Starting phenix.real_space_refine on Thu Mar 5 20:49:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mdo_23776/03_2026/7mdo_23776.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mdo_23776/03_2026/7mdo_23776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mdo_23776/03_2026/7mdo_23776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mdo_23776/03_2026/7mdo_23776.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mdo_23776/03_2026/7mdo_23776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mdo_23776/03_2026/7mdo_23776.map" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.073 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 12 5.49 5 S 132 5.16 5 C 15786 2.51 5 N 4380 2.21 5 O 4788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 107 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25098 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4156 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 502} Chain breaks: 2 Chain: "B" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4156 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 502} Chain breaks: 2 Chain: "C" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4156 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 502} Chain breaks: 2 Chain: "D" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4156 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 502} Chain breaks: 2 Chain: "E" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4156 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 502} Chain breaks: 2 Chain: "F" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4156 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 502} Chain breaks: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.51, per 1000 atoms: 0.22 Number of scatterers: 25098 At special positions: 0 Unit cell: (145.08, 141.96, 95.16, 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 132 16.00 P 12 15.00 O 4788 8.00 N 4380 7.00 C 15786 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 1.0 seconds 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5988 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 13 sheets defined 53.2% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.503A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 226 removed outlier: 5.353A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 228 through 233 removed outlier: 3.793A pdb=" N ALA A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.611A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 removed outlier: 3.671A pdb=" N MET A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 276' Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.750A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 333 removed outlier: 3.642A pdb=" N ASP A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.644A pdb=" N LYS A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 482 through 493 Processing helix chain 'A' and resid 493 through 499 Processing helix chain 'A' and resid 499 through 506 Processing helix chain 'A' and resid 526 through 534 removed outlier: 4.040A pdb=" N ALA A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 555 through 569 Processing helix chain 'A' and resid 579 through 582 removed outlier: 3.563A pdb=" N ILE A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 579 through 582' Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 649 through 663 removed outlier: 3.784A pdb=" N LYS A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 Processing helix chain 'A' and resid 683 through 703 Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 750 through 763 removed outlier: 4.008A pdb=" N LYS A 754 " --> pdb=" O ASN A 750 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE A 758 " --> pdb=" O LYS A 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 226 removed outlier: 5.297A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.741A pdb=" N ALA B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 removed outlier: 3.567A pdb=" N ALA B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 276 removed outlier: 3.817A pdb=" N MET B 275 " --> pdb=" O PRO B 272 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 276 " --> pdb=" O GLU B 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 276' Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.525A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.758A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 326 Processing helix chain 'B' and resid 327 through 333 removed outlier: 3.656A pdb=" N ASP B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 384 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.703A pdb=" N LYS B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 482 through 493 Processing helix chain 'B' and resid 493 through 499 Processing helix chain 'B' and resid 499 through 506 Processing helix chain 'B' and resid 526 through 536 removed outlier: 3.725A pdb=" N ALA B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 555 through 569 Processing helix chain 'B' and resid 579 through 582 removed outlier: 3.624A pdb=" N ILE B 582 " --> pdb=" O LEU B 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 579 through 582' Processing helix chain 'B' and resid 599 through 608 Processing helix chain 'B' and resid 649 through 663 removed outlier: 3.710A pdb=" N LYS B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 677 Processing helix chain 'B' and resid 683 through 703 Processing helix chain 'B' and resid 732 through 741 Processing helix chain 'B' and resid 750 through 763 removed outlier: 3.897A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE B 758 " --> pdb=" O LYS B 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.552A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 226 removed outlier: 5.407A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 228 through 233 removed outlier: 3.737A pdb=" N ALA C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 removed outlier: 3.610A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 276 removed outlier: 3.630A pdb=" N MET C 275 " --> pdb=" O PRO C 272 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER C 276 " --> pdb=" O GLU C 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 272 through 276' Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.565A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.773A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 333 removed outlier: 4.884A pdb=" N GLN C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 328 " --> pdb=" O ILE C 324 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 384 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 407 through 425 removed outlier: 3.559A pdb=" N LYS C 425 " --> pdb=" O GLN C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 482 through 493 removed outlier: 3.552A pdb=" N GLU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 499 Processing helix chain 'C' and resid 499 through 506 Processing helix chain 'C' and resid 526 through 535 removed outlier: 3.870A pdb=" N ALA C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 555 through 569 Processing helix chain 'C' and resid 579 through 582 removed outlier: 3.641A pdb=" N ILE C 582 " --> pdb=" O LEU C 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 579 through 582' Processing helix chain 'C' and resid 599 through 608 Processing helix chain 'C' and resid 649 through 663 removed outlier: 3.674A pdb=" N LYS C 663 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 677 Processing helix chain 'C' and resid 683 through 703 Processing helix chain 'C' and resid 732 through 741 Processing helix chain 'C' and resid 750 through 763 removed outlier: 3.981A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE C 758 " --> pdb=" O LYS C 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 226 removed outlier: 5.291A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 228 through 233 removed outlier: 3.834A pdb=" N ALA D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 removed outlier: 3.629A pdb=" N ALA D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 276 removed outlier: 3.609A pdb=" N MET D 275 " --> pdb=" O PRO D 272 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER D 276 " --> pdb=" O GLU D 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 272 through 276' Processing helix chain 'D' and resid 280 through 296 Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.754A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 326 Processing helix chain 'D' and resid 327 through 333 removed outlier: 3.671A pdb=" N ASP D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 384 Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 407 through 425 removed outlier: 3.599A pdb=" N LYS D 425 " --> pdb=" O GLN D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 482 through 493 Processing helix chain 'D' and resid 493 through 499 Processing helix chain 'D' and resid 499 through 506 Processing helix chain 'D' and resid 526 through 535 removed outlier: 3.893A pdb=" N ALA D 530 " --> pdb=" O LEU D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 555 through 569 Processing helix chain 'D' and resid 578 through 582 removed outlier: 3.656A pdb=" N ILE D 582 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 608 Processing helix chain 'D' and resid 649 through 663 removed outlier: 3.782A pdb=" N LYS D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 677 Processing helix chain 'D' and resid 683 through 703 Processing helix chain 'D' and resid 732 through 741 Processing helix chain 'D' and resid 750 through 763 removed outlier: 3.944A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE D 758 " --> pdb=" O LYS D 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.576A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 226 removed outlier: 5.377A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 228 through 233 removed outlier: 3.800A pdb=" N ALA E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 removed outlier: 3.586A pdb=" N ALA E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 276 removed outlier: 3.831A pdb=" N MET E 275 " --> pdb=" O PRO E 272 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER E 276 " --> pdb=" O GLU E 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 272 through 276' Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.572A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.770A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 326 Processing helix chain 'E' and resid 327 through 333 removed outlier: 3.700A pdb=" N ASP E 333 " --> pdb=" O LEU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 384 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 407 through 425 removed outlier: 3.641A pdb=" N LYS E 425 " --> pdb=" O GLN E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 445 Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'E' and resid 482 through 493 Processing helix chain 'E' and resid 493 through 499 Processing helix chain 'E' and resid 499 through 506 Processing helix chain 'E' and resid 526 through 535 removed outlier: 3.866A pdb=" N ALA E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 Processing helix chain 'E' and resid 555 through 569 Processing helix chain 'E' and resid 579 through 582 removed outlier: 3.604A pdb=" N ILE E 582 " --> pdb=" O LEU E 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 579 through 582' Processing helix chain 'E' and resid 599 through 608 Processing helix chain 'E' and resid 649 through 663 removed outlier: 3.676A pdb=" N LYS E 663 " --> pdb=" O ALA E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 676 Processing helix chain 'E' and resid 683 