Starting phenix.real_space_refine on Mon Oct 14 20:12:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur8_42487/10_2024/8ur8_42487.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur8_42487/10_2024/8ur8_42487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur8_42487/10_2024/8ur8_42487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur8_42487/10_2024/8ur8_42487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur8_42487/10_2024/8ur8_42487.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur8_42487/10_2024/8ur8_42487.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 11964 2.51 5 N 3088 2.21 5 O 3612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 18752 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Chain: "B" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Chain: "C" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Chain: "D" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 16 residue: pdb=" N ARG A 78 " occ=0.86 ... (9 atoms not shown) pdb=" NH2 ARG A 78 " occ=0.86 residue: pdb=" N GLY A 79 " occ=0.82 ... (2 atoms not shown) pdb=" O GLY A 79 " occ=0.82 residue: pdb=" N GLY A 80 " occ=0.83 ... (2 atoms not shown) pdb=" O GLY A 80 " occ=0.83 residue: pdb=" N ARG A 81 " occ=0.62 ... (9 atoms not shown) pdb=" NH2 ARG A 81 " occ=0.62 residue: pdb=" N ARG B 78 " occ=0.86 ... (9 atoms not shown) pdb=" NH2 ARG B 78 " occ=0.86 residue: pdb=" N GLY B 79 " occ=0.82 ... (2 atoms not shown) pdb=" O GLY B 79 " occ=0.82 residue: pdb=" N GLY B 80 " occ=0.83 ... (2 atoms not shown) pdb=" O GLY B 80 " occ=0.83 residue: pdb=" N ARG B 81 " occ=0.62 ... (9 atoms not shown) pdb=" NH2 ARG B 81 " occ=0.62 residue: pdb=" N ARG C 78 " occ=0.86 ... (9 atoms not shown) pdb=" NH2 ARG C 78 " occ=0.86 residue: pdb=" N GLY C 79 " occ=0.82 ... (2 atoms not shown) pdb=" O GLY C 79 " occ=0.82 residue: pdb=" N GLY C 80 " occ=0.83 ... (2 atoms not shown) pdb=" O GLY C 80 " occ=0.83 residue: pdb=" N ARG C 81 " occ=0.62 ... (9 atoms not shown) pdb=" NH2 ARG C 81 " occ=0.62 ... (remaining 4 not shown) Time building chain proxies: 10.66, per 1000 atoms: 0.57 Number of scatterers: 18752 At special positions: 0 Unit cell: (130.5, 140.94, 87.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 3612 8.00 N 3088 7.00 C 11964 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: 4.63 Conformation dependent library (CDL) restraints added in 2.5 seconds 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4408 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 18 sheets defined 43.3% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 7 through 12 removed outlier: 3.572A pdb=" N PHE A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 12 " --> pdb=" O TYR A 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 7 through 12' Processing helix chain 'A' and resid 19 through 23 Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 157 through 162 removed outlier: 4.080A pdb=" N ASP A 162 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.598A pdb=" N PHE A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.561A pdb=" N ILE A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 187 " --> pdb=" O TRP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 206 through 209 removed outlier: 3.747A pdb=" N ILE A 209 " --> pdb=" O VAL A 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 209' Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 229 through 240 Processing helix chain 'A' and resid 313 through 324 removed outlier: 3.621A pdb=" N ARG A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.611A pdb=" N GLY A 330 " --> pdb=" O PRO A 327 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASN A 331 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 removed outlier: 3.650A pdb=" N GLN A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 366 removed outlier: 3.505A pdb=" N ILE A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 431 through 443 Processing helix chain 'A' and resid 449 through 457 removed outlier: 3.913A pdb=" N LEU A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 524 removed outlier: 3.583A pdb=" N SER A 511 " --> pdb=" O THR A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 537 Processing helix chain 'A' and resid 538 through 550 removed outlier: 3.646A pdb=" N ASN A 550 " --> pdb=" O ILE A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 562 through 576 Processing helix chain 'A' and resid 579 through 588 Processing helix chain 'B' and resid 7 through 12 removed outlier: 3.639A pdb=" N PHE B 11 " --> pdb=" O ASN B 7 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B 12 " --> pdb=" O TYR B 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 7 through 12' Processing helix chain 'B' and resid 19 through 23 Processing helix chain 'B' and resid 31 through 44 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 143 through 155 Processing helix chain 'B' and resid 157 through 162 removed outlier: 3.970A pdb=" N ASP B 162 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.627A pdb=" N THR B 185 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 187 " --> pdb=" O TRP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 206 through 209 removed outlier: 3.774A pdb=" N ILE B 209 " --> pdb=" O VAL B 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 206 through 209' Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 229 through 240 Processing helix chain 'B' and resid 313 through 326 removed outlier: 3.597A pdb=" N ARG B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN B 325 " --> pdb=" O ASN B 321 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 331 removed outlier: 3.943A pdb=" N GLY B 330 " --> pdb=" O PRO B 327 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ASN B 331 " --> pdb=" O GLU B 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 327 through 331' Processing helix chain 'B' and resid 332 through 337 removed outlier: 3.649A pdb=" N GLN B 337 " --> pdb=" O ASP B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 366 Processing helix chain 'B' and resid 368 through 372 removed outlier: 4.402A pdb=" N GLY B 372 " --> pdb=" O PRO B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 431 through 443 Processing helix