 144 TYR cc_start: 0.7015 (m-10) cc_final: 0.6690 (m-10) REVERT: D 259 PHE cc_start: 0.6866 (t80) cc_final: 0.6629 (t80) REVERT: D 304 MET cc_start: 0.7830 (mmm) cc_final: 0.7482 (tpt) REVERT: D 343 LYS cc_start: 0.8090 (tppp) cc_final: 0.7626 (tptp) REVERT: D 361 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.7679 (m-80) REVERT: D 409 GLU cc_start: 0.7921 (tt0) cc_final: 0.7642 (mt-10) REVERT: D 433 ASP cc_start: 0.8591 (t70) cc_final: 0.8345 (t0) REVERT: D 463 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7937 (m-40) REVERT: D 502 ILE cc_start: 0.8438 (mt) cc_final: 0.8220 (mt) REVERT: D 517 HIS cc_start: 0.7604 (t-170) cc_final: 0.7030 (t-90) REVERT: D 588 ILE cc_start: 0.7990 (tp) cc_final: 0.7648 (mt) outliers start: 41 outliers final: 20 residues processed: 315 average time/residue: 0.2786 time to fit residues: 130.4341 Evaluate side-chains 295 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 267 time to evaluate : 1.656 ------------------------------------------------------------------------------- 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 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 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 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 C residue 134 ILE Chi-restraints excluded: chain C residue 151 ILE 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 D residue 134 ILE Chi-restraints excluded: chain D residue 151 ILE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 107 optimal weight: 0.8980 chunk 177 optimal weight: 0.7980 chunk 197 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 463 ASN B 156 ASN B 463 ASN C 156 ASN C 463 ASN D 463 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.167259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.139640 restraints weight = 17485.333| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.43 r_work: 0.3273 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16008 Z= 0.177 Angle : 0.548 8.642 21712 Z= 0.283 Chirality : 0.040 0.126 2440 Planarity : 0.003 0.040 2716 Dihedral : 13.835 149.697 2412 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.77 % Allowed : 10.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.19), residues: 2008 helix: 1.28 (0.14), residues: 1392 sheet: 2.43 (0.41), residues: 112 loop : -0.83 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 281 HIS 0.005 0.001 HIS A 432 PHE 0.012 0.001 PHE D 143 TYR 0.014 0.001 TYR B 411 ARG 0.004 0.000 ARG B 554 *********************** 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 317 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 277 time to evaluate : 1.737 Fit side-chains REVERT: A 117 GLN cc_start: 0.5999 (mt0) cc_final: 0.4676 (tp-100) REVERT: A 123 GLU cc_start: 0.5970 (tp30) cc_final: 0.5613 (tp30) REVERT: A 144 TYR cc_start: 0.6838 (m-10) cc_final: 0.6608 (m-10) REVERT: A 149 MET cc_start: 0.7633 (mmp) cc_final: 0.7265 (mmp) REVERT: A 153 MET cc_start: 0.7396 (ttm) cc_final: 0.7179 (mtt) REVERT: A 259 PHE cc_start: 0.6798 (t80) cc_final: 0.6530 (t80) REVERT: A 304 MET cc_start: 0.7691 (mmm) cc_final: 0.7318 (tpt) REVERT: A 361 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7717 (m-80) REVERT: A 433 ASP cc_start: 0.8454 (t70) cc_final: 0.8225 (t0) REVERT: A 463 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.8079 (m-40) REVERT: A 473 MET cc_start: 0.6933 (ttp) cc_final: 0.6370 (ttm) REVERT: A 517 HIS cc_start: 0.7478 (t-170) cc_final: 0.6944 (t-90) REVERT: A 541 ILE cc_start: 0.7612 (mm) cc_final: 0.7307 (mt) REVERT: A 588 ILE cc_start: 0.7868 (tp) cc_final: 0.7533 (mt) REVERT: B 117 GLN cc_start: 0.6093 (mt0) cc_final: 0.4784 (tp-100) REVERT: B 123 GLU cc_start: 0.5899 (tp30) cc_final: 0.5531 (tp30) REVERT: B 144 TYR cc_start: 0.6834 (m-10) cc_final: 0.6576 (m-10) REVERT: B 149 MET cc_start: 0.7634 (mmp) cc_final: 0.7266 (mmp) REVERT: B 153 MET cc_start: 0.7461 (ttm) cc_final: 0.7244 (mtt) REVERT: B 259 PHE cc_start: 0.6803 (t80) cc_final: 0.6564 (t80) REVERT: B 304 MET cc_start: 0.7708 (mmm) cc_final: 0.7334 (tpt) REVERT: B 361 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.7713 (m-80) REVERT: B 433 ASP cc_start: 0.8444 (t70) cc_final: 0.8213 (t0) REVERT: B 463 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.8074 (m-40) REVERT: B 473 MET cc_start: 0.6995 (ttp) cc_final: 0.6432 (ttm) REVERT: B 502 ILE cc_start: 0.8352 (mt) cc_final: 0.8144 (mt) REVERT: B 517 HIS cc_start: 0.7424 (t-170) cc_final: 0.6892 (t-90) REVERT: B 541 ILE cc_start: 0.7626 (mm) cc_final: 0.7318 (mt) REVERT: B 588 ILE cc_start: 0.7864 (tp) cc_final: 0.7528 (mt) REVERT: C 117 GLN cc_start: 0.6048 (mt0) cc_final: 0.4744 (tp-100) REVERT: C 123 GLU cc_start: 0.5903 (tp30) cc_final: 0.5534 (tp30) REVERT: C 144 TYR cc_start: 0.6847 (m-10) cc_final: 0.6589 (m-10) REVERT: C 149 MET cc_start: 0.7629 (mmp) cc_final: 0.7263 (mmp) REVERT: C 153 MET cc_start: 0.7468 (ttm) cc_final: 0.7257 (mtt) REVERT: C 259 PHE cc_start: 0.6800 (t80) cc_final: 0.6567 (t80) REVERT: C 361 