through 703 Processing helix chain 'E' and resid 732 through 741 Processing helix chain 'E' and resid 750 through 763 removed outlier: 3.911A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE E 758 " --> pdb=" O LYS E 754 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 226 removed outlier: 5.355A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 228 through 233 removed outlier: 3.602A pdb=" N ALA F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 263 removed outlier: 3.615A pdb=" N ALA F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 276 removed outlier: 3.689A pdb=" N MET F 275 " --> pdb=" O PRO F 272 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER F 276 " --> pdb=" O GLU F 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 272 through 276' Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.570A pdb=" N ASN F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.777A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 333 removed outlier: 4.854A pdb=" N GLN F 327 " --> pdb=" O ARG F 323 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU F 328 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N THR F 330 " --> pdb=" O SER F 326 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP F 333 " --> pdb=" O LEU F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 384 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 407 through 425 removed outlier: 3.571A pdb=" N LYS F 425 " --> pdb=" O GLN F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 445 Processing helix chain 'F' and resid 448 through 458 Processing helix chain 'F' and resid 482 through 493 Processing helix chain 'F' and resid 493 through 499 Processing helix chain 'F' and resid 499 through 506 Processing helix chain 'F' and resid 526 through 535 removed outlier: 3.911A pdb=" N ALA F 530 " --> pdb=" O LEU F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 Processing helix chain 'F' and resid 555 through 569 Processing helix chain 'F' and resid 579 through 582 removed outlier: 3.678A pdb=" N ILE F 582 " --> pdb=" O LEU F 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 579 through 582' Processing helix chain 'F' and resid 599 through 608 Processing helix chain 'F' and resid 649 through 663 removed outlier: 3.704A pdb=" N LYS F 663 " --> pdb=" O ALA F 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 677 Processing helix chain 'F' and resid 683 through 703 Processing helix chain 'F' and resid 732 through 741 Processing helix chain 'F' and resid 750 through 763 removed outlier: 3.983A pdb=" N LYS F 754 " --> pdb=" O ASN F 750 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE F 758 " --> pdb=" O LYS F 754 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.105A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR A 347 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.481A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.086A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR B 347 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.407A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 270 removed outlier: 7.369A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR C 347 " --> pdb=" O LEU C 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.532A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 270 removed outlier: 7.109A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR D 347 " --> pdb=" O LEU D 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 621 through 623 removed outlier: 5.600A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.526A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.977A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR E 347 " --> pdb=" O LEU E 243 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.526A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 265 through 270 removed outlier: 5.992A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR F 347 " --> pdb=" O LEU F 243 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.486A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1017 hydrogen bonds defined for protein. 3039 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: 4.06 Time building geometry restraints manager: 2.26 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: 8324 1.34 - 1.46: 3273 1.46 - 1.57: 13681 1.57 - 1.69: 18 1.69 - 1.81: 222 Bond restraints: 25518 Sorted by residual: bond pdb=" C TYR C 495 " pdb=" N PRO C 496 " ideal model delta sigma weight residual 1.336 1.357 -0.022 1.23e-02 6.61e+03 3.14e+00 bond pdb=" C TYR F 495 " pdb=" N PRO F 496 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.23e-02 6.61e+03 3.01e+00 bond pdb=" C TYR E 495 " pdb=" N PRO E 496 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.23e-02 6.61e+03 2.71e+00 bond pdb=" CA VAL B 343 " pdb=" CB VAL B 343 " ideal model delta sigma weight residual 1.533 1.552 -0.019 1.19e-02 7.06e+03 2.58e+00 bond pdb=" C TYR A 495 " pdb=" N PRO A 496 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.28e+00 ... (remaining 25513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 33143 2.41 - 4.83: 1100 4.83 - 7.24: 184 7.24 - 9.65: 38 9.65 - 12.07: 17 Bond angle restraints: 34482 Sorted by residual: angle pdb=" N MET B 275 " pdb=" CA MET B 275 " pdb=" C MET B 275 " ideal model delta sigma weight residual 114.75 106.21 8.54 1.26e+00 6.30e-01 4.59e+01 angle pdb=" N MET E 275 " pdb=" CA MET E 275 " pdb=" C MET E 275 " ideal model delta sigma weight residual 114.75 106.24 8.51 1.26e+00 6.30e-01 4.56e+01 angle pdb=" N MET A 275 " pdb=" CA MET A 275 " pdb=" C MET A 275 " ideal model delta sigma weight residual 114.75 106.28 8.47 1.26e+00 6.30e-01 4.52e+01 angle pdb=" N MET C 275 " pdb=" CA MET C 275 " pdb=" C MET C 275 " ideal model delta sigma weight residual 114.75 106.56 8.19 1.26e+00 6.30e-01 4.22e+01 angle pdb=" N MET F 275 " pdb=" CA MET F 275 " pdb=" C MET F 275 " ideal model delta sigma weight residual 114.75 106.63 8.12 1.26e+00 6.30e-01 4.15e+01 ... (remaining 34477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.08: 14728 25.08 - 50.17: 960 50.17 - 75.25: 103 75.25 - 100.33: 7 100.33 - 125.41: 6 Dihedral angle restraints: 15804 sinusoidal: 6612 harmonic: 9192 Sorted by residual: dihedral pdb=" O1B ADP E 901 " pdb=" O3A ADP E 901 " pdb=" PB ADP E 901 " pdb=" PA ADP E 901 " ideal model delta sinusoidal sigma weight residual -60.00 65.41 -125.41 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" O1B ADP D 901 " pdb=" O3A ADP D 901 " pdb=" PB ADP D 901 " pdb=" PA ADP D 901 " ideal model delta sinusoidal sigma weight residual -60.00 65.16 -125.17 1 2.00e+01 2.50e-03 3.78e+01 dihedral pdb=" O1B ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PB ADP B 901 " pdb=" PA ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 65.11 -125.12 1 2.00e+01 2.50e-03 3.78e+01 ... (remaining 15801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3339 0.083 - 0.166: 465 0.166 - 0.249: 62 0.249 - 0.332: 19 0.332 - 0.415: 9 Chirality restraints: 3894 Sorted by residual: chirality pdb=" CB ILE D 620 " pdb=" CA ILE D 620 " pdb=" CG1 ILE D 620 " pdb=" CG2 ILE D 620 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" CB ILE B 620 " pdb=" CA ILE B 620 " pdb=" CG1 ILE B 620 " pdb=" CG2 ILE B 620 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CB ILE A 620 " pdb=" CA ILE A 620 " pdb=" CG1 ILE A 620 " pdb=" CG2 ILE A 620 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.19e+00 ... (remaining 3891 not shown) Planarity restraints: 4524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 327 " -0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C GLN A 327 " 0.061 2.00e-02 2.50e+03 pdb=" O GLN A 327 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU A 328 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 327 " 0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C GLN E 327 " -0.061 2.00e-02 2.50e+03 pdb=" O GLN E 327 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU E 328 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 327 " 0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C GLN D 327 " -0.061 2.00e-02 2.50e+03 pdb=" O GLN D 327 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU D 328 " 0.021 2.00e-02 2.50e+03 ... (remaining 4521 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 6895 2.81 - 3.33: 23990 3.33 - 3.85: 42884 3.85 - 4.38: 49368 4.38 - 4.90: 79009 Nonbonded interactions: 202146 Sorted by model distance: nonbonded pdb=" O PRO F 246 " pdb=" OG1 THR F 249 " model vdw 2.283 3.040 nonbonded pdb=" O PRO C 246 " pdb=" OG1 THR C 249 " model vdw 2.286 3.040 nonbonded pdb=" O PRO B 246 " pdb=" OG1 THR B 249 " model vdw 2.291 3.040 nonbonded pdb=" O PRO E 246 " pdb=" OG1 THR E 249 " model vdw 2.293 3.040 nonbonded pdb=" O GLU F 546 " pdb=" OG1 THR F 549 " model vdw 2.303 3.040 ... (remaining 202141 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 group one per residue 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: 0.910 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 20.640 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 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 : 0.005 0.045 25518 Z= 0.226 Angle : 1.058 12.067 34482 Z= 0.567 Chirality : 0.064 0.415 3894 Planarity : 0.008 0.084 4524 Dihedral : 15.751 125.415 9816 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.13), residues: 3150 helix: -2.46 (0.10), residues: 1590 sheet: -2.22 (0.27), residues: 336 loop : -0.88 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 239 TYR 0.016 0.002 TYR D 244 PHE 0.015 0.002 PHE C 503 TRP 0.020 0.002 TRP A 476 HIS 0.013 0.002 HIS E 735 Details of bonding type rmsd covalent geometry : bond 0.00463 (25518) covalent geometry : angle 1.05812 (34482) hydrogen bonds : bond 0.15675 ( 1017) hydrogen bonds : angle 7.73155 ( 3039) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 954 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 LEU cc_start: 0.9139 (tp) cc_final: 0.8810 (tp) REVERT: A 241 ILE cc_start: 0.9394 (pt) cc_final: 0.9016 (pt) REVERT: A 278 LEU cc_start: 0.8657 (pp) cc_final: 0.7994 (mt) REVERT: A 283 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7682 (tm-30) REVERT: A 312 LYS cc_start: 0.9141 (tptt) cc_final: 0.8897 (tptt) REVERT: A 347 THR cc_start: 0.7932 (t) cc_final: 0.7675 (t) REVERT: A 449 MET cc_start: 0.8244 (mmm) cc_final: 0.7902 (tpt) REVERT: A 450 ASP cc_start: 0.8227 (p0) cc_final: 0.8019 (t0) REVERT: A 484 ASP cc_start: 0.8202 (p0) cc_final: 0.7773 (p0) REVERT: A 486 LYS cc_start: 0.8502 (mttt) cc_final: 0.8053 (mtpt) REVERT: A 488 GLU cc_start: 0.8175 (tp30) cc_final: 0.7941 (tp30) REVERT: A 503 PHE cc_start: 0.6505 (t80) cc_final: 0.6254 (t80) REVERT: A 543 LYS cc_start: 0.9304 (mmtp) cc_final: 0.8405 (mmtt) REVERT: A 546 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8681 (mp0) REVERT: A 549 THR cc_start: 0.5819 (p) cc_final: 0.5534 (p) REVERT: A 558 ASN cc_start: 0.7624 (m-40) cc_final: 0.7352 (m110) REVERT: A 565 LYS cc_start: 0.8944 (tptp) cc_final: 0.8728 (tptt) REVERT: A 678 MET cc_start: 0.6726 (ptp) cc_final: 0.6427 (ptm) REVERT: A 689 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7327 (tm-30) REVERT: A 690 ILE cc_start: 0.8940 (mm) cc_final: 0.8341 (mm) REVERT: A 692 GLN cc_start: 0.8447 (tp40) cc_final: 0.7970 (tm-30) REVERT: A 761 THR cc_start: 0.6881 (m) cc_final: 0.6491 (m) REVERT: B 217 LYS cc_start: 0.8542 (mtmm) cc_final: 0.8291 (mmtp) REVERT: B 225 ARG cc_start: 0.8447 (mmm-85) cc_final: 0.8185 (ttt180) REVERT: B 278 LEU cc_start: 0.8599 (pp) cc_final: 0.7582 (mt) REVERT: B 306 LEU cc_start: 0.9293 (tt) cc_final: 0.8842 (tp) REVERT: B 349 ARG cc_start: 0.8279 (mtm180) cc_final: 0.7972 (mtp85) REVERT: B 403 THR cc_start: 0.8492 (p) cc_final: 0.8241 (t) REVERT: B 417 GLU cc_start: 0.8578 (tp30) cc_final: 0.8309 (tp30) REVERT: B 484 ASP cc_start: 0.8487 (p0) cc_final: 0.8000 (p0) REVERT: B 508 MET cc_start: 0.0762 (mtt) cc_final: -0.0871 (mtt) REVERT: B 543 LYS cc_start: 0.9292 (mmtp) cc_final: 0.8302 (mmtm) REVERT: B 558 ASN cc_start: 0.7486 (m-40) cc_final: 0.6969 (m110) REVERT: B 560 ARG cc_start: 0.8294 (mtp-110) cc_final: 0.8084 (mtp-110) REVERT: B 662 ARG cc_start: 0.8333 (ttt90) cc_final: 0.8021 (ttt90) REVERT: B 678 MET cc_start: 0.7559 (ptp) cc_final: 0.7066 (ptp) REVERT: B 689 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7436 (tm-30) REVERT: B 690 ILE cc_start: 0.8677 (mm) cc_final: 0.8224 (mm) REVERT: B 700 ARG cc_start: 0.8785 (ttp-170) cc_final: 0.8491 (ttm170) REVERT: C 203 TYR cc_start: 0.7845 (m-10) cc_final: 0.7597 (m-10) REVERT: C 241 ILE cc_start: 0.9226 (pt) cc_final: 0.8850 (pt) REVERT: C 252 THR cc_start: 0.8639 (p) cc_final: 0.8318 (p) REVERT: C 256 ARG cc_start: 0.8498 (ttm170) cc_final: 0.8087 (ttm110) REVERT: C 262 THR cc_start: 0.8400 (m) cc_final: 0.7841 (t) REVERT: C 278 LEU cc_start: 0.8938 (pp) cc_final: 0.8556 (mt) REVERT: C 283 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7251 (tm-30) REVERT: C 306 LEU cc_start: 0.9135 (tt) cc_final: 0.8754 (tt) REVERT: C 332 MET cc_start: 0.8824 (mmp) cc_final: 0.8595 (mmm) REVERT: C 442 MET cc_start: 0.7643 (tmm) cc_final: 0.7044 (tmm) REVERT: C 482 LEU cc_start: 0.7312 (mp) cc_final: 0.7100 (mt) REVERT: C 486 LYS cc_start: 0.8369 (mttt) cc_final: 0.7792 (mmmt) REVERT: C 508 MET cc_start: 0.2332 (mtt) cc_final: 0.1474 (mtt) REVERT: C 543 LYS cc_start: 0.9127 (mmtp) cc_final: 0.8392 (mmmm) REVERT: C 560 ARG cc_start: 0.8175 (mtp-110) cc_final: 0.7863 (mtp-110) REVERT: C 562 ILE cc_start: 0.9248 (pt) cc_final: 0.9017 (tp) REVERT: C 611 MET cc_start: 0.7808 (mmp) cc_final: 0.7524 (mmp) REVERT: C 678 MET cc_start: 0.7732 (ptp) cc_final: 0.7213 (ptt) REVERT: C 689 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7827 (tm-30) REVERT: C 690 ILE cc_start: 0.8724 (mm) cc_final: 0.8147 (mm) REVERT: C 732 ARG cc_start: 0.3286 (mtm-85) cc_final: 0.2880 (mtp85) REVERT: D 203 TYR cc_start: 0.8156 (m-10) cc_final: 0.7784 (m-10) REVERT: D 221 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7503 (tm-30) REVERT: D 241 ILE cc_start: 0.9392 (pt) cc_final: 0.9174 (pt) REVERT: D 283 GLU cc_start: 0.7981 (tm-30) cc_final: 0.6550 (tm-30) REVERT: D 305 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7455 (mm-30) REVERT: D 306 LEU cc_start: 0.9138 (tt) cc_final: 0.8817 (tp) REVERT: D 352 SER cc_start: 0.9224 (m) cc_final: 0.8478 (p) REVERT: D 395 ASP cc_start: 0.8399 (m-30) cc_final: 0.7867 (p0) REVERT: D 484 ASP cc_start: 0.8757 (p0) cc_final: 0.7949 (p0) REVERT: D 543 LYS cc_start: 0.9224 (mmtp) cc_final: 0.8269 (mmmm) REVERT: D 546 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8750 (mp0) REVERT: D 611 MET cc_start: 0.7824 (mmp) cc_final: 0.7222 (mmm) REVERT: D 634 LEU cc_start: 0.7785 (tp) cc_final: 0.7552 (tt) REVERT: D 678 MET cc_start: 0.7275 (ptp) cc_final: 0.7012 (ptm) REVERT: D 689 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7395 (tm-30) REVERT: D 690 ILE cc_start: 0.8783 (mm) cc_final: 0.8102 (mm) REVERT: E 241 ILE cc_start: 0.9368 (pt) cc_final: 0.9156 (pt) REVERT: E 306 LEU cc_start: 0.9245 (tt) cc_final: 0.8791 (tp) REVERT: E 312 LYS cc_start: 0.9287 (tptt) cc_final: 0.9058 (tptt) REVERT: E 344 MET cc_start: 0.7997 (mtt) cc_final: 0.7793 (mtt) REVERT: E 478 ASP cc_start: 0.7003 (m-30) cc_final: 0.6335 (t0) REVERT: E 486 LYS cc_start: 0.8481 (mttt) cc_final: 0.8096 (mmmt) REVERT: E 494 GLN cc_start: 0.8240 (tp-100) cc_final: 0.8037 (mm110) REVERT: E 508 MET cc_start: 0.0455 (mtt) cc_final: -0.1332 (mtt) REVERT: E 526 LEU cc_start: 0.8307 (mt) cc_final: 0.8092 (mp) REVERT: E 542 ILE cc_start: 0.8856 (tp) cc_final: 0.8609 (tp) REVERT: E 546 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8713 (mp0) REVERT: E 558 ASN cc_start: 0.7504 (m-40) cc_final: 0.6990 (m-40) REVERT: E 560 ARG cc_start: 0.8225 (mtp-110) cc_final: 0.8000 (mtp-110) REVERT: E 608 MET cc_start: 0.8685 (ppp) cc_final: 0.8425 (ppp) REVERT: E 611 MET cc_start: 0.7712 (mmp) cc_final: 0.7385 (mmm) REVERT: E 643 ILE cc_start: 0.8330 (tp) cc_final: 0.7609 (mm) REVERT: E 651 LYS cc_start: 0.9157 (ptpt) cc_final: 0.8139 (pttp) REVERT: E 662 ARG cc_start: 0.8440 (ttt90) cc_final: 0.7977 (tmm160) REVERT: E 678 MET cc_start: 0.7383 (ptp) cc_final: 0.6913 (ptm) REVERT: F 203 TYR cc_start: 0.8046 (m-10) cc_final: 0.7603 (m-10) REVERT: F 221 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7568 (tm-30) REVERT: F 222 LEU cc_start: 0.9017 (tp) cc_final: 0.8768 (tp) REVERT: F 239 ARG cc_start: 0.7731 (mtp-110) cc_final: 0.7365 (mtm180) REVERT: F 241 ILE cc_start: 0.9262 (pt) cc_final: 0.8881 (pt) REVERT: F 278 LEU cc_start: 0.8826 (pp) cc_final: 0.7890 (mt) REVERT: F 307 ASP cc_start: 0.7315 (m-30) cc_final: 0.7106 (m-30) REVERT: F 312 LYS cc_start: 0.8920 (tptt) cc_final: 0.8618 (tppt) REVERT: F 327 GLN cc_start: 0.7255 (tp40) cc_final: 0.6676 (mm-40) REVERT: F 484 ASP cc_start: 0.8679 (p0) cc_final: 0.8258 (p0) REVERT: F 503 PHE cc_start: 0.6829 (t80) cc_final: 0.6503 (t80) REVERT: F 543 LYS cc_start: 0.9076 (mmtp) cc_final: 0.8379 (mmmt) REVERT: F 546 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8477 (mp0) REVERT: F 700 ARG cc_start: 0.8196 (ttp-170) cc_final: 0.7991 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 954 average time/residue: 0.1903 time to fit residues: 271.0520 Evaluate side-chains 665 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 665 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 0.0980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN A 458 GLN A 602 ASN B 404 HIS B 421 GLN B 458 GLN B 499 HIS ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN C 337 GLN C 421 GLN C 458 GLN ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN D 337 GLN D 421 GLN D 458 GLN D 533 ASN D 602 ASN E 285 ASN E 401 ASN E 421 GLN E 458 GLN ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN F 285 ASN F 458 GLN F 499 HIS F 533 ASN F 602 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.119717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.098966 restraints weight = 75980.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.102136 restraints weight = 45041.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.104340 restraints weight = 30525.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.105852 restraints weight = 22716.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.106952 restraints weight = 18105.589| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25518 Z= 0.140 Angle : 0.693 8.079 34482 Z= 0.351 Chirality : 0.045 0.162 3894 Planarity : 0.006 0.078 4524 Dihedral : 9.245 117.287 3480 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.30 % Allowed : 4.61 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.15), residues: 3150 helix: -1.01 (0.12), residues: 1584 sheet: -1.88 (0.29), residues: 318 loop : -0.52 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 465 TYR 0.020 0.002 TYR B 244 PHE 0.020 0.001 PHE E 506 TRP 0.010 0.001 TRP D 476 HIS 0.005 0.001 HIS E 735 Details of bonding type rmsd covalent geometry : bond 0.00306 (25518) covalent geometry : angle 0.69289 (34482) hydrogen bonds : bond 0.04201 ( 1017) hydrogen bonds : angle 5.60135 ( 3039) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 746 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.7904 (m-10) cc_final: 0.7282 (m-10) REVERT: A 218 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8446 (tm-30) REVERT: A 222 LEU cc_start: 0.8876 (tp) cc_final: 0.8470 (tp) REVERT: A 332 MET cc_start: 0.9245 (mmm) cc_final: 0.8911 (mmt) REVERT: A 349 ARG cc_start: 0.8295 (tpp80) cc_final: 0.7562 (mtm180) REVERT: A 359 ARG cc_start: 0.7474 (ttt180) cc_final: 0.7249 (ttt180) REVERT: A 395 ASP cc_start: 0.8450 (m-30) cc_final: 0.7563 (m-30) REVERT: A 403 THR cc_start: 0.8857 (p) cc_final: 0.8599 (t) REVERT: A 484 ASP cc_start: 0.7868 (p0) cc_final: 0.6823 (p0) REVERT: A 526 LEU cc_start: 0.8098 (mt) cc_final: 0.7789 (mp) REVERT: A 543 LYS cc_start: 0.9352 (mmtp) cc_final: 0.9098 (mmtt) REVERT: A 634 LEU cc_start: 0.7385 (tp) cc_final: 0.7177 (tp) REVERT: A 678 MET cc_start: 0.6599 (ptp) cc_final: 0.6084 (ptt) REVERT: A 689 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7568 (tm-30) REVERT: A 692 GLN cc_start: 0.8325 (tp40) cc_final: 0.7946 (tm-30) REVERT: B 225 ARG cc_start: 0.8675 (mmm-85) cc_final: 0.8071 (ttt180) REVERT: B 260 ASN cc_start: 0.8541 (m-40) cc_final: 0.7529 (m-40) REVERT: B 291 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7915 (mt-10) REVERT: B 309 ILE cc_start: 0.9294 (mp) cc_final: 0.9003 (mt) REVERT: B 312 LYS cc_start: 0.9239 (ptpp) cc_final: 0.8855 (ptpp) REVERT: B 403 THR cc_start: 0.8285 (p) cc_final: 0.7909 (t) REVERT: B 410 ASP cc_start: 0.8244 (p0) cc_final: 0.7959 (p0) REVERT: B 508 MET cc_start: 0.0353 (mtt) cc_final: -0.0345 (mtt) REVERT: B 543 LYS cc_start: 0.9138 (mmtp) cc_final: 0.8400 (mmtm) REVERT: B 546 GLU cc_start: 0.8906 (mp0) cc_final: 0.8389 (mp0) REVERT: B 550 MET cc_start: 0.5284 (mmp) cc_final: 0.4955 (mtm) REVERT: B 559 VAL cc_start: 0.8817 (t) cc_final: 0.8206 (t) REVERT: B 651 LYS cc_start: 0.9146 (ptpt) cc_final: 0.8871 (ptpt) REVERT: B 689 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7470 (tm-30) REVERT: B 690 ILE cc_start: 0.8629 (mm) cc_final: 0.8133 (mm) REVERT: B 700 ARG cc_start: 0.8819 (ttp-170) cc_final: 0.8578 (ttm170) REVERT: B 757 MET cc_start: 0.7461 (tmm) cc_final: 0.7211 (tmm) REVERT: C 219 MET cc_start: 0.8030 (tpp) cc_final: 0.7805 (tpp) REVERT: C 244 TYR cc_start: 0.8084 (p90) cc_final: 0.7864 (p90) REVERT: C 252 THR cc_start: 0.8580 (p) cc_final: 0.8289 (p) REVERT: C 256 ARG cc_start: 0.8291 (ttm170) cc_final: 0.8076 (ttm110) REVERT: C 267 PHE cc_start: 0.7995 (t80) cc_final: 0.7782 (t80) REVERT: C 312 LYS cc_start: 0.9089 (ptpt) cc_final: 0.8742 (ptpt) REVERT: C 442 MET cc_start: 0.7563 (tmm) cc_final: 0.7256 (tmm) REVERT: C 450 ASP cc_start: 0.8327 (p0) cc_final: 0.8110 (t0) REVERT: C 486 LYS cc_start: 0.8750 (mttt) cc_final: 0.8239 (mmmt) REVERT: C 508 MET cc_start: 0.2116 (mtt) cc_final: 0.1546 (mtt) REVERT: C 543 LYS cc_start: 0.9181 (mmtp) cc_final: 0.8530 (mmtp) REVERT: C 546 GLU cc_start: 0.8892 (mp0) cc_final: 0.8467 (mp0) REVERT: C 565 LYS cc_start: 0.9223 (mtpt) cc_final: 0.8705 (mmmt) REVERT: D 203 TYR cc_start: 0.8029 (m-10) cc_final: 0.7664 (m-10) REVERT: D 288 LYS cc_start: 0.9012 (mppt) cc_final: 0.8776 (mttt) REVERT: D 312 LYS cc_start: 0.8987 (ptpp) cc_final: 0.8559 (ptpp) REVERT: D 392 ASP cc_start: 0.7165 (p0) cc_final: 0.6921 (p0) REVERT: D 404 HIS cc_start: 0.7939 (p90) cc_final: 0.7627 (p90) REVERT: D 484 ASP cc_start: 0.8600 (p0) cc_final: 0.7420 (p0) REVERT: D 542 ILE cc_start: 0.8975 (tp) cc_final: 0.8765 (tp) REVERT: D 546 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8633 (mp0) REVERT: D 562 ILE cc_start: 0.9121 (tp) cc_final: 0.8895 (tp) REVERT: D 611 MET cc_start: 0.7498 (mmp) cc_final: 0.7219 (mmm) REVERT: D 668 LYS cc_start: 0.7902 (tttt) cc_final: 0.7433 (tptt) REVERT: D 678 MET cc_start: 0.7287 (ptp) cc_final: 0.6508 (ptt) REVERT: D 689 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7463 (tm-30) REVERT: D 690 ILE cc_start: 0.8890 (mm) cc_final: 0.8268 (mm) REVERT: E 222 LEU cc_start: 0.9017 (tp) cc_final: 0.8760 (tp) REVERT: E 281 GLU cc_start: 0.8386 (mp0) cc_final: 0.8099 (mp0) REVERT: E 287 ARG cc_start: 0.8206 (mmm160) cc_final: 0.7811 (mmm-85) REVERT: E 306 LEU cc_start: 0.9464 (tt) cc_final: 0.9253 (tp) REVERT: E 478 ASP cc_start: 0.6842 (m-30) cc_final: 