chain 'B' and resid 449 through 456 removed outlier: 3.730A pdb=" N LEU B 453 " --> pdb=" O LYS B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 524 removed outlier: 3.615A pdb=" N SER B 511 " --> pdb=" O THR B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 537 Processing helix chain 'B' and resid 538 through 550 removed outlier: 3.673A pdb=" N ASN B 550 " --> pdb=" O ILE B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 559 Processing helix chain 'B' and resid 562 through 576 removed outlier: 3.507A pdb=" N GLY B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS B 575 " --> pdb=" O GLY B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 588 Processing helix chain 'C' and resid 7 through 12 removed outlier: 3.602A pdb=" N PHE C 11 " --> pdb=" O ASN C 7 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA C 12 " --> pdb=" O TYR C 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 7 through 12' Processing helix chain 'C' and resid 19 through 23 Processing helix chain 'C' and resid 31 through 44 Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'C' and resid 106 through 115 Processing helix chain 'C' and resid 143 through 156 Processing helix chain 'C' and resid 157 through 162 removed outlier: 4.062A pdb=" N ASP C 162 " --> pdb=" O GLU C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 177 through 187 removed outlier: 3.658A pdb=" N THR C 185 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE C 187 " --> pdb=" O TRP C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 205 Processing helix chain 'C' and resid 206 through 209 removed outlier: 3.779A pdb=" N ILE C 209 " --> pdb=" O VAL C 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 206 through 209' Processing helix chain 'C' and resid 224 through 229 Processing helix chain 'C' and resid 229 through 240 Processing helix chain 'C' and resid 313 through 326 removed outlier: 3.625A pdb=" N ARG C 324 " --> pdb=" O LYS C 320 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN C 325 " --> pdb=" O ASN C 321 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 331 removed outlier: 3.913A pdb=" N GLY C 330 " --> pdb=" O PRO C 327 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ASN C 331 " --> pdb=" O GLU C 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 327 through 331' Processing helix chain 'C' and resid 332 through 337 removed outlier: 3.666A pdb=" N GLN C 337 " --> pdb=" O ASP C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 366 Processing helix chain 'C' and resid 368 through 372 removed outlier: 4.346A pdb=" N GLY C 372 " --> pdb=" O PRO C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 430 Processing helix chain 'C' and resid 431 through 443 Processing helix chain 'C' and resid 449 through 456 removed outlier: 3.761A pdb=" N LEU C 453 " --> pdb=" O LYS C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 524 removed outlier: 3.617A pdb=" N SER C 511 " --> pdb=" O THR C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 537 Processing helix chain 'C' and resid 538 through 550 removed outlier: 3.687A pdb=" N ASN C 550 " --> pdb=" O ILE C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 559 Processing helix chain 'C' and resid 562 through 576 removed outlier: 3.641A pdb=" N LYS C 575 " --> pdb=" O GLY C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 588 Processing helix chain 'D' and resid 7 through 12 removed outlier: 3.587A pdb=" N PHE D 11 " --> pdb=" O ASN D 7 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA D 12 " --> pdb=" O TYR D 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 7 through 12' Processing helix chain 'D' and resid 19 through 23 Processing helix chain 'D' and resid 31 through 44 Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 87 through 94 Processing helix chain 'D' and resid 106 through 118 Processing helix chain 'D' and resid 143 through 155 Processing helix chain 'D' and resid 157 through 162 removed outlier: 4.090A pdb=" N ASP D 162 " --> pdb=" O GLU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 176 removed outlier: 3.588A pdb=" N PHE D 175 " --> pdb=" O SER D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 187 removed outlier: 3.550A pdb=" N ILE D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR D 185 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE D 187 " --> pdb=" O TRP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 206 through 209 removed outlier: 3.771A pdb=" N ILE D 209 " --> pdb=" O VAL D 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 206 through 209' Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 229 through 240 Processing helix chain 'D' and resid 313 through 326 removed outlier: 3.629A pdb=" N ARG D 324 " --> pdb=" O LYS D 320 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN D 325 " --> pdb=" O ASN D 321 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.638A pdb=" N GLY D 330 " --> pdb=" O PRO D 327 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASN D 331 " --> pdb=" O GLU D 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 327 through 331' Processing helix chain 'D' and resid 332 through 337 removed outlier: 3.642A pdb=" N GLN D 337 " --> pdb=" O ASP D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 366 Processing helix chain 'D' and resid 426 through 430 Processing helix chain 'D' and resid 431 through 443 Processing helix chain 'D' and resid 449 through 457 removed outlier: 3.976A pdb=" N LEU D 453 " --> pdb=" O LYS D 449 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D 454 " --> pdb=" O ILE D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 524 removed outlier: 3.566A pdb=" N SER D 511 " --> pdb=" O THR D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 537 Processing helix chain 'D' and resid 538 through 550 removed outlier: 3.642A pdb=" N ASN D 550 " --> pdb=" O ILE D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 559 Processing helix chain 'D' and resid 562 through 576 removed outlier: 3.537A pdb=" N ALA D 568 " --> pdb=" O MET D 564 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS D 574 " --> pdb=" O ALA D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 588 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 