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: C 433 ASP cc_start: 0.8435 (t70) cc_final: 0.8200 (t0) REVERT: C 463 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.8090 (m-40) REVERT: C 473 MET cc_start: 0.7017 (ttp) cc_final: 0.6422 (ttm) REVERT: C 502 ILE cc_start: 0.8344 (mt) cc_final: 0.8137 (mt) REVERT: C 517 HIS cc_start: 0.7274 (t70) cc_final: 0.6846 (t-90) REVERT: C 541 ILE cc_start: 0.7593 (mm) cc_final: 0.7329 (mt) REVERT: C 588 ILE cc_start: 0.7918 (tp) cc_final: 0.7574 (mt) REVERT: D 117 GLN cc_start: 0.6094 (mt0) cc_final: 0.4757 (tp-100) REVERT: D 125 GLU cc_start: 0.6583 (tp30) cc_final: 0.6300 (tp30) REVERT: D 144 TYR cc_start: 0.6821 (m-10) cc_final: 0.6561 (m-10) REVERT: D 149 MET cc_start: 0.7634 (mmp) cc_final: 0.7270 (mmp) REVERT: D 153 MET cc_start: 0.7456 (ttm) cc_final: 0.7239 (mtt) REVERT: D 259 PHE cc_start: 0.6809 (t80) cc_final: 0.6574 (t80) REVERT: D 304 MET cc_start: 0.7676 (mmm) cc_final: 0.7296 (tpt) REVERT: D 361 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.7707 (m-80) REVERT: D 433 ASP cc_start: 0.8461 (t70) cc_final: 0.8223 (t0) REVERT: D 463 ASN cc_start: 0.8337 (OUTLIER) cc_final: 0.8101 (m-40) REVERT: D 473 MET cc_start: 0.6958 (ttp) cc_final: 0.6388 (ttm) REVERT: D 502 ILE cc_start: 0.8342 (mt) cc_final: 0.8135 (mt) REVERT: D 517 HIS cc_start: 0.7469 (t-170) cc_final: 0.6914 (t-90) REVERT: D 541 ILE cc_start: 0.7625 (mm) cc_final: 0.7319 (mt) REVERT: D 588 ILE cc_start: 0.7865 (tp) cc_final: 0.7528 (mt) outliers start: 40 outliers final: 19 residues processed: 301 average time/residue: 0.2619 time to fit residues: 118.8625 Evaluate side-chains 287 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 260 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE 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 B residue 134 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 C residue 134 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 164 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN B 463 ASN C 463 ASN D 463 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.163882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.132607 restraints weight = 17745.806| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.21 r_work: 0.3164 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16008 Z= 0.222 Angle : 0.548 8.198 21712 Z= 0.282 Chirality : 0.040 0.127 2440 Planarity : 0.004 0.042 2716 Dihedral : 13.786 150.142 2412 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.19 % Allowed : 10.11 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.19), residues: 2008 helix: 1.43 (0.14), residues: 1392 sheet: 2.29 (0.41), residues: 112 loop : -0.92 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 281 HIS 0.005 0.001 HIS D 432 PHE 0.013 0.001 PHE D 236 TYR 0.013 0.001 TYR C 411 ARG 0.006 0.000 ARG A 554 *********************** 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 314 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 268 time to evaluate : 1.707 Fit side-chains REVERT: A 117 GLN cc_start: 0.6209 (mt0) cc_final: 0.4881 (tp-100) REVERT: A 123 GLU cc_start: 0.6022 (tp30) cc_final: 0.5648 (tp30) REVERT: A 125 GLU cc_start: 0.6643 (tp30) cc_final: 0.6370 (tp30) REVERT: A 144 TYR cc_start: 0.6934 (m-10) cc_final: 0.6704 (m-10) REVERT: A 236 PHE cc_start: 0.5523 (t80) cc_final: 0.5306 (t80) REVERT: A 259 PHE cc_start: 0.6845 (t80) cc_final: 0.6549 (t80) REVERT: A 304 MET cc_start: 0.7781 (mmm) cc_final: 0.7389 (tpt) REVERT: A 343 LYS cc_start: 0.7881 (tppp) cc_final: 0.7496 (tptt) REVERT: A 361 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: A 463 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8246 (m-40) REVERT: A 473 MET cc_start: 0.6968 (ttp) cc_final: 0.6424 (ttm) REVERT: A 517 HIS cc_start: 0.7491 (t-170) cc_final: 0.6994 (t-90) REVERT: A 541 ILE cc_start: 0.7693 (mm) cc_final: 0.7422 (mt) REVERT: A 585 THR cc_start: 0.8079 (t) cc_final: 0.7873 (p) REVERT: A 588 ILE cc_start: 0.7949 (tp) cc_final: 0.7608 (mt) REVERT: B 117 GLN cc_start: 0.6130 (mt0) cc_final: 0.4812 (tp-100) REVERT: B 123 GLU cc_start: 0.5983 (tp30) cc_final: 0.5625 (tp30) REVERT: B 125 GLU cc_start: 0.6674 (tp30) cc_final: 0.6341 (tp30) REVERT: B 144 TYR cc_start: 0.6916 (m-10) cc_final: 0.6654 (m-10) REVERT: B 236 PHE cc_start: 0.5504 (t80) cc_final: 0.5289 (t80) REVERT: B 259 PHE cc_start: 0.6839 (t80) cc_final: 0.6550 (t80) REVERT: B 304 MET cc_start: 0.7786 (mmm) cc_final: 0.7387 (tpt) REVERT: B 343 LYS cc_start: 0.7892 (tppp) cc_final: 0.7509 (tptt) REVERT: B 361 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.7778 (m-80) REVERT: B 463 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.8238 (m-40) REVERT: B 473 MET cc_start: 0.6988 (ttp) cc_final: 0.6446 (ttm) REVERT: B 502 ILE cc_start: 0.8395 (mt) cc_final: 0.8172 (mt) REVERT: B 517 HIS cc_start: 0.7469 (t-170) cc_final: 0.6972 (t-90) REVERT: B 541 ILE cc_start: 0.7704 (mm) cc_final: 0.7436 (mt) REVERT: B 585 THR cc_start: 0.8088 (t) cc_final: 0.7887 (p) REVERT: B 588 ILE cc_start: 0.7937 (tp) cc_final: 0.7593 (mt) REVERT: C 117 GLN cc_start: 0.6152 (mt0) cc_final: 0.4818 (tp-100) REVERT: C 123 GLU cc_start: 0.5936 (tp30) cc_final: 0.5566 (tp30) REVERT: C 125 GLU cc_start: 0.6676 (tp30) cc_final: 0.6341 (tp30) REVERT: C 144 TYR cc_start: 0.6917 (m-10) cc_final: 0.6652 (m-10) REVERT: C 233 ASP cc_start: 0.7281 (p0) cc_final: 0.7073 (p0) REVERT: C 236 PHE cc_start: 0.5499 (t80) cc_final: 0.5293 (t80) REVERT: C 259 PHE cc_start: 0.6829 (t80) cc_final: 0.6565 (t80) REVERT: C 361 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.7833 (m-80) REVERT: C 463 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8252 (m-40) REVERT: C 473 MET cc_start: 0.7001 (ttp) cc_final: 0.6467 (ttm) REVERT: C 502 ILE cc_start: 0.8390 (mt) cc_final: 0.8164 (mt) REVERT: C 517 HIS cc_start: 0.7343 (t70) cc_final: 0.7131 (t-90) REVERT: C 588 ILE cc_start: 0.7943 (tp) cc_final: 0.7582 (mt) REVERT: D 117 GLN cc_start: 0.6198 (mt0) cc_final: 0.4845 (tp-100) REVERT: D 125 GLU cc_start: 0.6667 (tp30) cc_final: 0.6396 (tp30) REVERT: D 144 TYR cc_start: 0.6895 (m-10) cc_final: 0.6629 (m-10) REVERT: D 259 PHE cc_start: 0.6831 (t80) cc_final: 0.6563 (t80) REVERT: D 304 MET cc_start: 0.7781 (mmm) cc_final: 0.7384 (tpt) REVERT: D 361 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7769 (m-80) REVERT: D 409 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7428 (mt-10) REVERT: D 446 GLU cc_start: 0.7620 (tt0) cc_final: 0.7363 (tt0) REVERT: D 463 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8267 (m-40) REVERT: D 473 MET cc_start: 0.6967 (ttp) cc_final: 0.6425 (ttm) REVERT: D 502 ILE cc_start: 0.8390 (mt) cc_final: 0.8166 (mt) REVERT: D 517 HIS cc_start: 0.7495 (t-170) cc_final: 0.6986 (t-90) REVERT: D 541 ILE cc_start: 0.7697 (mm) cc_final: 0.7420 (mt) REVERT: D 585 THR cc_start: 0.8060 (t) cc_final: 0.7857 (p) REVERT: D 588 ILE cc_start: 0.7954 (tp) cc_final: 0.7610 (mt) outliers start: 46 outliers final: 29 residues processed: 293 average time/residue: 0.2720 time to fit residues: 119.2747 Evaluate side-chains 292 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 255 time to evaluate : 2.018 ------------------------------------------------------------------------------- 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 427 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 463 ASN 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 427 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 463 ASN 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 427 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 463 ASN 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 427 MET Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 463 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 199 optimal weight: 30.0000 chunk 88 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 111 optimal weight: 20.0000 chunk 64 optimal weight: 0.8980 chunk 177 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 HIS A 440 GLN A 463 ASN B 432 HIS B 437 HIS B 440 GLN B 463 ASN C 432 HIS C 437 HIS C 440 GLN C 463 ASN D 432 HIS D 437 HIS D 463 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.165408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.132910 restraints weight = 17598.156| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.05 r_work: 0.3175 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16008 Z= 0.167 Angle : 0.537 8.274 21712 Z= 0.277 Chirality : 0.040 0.155 2440 Planarity : 0.003 0.042 2716 Dihedral : 13.596 149.314 2412 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.94 % Allowed : 12.12 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.19), residues: 2008 helix: 1.60 (0.14), residues: 1392 sheet: 2.33 (0.41), residues: 112 loop : -0.93 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 281 HIS 0.005 0.001 HIS A 432 PHE 0.011 0.001 PHE C 143 TYR 0.016 0.001 TYR B 411 ARG 0.006 0.000 ARG A 554 *********************** 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 291 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 263 time to evaluate : 1.708 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.7568 (mmp) cc_final: 0.7203 (mmp) REVERT: A 259 PHE cc_start: 0.6716 (t80) cc_final: 0.6289 (t80) REVERT: A 262 ILE cc_start: 0.8019 (mp) cc_final: 0.7517 (tt) REVERT: A 304 MET cc_start: 0.7658 (mmm) cc_final: 0.7235 (tpt) REVERT: A 361 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.7839 (m-80) REVERT: A 398 GLN cc_start: 0.7878 (mt0) cc_final: 0.7500 (mt0) REVERT: A 446 GLU cc_start: 0.7571 (tt0) cc_final: 0.7306 (tt0) REVERT: A 463 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8211 (m-40) REVERT: A 473 MET cc_start: 0.6908 (ttp) cc_final: 0.6331 (ttm) REVERT: A 517 HIS cc_start: 0.7382 (t-170) cc_final: 0.6881 (t-90) REVERT: A 585 THR cc_start: 0.8047 (t) cc_final: 0.7841 (p) REVERT: A 588 ILE cc_start: 0.7899 (tp) cc_final: 0.7577 (mt) REVERT: A 593 ARG cc_start: 0.7502 (ttm110) cc_final: 0.7198 (ttp-110) REVERT: B 123 GLU cc_start: 0.5955 (tp30) cc_final: 0.5593 (tp30) REVERT: B 125 GLU cc_start: 0.6596 (tp30) cc_final: 0.6341 (tp30) REVERT: B 149 MET cc_start: 0.7598 (mmp) cc_final: 0.7229 (mmp) REVERT: B 259 PHE cc_start: 0.6719 (t80) cc_final: 0.6487 (t80) REVERT: B 304 MET cc_start: 0.7671 (mmm) cc_final: 0.7239 (tpt) REVERT: B 361 TYR cc_start: 0.8209 (OUTLIER) cc_final: 0.7831 (m-80) REVERT: B 398 GLN cc_start: 0.7879 (mt0) cc_final: 0.7503 (mt0) REVERT: B 446 GLU cc_start: 0.7570 (tt0) cc_final: 0.7301 (tt0) REVERT: B 463 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.8214 (m-40) REVERT: B 487 MET cc_start: 0.7982 (ttm) cc_final: 0.7715 (ttm) REVERT: B 502 ILE cc_start: 0.8352 (mt) cc_final: 0.8127 (mt) REVERT: B 517 HIS cc_start: 0.7343 (t-170) cc_final: 0.6845 (t-90) REVERT: B 585 THR cc_start: 0.8063 (t) cc_final: 0.7852 (p) REVERT: B 588 ILE cc_start: 0.7900 (tp) cc_final: 0.7550 (mt) REVERT: C 123 GLU cc_start: 0.5973 (tp30) cc_final: 0.5629 (tp30) REVERT: C 125 GLU cc_start: 0.6604 (tp30) cc_final: 0.6344 (tp30) REVERT: C 149 MET cc_start: 0.7590 (mmp) cc_final: 0.7229 (mmp) REVERT: C 233 ASP cc_start: 0.7115 (p0) cc_final: 0.6907 (p0) REVERT: C 259 PHE cc_start: 0.6815 (t80) cc_final: 0.6509 (t80) REVERT: C 361 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7796 (m-80) REVERT: C 463 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8217 (m-40) REVERT: C 473 MET cc_start: 0.6979 (ttp) cc_final: 0.6528 (ttm) REVERT: C 487 MET cc_start: 0.8033 (ttm) cc_final: 0.7760 (ttm) REVERT: C 502 ILE cc_start: 0.8346 (mt) cc_final: 0.8119 (mt) REVERT: C 517 HIS cc_start: 0.7252 (t70) cc_final: 0.7052 (t-90) REVERT: C 588 ILE cc_start: 0.7906 (tp) cc_final: 0.7553 (pt) REVERT: D 149 MET cc_start: 0.7603 (mmp) cc_final: 0.7234 (mmp) REVERT: D 259 PHE cc_start: 0.6713 (t80) cc_final: 0.6472 (t80) REVERT: D 304 MET cc_start: 0.7659 (mmm) cc_final: 0.7219 (tpt) REVERT: D 361 TYR cc_start: 0.8183 (OUTLIER) cc_final: 0.7808 (m-80) REVERT: D 409 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7324 (mt-10) REVERT: D 446 GLU cc_start: 0.7576 (tt0) cc_final: 0.7320 (tt0) REVERT: D 463 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8233 (m-40) REVERT: D 473 MET cc_start: 0.6937 (ttp) cc_final: 0.6368 (ttm) REVERT: D 502 ILE cc_start: 0.8348 (mt) cc_final: 0.8125 (mt) REVERT: D 517 HIS cc_start: 0.7395 (t-170) cc_final: 0.6878 (t-90) REVERT: D 541 ILE cc_start: 0.7613 (mm) cc_final: 0.7338 (mt) REVERT: D 588 ILE cc_start: 0.7895 (tp) cc_final: 0.7578 (pt) REVERT: D 593 ARG cc_start: 0.7497 (ttm110) cc_final: 0.7186 (ttp-110) outliers start: 28 outliers final: 16 residues processed: 275 average time/residue: 0.2848 time to fit residues: 118.3012 Evaluate side-chains 288 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 264 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE 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 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 C residue 151 ILE 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 D residue 151 ILE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 33 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 189 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 463 ASN B 117 GLN B 463 ASN C 117 GLN C 463 ASN D 117 GLN D 136 HIS D 463 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.164073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.134133 restraints weight = 17765.324| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.96 r_work: 0.3191 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 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 0.032 16008 Z= 0.200 Angle : 0.538 8.261 21712 Z= 0.277 Chirality : 0.040 0.157 2440 Planarity : 0.004 0.042 2716 Dihedral : 13.544 149.763 2412 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.59 % Allowed : 13.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.19), residues: 2008 helix: 1.68 (0.14), residues: 1392 sheet: 2.21 (0.42), residues: 112 loop : -0.96 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 281 HIS 0.006 0.001 HIS D 432 PHE 0.010 0.001 PHE C 514 TYR 0.014 0.001 TYR A 411 ARG 0.007 0.000 ARG A 554 *********************** 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 288 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 265 time to evaluate : 1.348 Fit side-chains REVERT: A 149 MET cc_start: 0.7438 (mmp) cc_final: 0.7139 (mmp) REVERT: A 233 ASP cc_start: 0.7287 (p0) cc_final: 0.7082 (p0) REVERT: A 259 PHE cc_start: 0.6789 (t80) cc_final: 0.6282 (t80) REVERT: A 262 ILE cc_start: 0.8055 (mp) cc_final: 0.7555 (tt) REVERT: A 304 MET cc_start: 0.7671 (mmm) cc_final: 0.7231 (tpt) REVERT: A 446 GLU cc_start: 0.7562 (tt0) cc_final: 0.7296 (tt0) REVERT: A 463 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.8024 (m110) REVERT: A 473 MET cc_start: 0.6970 (ttp) cc_final: 0.6384 (ttm) REVERT: A 487 MET cc_start: 0.7987 (ttm) cc_final: 0.7706 (ttm) REVERT: A 517 HIS cc_start: 0.7353 (t-170) cc_final: 0.6855 (t-90) REVERT: A 588 ILE cc_start: 0.7958 (tp) cc_final: 0.7640 (pt) REVERT: A 593 ARG