0.6137 (t0) REVERT: E 508 MET cc_start: -0.0390 (mtt) cc_final: -0.0744 (mtt) REVERT: E 560 ARG cc_start: 0.8284 (mtp-110) cc_final: 0.8045 (mtp180) REVERT: E 601 ILE cc_start: 0.8669 (mt) cc_final: 0.8456 (mt) REVERT: E 643 ILE cc_start: 0.8382 (tp) cc_final: 0.7949 (pt) REVERT: E 651 LYS cc_start: 0.9082 (ptpt) cc_final: 0.8085 (pttp) REVERT: E 662 ARG cc_start: 0.8476 (ttt90) cc_final: 0.8076 (tmm160) REVERT: E 757 MET cc_start: 0.7303 (ttp) cc_final: 0.7065 (ppp) REVERT: F 205 ASP cc_start: 0.8224 (m-30) cc_final: 0.7582 (t0) REVERT: F 222 LEU cc_start: 0.9002 (tp) cc_final: 0.8762 (tp) REVERT: F 287 ARG cc_start: 0.7800 (mmm160) cc_final: 0.7056 (mmm-85) REVERT: F 305 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7930 (mm-30) REVERT: F 306 LEU cc_start: 0.9490 (tt) cc_final: 0.9283 (tt) REVERT: F 312 LYS cc_start: 0.8724 (tptt) cc_final: 0.8520 (tppt) REVERT: F 484 ASP cc_start: 0.8393 (p0) cc_final: 0.7722 (p0) REVERT: F 494 GLN cc_start: 0.7576 (tp-100) cc_final: 0.7353 (tp40) REVERT: F 499 HIS cc_start: 0.7734 (m90) cc_final: 0.7331 (m-70) REVERT: F 543 LYS cc_start: 0.9076 (mmtp) cc_final: 0.7741 (mmtt) REVERT: F 546 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8437 (mp0) REVERT: F 550 MET cc_start: 0.6109 (mmp) cc_final: 0.5680 (mmp) REVERT: F 560 ARG cc_start: 0.8417 (mtp-110) cc_final: 0.8144 (mtp-110) REVERT: F 561 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8258 (mm-30) outliers start: 8 outliers final: 1 residues processed: 753 average time/residue: 0.1859 time to fit residues: 209.6806 Evaluate side-chains 592 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 591 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 119 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 209 optimal weight: 0.7980 chunk 287 optimal weight: 0.9980 chunk 192 optimal weight: 9.9990 chunk 294 optimal weight: 0.2980 chunk 300 optimal weight: 2.9990 chunk 235 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 GLN E 602 ASN F 458 GLN F 602 ASN F 692 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.119774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.099021 restraints weight = 77450.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.102156 restraints weight = 45753.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.104300 restraints weight = 31004.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.105778 restraints weight = 23148.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.106842 restraints weight = 18593.501| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25518 Z= 0.138 Angle : 0.684 13.461 34482 Z= 0.344 Chirality : 0.045 0.147 3894 Planarity : 0.006 0.119 4524 Dihedral : 8.978 115.113 3480 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.04 % Allowed : 5.13 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.15), residues: 3150 helix: -0.57 (0.12), residues: 1578 sheet: -1.96 (0.30), residues: 288 loop : -0.47 (0.19), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 465 TYR 0.014 0.001 TYR C 244 PHE 0.024 0.002 PHE C 742 TRP 0.011 0.002 TRP F 476 HIS 0.007 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00310 (25518) covalent geometry : angle 0.68412 (34482) hydrogen bonds : bond 0.03842 ( 1017) hydrogen bonds : angle 5.39087 ( 3039) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 707 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.7856 (m-10) cc_final: 0.7173 (m-10) REVERT: A 219 MET cc_start: 0.7662 (tpt) cc_final: 0.7352 (tpp) REVERT: A 222 LEU cc_start: 0.8778 (tp) cc_final: 0.8446 (tp) REVERT: A 403 THR cc_start: 0.8930 (p) cc_final: 0.8691 (t) REVERT: A 449 MET cc_start: 0.7885 (mmm) cc_final: 0.7524 (mmm) REVERT: A 499 HIS cc_start: 0.6957 (m170) cc_final: 0.6716 (m170) REVERT: A 526 LEU cc_start: 0.8022 (mt) cc_final: 0.7673 (mp) REVERT: A 543 LYS cc_start: 0.9475 (mmtp) cc_final: 0.9253 (mmtt) REVERT: A 560 ARG cc_start: 0.8259 (mtp180) cc_final: 0.7875 (mtp-110) REVERT: A 577 ASP cc_start: 0.7633 (p0) cc_final: 0.7430 (p0) REVERT: A 678 MET cc_start: 0.6615 (ptp) cc_final: 0.6092 (ptt) REVERT: A 692 GLN cc_start: 0.8435 (tp40) cc_final: 0.8003 (tm-30) REVERT: A 757 MET cc_start: 0.7212 (ppp) cc_final: 0.6895 (ppp) REVERT: B 205 ASP cc_start: 0.7850 (t70) cc_final: 0.7621 (t0) REVERT: B 225 ARG cc_start: 0.8607 (mmm-85) cc_final: 0.7912 (ttt180) REVERT: B 252 THR cc_start: 0.8661 (p) cc_final: 0.8412 (t) REVERT: B 312 LYS cc_start: 0.9198 (ptpp) cc_final: 0.8894 (ptpp) REVERT: B 403 THR cc_start: 0.8477 (p) cc_final: 0.8089 (t) REVERT: B 508 MET cc_start: 0.0573 (mtt) cc_final: -0.0419 (mtt) REVERT: B 543 LYS cc_start: 0.9200 (mmtp) cc_final: 0.8410 (mmtm) REVERT: B 546 GLU cc_start: 0.8890 (mp0) cc_final: 0.8356 (mp0) REVERT: B 550 MET cc_start: 0.5705 (mmp) cc_final: 0.5436 (ttm) REVERT: B 559 VAL cc_start: 0.8818 (t) cc_final: 0.8205 (t) REVERT: B 634 LEU cc_start: 0.7877 (tt) cc_final: 0.7561 (tt) REVERT: B 651 LYS cc_start: 0.9150 (ptpt) cc_final: 0.8784 (ptpt) REVERT: B 678 MET cc_start: 0.7469 (ptp) cc_final: 0.6650 (ptm) REVERT: B 689 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7356 (tm-30) REVERT: B 690 ILE cc_start: 0.8508 (mm) cc_final: 0.8044 (mm) REVERT: C 241 ILE cc_start: 0.9162 (pt) cc_final: 0.8924 (pt) REVERT: C 244 TYR cc_start: 0.8094 (p90) cc_final: 0.7843 (p90) REVERT: C 252 THR cc_start: 0.8589 (p) cc_final: 0.8223 (p) REVERT: C 253 LEU cc_start: 0.9048 (mp) cc_final: 0.8721 (mt) REVERT: C 267 PHE cc_start: 0.7995 (t80) cc_final: 0.7635 (t80) REVERT: C 306 LEU cc_start: 0.9523 (tt) cc_final: 0.9306 (tt) REVERT: C 312 LYS cc_start: 0.9106 (ptpt) cc_final: 0.8838 (ptpt) REVERT: C 442 MET cc_start: 0.7508 (tmm) cc_final: 0.7255 (tmm) REVERT: C 450 ASP cc_start: 0.8257 (p0) cc_final: 0.8041 (t0) REVERT: C 484 ASP cc_start: 0.8760 (p0) cc_final: 0.8407 (p0) REVERT: C 543 LYS cc_start: 0.9183 (mmtp) cc_final: 0.8439 (mmtp) REVERT: C 546 GLU cc_start: 0.8764 (mp0) cc_final: 0.8405 (mp0) REVERT: C 560 ARG cc_start: 0.8086 (mtp-110) cc_final: 0.7758 (mtp-110) REVERT: C 565 LYS cc_start: 0.9197 (mtpt) cc_final: 0.8431 (mmmt) REVERT: D 221 GLU cc_start: 0.7399 (tm-30) cc_final: 0.7187 (tm-30) REVERT: D 312 LYS cc_start: 0.9245 (ptpp) cc_final: 0.8816 (ptpp) REVERT: D 404 HIS cc_start: 0.7868 (p90) cc_final: 0.7596 (p90) REVERT: D 449 MET cc_start: 0.7791 (mmm) cc_final: 0.7498 (mmm) REVERT: D 508 MET cc_start: 0.0505 (mtt) cc_final: -0.0041 (mtt) REVERT: D 543 LYS cc_start: 0.9242 (mmtp) cc_final: 0.8189 (mmmt) REVERT: D 546 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8552 (mp0) REVERT: D 561 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8013 (mm-30) REVERT: D 565 LYS cc_start: 0.9197 (mtpt) cc_final: 0.8954 (tptt) REVERT: D 611 MET cc_start: 0.7474 (mmp) cc_final: 0.7205 (mmm) REVERT: D 678 MET cc_start: 0.7047 (ptp) cc_final: 0.6366 (ptm) REVERT: D 689 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7442 (tm-30) REVERT: D 690 ILE cc_start: 0.8886 (mm) cc_final: 0.8280 (mm) REVERT: E 218 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8215 (tm-30) REVERT: E 219 MET cc_start: 0.8436 (tpp) cc_final: 0.8211 (tpp) REVERT: E 287 ARG cc_start: 0.8292 (mmm160) cc_final: 0.7952 (mmm-85) REVERT: E 306 LEU cc_start: 0.9427 (tt) cc_final: 0.9214 (tp) REVERT: E 332 MET cc_start: 0.8913 (mmm) cc_final: 0.8313 (mmm) REVERT: E 411 LEU cc_start: 0.9017 (mp) cc_final: 0.8629 (mm) REVERT: E 478 ASP cc_start: 0.7041 (m-30) cc_final: 0.6349 (t0) REVERT: E 529 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8218 (mmmt) REVERT: E 543 LYS cc_start: 0.9217 (mmtp) cc_final: 0.8205 (mmmm) REVERT: E 560 ARG cc_start: 0.8249 (mtp-110) cc_final: 0.7938 (mtp-110) REVERT: E 565 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8624 (mtmt) REVERT: E 601 ILE cc_start: 0.8665 (mt) cc_final: 0.8393 (mt) REVERT: E 643 ILE cc_start: 0.8336 (tp) cc_final: 0.7950 (pt) REVERT: E 651 LYS cc_start: 0.9063 (ptpt) cc_final: 0.8077 (pttp) REVERT: F 205 ASP cc_start: 0.8280 (m-30) cc_final: 0.7644 (t0) REVERT: F 273 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7928 (tm-30) REVERT: F 287 ARG cc_start: 0.7842 (mmm160) cc_final: 0.7296 (mmm-85) REVERT: F 306 LEU cc_start: 0.9485 (tt) cc_final: 0.9216 (tt) REVERT: F 312 LYS cc_start: 0.8748 (tptt) cc_final: 0.8531 (tppt) REVERT: F 368 ASP cc_start: 0.8182 (t0) cc_final: 0.7981 (t0) REVERT: F 449 MET cc_start: 0.7997 (mmm) cc_final: 0.7679 (mmm) REVERT: F 484 ASP cc_start: 0.8554 (p0) cc_final: 0.7832 (p0) REVERT: F 494 GLN cc_start: 0.7693 (tp-100) cc_final: 0.7455 (tp40) REVERT: F 543 LYS cc_start: 0.9195 (mmtp) cc_final: 0.8184 (mmtt) REVERT: F 546 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8390 (mp0) REVERT: F 550 MET cc_start: 0.5958 (mmp) cc_final: 0.5465 (mmp) REVERT: F 560 ARG cc_start: 0.8444 (mtp-110) cc_final: 0.7935 (mtp-110) REVERT: F 757 MET cc_start: 0.7421 (ttt) cc_final: 0.7078 (ppp) outliers start: 1 outliers final: 0 residues processed: 708 average time/residue: 0.1822 time to fit residues: 193.8699 Evaluate side-chains 544 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 298 optimal weight: 0.8980 chunk 267 optimal weight: 0.0770 chunk 59 optimal weight: 0.2980 chunk 4 optimal weight: 3.9990 chunk 284 optimal weight: 6.9990 chunk 57 optimal weight: 0.1980 chunk 171 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 308 optimal weight: 6.9990 chunk 238 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN A 602 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN D 285 ASN D 602 ASN E 285 ASN E 327 GLN E 421 GLN E 602 ASN F 285 ASN ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.119301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.099374 restraints weight = 75335.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.102536 restraints weight = 43868.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.104710 restraints weight = 29245.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.106235 restraints weight = 21401.