245 removed outlier: 6.292A pdb=" N ILE A 52 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLU A 245 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE A 54 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA A 25 " --> pdb=" O HIS A 53 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU A 55 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU A 27 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER A 24 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N PHE A 287 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR A 26 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N THR A 289 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE A 28 " --> pdb=" O THR A 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 133 removed outlier: 4.374A pdb=" N MET A 389 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 413 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL A 346 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 248 through 257 removed outlier: 5.983A pdb=" N VAL A 250 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASP A 270 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A 252 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 266 " --> pdb=" O LYS A 254 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASP A 256 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA A 264 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AA6, first strand: chain 'B' and resid 243 through 245 removed outlier: 6.307A pdb=" N ILE B 52 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLU B 245 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE B 54 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA B 25 " --> pdb=" O HIS B 53 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU B 55 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU B 27 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N SER B 24 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N PHE B 287 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR B 26 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N THR B 289 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE B 28 " --> pdb=" O THR B 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 84 Processing sheet with id=AA8, first strand: chain 'B' and resid 132 through 133 removed outlier: 4.474A pdb=" N MET B 389 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA B 413 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL B 346 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 248 through 257 removed outlier: 5.995A pdb=" N VAL B 250 " --> pdb=" O ASP B 270 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP B 270 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 252 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 266 " --> pdb=" O LYS B 254 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASP B 256 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ALA B 264 " --> pdb=" O ASP B 256 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 4 Processing sheet with id=AB2, first strand: chain 'C' and resid 243 through 245 removed outlier: 6.300A pdb=" N ILE C 52 " --> pdb=" O GLN C 243 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLU C 245 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE C 54 " --> pdb=" O GLU C 245 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER C 24 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE C 287 " --> pdb=" O SER C 24 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TYR C 26 " --> pdb=" O PHE C 287 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N THR C 289 " --> pdb=" O TYR C 26 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE C 28 " --> pdb=" O THR C 289 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 83 through 84 Processing sheet with id=AB4, first strand: chain 'C' and resid 132 through 133 removed outlier: 4.474A pdb=" N MET C 389 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA C 413 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL C 346 " --> pdb=" O ALA C 413 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 248 through 257 removed outlier: 5.994A pdb=" N VAL C 250 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASP C 270 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP C 252 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU C 266 " --> pdb=" O LYS C 254 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ASP C 256 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ALA C 264 " --> pdb=" O ASP C 256 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 4 Processing sheet with id=AB7, first strand: chain 'D' and resid 243 through 245 removed outlier: 6.261A pdb=" N ILE D 52 " --> pdb=" O GLN D 243 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLU D 245 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILE D 54 " --> pdb=" O GLU D 245 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA D 25 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU D 55 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU D 27 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER D 24 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N PHE D 287 " --> pdb=" O SER D 24 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR D 26 " --> pdb=" O PHE D 287 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N THR D 289 " --> pdb=" O TYR D 26 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE D 28 " --> pdb=" O THR D 289 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 132 through 133 removed outlier: 4.380A pdb=" N MET D 389 " --> pdb=" O ILE D 382 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA D 413 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL D 346 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 248 through 257 removed outlier: 6.016A pdb=" N VAL D 250 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASP D 270 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP D 252 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU D 266 " --> pdb=" O LYS D 254 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASP D 256 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA D 264 " --> pdb=" O ASP D 256 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1869 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.67 Time building geometry restraints manager: 5.