cc_start: 0.7511 (ttm110) cc_final: 0.7238 (ttp-110) REVERT: B 123 GLU cc_start: 0.6047 (tp30) cc_final: 0.5703 (tp30) REVERT: B 125 GLU cc_start: 0.6631 (tp30) cc_final: 0.6369 (tp30) REVERT: B 149 MET cc_start: 0.7444 (mmp) cc_final: 0.7137 (mmp) REVERT: B 233 ASP cc_start: 0.7297 (p0) cc_final: 0.7088 (p0) REVERT: B 259 PHE cc_start: 0.6748 (t80) cc_final: 0.6373 (t80) REVERT: B 262 ILE cc_start: 0.8042 (mp) cc_final: 0.7634 (tt) REVERT: B 304 MET cc_start: 0.7691 (mmm) cc_final: 0.7258 (tpt) REVERT: B 446 GLU cc_start: 0.7579 (tt0) cc_final: 0.7313 (tt0) REVERT: B 463 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.7929 (m110) REVERT: B 473 MET cc_start: 0.7005 (ttp) cc_final: 0.6458 (ttm) REVERT: B 487 MET cc_start: 0.7986 (ttm) cc_final: 0.7659 (ttm) REVERT: B 502 ILE cc_start: 0.8347 (mt) cc_final: 0.8125 (mt) REVERT: B 517 HIS cc_start: 0.7309 (t-170) cc_final: 0.6821 (t-90) REVERT: B 588 ILE cc_start: 0.7947 (tp) cc_final: 0.7636 (pt) REVERT: C 123 GLU cc_start: 0.5973 (tp30) cc_final: 0.5615 (tp30) REVERT: C 125 GLU cc_start: 0.6643 (tp30) cc_final: 0.6383 (tp30) REVERT: C 149 MET cc_start: 0.7463 (mmp) cc_final: 0.7169 (mmp) REVERT: C 259 PHE cc_start: 0.6808 (t80) cc_final: 0.6529 (t80) REVERT: C 463 ASN cc_start: 0.8426 (OUTLIER) cc_final: 0.7929 (m110) REVERT: C 473 MET cc_start: 0.7011 (ttp) cc_final: 0.6537 (ttm) REVERT: C 487 MET cc_start: 0.7969 (ttm) cc_final: 0.7634 (ttm) REVERT: C 502 ILE cc_start: 0.8353 (mt) cc_final: 0.8126 (mt) REVERT: C 588 ILE cc_start: 0.7955 (tp) cc_final: 0.7612 (pt) REVERT: D 149 MET cc_start: 0.7472 (mmp) cc_final: 0.7172 (mmp) REVERT: D 233 ASP cc_start: 0.7280 (p0) cc_final: 0.7069 (p0) REVERT: D 236 PHE cc_start: 0.5496 (t80) cc_final: 0.5253 (t80) REVERT: D 259 PHE cc_start: 0.6726 (t80) cc_final: 0.6361 (t80) REVERT: D 262 ILE cc_start: 0.8003 (mp) cc_final: 0.7638 (tt) REVERT: D 304 MET cc_start: 0.7653 (mmm) cc_final: 0.7217 (tpt) REVERT: D 409 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7323 (mt-10) REVERT: D 446 GLU cc_start: 0.7597 (tt0) cc_final: 0.7342 (tt0) REVERT: D 463 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.7950 (m110) REVERT: D 473 MET cc_start: 0.6996 (ttp) cc_final: 0.6441 (ttm) REVERT: D 487 MET cc_start: 0.7984 (ttm) cc_final: 0.7704 (ttm) REVERT: D 502 ILE cc_start: 0.8338 (mt) cc_final: 0.8125 (mt) REVERT: D 517 HIS cc_start: 0.7337 (t-170) cc_final: 0.6836 (t-90) REVERT: D 588 ILE cc_start: 0.7942 (tp) cc_final: 0.7618 (pt) REVERT: D 593 ARG cc_start: 0.7516 (ttm110) cc_final: 0.7240 (ttp-110) outliers start: 23 outliers final: 16 residues processed: 272 average time/residue: 0.2723 time to fit residues: 111.1937 Evaluate side-chains 287 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 267 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 463 ASN 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 B residue 463 ASN 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 445 ASP Chi-restraints excluded: chain C residue 463 ASN 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 445 ASP Chi-restraints excluded: chain D residue 463 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 89 optimal weight: 0.9990 chunk 160 optimal weight: 0.0010 chunk 8 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 463 ASN B 117 GLN B 432 HIS B 463 ASN C 117 GLN C 432 HIS C 463 ASN D 117 GLN D 432 HIS D 463 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.164985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.125871 restraints weight = 17605.759| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.67 r_work: 0.3234 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16008 Z= 0.168 Angle : 0.527 8.303 21712 Z= 0.271 Chirality : 0.040 0.160 2440 Planarity : 0.003 0.042 2716 Dihedral : 13.334 149.271 2404 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.39 % Allowed : 13.85 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.19), residues: 2008 helix: 1.75 (0.14), residues: 1392 sheet: 2.26 (0.43), residues: 112 loop : -0.95 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 281 HIS 0.006 0.001 HIS A 432 PHE 0.011 0.001 PHE A 464 TYR 0.015 0.001 TYR B 411 ARG 0.006 0.000 ARG A 554 *********************** 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 288 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 268 time to evaluate : 2.025 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.7548 (mmp) cc_final: 0.7217 (mmp) REVERT: A 233 ASP cc_start: 0.7146 (p0) cc_final: 0.6935 (p0) REVERT: A 259 PHE cc_start: 0.6786 (t80) cc_final: 0.6302 (t80) REVERT: A 262 ILE cc_start: 0.8099 (mp) cc_final: 0.7610 (tt) REVERT: A 304 MET cc_start: 0.7806 (mmm) cc_final: 0.7545 (tpt) REVERT: A 446 GLU cc_start: 0.7661 (tt0) cc_final: 0.7399 (tt0) REVERT: A 463 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8112 (m110) REVERT: A 473 MET cc_start: 0.7064 (ttp) cc_final: 0.6575 (ttm) REVERT: A 487 MET cc_start: 0.8056 (ttm) cc_final: 0.7739 (ttm) REVERT: A 517 HIS cc_start: 0.7518 (t-170) cc_final: 0.6997 (t-90) REVERT: A 588 ILE cc_start: 0.7931 (tp) cc_final: 0.7607 (pt) REVERT: A 593 ARG cc_start: 0.7487 (ttm110) cc_final: 0.7229 (ttp-110) REVERT: B 123 GLU cc_start: 0.6072 (tp30) cc_final: 0.5734 (tp30) REVERT: B 125 GLU cc_start: 0.6615 (tp30) cc_final: 0.6362 (tp30) REVERT: B 149 MET cc_start: 0.7553 (mmp) cc_final: 0.7210 (mmp) REVERT: B 259 PHE cc_start: 0.6755 (t80) cc_final: 0.6398 (t80) REVERT: B 262 ILE cc_start: 0.8005 (mp) cc_final: 0.7613 (tt) REVERT: B 304 MET cc_start: 0.7810 (mmm) cc_final: 0.7548 (tpt) REVERT: B 446 GLU cc_start: 0.7669 (tt0) cc_final: 0.7410 (tt0) REVERT: B 463 ASN cc_start: 0.8579 (OUTLIER) cc_final: 0.8050 (m110) REVERT: B 473 MET cc_start: 0.7118 (ttp) cc_final: 0.6625 (ttm) REVERT: B 487 MET cc_start: 0.8094 (ttm) cc_final: 0.7741 (ttm) REVERT: B 502 ILE cc_start: 0.8422 (mt) cc_final: 0.8207 (mt) REVERT: B 517 HIS cc_start: 0.7500 (t-170) cc_final: 0.6983 (t-90) REVERT: B 588 ILE cc_start: 0.7904 (tp) cc_final: 0.7577 (pt) REVERT: B 593 ARG cc_start: 0.7451 (ttm110) cc_final: 0.7233 (ttp-110) REVERT: C 123 GLU cc_start: 0.6048 (tp30) cc_final: 0.5728 (tp30) REVERT: C 125 GLU cc_start: 0.6604 (tp30) cc_final: 0.6345 (tp30) REVERT: C 149 MET cc_start: 0.7573 (mmp) cc_final: 0.7226 (mmp) REVERT: C 259 PHE cc_start: 0.6747 (t80) cc_final: 0.6311 (t80) REVERT: C 262 ILE cc_start: 0.8042 (mp) cc_final: 0.7615 (tt) REVERT: C 463 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8067 (m110) REVERT: C 473 MET cc_start: 0.7109 (ttp) cc_final: 0.6616 (ttm) REVERT: C 487 MET cc_start: 0.8072 (ttm) cc_final: 0.7703 (ttm) REVERT: C 502 ILE cc_start: 0.8429 (mt) cc_final: 0.8211 (mt) REVERT: C 588 ILE cc_start: 0.7910 (tp) cc_final: 0.7589 (pt) REVERT: D 149 MET cc_start: 0.7569 (mmp) cc_final: 0.7234 (mmp) REVERT: D 236 PHE cc_start: 0.5314 (t80) cc_final: 0.5112 (t80) REVERT: D 259 PHE cc_start: 0.6856 (t80) cc_final: 0.6490 (t80) REVERT: D 262 ILE cc_start: 0.8030 (mp) cc_final: 0.7636 (tt) REVERT: D 304 MET cc_start: 0.7796 (mmm) cc_final: 0.7534 (tpt) REVERT: D 409 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7510 (mt-10) REVERT: D 446 GLU cc_start: 0.7699 (tt0) cc_final: 0.7447 (tt0) REVERT: D 463 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8090 (m110) REVERT: D 473 MET cc_start: 0.7107 (ttp) cc_final: 0.6611 (ttm) REVERT: D 487 MET cc_start: 0.8063 (ttm) cc_final: 0.7742 (ttm) REVERT: D 502 ILE cc_start: 0.8408 (mt) cc_final: 0.8193 (mt) REVERT: D 517 HIS cc_start: 0.7516 (t-170) cc_final: 0.6980 (t-90) REVERT: D 588 ILE cc_start: 0.7903 (tp) cc_final: 0.7573 (pt) REVERT: D 593 ARG cc_start: 0.7479 (ttm110) cc_final: 0.7219 (ttp-110) outliers start: 20 outliers final: 13 residues processed: 278 average time/residue: 0.2766 time to fit residues: 115.3908 Evaluate side-chains 288 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 271 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 463 ASN 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 B residue 463 ASN Chi-restraints excluded: chain C residue 281 TRP 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 D residue 281 TRP Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 463 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 156 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 160 optimal weight: 0.0010 chunk 143 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 84 optimal weight: 0.0980 chunk 67 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 432 HIS A 463 ASN B 117 GLN B 463 ASN B 517 HIS C 117 GLN C 432 HIS C 463 ASN D 117 GLN D 156 ASN D 432 HIS D 463 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.166362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.135613 restraints weight = 17682.987| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.91 r_work: 0.3230 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16008 Z= 0.144 Angle : 0.516 8.394 21712 Z= 0.265 Chirality : 0.039 0.157 2440 Planarity : 0.003 0.042 2716 Dihedral : 13.056 148.561 2404 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.39 % Allowed : 14.34 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.19), residues: 2008 helix: 1.85 (0.14), residues: 1400 sheet: 2.42 (0.43), residues: 112 loop : -0.83 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 281 HIS 0.006 0.001 HIS B 432 PHE 0.012 0.001 PHE A 464 TYR 0.016 0.001 TYR A 411 ARG 0.008 0.000 ARG A 554 *********************** 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 295 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 275 time to evaluate : 1.764 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.7446 (mmp) cc_final: 0.7143 (mmp) REVERT: A 259 PHE cc_start: 0.6823 (t80) cc_final: 0.6317 (t80) REVERT: A 262 ILE cc_start: 0.8074 (mt) cc_final: 0.7590 (tt) REVERT: A 304 MET cc_start: 0.7648 (mmm) cc_final: 0.7333 (tpt) REVERT: A 446 GLU cc_start: 0.7606 (tt0) cc_final: 0.7371 (tt0) REVERT: A 463 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8056 (m110) REVERT: A 473 MET cc_start: 0.6932 (ttp) cc_final: 0.6566 (ttm) REVERT: A 487 MET cc_start: 0.8003 (ttm) cc_final: 0.7637 (ttm) REVERT: A 517 HIS cc_start: 0.7254 (t-170) cc_final: 0.6805 (t-90) REVERT: A 588 ILE cc_start: 0.7966 (tp) cc_final: 0.7655 (pt) REVERT: A 593 ARG cc_start: 0.7380 (ttm110) cc_final: 0.7107 (ttp-110) REVERT: B 123 GLU cc_start: 0.6019 (tp30) cc_final: 0.5713 (tp30) REVERT: B 125 GLU cc_start: 0.6613 (tp30) cc_final: 0.6358 (tp30) REVERT: B 149 MET cc_start: 0.7465 (mmp) cc_final: 0.7118 (mmp) REVERT: B 259 PHE cc_start: 0.6730 (t80) cc_final: 0.6341 (t80) REVERT: B 262 ILE cc_start: 0.8004 (mp) cc_final: 0.7624 (tt) REVERT: B 304 MET cc_start: 0.7664 (mmm) cc_final: 0.7355 (tpt) REVERT: B 312 ASP cc_start: 0.7821 (t0) cc_final: 0.7618 (t0) REVERT: B 404 ARG cc_start: 0.7656 (tpp80) cc_final: 0.7285 (tpp80) REVERT: B 446 GLU cc_start: 0.7568 (tt0) cc_final: 0.7329 (tt0) REVERT: B 463 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8008 (m110) REVERT: B 473 MET cc_start: 0.6955 (ttp) cc_final: 0.6589 (ttm) REVERT: B 487 MET cc_start: 0.7988 (ttm) cc_final: 0.7599 (ttm) REVERT: B 502 ILE cc_start: 0.8349 (mt) cc_final: 0.8139 (mt) REVERT: B 517 HIS cc_start: 0.7249 (t70) cc_final: 0.6949 (t-90) REVERT: B 588 ILE cc_start: 0.7986 (tp) cc_final: 0.7644 (pt) REVERT: B 593 ARG cc_start: 0.7428 (ttm110) cc_final: 0.7219 (ttp-110) REVERT: C 123 GLU cc_start: 0.6015 (tp30) cc_final: 0.5703 (tp30) REVERT: C 125 GLU cc_start: 0.6620 (tp30) cc_final: 0.6368 (tp30) REVERT: C 149 MET cc_start: 0.7459 (mmp) cc_final: 0.7123 (mmp) REVERT: C 259 PHE cc_start: 0.6822 (t80) cc_final: 0.6345 (t80) REVERT: C 262 ILE cc_start: 0.7962 (mp) cc_final: 0.7592 (tt) REVERT: C 463 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8018 (m110) REVERT: C 473 MET cc_start: 0.6944 (ttp) cc_final: 0.6572 (ttm) REVERT: C 487 MET cc_start: 0.7983 (ttm) cc_final: 0.7576 (ttm) REVERT: C 502 ILE cc_start: 0.8355 (mt) cc_final: 0.8147 (mt) REVERT: C 588 ILE cc_start: 0.7997 (tp) cc_final: 0.7645 (pt) REVERT: C 593 ARG cc_start: 0.7452 (ttm110) cc_final: 0.7238 (ttp-110) REVERT: D 149 MET cc_start: 0.7477 (mmp) cc_final: 0.7134 (mmp) REVERT: D 259 PHE cc_start: 0.6773 (t80) cc_final: 0.6378 (t80) REVERT: D 262 ILE cc_start: 0.8003 (mp) cc_final: 0.7618 (tt) REVERT: D 304 MET cc_start: 0.7632 (mmm) cc_final: 0.7319 (tpt) REVERT: D 404 ARG cc_start: 0.7646 (tpp80) cc_final: 0.7279 (tpp80) REVERT: D 409 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7402 (mt-10) REVERT: D 446 GLU cc_start: 0.7602 (tt0) cc_final: 0.7366 (tt0) REVERT: D 463 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.8020 (m110) REVERT: D 473 MET cc_start: 0.6941 (ttp) cc_final: 0.6570 (ttm) REVERT: D 487 MET cc_start: 0.8005 (ttm) cc_final: 0.7650 (ttm) REVERT: D 502 ILE cc_start: 0.8344 (mt) cc_final: 0.8135 (mt) REVERT: D 517 HIS cc_start: 0.7353 (t-170) cc_final: 0.6869 (t-90) REVERT: D 588 ILE cc_start: 0.7996 (tp) cc_final: 0.7645 (pt) REVERT: D 593 ARG cc_start: 0.7367 (ttm110) cc_final: 0.7094 (ttp-110) outliers start: 20 outliers final: 9 residues processed: 285 average time/residue: 0.2857 time to fit residues: 120.6793 Evaluate side-chains 283 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 270 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 TRP Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 463 ASN 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 C residue 463 ASN Chi-restraints excluded: chain D residue 281 TRP Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 463 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 8 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 73 optimal weight: 0.0170 chunk 97 optimal weight: 0.0070 chunk 36 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 463 ASN B 117 GLN B 432 HIS B 463 ASN C 117 GLN C 463 ASN D 117 GLN D 463 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.166941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.125660 restraints weight = 17801.489| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.85 r_work: 0.3221 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16008 Z= 0.150 Angle : 0.520 8.424 21712 Z= 0.267 Chirality : 0.040 0.162 2440 Planarity : 0.003 0.042 2716 Dihedral : 12.883 148.511 2404 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.90 % Allowed : 14.82 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.19), residues: 2008 helix: 1.89 (0.14), residues: 1400 sheet: 2.45 (0.43), residues: 112 loop : -0.77 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 281 HIS 0.006 0.001 HIS A 432 PHE 0.016 0.001 PHE A 464 TYR 0.015 0.001 TYR B 411 ARG 0.008 0.000 ARG A 554 ********************** 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 286 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 273 time to evaluate : 1.823 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.7460 (mmp) cc_final: 0.7156 (mmp) REVERT: A 259 PHE cc_start: 0.6794 (t80) cc_final: 0.6315 (t80) REVERT: A 262 ILE cc_start: 0.8062 (mt) cc_final: 0.7587 (tt) REVERT: A 304 MET cc_start: 0.7659 (mmm) cc_final: 0.7347 (tpt) REVERT: A 446 GLU cc_start: 0.7621 (tt0) cc_final: 0.7385 (tt0) REVERT: A 463 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.7975 (m110) REVERT: A 473 MET cc_start: 0.6905 (ttp) cc_final: 0.6555 (ttm) REVERT: A 487 MET cc_start: 0.8022 (ttm) cc_final: 0.7623 (ttm) REVERT: A 517 HIS cc_start: 0.7210 (t-170) cc_final: 0.6765 (t-90) REVERT: A 573 LEU cc_start: 0.7205 (mm) cc_final: 0.6920 (mt) REVERT: A 588 ILE cc_start: 0.7973 (tp) cc_final: 0.7628 (pt) REVERT: A 593 ARG cc_start: 0.7356 (ttm110) cc_final: 0.7089 (ttp-110) REVERT: B 123 GLU cc_start: 0.5997 (tp30) cc_final: 0.5707 (tp30) REVERT: B 149 MET cc_start: 0.7460 (mmp) cc_final: 0.7135 (mmp) REVERT: B 259 PHE cc_start: 0.6670 (t80) cc_final: 0.6283 (t80) REVERT: B 262 ILE cc_start: 0.7977 (mp) cc_final: 0.7592 (tt) REVERT: B 304 MET cc_start: 0.7645 (mmm) cc_final: 0.7336 (tpt) REVERT: B 312 ASP cc_start: 0.7862 (t0) cc_final: 0.7655 (t0) REVERT: B 404 ARG cc_start: 0.7683 (tpp80) cc_final: 0.7373 (tpp80) REVERT: B 446 GLU cc_start: 0.7591 (tt0) cc_final: 0.7350 (tt0) REVERT: B 463 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.7980 (m110) REVERT: B 473 MET cc_start: 0.6938 (ttp) cc_final: 0.6583 (ttm) REVERT: B 487 MET cc_start: 0.7989 (ttm) cc_final: 0.7570 (ttm) REVERT: B 517 HIS cc_start: 0.7313 (t70) cc_final: 0.6973 (t-90) REVERT: B 573 LEU cc_start: 0.7249 (mm) cc_final: 0.6986 (mt) REVERT: B 588 ILE cc_start: 0.7982 (tp) cc_final: 0.7620 (pt) REVERT: B 593 ARG cc_start: 0.7468 (ttm110) cc_final: 0.7259 (ttp-110) REVERT: C 123 GLU cc_start: 0.5993 (tp30) cc_final: 0.5702 (tp30) REVERT: C 125 GLU cc_start: 0.6526 (tp30) cc_final: 0.6259 (tp30) REVERT: C 149 MET cc_start: 0.7460 (mmp) cc_final: 0.7132 (mmp) REVERT: C 259 PHE cc_start: 0.6681 (t80) cc_final: 0.6264 (t80) REVERT: C 262 ILE cc_start: 0.7973 (mp) cc_final: 0.7592 (tt) REVERT: C 463 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.7910 (m110) REVERT: C 473 MET cc_start: 0.7016 (ttp) cc_final: 0.6705 (ttm) REVERT: C 487 MET cc_start: 0.7973 (ttm) cc_final: 0.7562 (ttm) REVERT: C 573 LEU cc_start: 0.7243 (mm) cc_final: 0.6992 (mt) REVERT: C 588 ILE cc_start: 0.7963 (tp) cc_final: 0.7599 (pt) REVERT: C 593 ARG cc_start: 0.7464 (ttm110) cc_final: 0.7252 (ttp-110) REVERT: D 149 MET cc_start: 0.7481 (mmp) cc_final: 0.7150 (mmp) REVERT: D 259 PHE cc_start: 0.6676 (t80) cc_final: 0.6308 (t80) REVERT: D 262 ILE cc_start: 0.7979 (mp) cc_final: 0.7594 (tt) REVERT: D 304 MET cc_start: 0.7644 (mmm) cc_final: 0.7333 (tpt) REVERT: D 404 ARG cc_start: 0.7673 (tpp80) cc_final: 0.7360 (tpp80) REVERT: D 409 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7358 (mt-10) REVERT: D 446 GLU cc_start: 0.7622 (tt0) cc_final: 0.7387 (tt0) REVERT: D 463 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.7912 (m110) REVERT: D 473 MET cc_start: 0.6931 (ttp) cc_final: 0.6570 (ttm) REVERT: D 487 MET cc_start: 0.7992 (ttm) cc_final: 0.7591 (ttm) REVERT: D 517 HIS cc_start: 0.7388 (t-170) cc_final: 0.6899 (t-90) REVERT: D 588 ILE cc_start: 0.7973 (tp) cc_final: 0.7625 (pt) REVERT: D 593 ARG cc_start: 0.7345 (ttm110) cc_final: 0.7078 (ttp-110) outliers start: 13 outliers final: 9 residues processed: 280 average time/residue: 0.2820 time to fit residues: 116.8802 Evaluate side-chains 282 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 269 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 TRP Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 463 ASN 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 C residue 463 ASN Chi-restraints excluded: chain D residue 281 TRP Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 463 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 95 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 175 optimal weight: 0.7980 chunk 64 optimal weight: 0.3980 chunk 190 optimal weight: 0.0770 chunk 116 optimal weight: 0.0270 chunk 112 optimal weight: 7.9990 chunk 118 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 432 HIS A 463 ASN B 117 GLN B 432 HIS B 463 ASN C 117 GLN C 463 ASN D 117 GLN D 463 ASN D 517 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.167752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.137276 restraints weight = 17615.579| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.90 r_work: 0.3229 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16008 Z= 0.139 Angle : 0.512 8.463 21712 Z= 0.262 Chirality : 0.039 0.159 2440 Planarity : 0.003 0.042 2716 Dihedral : 12.721 148.303 2404 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.90 % Allowed : 14.89 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.19), residues: 2008 helix: 1.93 (0.14), residues: 1400 sheet: 2.47 (0.43), residues: 112 loop : -0.73 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 281 HIS 0.005 0.001 HIS C 432 PHE 0.016 0.001 PHE D 464 TYR 0.015 0.001 TYR A 411 ARG 0.008 0.000 ARG A 554 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7768.10 seconds wall clock time: 141 minutes 51.01 seconds (8511.01 seconds total)