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.107349 restraints weight = 16829.553| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25518 Z= 0.125 Angle : 0.672 7.423 34482 Z= 0.336 Chirality : 0.045 0.165 3894 Planarity : 0.005 0.072 4524 Dihedral : 8.828 122.589 3480 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.15), residues: 3150 helix: -0.29 (0.13), residues: 1572 sheet: -2.14 (0.33), residues: 234 loop : -0.48 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 359 TYR 0.015 0.001 TYR C 244 PHE 0.023 0.001 PHE E 742 TRP 0.014 0.002 TRP A 476 HIS 0.007 0.001 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00279 (25518) covalent geometry : angle 0.67210 (34482) hydrogen bonds : bond 0.03674 ( 1017) hydrogen bonds : angle 5.19429 ( 3039) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 696 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.7785 (m-10) cc_final: 0.7242 (m-10) REVERT: A 222 LEU cc_start: 0.8745 (tp) cc_final: 0.8544 (tp) REVERT: A 305 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8300 (mm-30) REVERT: A 484 ASP cc_start: 0.8382 (p0) cc_final: 0.7591 (p0) REVERT: A 486 LYS cc_start: 0.8670 (tttt) cc_final: 0.8129 (mtpt) REVERT: A 489 LEU cc_start: 0.8916 (mt) cc_final: 0.8666 (mt) REVERT: A 526 LEU cc_start: 0.7770 (mt) cc_final: 0.7484 (mp) REVERT: A 543 LYS cc_start: 0.9488 (mmtp) cc_final: 0.9218 (mmtt) REVERT: A 678 MET cc_start: 0.6636 (ptp) cc_final: 0.6110 (ptt) REVERT: A 757 MET cc_start: 0.7184 (ppp) cc_final: 0.6813 (ppp) REVERT: B 225 ARG cc_start: 0.8648 (mmm-85) cc_final: 0.7922 (ttt180) REVERT: B 252 THR cc_start: 0.8608 (p) cc_final: 0.8385 (t) REVERT: B 305 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8031 (mm-30) REVERT: B 312 LYS cc_start: 0.9115 (ptpp) cc_final: 0.8868 (ptpp) REVERT: B 368 ASP cc_start: 0.8084 (t0) cc_final: 0.7868 (t70) REVERT: B 403 THR cc_start: 0.8451 (p) cc_final: 0.8089 (t) REVERT: B 411 LEU cc_start: 0.9002 (mt) cc_final: 0.8717 (mt) REVERT: B 417 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7025 (mm-30) REVERT: B 508 MET cc_start: 0.0713 (mtt) cc_final: -0.0196 (mtt) REVERT: B 543 LYS cc_start: 0.9211 (mmtp) cc_final: 0.8821 (mmtm) REVERT: B 559 VAL cc_start: 0.8690 (t) cc_final: 0.8163 (t) REVERT: B 642 LEU cc_start: 0.9066 (pp) cc_final: 0.8817 (mp) REVERT: B 651 LYS cc_start: 0.9158 (ptpt) cc_final: 0.8854 (ptpt) REVERT: B 678 MET cc_start: 0.7360 (ptp) cc_final: 0.6514 (ptt) REVERT: B 689 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7376 (tm-30) REVERT: C 219 MET cc_start: 0.8285 (tpp) cc_final: 0.7433 (tpp) REVERT: C 244 TYR cc_start: 0.7968 (p90) cc_final: 0.7557 (p90) REVERT: C 278 LEU cc_start: 0.8722 (mt) cc_final: 0.8287 (mt) REVERT: C 281 GLU cc_start: 0.8479 (mp0) cc_final: 0.7972 (mp0) REVERT: C 306 LEU cc_start: 0.9566 (tt) cc_final: 0.9286 (tt) REVERT: C 442 MET cc_start: 0.7452 (tmm) cc_final: 0.7208 (tmm) REVERT: C 449 MET cc_start: 0.8386 (mmm) cc_final: 0.8012 (mmm) REVERT: C 484 ASP cc_start: 0.8582 (p0) cc_final: 0.8189 (p0) REVERT: C 508 MET cc_start: 0.2129 (mtt) cc_final: 0.1470 (mtt) REVERT: C 543 LYS cc_start: 0.9132 (mmtp) cc_final: 0.8184 (mmtm) REVERT: C 565 LYS cc_start: 0.9199 (mtpt) cc_final: 0.8397 (mmmt) REVERT: D 219 MET cc_start: 0.8074 (tpp) cc_final: 0.7676 (tpp) REVERT: D 221 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7437 (tm-30) REVERT: D 312 LYS cc_start: 0.9176 (ptpp) cc_final: 0.8797 (ptpp) REVERT: D 404 HIS cc_start: 0.7808 (p90) cc_final: 0.7570 (p90) REVERT: D 484 ASP cc_start: 0.8298 (p0) cc_final: 0.7511 (p0) REVERT: D 508 MET cc_start: 0.0242 (mtt) cc_final: -0.0007 (mtt) REVERT: D 543 LYS cc_start: 0.9252 (mmtp) cc_final: 0.8082 (mmmm) REVERT: D 546 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8503 (mp0) REVERT: D 562 ILE cc_start: 0.8950 (tp) cc_final: 0.8392 (tp) REVERT: D 579 LEU cc_start: 0.8408 (mt) cc_final: 0.8180 (mt) REVERT: D 678 MET cc_start: 0.7034 (ptp) cc_final: 0.6279 (ptt) REVERT: D 690 ILE cc_start: 0.8863 (mm) cc_final: 0.8254 (mm) REVERT: D 700 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7822 (ttp-110) REVERT: E 218 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8316 (tm-30) REVERT: E 219 MET cc_start: 0.8386 (tpp) cc_final: 0.8185 (tpp) REVERT: E 287 ARG cc_start: 0.8124 (mmm160) cc_final: 0.7826 (mmm-85) REVERT: E 331 LEU cc_start: 0.9290 (mm) cc_final: 0.9062 (mm) REVERT: E 332 MET cc_start: 0.9031 (mmm) cc_final: 0.8333 (mmm) REVERT: E 543 LYS cc_start: 0.8864 (mmtp) cc_final: 0.8056 (mmtp) REVERT: E 546 GLU cc_start: 0.8576 (mp0) cc_final: 0.8240 (mp0) REVERT: E 560 ARG cc_start: 0.8166 (mtp-110) cc_final: 0.7842 (mtp-110) REVERT: E 565 LYS cc_start: 0.8850 (mtpt) cc_final: 0.8601 (mtmt) REVERT: E 601 ILE cc_start: 0.8577 (mt) cc_final: 0.8336 (mt) REVERT: E 634 LEU cc_start: 0.7615 (tt) cc_final: 0.7218 (tt) REVERT: E 757 MET cc_start: 0.6720 (ppp) cc_final: 0.6368 (ppp) REVERT: F 205 ASP cc_start: 0.8282 (m-30) cc_final: 0.7668 (t0) REVERT: F 219 MET cc_start: 0.8469 (tpp) cc_final: 0.8137 (tpp) REVERT: F 241 ILE cc_start: 0.9175 (pt) cc_final: 0.8971 (pt) REVERT: F 273 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7951 (tm-30) REVERT: F 287 ARG cc_start: 0.7812 (mmm160) cc_final: 0.7427 (mmm-85) REVERT: F 306 LEU cc_start: 0.9524 (tt) cc_final: 0.9307 (tt) REVERT: F 312 LYS cc_start: 0.8605 (tptt) cc_final: 0.8384 (tppt) REVERT: F 368 ASP cc_start: 0.8192 (t0) cc_final: 0.7937 (t0) REVERT: F 484 ASP cc_start: 0.8499 (p0) cc_final: 0.7811 (p0) REVERT: F 499 HIS cc_start: 0.7522 (m90) cc_final: 0.7315 (m-70) REVERT: F 508 MET cc_start: 0.0682 (mtt) cc_final: 0.0412 (mtt) REVERT: F 543 LYS cc_start: 0.9231 (mmtp) cc_final: 0.8135 (mmtt) REVERT: F 546 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8377 (mp0) REVERT: F 550 MET cc_start: 0.5896 (mmp) cc_final: 0.5432 (mmp) REVERT: F 560 ARG cc_start: 0.8346 (mtp-110) cc_final: 0.7958 (mtp-110) REVERT: F 606 THR cc_start: 0.9129 (p) cc_final: 0.8827 (p) outliers start: 0 outliers final: 0 residues processed: 696 average time/residue: 0.1824 time to fit residues: 193.9145 Evaluate side-chains 556 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 556 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 6.9990 chunk 226 optimal weight: 0.0980 chunk 274 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN C 692 GLN D 285 ASN D 602 ASN E 602 ASN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.115808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.095943 restraints weight = 75365.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.098877 restraints weight = 45243.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.100910 restraints weight = 30956.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.102308 restraints weight = 23180.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.103282 restraints weight = 18617.894| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 25518 Z= 0.216 Angle : 0.737 7.728 34482 Z= 0.378 Chirality : 0.046 0.180 3894 Planarity : 0.006 0.065 4524 Dihedral : 8.638 112.327 3480 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.15), residues: 3150 helix: -0.40 (0.12), residues: 1608 sheet: -2.03 (0.27), residues: 306 loop : -0.16 (0.20), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 465 TYR 0.017 0.002 TYR B 495 PHE 0.034 0.002 PHE A 618 TRP 0.013 0.002 TRP D 454 HIS 0.012 0.002 HIS C 735 Details of bonding type rmsd covalent geometry : bond 0.00457 (25518) covalent geometry : angle 0.73653 (34482) hydrogen bonds : bond 0.03920 ( 1017) hydrogen bonds : angle 5.35417 ( 3039) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 660 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.7960 (m-10) cc_final: 0.7248 (m-10) REVERT: A 305 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8477 (mm-30) REVERT: A 359 ARG cc_start: 0.7742 (ttt-90) cc_final: 0.7463 (ttt90) REVERT: A 526 LEU cc_start: 0.8126 (mt) cc_final: 0.7850 (mp) REVERT: A 543 LYS cc_start: 0.9472 (mmtp) cc_final: 0.9181 (mmtt) REVERT: A 560 ARG cc_start: 0.8481 (mtp180) cc_final: 0.8006 (mtp180) REVERT: A 577 ASP cc_start: 0.7818 (p0) cc_final: 0.7267 (p0) REVERT: A 578 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7557 (mm-30) REVERT: A 634 LEU cc_start: 0.7624 (tp) cc_final: 0.7267 (tp) REVERT: A 678 MET cc_start: 0.6673 (ptp) cc_final: 0.6156 (ptt) REVERT: A 757 MET cc_start: 0.7267 (ppp) cc_final: 0.6891 (ppp) REVERT: B 225 ARG cc_start: 0.8350 (mmm-85) cc_final: 0.8102 (ttt180) REVERT: B 305 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8225 (mm-30) REVERT: B 312 LYS cc_start: 0.9247 (ptpp) cc_final: 0.8976 (ptpp) REVERT: B 543 LYS cc_start: 0.9215 (mmtp) cc_final: 0.8842 (mmtm) REVERT: B 550 MET cc_start: 0.7119 (tpp) cc_final: 0.6660 (tpp) REVERT: B 563 PHE cc_start: 0.8364 (t80) cc_final: 0.7885 (t80) REVERT: B 642 LEU cc_start: 0.9121 (pp) cc_final: 0.8818 (mp) REVERT: B 678 MET cc_start: 0.7603 (ptp) cc_final: 0.7397 (ptm) REVERT: B 689 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7487 (tm-30) REVERT: C 219 MET cc_start: 0.8436 (tpp) cc_final: 0.7610 (tpp) REVERT: C 273 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8151 (tm-30) REVERT: C 278 LEU cc_start: 0.8887 (mt) cc_final: 0.8541 (mt) REVERT: C 281 GLU cc_start: 0.8538 (mp0) cc_final: 0.8029 (mp0) REVERT: C 306 LEU cc_start: 0.9581 (tt) cc_final: 0.9264 (tt) REVERT: C 312 LYS cc_start: 0.9195 (ptpp) cc_final: 0.8969 (ptpp) REVERT: C 368 ASP cc_start: 0.8436 (t0) cc_final: 0.8194 (t0) REVERT: C 486 LYS cc_start: 0.8795 (mttt) cc_final: 0.8520 (mmmt) REVERT: C 542 ILE cc_start: 0.8587 (tp) cc_final: 0.8333 (tp) REVERT: C 543 LYS cc_start: 0.8549 (mmtp) cc_final: 0.8264 (mmtm) REVERT: C 546 GLU cc_start: 0.8207 (pm20) cc_final: 0.7725 (pm20) REVERT: C 550 MET cc_start: 0.4662 (mmp) cc_final: 0.4210 (ttm) REVERT: C 560 ARG cc_start: 0.8283 (mtp-110) cc_final: 0.8071 (mtp-110) REVERT: C 565 LYS cc_start: 0.9356 (mtpt) cc_final: 0.8668 (mmmt) REVERT: D 219 MET cc_start: 0.8079 (tpp) cc_final: 0.7651 (tpp) REVERT: D 221 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7415 (tm-30) REVERT: D 306 LEU cc_start: 0.9504 (tp) cc_final: 0.9267 (tp) REVERT: D 312 LYS cc_start: 0.9253 (ptpp) cc_final: 0.8917 (ptpp) REVERT: D 404 HIS cc_start: 0.8147 (p90) cc_final: 0.7824 (p90) REVERT: D 484 ASP cc_start: 0.8118 (p0) cc_final: 0.6786 (p0) REVERT: D 488 GLU cc_start: 0.8474 (mp0) cc_final: 0.8147 (mp0) REVERT: D 508 MET cc_start: 0.0567 (mtt) cc_final: 0.0170 (mtt) REVERT: D 543 LYS cc_start: 0.9225 (mmtp) cc_final: 0.8177 (mmmm) REVERT: D 546 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8505 (mp0) REVERT: D 611 MET cc_start: 0.7356 (mmm) cc_final: 0.7110 (mmm) REVERT: D 678 MET cc_start: 0.7087 (ptp) cc_final: 0.6329 (ptt) REVERT: D 690 ILE cc_start: 0.8923 (mm) cc_final: 0.8400 (mm) REVERT: D 700 ARG cc_start: 0.8243 (ttp80) cc_final: 0.7807 (ttm170) REVERT: E 218 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8454 (tm-30) REVERT: E 287 ARG cc_start: 0.8438 (mmm160) cc_final: 0.7925 (mmm-85) REVERT: E 332 MET cc_start: 0.8971 (mmm) cc_final: 0.8402 (mmm) REVERT: E 333 ASP cc_start: 0.8208 (m-30) cc_final: 0.7983 (m-30) REVERT: E 364 ASP cc_start: 0.8152 (m-30) cc_final: 0.7608 (p0) REVERT: E 411 LEU cc_start: 0.9140 (mp) cc_final: 0.8675 (mm) REVERT: E 543 LYS cc_start: 0.9167 (mmtp) cc_final: 0.8814 (mmpt) REVERT: E 546 GLU cc_start: 0.8862 (mp0) cc_final: 0.8548 (mp0) REVERT: E 560 ARG cc_start: 0.8251 (mtp-110) cc_final: 0.7921 (mtp-110) REVERT: E 565 LYS cc_start: 0.9041 (mtpt) cc_final: 0.8748 (mtmt) REVERT: E 601 ILE cc_start: 0.8695 (mt) cc_final: 0.8411 (mt) REVERT: E 651 LYS cc_start: 0.9147 (ptpt) cc_final: 0.8293 (pttp) REVERT: E 757 MET cc_start: 0.6818 (ppp) cc_final: 0.6520 (ppp) REVERT: F 273 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8031 (tm-30) REVERT: F 305 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8172 (mm-30) REVERT: F 306 LEU cc_start: 0.9434 (tt) cc_final: 0.9230 (tt) REVERT: F 312 LYS cc_start: 0.9022 (tptt) cc_final: 0.8583 (tppt) REVERT: F 484 ASP cc_start: 0.8470 (p0) cc_final: 0.7688 (p0) REVERT: F 499 HIS cc_start: 0.7656 (m90) cc_final: 0.7368 (m-70) REVERT: F 543 LYS cc_start: 0.9282 (mmtp) cc_final: 0.8174 (mmtm) REVERT: F 546 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8386 (mp0) REVERT: F 550 MET cc_start: 0.6161 (mmp) cc_final: 0.5563 (mmp) REVERT: F 560 ARG cc_start: 0.8603 (mtp-110) cc_final: 0.8239 (mtp-110) REVERT: F 578 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7649 (mm-30) REVERT: F 662 ARG cc_start: 0.8357 (ttt90) cc_final: 0.8014 (ttt90) outliers start: 0 outliers final: 0 residues processed: 660 average time/residue: 0.1821 time to fit residues: 182.6332 Evaluate side-chains 527 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 527 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 211 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 270 optimal weight: 0.0770 chunk 113 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 overall best weight: 0.7938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN B 660 ASN C 602 ASN D 458 GLN D 602 ASN ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 692 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.117418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.097114 restraints weight = 77441.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.100283 restraints weight = 44791.