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6064 1.34 - 1.45: 3267 1.45 - 1.57: 9709 1.57 - 1.69: 0 1.69 - 1.80: 144 Bond restraints: 19184 Sorted by residual: bond pdb=" CB GLU B 110 " pdb=" CG GLU B 110 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.21e+00 bond pdb=" CB GLU C 110 " pdb=" CG GLU C 110 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.78e+00 bond pdb=" CB GLU D 110 " pdb=" CG GLU D 110 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.37e+00 bond pdb=" CB GLU A 110 " pdb=" CG GLU A 110 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.26e+00 bond pdb=" CG1 ILE C 427 " pdb=" CD1 ILE C 427 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.62e+00 ... (remaining 19179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 25211 1.57 - 3.13: 677 3.13 - 4.70: 73 4.70 - 6.26: 33 6.26 - 7.83: 2 Bond angle restraints: 25996 Sorted by residual: angle pdb=" N VAL D 169 " pdb=" CA VAL D 169 " pdb=" C VAL D 169 " ideal model delta sigma weight residual 113.71 110.08 3.63 9.50e-01 1.11e+00 1.46e+01 angle pdb=" N VAL A 169 " pdb=" CA VAL A 169 " pdb=" C VAL A 169 " ideal model delta sigma weight residual 113.53 109.88 3.65 9.80e-01 1.04e+00 1.39e+01 angle pdb=" N VAL C 169 " pdb=" CA VAL C 169 " pdb=" C VAL C 169 " ideal model delta sigma weight residual 113.53 109.95 3.58 9.80e-01 1.04e+00 1.34e+01 angle pdb=" N VAL B 169 " pdb=" CA VAL B 169 " pdb=" C VAL B 169 " ideal model delta sigma weight residual 113.53 109.98 3.55 9.80e-01 1.04e+00 1.31e+01 angle pdb=" C GLN C 396 " pdb=" N GLN C 397 " pdb=" CA GLN C 397 " ideal model delta sigma weight residual 121.70 127.03 -5.33 1.80e+00 3.09e-01 8.76e+00 ... (remaining 25991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.69: 10162 14.69 - 29.38: 980 29.38 - 44.08: 269 44.08 - 58.77: 49 58.77 - 73.46: 32 Dihedral angle restraints: 11492 sinusoidal: 4672 harmonic: 6820 Sorted by residual: dihedral pdb=" CA ASP B 503 " pdb=" C ASP B 503 " pdb=" N THR B 504 " pdb=" CA THR B 504 " ideal model delta harmonic sigma weight residual 180.00 -158.52 -21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ASP C 503 " pdb=" C ASP C 503 " pdb=" N THR C 504 " pdb=" CA THR C 504 " ideal model delta harmonic sigma weight residual 180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ASP A 503 " pdb=" C ASP A 503 " pdb=" N THR A 504 " pdb=" CA THR A 504 " ideal model delta harmonic sigma weight residual -180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 11489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1430 0.033 - 0.067: 975 0.067 - 0.100: 284 0.100 - 0.133: 133 0.133 - 0.167: 30 Chirality restraints: 2852 Sorted by residual: chirality pdb=" CA ILE B 380 " pdb=" N ILE B 380 " pdb=" C ILE B 380 " pdb=" CB ILE B 380 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA LYS D 589 " pdb=" N LYS D 589 " pdb=" C LYS D 589 " pdb=" CB LYS D 589 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA LYS B 589 " pdb=" N LYS B 589 " pdb=" C LYS B 589 " pdb=" CB LYS B 589 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 2849 not shown) Planarity restraints: 3336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 201 " 0.009 2.00e-02 2.50e+03 1.15e-02 2.65e+00 pdb=" CG TYR B 201 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 201 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 201 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 201 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 201 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 201 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 201 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 201 " -0.011 2.00e-02 2.50e+03 1.09e-02 2.38e+00 pdb=" CG TYR A 201 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 201 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 201 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 201 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 201 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 201 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 201 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 201 " 0.011 2.00e-02 2.50e+03 9.79e-03 1.92e+00 pdb=" CG TYR D 201 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR D 201 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR D 201 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR D 201 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR D 201 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 201 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 201 " 0.001 2.00e-02 2.50e+03 ... (remaining 3333 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4338 2.77 - 3.30: 17550 3.30 - 3.84: 32520 3.84 - 4.37: 40568 4.37 - 4.90: 67775 Nonbonded interactions: 162751 Sorted by model distance: nonbonded pdb=" OD2 ASP C 44 " pdb=" OH TYR C 520 " model vdw 2.241 3.040 nonbonded pdb=" OD2 ASP B 44 " pdb=" OH TYR B 520 " model vdw 2.241 3.040 nonbonded pdb=" OD2 ASP A 44 " pdb=" OH TYR A 520 " model vdw 2.250 3.040 nonbonded pdb=" O GLU B 356 " pdb=" OG1 THR B 360 " model vdw 2.261 3.040 nonbonded pdb=" OD2 ASP D 44 " pdb=" OH TYR D 520 " model vdw 2.263 3.040 ... (remaining 162746 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.62 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.700 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 42.070 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 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 : 0.006 0.054 19184 Z= 0.414 Angle : 0.636 7.830 25996 Z= 0.353 Chirality : 0.049 0.167 2852 Planarity : 0.004 0.033 3336 Dihedral : 13.526 73.458 7084 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: -0.82 (0.17), residues: 2300 helix: -1.11 (0.16), residues: 776 sheet: 0.07 (0.33), residues: 304 loop : -0.16 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 91 HIS 0.005 0.001 HIS A 588 PHE 0.017 0.002 PHE D 189 TYR 0.028 0.002 TYR B 201 ARG 0.004 0.001 ARG C 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 2.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.8160 (t70) cc_final: 0.7867 (t0) REVERT: A 132 GLN cc_start: 0.8786 (mp10) cc_final: 0.8281 (mp10) REVERT: A 159 GLU cc_start: 0.9048 (mp0) cc_final: 0.8749 (mp0) REVERT: A 359 ASP cc_start: 0.9320 (m-30) cc_final: 0.9066 (m-30) REVERT: A 473 MET cc_start: 0.9491 (mmm) cc_final: 0.9189 (mmm) REVERT: A 526 ASP cc_start: 0.8557 (t70) cc_final: 0.8009 (t0) REVERT: B 82 GLU cc_start: 0.7249 (pm20) cc_final: 0.7024 (pm20) REVERT: B 88 GLU cc_start: 0.9332 (mm-30) cc_final: 0.8844 (mm-30) REVERT: B 151 LEU cc_start: 0.8512 (mt) cc_final: 0.8262 (mp) REVERT: B 159 GLU cc_start: 0.9064 (mp0) cc_final: 0.8688 (pm20) REVERT: B 253 ILE cc_start: 0.9433 (mt) cc_final: 0.9194 (mp) REVERT: B 401 ASP cc_start: 0.8711 (m-30) cc_final: 0.8404 (p0) REVERT: C 159 GLU cc_start: 0.9065 (mp0) cc_final: 0.8789 (pm20) REVERT: C 253 ILE cc_start: 0.9424 (mt) cc_final: 0.9178 (mp) REVERT: D 117 GLU cc_start: 0.9094 (pt0) cc_final: 0.8604 (pp20) REVERT: D 132 GLN cc_start: 0.8862 (mp10) cc_final: 0.8330 (mp10) REVERT: D 159 GLU cc_start: 0.9085 (mp0) cc_final: 0.8713 (mp0) REVERT: D 359 ASP cc_start: 0.9319 (m-30) cc_final: 0.9061 (m-30) REVERT: D 452 ASP cc_start: 0.8904 (p0) cc_final: 0.8351 (t0) REVERT: D 473 MET cc_start: 0.9488 (mmm) cc_final: 0.9210 (mmm) REVERT: D 534 ASN cc_start: 0.9547 (p0) cc_final: 0.9096 (p0) outliers start: 0 outliers final: 1 residues processed: 226 average time/residue: 1.8793 time to fit residues: 463.7733 Evaluate side-chains 114 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 1.9990 chunk 172 optimal weight: 0.0970 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 178 optimal weight: 0.0980 chunk 69 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 22 ASN B 240 HIS B 442 HIS C 22 ASN C 240 HIS C 442 HIS C 486 HIS D 240 HIS D 331 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19184 Z= 0.188 Angle : 0.508 6.303 25996 Z= 0.271 Chirality : 0.043 0.161 2852 Planarity : 0.003 0.034 3336 Dihedral : 4.262 16.621 2506 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.82 % Allowed : 7.50 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.17 (0.18), residues: 2300 helix: 0.32 (0.18), residues: 796 sheet: 0.20 (0.33), residues: 284 loop : 0.09 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 192 HIS 0.003 0.001 HIS A 588 PHE 0.023 0.001 PHE A 506 TYR 0.011 0.001 TYR B 223 ARG 0.011 0.001 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8865 (mp10) cc_final: 0.8223 (mp10) REVERT: A 159 GLU cc_start: 0.9142 (mp0) cc_final: 0.8906 (mp0) REVERT: A 359 ASP cc_start: 0.9171 (m-30) cc_final: 0.8867 (m-30) REVERT: A 430 CYS cc_start: 0.9041 (m) cc_final: 0.8466 (m) REVERT: A 473 MET cc_start: 0.9500 (mmm) cc_final: 0.9195 (mmm) REVERT: A 526 ASP cc_start: 0.8785 (t70) cc_final: 0.8509 (p0) REVERT: A 557 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8332 (mp0) REVERT: B 159 GLU cc_start: 0.9124 (mp0) cc_final: 0.8898 (pm20) REVERT: B 401 ASP cc_start: 0.8668 (m-30) cc_final: 0.8382 (p0) REVERT: B 564 MET cc_start: 0.8924 (mmm) cc_final: 0.8523 (tmt) REVERT: B 583 SER cc_start: 0.8600 (m) cc_final: 0.8357 (p) REVERT: C 253 ILE cc_start: 0.9377 (mt) cc_final: 0.9082 (mm) REVERT: C 583 SER cc_start: 0.8568 (m) cc_final: 0.8333 (p) REVERT: D 132 GLN cc_start: 0.8908 (mp10) cc_final: 0.8262 (mp10) REVERT: D 159 GLU cc_start: 0.9137 (mp0) cc_final: 0.8786 (mp0) REVERT: D 359 ASP cc_start: 0.9153 (m-30) cc_final: 0.8839 (m-30) REVERT: D 430 CYS cc_start: 0.9087 (m) cc_final: 0.8509 (m) REVERT: D 452 ASP cc_start: 0.8827 (p0) cc_final: 0.8423 (t0) REVERT: D 473 MET cc_start: 0.9495 (mmm) cc_final: 0.9216 (mmm) REVERT: D 557 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8077 (mp0) outliers start: 17 outliers final: 4 residues processed: 156 average time/residue: 1.6494 time to fit residues: 285.5757 Evaluate side-chains 115 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 508 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 224 optimal weight: 0.7980 chunk 184 optimal weight: 0.6980 chunk 205 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 486 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 19184 Z= 0.318 Angle : 0.522 6.184 25996 Z= 0.278 Chirality : 0.045 0.160 2852 Planarity : 0.003 0.031 3336 Dihedral : 4.231 16.929 2504 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.15 % Allowed : 9.62 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.49 (0.18), residues: 2300 helix: 0.95 (0.19), residues: 796 sheet: -0.21 (0.32), residues: 304 loop : 0.17 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 113 HIS 0.005 0.001 HIS C 588 PHE 0.027 0.001 PHE A 506 TYR 0.016 0.001 TYR D 236 ARG 0.006 0.001 ARG C 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8877 (mp10) cc_final: 0.8157 (mp10) REVERT: A 159 GLU cc_start: 0.9178 (mp0) cc_final: 0.8921 (mp0) REVERT: A 359 ASP cc_start: 0.9138 (m-30) cc_final: 0.8869 (m-30) REVERT: A 430 CYS cc_start: 0.9118 (m) cc_final: 0.8600 (m) REVERT: A 473 MET cc_start: 0.9474 (mmm) cc_final: 0.9247 (mmm) REVERT: A 526 ASP cc_start: 0.8834 (t70) cc_final: 0.8434 (p0) REVERT: A 557 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8358 (mp0) REVERT: B 401 ASP cc_start: 0.8676 (m-30) cc_final: 0.8373 (p0) REVERT: C 82 GLU cc_start: 0.7672 (pm20) cc_final: 0.7366 (pm20) REVERT: C 253 ILE cc_start: 0.9332 (mt) cc_final: 0.9118 (mm) REVERT: C 506 PHE cc_start: 0.8979 (t80) cc_final: 0.8776 (t80) REVERT: D 132 GLN cc_start: 0.8843 (mp10) cc_final: 0.8076 (mp10) REVERT: D 159 GLU cc_start: 0.9136 (mp0) cc_final: 0.8829 (mp0) REVERT: D 359 ASP cc_start: 0.9141 (m-30) cc_final: 0.8788 (m-30) REVERT: D 430 CYS cc_start: 0.9138 (m) cc_final: 0.8603 (m) REVERT: D 473 MET cc_start: 0.9457 (mmm) cc_final: 0.9229 (mmm) REVERT: D 526 ASP cc_start: 0.8599 (p0) cc_final: 0.8259 (p0) outliers start: 24 outliers final: 5 residues processed: 128 average time/residue: 1.6007 time to fit residues: 228.5910 Evaluate side-chains 98 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 452 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 208 optimal weight: 0.5980 chunk 220 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 402 GLN D 240 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19184 Z= 0.160 Angle : 0.459 6.841 25996 Z= 0.244 Chirality : 0.042 0.151 2852 Planarity : 0.003 0.030 3336 Dihedral : 3.936 17.526 2504 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.01 % Allowed : 10.58 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.73 (0.18), residues: 2300 helix: 1.23 (0.19), residues: 796 sheet: 0.01 (0.33), residues: 284 loop : 0.22 (0.19), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 316 HIS 0.003 0.001 HIS C 588 PHE 0.017 0.001 PHE A 506 TYR 0.012 0.001 TYR D 223 ARG 0.004 0.000 ARG C 324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 2.