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.102383 restraints weight = 30013.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.103868 restraints weight = 22285.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.104945 restraints weight = 17755.919| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25518 Z= 0.137 Angle : 0.694 7.554 34482 Z= 0.347 Chirality : 0.046 0.195 3894 Planarity : 0.005 0.076 4524 Dihedral : 8.509 111.408 3480 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.04 % Allowed : 2.83 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.15), residues: 3150 helix: -0.39 (0.13), residues: 1614 sheet: -1.90 (0.29), residues: 288 loop : -0.27 (0.20), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 638 TYR 0.015 0.001 TYR D 517 PHE 0.027 0.001 PHE B 576 TRP 0.012 0.002 TRP E 476 HIS 0.009 0.001 HIS C 735 Details of bonding type rmsd covalent geometry : bond 0.00307 (25518) covalent geometry : angle 0.69411 (34482) hydrogen bonds : bond 0.03705 ( 1017) hydrogen bonds : angle 5.15625 ( 3039) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 674 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.8014 (tpt) cc_final: 0.7425 (tpp) REVERT: A 278 LEU cc_start: 0.8489 (mt) cc_final: 0.7759 (mt) REVERT: A 288 LYS cc_start: 0.8931 (mptt) cc_final: 0.8582 (mmtm) REVERT: A 305 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8371 (mm-30) REVERT: A 403 THR cc_start: 0.8935 (p) cc_final: 0.8657 (t) REVERT: A 486 LYS cc_start: 0.8482 (tttt) cc_final: 0.8036 (mtpt) REVERT: A 494 GLN cc_start: 0.7646 (mm110) cc_final: 0.7313 (tp40) REVERT: A 526 LEU cc_start: 0.7933 (mt) cc_final: 0.7656 (mp) REVERT: A 543 LYS cc_start: 0.9489 (mmtp) cc_final: 0.9201 (mmtt) REVERT: A 560 ARG cc_start: 0.8291 (mtp180) cc_final: 0.7760 (mtp-110) REVERT: A 619 ILE cc_start: 0.9490 (mm) cc_final: 0.9249 (pt) REVERT: A 678 MET cc_start: 0.6588 (ptp) cc_final: 0.6099 (ptt) REVERT: A 757 MET cc_start: 0.7178 (ppp) cc_final: 0.6845 (ppp) REVERT: B 225 ARG cc_start: 0.8381 (mmm-85) cc_final: 0.7704 (ttt180) REVERT: B 305 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8203 (mm-30) REVERT: B 312 LYS cc_start: 0.9238 (ptpp) cc_final: 0.8923 (ptpp) REVERT: B 332 MET cc_start: 0.8942 (mmm) cc_final: 0.8537 (mmm) REVERT: B 411 LEU cc_start: 0.9231 (mt) cc_final: 0.8930 (mt) REVERT: B 450 ASP cc_start: 0.7549 (p0) cc_final: 0.7168 (p0) REVERT: B 543 LYS cc_start: 0.9182 (mmtp) cc_final: 0.8802 (mmtm) REVERT: B 564 ASP cc_start: 0.8885 (m-30) cc_final: 0.8603 (m-30) REVERT: B 565 LYS cc_start: 0.9105 (mptt) cc_final: 0.8583 (mmmt) REVERT: B 642 LEU cc_start: 0.9089 (pp) cc_final: 0.8785 (mp) REVERT: B 662 ARG cc_start: 0.8196 (ttt90) cc_final: 0.7932 (ttt90) REVERT: B 668 LYS cc_start: 0.7401 (mttt) cc_final: 0.6706 (mptt) REVERT: B 689 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7374 (tm-30) REVERT: B 740 MET cc_start: 0.2539 (ptt) cc_final: 0.2172 (ptm) REVERT: C 241 ILE cc_start: 0.9165 (pt) cc_final: 0.8946 (pt) REVERT: C 273 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7946 (tm-30) REVERT: C 278 LEU cc_start: 0.8749 (mt) cc_final: 0.8389 (mt) REVERT: C 281 GLU cc_start: 0.8408 (mp0) cc_final: 0.7916 (mp0) REVERT: C 306 LEU cc_start: 0.9480 (tt) cc_final: 0.9255 (tt) REVERT: C 388 MET cc_start: 0.4721 (mtp) cc_final: 0.4436 (mtt) REVERT: C 492 LEU cc_start: 0.7586 (mm) cc_final: 0.7322 (mt) REVERT: C 508 MET cc_start: 0.1524 (mtt) cc_final: 0.0835 (mtt) REVERT: C 542 ILE cc_start: 0.8823 (tp) cc_final: 0.8608 (tp) REVERT: C 543 LYS cc_start: 0.9014 (mmtp) cc_final: 0.8487 (mmtp) REVERT: C 546 GLU cc_start: 0.8440 (pm20) cc_final: 0.8214 (pm20) REVERT: C 550 MET cc_start: 0.4068 (mmp) cc_final: 0.3637 (ttm) REVERT: C 560 ARG cc_start: 0.8199 (mtp-110) cc_final: 0.7958 (mtp-110) REVERT: C 576 PHE cc_start: 0.7516 (t80) cc_final: 0.7257 (t80) REVERT: D 219 MET cc_start: 0.7979 (tpp) cc_final: 0.7553 (tpp) REVERT: D 221 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7298 (tm-30) REVERT: D 312 LYS cc_start: 0.9229 (ptpp) cc_final: 0.8877 (ptpp) REVERT: D 404 HIS cc_start: 0.7790 (p90) cc_final: 0.7520 (p90) REVERT: D 484 ASP cc_start: 0.8184 (p0) cc_final: 0.7383 (p0) REVERT: D 508 MET cc_start: 0.0241 (mtt) cc_final: 0.0006 (mtt) REVERT: D 543 LYS cc_start: 0.9288 (mmtp) cc_final: 0.8155 (mmmm) REVERT: D 546 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8494 (mp0) REVERT: D 611 MET cc_start: 0.7339 (mmm) cc_final: 0.7124 (mmm) REVERT: D 678 MET cc_start: 0.6893 (ptp) cc_final: 0.6171 (ptt) REVERT: D 690 ILE cc_start: 0.8914 (mm) cc_final: 0.8415 (mm) REVERT: E 218 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8140 (tm-30) REVERT: E 287 ARG cc_start: 0.8080 (mmm160) cc_final: 0.7672 (mmm-85) REVERT: E 316 THR cc_start: 0.7517 (p) cc_final: 0.7203 (p) REVERT: E 331 LEU cc_start: 0.9252 (mm) cc_final: 0.9017 (mm) REVERT: E 332 MET cc_start: 0.8872 (mmm) cc_final: 0.8288 (mmm) REVERT: E 399 VAL cc_start: 0.8531 (t) cc_final: 0.8317 (t) REVERT: E 411 LEU cc_start: 0.9050 (mp) cc_final: 0.8592 (mm) REVERT: E 546 GLU cc_start: 0.8703 (mp0) cc_final: 0.8453 (mp0) REVERT: E 560 ARG cc_start: 0.8333 (mtp-110) cc_final: 0.7946 (mtp-110) REVERT: E 565 LYS cc_start: 0.9015 (mtpt) cc_final: 0.8700 (mtmt) REVERT: E 601 ILE cc_start: 0.8801 (mt) cc_final: 0.8583 (mt) REVERT: E 651 LYS cc_start: 0.9130 (ptpt) cc_final: 0.8234 (pttp) REVERT: F 205 ASP cc_start: 0.8380 (m-30) cc_final: 0.7707 (t0) REVERT: F 273 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7855 (tm-30) REVERT: F 306 LEU cc_start: 0.9478 (tt) cc_final: 0.9216 (tt) REVERT: F 450 ASP cc_start: 0.7957 (m-30) cc_final: 0.7398 (t0) REVERT: F 484 ASP cc_start: 0.8389 (p0) cc_final: 0.7941 (p0) REVERT: F 499 HIS cc_start: 0.7521 (m90) cc_final: 0.7201 (m-70) REVERT: F 508 MET cc_start: 0.0667 (mtt) cc_final: 0.0453 (mtt) REVERT: F 542 ILE cc_start: 0.8756 (tp) cc_final: 0.8492 (tp) REVERT: F 546 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8291 (mp0) REVERT: F 550 MET cc_start: 0.5549 (mmp) cc_final: 0.5063 (mmp) REVERT: F 560 ARG cc_start: 0.8510 (mtp-110) cc_final: 0.8252 (mtp-110) REVERT: F 578 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7520 (mm-30) REVERT: F 662 ARG cc_start: 0.8287 (ttt90) cc_final: 0.7939 (ttt90) REVERT: F 689 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7689 (tm-30) outliers start: 1 outliers final: 0 residues processed: 675 average time/residue: 0.1777 time to fit residues: 185.0368 Evaluate side-chains 547 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 547 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 216 optimal weight: 0.3980 chunk 144 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 245 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 234 optimal weight: 1.9990 chunk 226 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 222 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN B 285 ASN B 602 ASN C 533 ASN C 602 ASN D 533 ASN D 602 ASN E 602 ASN E 692 GLN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.117507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.097546 restraints weight = 75394.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.100532 restraints weight = 46031.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.102617 restraints weight = 31720.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.104058 restraints weight = 23821.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.105081 restraints weight = 19085.676| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25518 Z= 0.144 Angle : 0.700 7.578 34482 Z= 0.351 Chirality : 0.045 0.174 3894 Planarity : 0.005 0.094 4524 Dihedral : 8.426 110.218 3480 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.16), residues: 3150 helix: -0.35 (0.13), residues: 1656 sheet: -1.88 (0.29), residues: 288 loop : -0.17 (0.21), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 287 TYR 0.013 0.002 TYR F 495 PHE 0.026 0.001 PHE C 267 TRP 0.016 0.002 TRP C 476 HIS 0.009 0.001 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00320 (25518) covalent geometry : angle 0.69964 (34482) hydrogen bonds : bond 0.03605 ( 1017) hydrogen bonds : angle 5.16738 ( 3039) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 666 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.8031 (tpt) cc_final: 0.7577 (tpp) REVERT: A 287 ARG cc_start: 0.8298 (mmm-85) cc_final: 0.8072 (mmm-85) REVERT: A 288 LYS cc_start: 0.9082 (mptt) cc_final: 0.8741 (mmtm) REVERT: A 305 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8436 (mm-30) REVERT: A 403 THR cc_start: 0.8961 (p) cc_final: 0.8610 (t) REVERT: A 484 ASP cc_start: 0.8354 (p0) cc_final: 0.7727 (p0) REVERT: A 486 LYS cc_start: 0.8454 (tttt) cc_final: 0.8020 (mtpt) REVERT: A 526 LEU cc_start: 0.8032 (mt) cc_final: 0.7765 (mp) REVERT: A 542 ILE cc_start: 0.9429 (tp) cc_final: 0.9228 (tp) REVERT: A 543 LYS cc_start: 0.9478 (mmtp) cc_final: 0.9211 (mmmt) REVERT: A 550 MET cc_start: 0.6984 (tpp) cc_final: 0.6753 (tpp) REVERT: A 561 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8541 (pp20) REVERT: A 564 ASP cc_start: 0.9027 (m-30) cc_final: 0.8809 (m-30) REVERT: A 578 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7797 (mm-30) REVERT: A 606 THR cc_start: 0.9458 (p) cc_final: 0.9187 (p) REVERT: A 619 ILE cc_start: 0.9504 (mm) cc_final: 0.9268 (pt) REVERT: A 678 MET cc_start: 0.6682 (ptp) cc_final: 0.6153 (ptt) REVERT: A 757 MET cc_start: 0.7207 (ppp) cc_final: 0.6866 (ppp) REVERT: B 205 ASP cc_start: 0.8050 (t70) cc_final: 0.7846 (t0) REVERT: B 225 ARG cc_start: 0.8562 (mmm-85) cc_final: 0.7797 (ttt180) REVERT: B 312 LYS cc_start: 0.9286 (ptpp) cc_final: 0.8909 (ptpp) REVERT: B 326 SER cc_start: 0.8248 (m) cc_final: 0.7502 (p) REVERT: B 332 MET cc_start: 0.9007 (mmm) cc_final: 0.8614 (mmm) REVERT: B 411 LEU cc_start: 0.9260 (mt) cc_final: 0.8952 (mt) REVERT: B 450 ASP cc_start: 0.7683 (p0) cc_final: 0.6940 (t70) REVERT: B 508 MET cc_start: 0.0175 (mtt) cc_final: -0.0082 (mtt) REVERT: B 543 LYS cc_start: 0.9358 (mmtp) cc_final: 0.9075 (mmtm) REVERT: B 560 ARG cc_start: 0.8269 (mmm160) cc_final: 0.7705 (mmm160) REVERT: B 563 PHE cc_start: 0.8165 (t80) cc_final: 0.7662 (t80) REVERT: B 642 LEU cc_start: 0.9109 (pp) cc_final: 0.8760 (mp) REVERT: B 662 ARG cc_start: 0.8196 (ttt90) cc_final: 0.7951 (ttt90) REVERT: B 668 LYS cc_start: 0.7454 (mttt) cc_final: 0.6638 (mttp) REVERT: B 689 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7597 (tm-30) REVERT: C 273 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8064 (tm-30) REVERT: C 278 LEU cc_start: 0.8824 (mt) cc_final: 0.8458 (mt) REVERT: C 281 GLU cc_start: 0.8530 (mp0) cc_final: 0.8031 (mp0) REVERT: C 288 LYS cc_start: 0.9360 (mptt) cc_final: 0.8730 (mmtm) REVERT: C 306 LEU cc_start: 0.9517 (tt) cc_final: 0.9288 (tt) REVERT: C 388 MET cc_start: 0.4719 (mtp) cc_final: 0.4444 (mtt) REVERT: C 484 ASP cc_start: 0.8766 (p0) cc_final: 0.8461 (p0) REVERT: C 486 LYS cc_start: 0.8746 (mtpp) cc_final: 0.8193 (mmmm) REVERT: C 508 MET cc_start: 0.1505 (mtt) cc_final: 0.0908 (mtt) REVERT: C 543 LYS cc_start: 0.8777 (mmtp) cc_final: 0.8539 (mmtp) REVERT: C 550 MET cc_start: 0.3749 (mmp) cc_final: 0.3504 (ttm) REVERT: C 560 ARG cc_start: 0.8243 (mtp-110) cc_final: 0.8021 (mtp-110) REVERT: C 562 ILE cc_start: 0.9236 (tp) cc_final: 0.8810 (tp) REVERT: C 576 PHE cc_start: 0.7506 (t80) cc_final: 0.7228 (t80) REVERT: C 627 ASP cc_start: 0.8024 (m-30) cc_final: 0.7819 (m-30) REVERT: C 642 LEU cc_start: 0.8863 (mp) cc_final: 0.8660 (mp) REVERT: D 219 MET cc_start: 0.8048 (tpp) cc_final: 0.7676 (tpp) REVERT: D 221 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7378 (tm-30) REVERT: D 306 LEU cc_start: 0.9521 (tp) cc_final: 0.9241 (tt) REVERT: D 312 LYS cc_start: 0.9290 (ptpp) cc_final: 0.8977 (ptpp) REVERT: D 404 HIS cc_start: 0.8029 (p90) cc_final: 0.7741 (p90) REVERT: D 484 ASP cc_start: 0.8353 (p0) cc_final: 0.7581 (p0) REVERT: D 508 MET cc_start: 0.0311 (mtt) cc_final: 0.0111 (mtt) REVERT: D 543 LYS cc_start: 0.9207 (mmtp) cc_final: 0.8116 (mmmm) REVERT: D 546 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8484 (mp0) REVERT: D 562 ILE cc_start: 0.9479 (tp) cc_final: 0.8970 (mm) REVERT: D 611 MET cc_start: 0.7253 (mmm) cc_final: 0.6989 (mmm) REVERT: D 678 MET cc_start: 0.7071 (ptp) cc_final: 0.6304 (ptt) REVERT: D 690 ILE cc_start: 0.8891 (mm) cc_final: 0.8377 (mm) REVERT: E 218 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8289 (tm-30) REVERT: E 287 ARG cc_start: 0.8312 (mmm160) cc_final: 0.7912 (mmm-85) REVERT: E 331 LEU cc_start: 0.9359 (mm) cc_final: 0.9150 (mm) REVERT: E 332 MET cc_start: 0.9070 (mmm) cc_final: 0.8349 (mmm) REVERT: E 411 LEU cc_start: 0.9095 (mp) cc_final: 0.8580 (mm) REVERT: E 529 LYS cc_start: 0.8323 (mmmt) cc_final: 0.7966 (tptt) REVERT: E 543 LYS cc_start: 0.9195 (mmtp) cc_final: 0.8729 (mmmt) REVERT: E 546 GLU cc_start: 0.8797 (mp0) cc_final: 0.8471 (mp0) REVERT: E 560 ARG cc_start: 0.8404 (mtp-110) cc_final: 0.7998 (mtp180) REVERT: E 565 LYS cc_start: 0.9093 (mtpt) cc_final: 0.8764 (mtmt) REVERT: E 609 ASP cc_start: 0.8493 (p0) cc_final: 0.8281 (p0) REVERT: E 651 LYS cc_start: 0.9133 (ptpt) cc_final: 0.8232 (pttp) REVERT: E 757 MET cc_start: 0.6844 (ppp) cc_final: 0.6502 (ppp) REVERT: F 205 ASP cc_start: 0.8467 (m-30) cc_final: 0.7808 (t0) REVERT: F 267 PHE cc_start: 0.8167 (t80) cc_final: 0.7959 (t80) REVERT: F 273 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7868 (tm-30) REVERT: F 306 LEU cc_start: 0.9472 (tt) cc_final: 0.9208 (tt) REVERT: F 312 LYS cc_start: 0.9153 (ptpt) cc_final: 0.8920 (ptpp) REVERT: F 411 LEU cc_start: 0.8972 (mp) cc_final: 0.8687 (mm) REVERT: F 450 ASP cc_start: 0.7780 (m-30) cc_final: 0.7266 (t0) REVERT: F 484 ASP cc_start: 0.8013 (p0) cc_final: 0.7680 (p0) REVERT: F 499 HIS cc_start: 0.7895 (m90) cc_final: 0.7629 (m-70) REVERT: F 542 ILE cc_start: 0.8752 (tp) cc_final: 0.8505 (tp) REVERT: F 546 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8294 (mp0) REVERT: F 550 MET cc_start: 0.5619 (mmp) cc_final: 0.5131 (mmp) REVERT: F 560 ARG cc_start: 0.8482 (mtp-110) cc_final: 0.8230 (mtp-110) REVERT: F 561 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8479 (tp30) REVERT: F 565 LYS cc_start: 0.9152 (ptmt) cc_final: 0.8915 (ptmt) REVERT: F 578 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7608 (mm-30) REVERT: F 635 ARG cc_start: 0.5378 (tpt170) cc_final: 0.4687 (tpt170) REVERT: F 662 ARG cc_start: 0.8249 (ttt90) cc_final: 0.7883 (ttt90) REVERT: F 689 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7690 (tm-30) outliers start: 0 outliers final: 0 residues processed: 666 average time/residue: 0.1823 time to fit residues: 185.2270 Evaluate side-chains 541 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 541 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 242 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 222 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 252 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 291 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN D 602 ASN E 602 ASN F 285 ASN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.117858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.098175 restraints weight = 75567.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.101151 restraints weight = 45586.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.103201 restraints weight = 31230.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.104628 restraints weight = 23347.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.105700 restraints weight = 18681.008| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 25518 Z= 0.142 Angle : 0.717 8.043 34482 Z= 0.359 Chirality : 0.046 0.193 3894 Planarity : 0.005 0.091 4524 Dihedral : 8.381 110.288 3480 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.16), residues: 3150 helix: -0.37 (0.12), residues: 1674 sheet: -1.79 (0.29), residues: 288 loop : -0.10 (0.21), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 638 TYR 0.021 0.002 TYR F 495 PHE 0.020 0.001 PHE B 576 TRP 0.011 0.002 TRP E 476 HIS 0.012 0.001 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00320 (25518) covalent geometry : angle 0.71746 (34482) hydrogen bonds : bond 0.03573 ( 1017) hydrogen bonds : angle 5.19743 ( 3039) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 649 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 LEU cc_start: 0.8632 (mm) cc_final: 0.8224 (mt) REVERT: A 305 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8301 (mm-30) REVERT: A 403 THR cc_start: 0.8907 (p) cc_final: 0.8590 (t) REVERT: A 476 TRP cc_start: 0.8373 (m100) cc_final: 0.8105 (m100) REVERT: A 484 ASP cc_start: 0.8413 (p0) cc_final: 0.7774 (p0) REVERT: A 486 LYS cc_start: 0.8407 (tttt) cc_final: 0.7756 (mtpt) REVERT: A 526 LEU cc_start: 0.7982 (mt) cc_final: 0.7721 (mp) REVERT: A 542 ILE cc_start: 0.9412 (tp) cc_final: 0.9178 (tp) REVERT: A 543 LYS cc_start: 0.9504 (mmtp) cc_final: 0.9299 (mmmt) REVERT: A 550 MET cc_start: 0.7246 (tpp) cc_final: 0.6909 (tpp) REVERT: A 560 ARG cc_start: 0.8270 (mtp-110) cc_final: 0.7846 (mtp-110) REVERT: A 561 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8577 (mt-10) REVERT: A 564 ASP cc_start: 0.9040 (m-30) cc_final: 0.8744 (m-30) REVERT: A 578 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7751 (mm-30) REVERT: A 619 ILE cc_start: 0.9467 (mm) cc_final: 0.9238 (pt) REVERT: A 634 LEU cc_start: 0.7637 (tt) cc_final: 0.7420 (tt) REVERT: A 678 MET cc_start: 0.6695 (ptp) cc_final: 0.6164 (ptt) REVERT: A 757 MET cc_start: 0.7160 (ppp) cc_final: 0.6851 (ppp) REVERT: B 219 MET cc_start: 0.8361 (tpp) cc_final: 0.7816 (tpp) REVERT: B 225 ARG cc_start: 0.8597 (mmm-85) cc_final: 0.7882 (ttt180) REVERT: B 305 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8312 (mm-30) REVERT: B 312 LYS cc_start: 0.9262 (ptpp) cc_final: 0.8798 (ptpp) REVERT: B 326 SER cc_start: 0.8135 (m) cc_final: 0.7504 (p) REVERT: B 332 MET cc_start: 0.8977 (mmm) cc_final: 0.8606 (mmm) REVERT: B 365 ARG cc_start: 0.7269 (mpt90) cc_final: 0.7068 (mpt180) REVERT: B 403 THR cc_start: 0.8605 (p) cc_final: 0.8251 (t) REVERT: B 411 LEU cc_start: 0.9300 (mt) cc_final: 0.9094 (mt) REVERT: B 561 GLU cc_start: 0.8943 (tt0) cc_final: 0.8719 (tt0) REVERT: B 563 PHE cc_start: 0.8141 (t80) cc_final: 0.7581 (t80) REVERT: B 642 LEU cc_start: 0.9106 (pp) cc_final: 0.8771 (mp) REVERT: B 662 ARG cc_start: 0.8107 (ttt90) cc_final: 0.7893 (ttt90) REVERT: B 668 LYS cc_start: 0.7315 (mttp) cc_final: 0.6815 (mttp) REVERT: B 689 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7574 (tm-30) REVERT: C 273 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8012 (tm-30) REVERT: C 288 LYS cc_start: 0.9308 (mptt) cc_final: 0.8693 (mmtp) REVERT: C 306 LEU cc_start: 0.9517 (tt) cc_final: 0.9304 (tt) REVERT: C 319 GLU cc_start: 0.8105 (tp30) cc_final: 0.7853 (tm-30) REVERT: C 388 MET cc_start: 0.4691 (mtp) cc_final: 0.4404 (mtt) REVERT: C 486 LYS cc_start: 0.8617 (mtpp) cc_final: 0.8084 (mmmm) REVERT: C 508 MET cc_start: 0.1445 (mtt) cc_final: 0.0832 (mtt) REVERT: C 560 ARG cc_start: 0.8259 (mtp-110) cc_final: 0.8059 (mtp-110) REVERT: C 576 PHE cc_start: 0.7429 (t80) cc_final: 0.7018 (t80) REVERT: C 577 ASP cc_start: 0.7974 (p0) cc_final: 0.7756 (p0) REVERT: C 642 LEU cc_start: 0.8831 (mp) cc_final: 0.8618 (mp) REVERT: C 668 LYS cc_start: 0.6898 (ptpt) cc_final: 0.6385 (ptpt) REVERT: D 219 MET cc_start: 0.7906 (tpp) cc_final: 0.7552 (tpp) REVERT: D 295 LYS cc_start: 0.9101 (ptpp) cc_final: 0.8846 (pttm) REVERT: D 305 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8193 (mm-30) REVERT: D 306 LEU cc_start: 0.9518 (tp) cc_final: 0.9205 (tt) REVERT: D 312 LYS cc_start: 0.9224 (ptpp) cc_final: 0.8794 (ptpp) REVERT: D 465 ARG cc_start: 0.6555 (mmt90) cc_final: 0.5552 (mmp80) REVERT: D 484 ASP cc_start: 0.8311 (p0) cc_final: 0.7491 (p0) REVERT: D 543 LYS cc_start: 0.9277 (mmtp) cc_final: 0.8145 (mmmm) REVERT: D 546 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8488 (mp0) REVERT: D 611 MET cc_start: 0.7239 (mmm) cc_final: 0.7003 (mmm) REVERT: D 678 MET cc_start: 0.7055 (ptp) cc_final: 0.6299 (ptt) REVERT: D 690 ILE cc_start: 0.8862 (mm) cc_final: 0.8361 (mm) REVERT: E 219 MET cc_start: 0.8572 (tpp) cc_final: 0.8044 (tpp) REVERT: E 287 ARG cc_start: 0.8076 (mmm160) cc_final: 0.7738 (mmm-85) REVERT: E 312 LYS cc_start: 0.9414 (ptpt) cc_final: 0.9144 (ptpp) REVERT: E 331 LEU cc_start: 0.9319 (mm) cc_final: 0.9035 (mm) REVERT: E 332 MET cc_start: 0.9043 (mmm) cc_final: 0.8339 (mmm) REVERT: E 411 LEU cc_start: 0.9076 (mp) cc_final: 0.8625 (mm) REVERT: E 529 LYS cc_start: 0.8312 (mmmt) cc_final: 0.7875 (tptt) REVERT: E 543 LYS cc_start: 0.9194 (mmtp) cc_final: 0.8773 (mmmt) REVERT: E 546 GLU cc_start: 0.8774 (mp0) cc_final: 0.8409 (mp0) REVERT: E 560 ARG cc_start: 0.8394 (mtp-110) cc_final: 0.8159 (mtp180) REVERT: E 601 ILE cc_start: 0.8995 (mt) cc_final: 0.8788 (mt) REVERT: E 651 LYS cc_start: 0.9137 (ptpt) cc_final: 0.8230 (pttp) REVERT: E 757 MET cc_start: 0.6843 (ppp) cc_final: 0.6509 (ppp) REVERT: F 205 ASP cc_start: 0.8397 (m-30) cc_final: 0.7772 (t0) REVERT: F 306 LEU cc_start: 0.9496 (tt) cc_final: 0.9203 (tt) REVERT: F 312 LYS cc_start: 0.9209 (ptpt) cc_final: 0.8894 (ptpp) REVERT: F 411 LEU cc_start: 0.8969 (mp) cc_final: 0.8683 (mm) REVERT: F 450 ASP cc_start: 0.7523 (m-30) cc_final: 0.7107 (t0) REVERT: F 484 ASP cc_start: 0.7892 (p0) cc_final: 0.7647 (p0) REVERT: F 499 HIS cc_start: 0.7856 (m90) cc_final: 0.7569 (m-70) REVERT: F 543 LYS cc_start: 0.9076 (mmtp) cc_final: 0.7903 (mmtm) REVERT: F 546 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8377 (mp0) REVERT: F 550 MET cc_start: 0.5609 (mmp) cc_final: 0.5111 (mmp) REVERT: F 565 LYS cc_start: 0.9103 (ptmt) cc_final: 0.8878 (ptmt) REVERT: F 662 ARG cc_start: 0.8200 (ttt90) cc_final: 0.7834 (ttt90) REVERT: F 668 LYS cc_start: 0.7559 (tptt) cc_final: 0.7331 (tptt) REVERT: F 689 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7689 (tm-30) outliers start: 0 outliers final: 0 residues processed: 649 average time/residue: 0.1863 time to fit residues: 183.3742 Evaluate side-chains 534 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 534 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 260 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 182 optimal weight: 0.5980 chunk 198 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 185 optimal weight: 9.9990 chunk 195 optimal weight: 0.9980 chunk 224 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 602 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN B 421 GLN B 602 ASN ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN D 602 ASN E 602 ASN F 327 GLN F 494 GLN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.117984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.098700 restraints weight = 75221.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.101483 restraints weight = 46588.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.103421 restraints weight = 32411.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.104770 restraints weight = 24503.