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8873 (mp10) cc_final: 0.8121 (mp10) REVERT: A 159 GLU cc_start: 0.9171 (mp0) cc_final: 0.8936 (mp0) REVERT: A 430 CYS cc_start: 0.8995 (m) cc_final: 0.8441 (m) REVERT: A 465 MET cc_start: 0.9666 (mtm) cc_final: 0.9312 (mtm) REVERT: A 473 MET cc_start: 0.9460 (mmm) cc_final: 0.9195 (mmm) REVERT: A 526 ASP cc_start: 0.8879 (t70) cc_final: 0.8480 (p0) REVERT: A 557 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8363 (mp0) REVERT: B 401 ASP cc_start: 0.8643 (m-30) cc_final: 0.8343 (p0) REVERT: B 506 PHE cc_start: 0.8883 (t80) cc_final: 0.8628 (t80) REVERT: B 526 ASP cc_start: 0.8442 (t70) cc_final: 0.7991 (t0) REVERT: C 82 GLU cc_start: 0.7567 (pm20) cc_final: 0.7257 (pm20) REVERT: C 465 MET cc_start: 0.9645 (mtm) cc_final: 0.9369 (mtm) REVERT: D 83 MET cc_start: 0.7642 (mtm) cc_final: 0.7339 (mtm) REVERT: D 117 GLU cc_start: 0.8257 (pp20) cc_final: 0.8057 (pp20) REVERT: D 132 GLN cc_start: 0.8866 (mp10) cc_final: 0.8132 (mp10) REVERT: D 159 GLU cc_start: 0.9158 (mp0) cc_final: 0.8863 (mp0) REVERT: D 359 ASP cc_start: 0.9091 (m-30) cc_final: 0.8722 (m-30) REVERT: D 430 CYS cc_start: 0.9034 (m) cc_final: 0.8474 (m) REVERT: D 465 MET cc_start: 0.9683 (mtm) cc_final: 0.9347 (mtm) REVERT: D 473 MET cc_start: 0.9442 (mmm) cc_final: 0.9229 (mmm) REVERT: D 526 ASP cc_start: 0.8603 (p0) cc_final: 0.8328 (p0) outliers start: 21 outliers final: 2 residues processed: 135 average time/residue: 1.4835 time to fit residues: 225.6628 Evaluate side-chains 96 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain D residue 452 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 GLN D 240 HIS D 521 GLN D 565 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 19184 Z= 0.320 Angle : 0.513 6.830 25996 Z= 0.272 Chirality : 0.045 0.153 2852 Planarity : 0.003 0.036 3336 Dihedral : 4.133 18.249 2504 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.91 % Allowed : 11.59 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.72 (0.18), residues: 2300 helix: 1.33 (0.19), residues: 796 sheet: -0.35 (0.32), residues: 304 loop : 0.25 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 113 HIS 0.005 0.001 HIS A 588 PHE 0.020 0.001 PHE A 506 TYR 0.017 0.001 TYR D 236 ARG 0.003 0.000 ARG D 199 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 2.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7694 (mtm) cc_final: 0.7268 (mtm) REVERT: A 132 GLN cc_start: 0.8851 (mp10) cc_final: 0.8095 (mp10) REVERT: A 159 GLU cc_start: 0.9182 (mp0) cc_final: 0.8924 (mp0) REVERT: A 198 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8700 (ttt) REVERT: A 245 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.7931 (mt-10) REVERT: A 430 CYS cc_start: 0.9101 (m) cc_final: 0.8601 (m) REVERT: A 465 MET cc_start: 0.9700 (mtm) cc_final: 0.9345 (mtm) REVERT: A 473 MET cc_start: 0.9442 (mmm) cc_final: 0.9206 (mmm) REVERT: A 526 ASP cc_start: 0.8957 (t70) cc_final: 0.8455 (p0) REVERT: B 401 ASP cc_start: 0.8653 (m-30) cc_final: 0.8415 (p0) REVERT: B 526 ASP cc_start: 0.8591 (t70) cc_final: 0.8165 (t0) REVERT: C 82 GLU cc_start: 0.7759 (pm20) cc_final: 0.7533 (pm20) REVERT: C 465 MET cc_start: 0.9635 (mtm) cc_final: 0.9336 (mtm) REVERT: D 83 MET cc_start: 0.7775 (mtm) cc_final: 0.7402 (mtm) REVERT: D 117 GLU cc_start: 0.8428 (pp20) cc_final: 0.8207 (pp20) REVERT: D 132 GLN cc_start: 0.8863 (mp10) cc_final: 0.8111 (mp10) REVERT: D 198 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8638 (ttt) REVERT: D 359 ASP cc_start: 0.9129 (m-30) cc_final: 0.8784 (m-30) REVERT: D 430 CYS cc_start: 0.9071 (m) cc_final: 0.8581 (m) REVERT: D 473 MET cc_start: 0.9440 (mmm) cc_final: 0.9214 (mmm) REVERT: D 526 ASP cc_start: 0.8611 (p0) cc_final: 0.8370 (p0) outliers start: 19 outliers final: 8 residues processed: 110 average time/residue: 1.5810 time to fit residues: 194.4910 Evaluate side-chains 99 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 452 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.4980 chunk 198 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 220 optimal weight: 0.9990 chunk 183 optimal weight: 0.0470 chunk 102 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 240 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19184 Z= 0.133 Angle : 0.452 7.881 25996 Z= 0.239 Chirality : 0.042 0.151 2852 Planarity : 0.003 0.033 3336 Dihedral : 3.797 18.120 2504 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.01 % Allowed : 12.02 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.89 (0.18), residues: 2300 helix: 1.44 (0.19), residues: 800 sheet: -0.12 (0.33), residues: 284 loop : 0.32 (0.19), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.002 0.001 HIS B 588 PHE 0.013 0.001 PHE A 506 TYR 0.011 0.001 TYR D 112 ARG 0.003 0.000 ARG C 324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7680 (mtm) cc_final: 0.7419 (mtm) REVERT: A 132 GLN cc_start: 0.8851 (mp10) cc_final: 0.8104 (mp10) REVERT: A 159 GLU cc_start: 0.9182 (mp0) cc_final: 0.8931 (mp0) REVERT: A 198 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8574 (ttt) REVERT: A 401 ASP cc_start: 0.8472 (t0) cc_final: 0.8119 (p0) REVERT: A 430 CYS cc_start: 0.8967 (m) cc_final: 0.8414 (m) REVERT: A 465 MET cc_start: 0.9674 (mtm) cc_final: 0.9367 (mtm) REVERT: A 473 MET cc_start: 0.9424 (mmm) cc_final: 0.9203 (mmm) REVERT: A 526 ASP cc_start: 0.8921 (t70) cc_final: 0.8410 (p0) REVERT: A 557 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8377 (mp0) REVERT: B 401 ASP cc_start: 0.8588 (m-30) cc_final: 0.8339 (p0) REVERT: B 526 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8159 (t0) REVERT: C 198 MET cc_start: 0.9373 (tpt) cc_final: 0.9124 (tpt) REVERT: C 465 MET cc_start: 0.9620 (mtm) cc_final: 0.9346 (mtm) REVERT: D 83 MET cc_start: 0.7673 (mtm) cc_final: 0.7277 (mtm) REVERT: D 117 GLU cc_start: 0.8355 (pp20) cc_final: 0.8116 (pp20) REVERT: D 132 GLN cc_start: 0.8877 (mp10) cc_final: 0.8133 (mp10) REVERT: D 198 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8557 (ttt) REVERT: D 203 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8276 (mmm) REVERT: D 355 LYS cc_start: 0.9080 (mmmm) cc_final: 0.8366 (tppp) REVERT: D 359 ASP cc_start: 0.9092 (m-30) cc_final: 0.8663 (m-30) REVERT: D 430 CYS cc_start: 0.8981 (m) cc_final: 0.8429 (m) REVERT: D 473 MET cc_start: 0.9414 (mmm) cc_final: 0.9201 (mmm) REVERT: D 526 ASP cc_start: 0.8561 (p0) cc_final: 0.8233 (p0) outliers start: 21 outliers final: 5 residues processed: 128 average time/residue: 1.4307 time to fit residues: 206.9324 Evaluate side-chains 110 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 452 ASP Chi-restraints excluded: chain D residue 564 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 219 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19184 Z= 0.292 Angle : 0.508 9.138 25996 Z= 0.268 Chirality : 0.045 0.188 2852 Planarity : 0.003 0.035 3336 Dihedral : 4.033 18.171 2504 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.87 % Allowed : 12.16 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.86 (0.18), residues: 2300 helix: 1.51 (0.19), residues: 796 sheet: -0.41 (0.31), residues: 304 loop : 0.32 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 344 HIS 0.004 0.001 HIS B 588 PHE 0.022 0.001 PHE D 506 TYR 0.016 0.001 TYR D 236 ARG 0.003 0.000 ARG D 199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7725 (mtm) cc_final: 0.7298 (mtm) REVERT: A 132 GLN cc_start: 0.8843 (mp10) cc_final: 0.8100 (mp10) REVERT: A 159 GLU cc_start: 0.9195 (mp0) cc_final: 0.8941 (mp0) REVERT: A 198 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8702 (ttt) REVERT: A 401 ASP cc_start: 0.8562 (t0) cc_final: 0.8304 (t0) REVERT: A 430 CYS cc_start: 0.9043 (m) cc_final: 0.8571 (m) REVERT: A 465 MET cc_start: 0.9698 (mtm) cc_final: 0.9350 (mtm) REVERT: A 473 MET cc_start: 0.9427 (mmm) cc_final: 0.9196 (mmm) REVERT: A 526 ASP cc_start: 0.8976 (t70) cc_final: 0.8387 (p0) REVERT: B 401 ASP cc_start: 0.8626 (m-30) cc_final: 0.8356 (p0) REVERT: B 506 PHE cc_start: 0.9026 (t80) cc_final: 0.8809 (t80) REVERT: B 526 ASP cc_start: 0.8657 (t70) cc_final: 0.8234 (t0) REVERT: C 82 GLU cc_start: 0.7650 (pm20) cc_final: 0.7374 (pm20) REVERT: C 465 MET cc_start: 0.9638 (mtm) cc_final: 0.9344 (mtm) REVERT: D 83 MET cc_start: 0.7783 (mtm) cc_final: 0.7399 (mtm) REVERT: D 117 GLU cc_start: 0.8478 (pp20) cc_final: 0.8215 (pp20) REVERT: D 132 GLN cc_start: 0.8862 (mp10) cc_final: 0.8136 (mp10) REVERT: D 198 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8671 (ttt) REVERT: D 203 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8312 (mmm) REVERT: D 355 LYS cc_start: 0.9111 (mmmm) cc_final: 0.8449 (tppp) REVERT: D 359 ASP cc_start: 0.9082 (m-30) cc_final: 0.8664 (m-30) REVERT: D 430 CYS cc_start: 0.9046 (m) cc_final: 0.8565 (m) REVERT: D 473 MET cc_start: 0.9384 (mmm) cc_final: 0.9149 (mmm) REVERT: D 526 ASP cc_start: 0.8619 (p0) cc_final: 0.8375 (p0) outliers start: 18 outliers final: 5 residues processed: 108 average time/residue: 1.5391 time to fit residues: 186.4241 Evaluate side-chains 100 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 452 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 0.0370 chunk 42 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19184 Z= 0.148 Angle : 0.456 9.596 25996 Z= 0.240 Chirality : 0.042 0.184 2852 Planarity : 0.003 0.034 3336 Dihedral : 3.797 18.076 2504 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.67 % Allowed : 12.45 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.96 (0.18), residues: 2300 helix: 1.59 (0.19), residues: 796 sheet: -0.37 (0.31), residues: 304 loop : 0.39 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 316 HIS 0.002 0.001 HIS B 588 PHE 0.017 0.001 PHE D 506 TYR 0.010 0.001 TYR D 112 ARG 0.005 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 2.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7723 (mtm) cc_final: 0.7397 (mtt) REVERT: A 132 GLN cc_start: 0.8860 (mp10) cc_final: 0.8121 (mp10) REVERT: A 159 GLU cc_start: 0.9188 (mp0) cc_final: 0.8938 (mp0) REVERT: A 198 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8586 (ttt) REVERT: A 401 ASP cc_start: 0.8470 (t0) cc_final: 0.8233 (t0) REVERT: A 430 CYS cc_start: 0.8973 (m) cc_final: 0.8460 (m) REVERT: A 465 MET cc_start: 0.9674 (mtm) cc_final: 0.9355 (mtm) REVERT: A 473 MET cc_start: 0.9403 (mmm) cc_final: 0.9184 (mmm) REVERT: A 526 ASP cc_start: 0.8905 (t70) cc_final: 0.8361 (p0) REVERT: A 557 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8385 (mp0) REVERT: A 564 MET cc_start: 0.8473 (pmm) cc_final: 0.8218 (tmm) REVERT: B 401 ASP cc_start: 0.8620 (m-30) cc_final: 0.8304 (p0) REVERT: B 526 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8114 (t0) REVERT: C 82 GLU cc_start: 0.7589 (pm20) cc_final: 0.7284 (pm20) REVERT: C 465 MET cc_start: 0.9604 (mtm) cc_final: 0.9343 (mtm) REVERT: D 83 MET cc_start: 0.7677 (mtm) cc_final: 0.7284 (mtm) REVERT: D 117 GLU cc_start: 0.8480 (pp20) cc_final: 0.8210 (pp20) REVERT: D 132 GLN cc_start: 0.8873 (mp10) cc_final: 0.8155 (mp10) REVERT: D 198 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8569 (ttt) REVERT: D 203 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8461 (mpp) REVERT: D 355 LYS cc_start: 0.9098 (mmmm) cc_final: 0.8391 (tppp) REVERT: D 359 ASP cc_start: 0.9066 (m-30) cc_final: 0.8636 (m-30) REVERT: D 430 CYS cc_start: 0.8989 (m) cc_final: 0.8470 (m) REVERT: D 473 MET cc_start: 0.9364 (mmm) cc_final: 0.9142 (mmm) REVERT: D 526 ASP cc_start: 0.8553 (p0) cc_final: 0.8233 (p0) outliers start: 14 outliers final: 5 residues processed: 111 average time/residue: 1.4831 time to fit residues: 186.2250 Evaluate side-chains 106 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 452 ASP Chi-restraints excluded: chain D residue 539 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 7.9990 chunk 210 optimal weight: 4.9990 chunk 192 optimal weight: 0.5980 chunk 204 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19184 Z= 0.215 Angle : 0.484 9.803 25996 Z= 0.254 Chirality : 0.043 0.183 2852 Planarity : 0.003 0.041 3336 Dihedral : 3.883 17.965 2504 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.58 % Allowed : 12.55 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.96 (0.18), residues: 2300 helix: 1.58 (0.19), residues: 796 sheet: -0.35 (0.31), residues: 304 loop : 0.39 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 344 HIS 0.003 0.001 HIS B 588 PHE 0.013 0.001 PHE A 506 TYR 0.011 0.001 TYR A 236 ARG 0.011 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 2.333 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.7695 (mtm) cc_final: 0.7256 (mtm) REVERT: A 132 GLN cc_start: 0.8864 (mp10) cc_final: 0.8137 (mp10) REVERT: A 159 GLU cc_start: 0.9196 (mp0) cc_final: 0.8949 (mp0) REVERT: A 198 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8682 (ttt) REVERT: A 401 ASP cc_start: 0.8492 (t0) cc_final: 0.8256 (t0) REVERT: A 430 CYS cc_start: 0.8986 (m) cc_final: 0.8510 (m) REVERT: A 437 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7420 (mp10) REVERT: A 465 MET cc_start: 0.9681 (mtm) cc_final: 0.9360 (mtm) REVERT: A 473 MET cc_start: 0.9419 (mmm) cc_final: 0.9194 (mmm) REVERT: A 526 ASP cc_start: 0.8919 (t70) cc_final: 0.8361 (p0) REVERT: A 564 MET cc_start: 0.8499 (pmm) cc_final: 0.8184 (tmm) REVERT: B 401 ASP cc_start: 0.8558 (m-30) cc_final: 0.8296 (p0) REVERT: B 526 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8228 (t0) REVERT: C 82 GLU cc_start: 0.7601 (pm20) cc_final: 0.7258 (pm20) REVERT: C 465 MET cc_start: 0.9610 (mtm) cc_final: 0.9358 (mtm) REVERT: D 83 MET cc_start: 0.7705 (mtm) cc_final: 0.7332 (mtm) REVERT: D 117 GLU cc_start: 0.8537 (pp20) cc_final: 0.8254 (pp20) REVERT: D 132 GLN cc_start: 0.8830 (mp10) cc_final: 0.8102 (mp10) REVERT: D 198 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8619 (ttt) REVERT: D 203 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8275 (mmm) REVERT: D 355 LYS cc_start: 0.9107 (mmmm) cc_final: 0.8428 (tppp) REVERT: D 359 ASP cc_start: 0.9074 (m-30) cc_final: 0.8638 (m-30) REVERT: D 430 CYS cc_start: 0.9001 (m) cc_final: 0.8516 (m) REVERT: D 473 MET cc_start: 0.9393 (mmm) cc_final: 0.9167 (mmm) REVERT: D 526 ASP cc_start: 0.8583 (p0) cc_final: 0.8265 (p0) outliers start: 12 outliers final: 5 residues processed: 103 average time/residue: 1.5190 time to fit residues: 176.6563 Evaluate side-chains 103 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 452 ASP Chi-restraints excluded: chain D residue 539 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 227 optimal weight: 0.3980 chunk 209 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19184 Z= 0.147 Angle : 0.462 10.576 25996 Z= 0.244 Chirality : 0.042 0.180 2852 Planarity : 0.003 0.068 3336 Dihedral : 3.783 17.886 2504 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.58 % Allowed : 12.69 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 1.04 (0.18), residues: 2300 helix: 1.63 (0.19), residues: 796 sheet: -0.28 (0.31), residues: 304 loop : 0.44 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 316 HIS 0.002 0.001 HIS B 588 PHE 0.023 0.001 PHE C 506 TYR 0.013 0.001 TYR C 471 ARG 0.017 0.000 ARG B 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 2.195 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.7789 (mtm) cc_final: 0.7463 (mtt) REVERT: A 132 GLN cc_start: 0.8827 (mp10) cc_final: 0.8090 (mp10) REVERT: A 159 GLU cc_start: 0.9192 (mp0) cc_final: 0.8944 (mp0) REVERT: A 198 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8394 (ttt) REVERT: A 401 ASP cc_start: 0.8386 (t0) cc_final: 0.8163 (t0) REVERT: A 430 CYS cc_start: 0.8977 (m) cc_final: 0.8495 (m) REVERT: A 437 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7340 (mp10) REVERT: A 465 MET cc_start: 0.9651 (mtm) cc_final: 0.9360 (mtm) REVERT: A 473 MET cc_start: 0.9403 (mmm) cc_final: 0.9181 (mmm) REVERT: A 526 ASP cc_start: 0.8912 (t70) cc_final: 0.8382 (p0) REVERT: A 557 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8395 (mp0) REVERT: A 564 MET cc_start: 0.8499 (pmm) cc_final: 0.8191 (tmm) REVERT: B 401 ASP cc_start: 0.8501 (m-30) cc_final: 0.8293 (p0) REVERT: B 526 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8121 (t0) REVERT: C 449 LYS cc_start: 0.9225 (ptpt) cc_final: 0.8969 (ptmm) REVERT: C 465 MET cc_start: 0.9591 (mtm) cc_final: 0.9346 (mtm) REVERT: D 83 MET cc_start: 0.7764 (mtm) cc_final: 0.7341 (mtm) REVERT: D 117 GLU cc_start: 0.8515 (pp20) cc_final: 0.8230 (pp20) REVERT: D 132 GLN cc_start: 0.8848 (mp10) cc_final: 0.8134 (mp10) REVERT: D 198 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8587 (ttt) REVERT: D 203 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8242 (mmm) REVERT: D 355 LYS cc_start: 0.9068 (mmmm) cc_final: 0.8354 (tppp) REVERT: D 359 ASP cc_start: 0.9064 (m-30) cc_final: 0.8624 (m-30) REVERT: D 430 CYS cc_start: 0.8992 (m) cc_final: 0.8490 (m) REVERT: D 473 MET cc_start: 0.9378 (mmm) cc_final: 0.9155 (mmm) REVERT: D 526 ASP cc_start: 0.8560 (p0) cc_final: 0.8235 (p0) outliers start: 12 outliers final: 6 residues processed: 110 average time/residue: 1.4520 time to fit residues: 180.1247 Evaluate side-chains 111 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 452 ASP Chi-restraints excluded: chain D residue 539 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.073026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.055202 restraints weight = 41432.333| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 3.15 r_work: 0.2571 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19184 Z= 0.301 Angle : 0.519 9.799 25996 Z= 0.275 Chirality : 0.045 0.174 2852 Planarity : 0.004 0.084 3336 Dihedral : 4.072 18.387 2504 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.72 % Allowed : 12.69 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.97 (0.18), residues: 2300 helix: 1.54 (0.19), residues: 800 sheet: -0.39 (0.31), residues: 304 loop : 0.45 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 113 HIS 0.004 0.001 HIS B 588 PHE 0.016 0.001 PHE A 506 TYR 0.038 0.001 TYR C 471 ARG 0.019 0.001 ARG C 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4721.29 seconds wall clock time: 87 minutes 40.60 seconds (5260.60 seconds total)