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.105666 restraints weight = 19773.828| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25518 Z= 0.143 Angle : 0.728 11.785 34482 Z= 0.362 Chirality : 0.046 0.200 3894 Planarity : 0.005 0.083 4524 Dihedral : 8.356 110.485 3480 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.04 % Allowed : 1.23 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.16), residues: 3150 helix: -0.28 (0.13), residues: 1620 sheet: -1.92 (0.29), residues: 288 loop : -0.04 (0.20), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 635 TYR 0.023 0.001 TYR F 495 PHE 0.027 0.001 PHE C 267 TRP 0.016 0.002 TRP F 476 HIS 0.012 0.001 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00323 (25518) covalent geometry : angle 0.72808 (34482) hydrogen bonds : bond 0.03592 ( 1017) hydrogen bonds : angle 5.22662 ( 3039) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 638 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8302 (mm-30) REVERT: A 403 THR cc_start: 0.8908 (p) cc_final: 0.8621 (t) REVERT: A 476 TRP cc_start: 0.8396 (m100) cc_final: 0.8139 (m100) REVERT: A 484 ASP cc_start: 0.8419 (p0) cc_final: 0.7892 (p0) REVERT: A 486 LYS cc_start: 0.8346 (tttt) cc_final: 0.7761 (mtpt) REVERT: A 526 LEU cc_start: 0.7986 (mt) cc_final: 0.7726 (mp) REVERT: A 542 ILE cc_start: 0.9403 (tp) cc_final: 0.9169 (tp) REVERT: A 543 LYS cc_start: 0.9511 (mmtp) cc_final: 0.9298 (mmmt) REVERT: A 550 MET cc_start: 0.7238 (tpp) cc_final: 0.6961 (tpp) REVERT: A 560 ARG cc_start: 0.8259 (mtp-110) cc_final: 0.7917 (mtp-110) REVERT: A 564 ASP cc_start: 0.8954 (m-30) cc_final: 0.8737 (m-30) REVERT: A 578 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7760 (mm-30) REVERT: A 619 ILE cc_start: 0.9458 (mm) cc_final: 0.9257 (pt) REVERT: A 678 MET cc_start: 0.6693 (ptp) cc_final: 0.6177 (ptt) REVERT: A 757 MET cc_start: 0.7131 (ppp) cc_final: 0.6921 (ppp) REVERT: B 218 GLU cc_start: 0.9111 (pp20) cc_final: 0.8274 (tm-30) REVERT: B 219 MET cc_start: 0.8318 (tpp) cc_final: 0.7987 (tpp) REVERT: B 225 ARG cc_start: 0.8586 (mmm-85) cc_final: 0.7830 (ttt180) REVERT: B 305 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8229 (mm-30) REVERT: B 312 LYS cc_start: 0.9211 (ptpp) cc_final: 0.8799 (ptpp) REVERT: B 326 SER cc_start: 0.8144 (m) cc_final: 0.7463 (p) REVERT: B 332 MET cc_start: 0.8939 (mmm) cc_final: 0.8723 (mmm) REVERT: B 403 THR cc_start: 0.8571 (p) cc_final: 0.8258 (t) REVERT: B 411 LEU cc_start: 0.9268 (mt) cc_final: 0.9067 (mt) REVERT: B 508 MET cc_start: -0.0189 (mtt) cc_final: -0.0561 (mtt) REVERT: B 561 GLU cc_start: 0.8886 (tt0) cc_final: 0.8190 (mt-10) REVERT: B 563 PHE cc_start: 0.8139 (t80) cc_final: 0.7515 (t80) REVERT: B 642 LEU cc_start: 0.9083 (pp) cc_final: 0.8791 (mp) REVERT: B 689 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7564 (tm-30) REVERT: C 288 LYS cc_start: 0.9309 (mptt) cc_final: 0.8703 (mmtp) REVERT: C 306 LEU cc_start: 0.9596 (tt) cc_final: 0.9301 (tt) REVERT: C 319 GLU cc_start: 0.8208 (tp30) cc_final: 0.7962 (tm-30) REVERT: C 388 MET cc_start: 0.4628 (mtp) cc_final: 0.4392 (mtt) REVERT: C 450 ASP cc_start: 0.8110 (m-30) cc_final: 0.7667 (t70) REVERT: C 484 ASP cc_start: 0.8751 (p0) cc_final: 0.8478 (p0) REVERT: C 486 LYS cc_start: 0.8606 (mtpp) cc_final: 0.8093 (mmmm) REVERT: C 508 MET cc_start: 0.2110 (mtt) cc_final: 0.1489 (mtt) REVERT: C 561 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8296 (tp30) REVERT: C 562 ILE cc_start: 0.9336 (tp) cc_final: 0.9133 (mt) REVERT: C 576 PHE cc_start: 0.7178 (t80) cc_final: 0.6701 (t80) REVERT: C 577 ASP cc_start: 0.7965 (p0) cc_final: 0.7671 (p0) REVERT: C 642 LEU cc_start: 0.8813 (mp) cc_final: 0.8605 (mp) REVERT: C 668 LYS cc_start: 0.6899 (ptpt) cc_final: 0.6378 (ptpt) REVERT: D 219 MET cc_start: 0.7911 (tpp) cc_final: 0.7614 (tpp) REVERT: D 221 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7155 (tm-30) REVERT: D 225 ARG cc_start: 0.8646 (mmm-85) cc_final: 0.7905 (ttt180) REVERT: D 305 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8157 (mm-30) REVERT: D 306 LEU cc_start: 0.9479 (tp) cc_final: 0.9242 (tt) REVERT: D 312 LYS cc_start: 0.9333 (ptpp) cc_final: 0.8916 (ptpp) REVERT: D 465 ARG cc_start: 0.6367 (mmt90) cc_final: 0.5744 (mmm160) REVERT: D 484 ASP cc_start: 0.8291 (p0) cc_final: 0.7741 (p0) REVERT: D 543 LYS cc_start: 0.9271 (mmtp) cc_final: 0.8134 (mmmm) REVERT: D 546 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8495 (mp0) REVERT: D 550 MET cc_start: 0.5115 (mmp) cc_final: 0.4621 (ttm) REVERT: D 611 MET cc_start: 0.7240 (mmm) cc_final: 0.7036 (mmm) REVERT: D 678 MET cc_start: 0.7046 (ptp) cc_final: 0.6296 (ptt) REVERT: D 690 ILE cc_start: 0.8850 (mm) cc_final: 0.8347 (mm) REVERT: D 700 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7794 (ttm170) REVERT: E 218 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8150 (tm-30) REVERT: E 219 MET cc_start: 0.8596 (tpp) cc_final: 0.7991 (tpp) REVERT: E 312 LYS cc_start: 0.9384 (ptpt) cc_final: 0.9137 (ptpp) REVERT: E 332 MET cc_start: 0.9087 (mmm) cc_final: 0.8823 (mmp) REVERT: E 411 LEU cc_start: 0.9035 (mp) cc_final: 0.8548 (mm) REVERT: E 529 LYS cc_start: 0.8294 (mmmt) cc_final: 0.7874 (tptt) REVERT: E 543 LYS cc_start: 0.9207 (mmtp) cc_final: 0.8785 (mmmt) REVERT: E 546 GLU cc_start: 0.8813 (mp0) cc_final: 0.8463 (mp0) REVERT: E 560 ARG cc_start: 0.8369 (mtp-110) cc_final: 0.8118 (mtp180) REVERT: E 651 LYS cc_start: 0.9135 (ptpt) cc_final: 0.8231 (pttp) REVERT: E 757 MET cc_start: 0.6802 (ppp) cc_final: 0.6520 (ppp) REVERT: F 205 ASP cc_start: 0.8344 (m-30) cc_final: 0.7744 (t0) REVERT: F 273 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7914 (tm-30) REVERT: F 312 LYS cc_start: 0.9210 (ptpt) cc_final: 0.8909 (ptpp) REVERT: F 450 ASP cc_start: 0.7622 (m-30) cc_final: 0.7159 (t0) REVERT: F 484 ASP cc_start: 0.8582 (p0) cc_final: 0.8140 (p0) REVERT: F 499 HIS cc_start: 0.7863 (m90) cc_final: 0.7578 (m-70) REVERT: F 543 LYS cc_start: 0.9176 (mmtp) cc_final: 0.7963 (mmtm) REVERT: F 546 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8311 (mp0) REVERT: F 550 MET cc_start: 0.5669 (mmp) cc_final: 0.5169 (mmp) REVERT: F 560 ARG cc_start: 0.8379 (mtp-110) cc_final: 0.8152 (mtp-110) REVERT: F 662 ARG cc_start: 0.8190 (ttt90) cc_final: 0.7744 (ttt90) REVERT: F 689 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7681 (tm-30) outliers start: 1 outliers final: 0 residues processed: 638 average time/residue: 0.1801 time to fit residues: 175.6668 Evaluate side-chains 514 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 514 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 36 optimal weight: 4.9990 chunk 280 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 267 optimal weight: 0.8980 chunk 218 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 270 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN C 602 ASN D 602 ASN ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN F 327 GLN F 340 HIS F 494 GLN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.117299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.097612 restraints weight = 76246.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.100566 restraints weight = 45999.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.102564 restraints weight = 31474.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.103942 restraints weight = 23621.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.104962 restraints weight = 19050.640| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25518 Z= 0.153 Angle : 0.743 13.051 34482 Z= 0.372 Chirality : 0.046 0.182 3894 Planarity : 0.005 0.059 4524 Dihedral : 8.349 110.109 3480 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.04 % Allowed : 0.63 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.16), residues: 3150 helix: -0.26 (0.13), residues: 1614 sheet: -1.38 (0.36), residues: 192 loop : -0.10 (0.20), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 638 TYR 0.023 0.002 TYR F 495 PHE 0.017 0.001 PHE B 576 TRP 0.013 0.002 TRP F 476 HIS 0.011 0.001 HIS D 735 Details of bonding type rmsd covalent geometry : bond 0.00342 (25518) covalent geometry : angle 0.74303 (34482) hydrogen bonds : bond 0.03624 ( 1017) hydrogen bonds : angle 5.29025 ( 3039) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 639 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8368 (mm-30) REVERT: A 403 THR cc_start: 0.9040 (p) cc_final: 0.8689 (t) REVERT: A 476 TRP cc_start: 0.8481 (m100) cc_final: 0.8233 (m100) REVERT: A 484 ASP cc_start: 0.8489 (p0) cc_final: 0.8022 (p0) REVERT: A 486 LYS cc_start: 0.8314 (tttt) cc_final: 0.7745 (mtpt) REVERT: A 526 LEU cc_start: 0.8034 (mt) cc_final: 0.7787 (mp) REVERT: A 542 ILE cc_start: 0.9390 (tp) cc_final: 0.9151 (tp) REVERT: A 543 LYS cc_start: 0.9493 (mmtp) cc_final: 0.9274 (mmmt) REVERT: A 550 MET cc_start: 0.7240 (tpp) cc_final: 0.6909 (tpp) REVERT: A 560 ARG cc_start: 0.8236 (mtp-110) cc_final: 0.7862 (mtp-110) REVERT: A 564 ASP cc_start: 0.8978 (m-30) cc_final: 0.8733 (m-30) REVERT: A 578 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7807 (mm-30) REVERT: A 619 ILE cc_start: 0.9467 (mm) cc_final: 0.9255 (pt) REVERT: A 678 MET cc_start: 0.6748 (ptp) cc_final: 0.6191 (ptt) REVERT: A 757 MET cc_start: 0.7183 (ppp) cc_final: 0.6962 (ppp) REVERT: B 218 GLU cc_start: 0.9065 (pp20) cc_final: 0.8840 (tm-30) REVERT: B 225 ARG cc_start: 0.8669 (mmm-85) cc_final: 0.7961 (ttt180) REVERT: B 305 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8422 (mm-30) REVERT: B 312 LYS cc_start: 0.9232 (ptpp) cc_final: 0.8819 (ptpp) REVERT: B 326 SER cc_start: 0.8178 (m) cc_final: 0.7502 (p) REVERT: B 332 MET cc_start: 0.9001 (mmm) cc_final: 0.8594 (mmm) REVERT: B 347 THR cc_start: 0.9242 (p) cc_final: 0.9030 (t) REVERT: B 403 THR cc_start: 0.8723 (p) cc_final: 0.8398 (t) REVERT: B 411 LEU cc_start: 0.9337 (mt) cc_final: 0.9098 (mt) REVERT: B 564 ASP cc_start: 0.8850 (m-30) cc_final: 0.8484 (m-30) REVERT: B 642 LEU cc_start: 0.9126 (pp) cc_final: 0.8647 (mp) REVERT: B 668 LYS cc_start: 0.7462 (mttp) cc_final: 0.7139 (mptt) REVERT: B 689 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7625 (tm-30) REVERT: B 757 MET cc_start: 0.7145 (ppp) cc_final: 0.6920 (ppp) REVERT: C 273 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8384 (tm-30) REVERT: C 288 LYS cc_start: 0.9235 (mptt) cc_final: 0.8542 (mmtp) REVERT: C 306 LEU cc_start: 0.9499 (tt) cc_final: 0.9281 (tt) REVERT: C 319 GLU cc_start: 0.8276 (tp30) cc_final: 0.8017 (tm-30) REVERT: C 388 MET cc_start: 0.4753 (mtp) cc_final: 0.4384 (mtt) REVERT: C 508 MET cc_start: 0.2329 (mtt) cc_final: 0.1292 (mtt) REVERT: C 542 ILE cc_start: 0.8869 (tp) cc_final: 0.8661 (tp) REVERT: C 560 ARG cc_start: 0.8206 (mtp-110) cc_final: 0.7913 (mtp180) REVERT: C 561 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8351 (tp30) REVERT: C 562 ILE cc_start: 0.9380 (tp) cc_final: 0.9078 (tp) REVERT: C 565 LYS cc_start: 0.9191 (ptmt) cc_final: 0.8781 (pttt) REVERT: C 576 PHE cc_start: 0.7158 (t80) cc_final: 0.6680 (t80) REVERT: C 577 ASP cc_start: 0.8063 (p0) cc_final: 0.7772 (p0) REVERT: C 642 LEU cc_start: 0.8868 (mp) cc_final: 0.8660 (mp) REVERT: D 219 MET cc_start: 0.7973 (tpp) cc_final: 0.7649 (tpp) REVERT: D 221 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7205 (tm-30) REVERT: D 225 ARG cc_start: 0.8702 (mmm-85) cc_final: 0.8099 (ttt180) REVERT: D 305 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8189 (mm-30) REVERT: D 306 LEU cc_start: 0.9530 (tp) cc_final: 0.9276 (tt) REVERT: D 312 LYS cc_start: 0.9353 (ptpp) cc_final: 0.8906 (ptpp) REVERT: D 465 ARG cc_start: 0.6299 (mmt90) cc_final: 0.5525 (mmm160) REVERT: D 484 ASP cc_start: 0.8587 (p0) cc_final: 0.7245 (p0) REVERT: D 543 LYS cc_start: 0.9265 (mmtp) cc_final: 0.8145 (mmmm) REVERT: D 546 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8489 (mp0) REVERT: D 550 MET cc_start: 0.5123 (mmp) cc_final: 0.4615 (ttm) REVERT: D 560 ARG cc_start: 0.8364 (mtp180) cc_final: 0.8150 (mmm160) REVERT: D 611 MET cc_start: 0.7158 (mmm) cc_final: 0.6892 (mmm) REVERT: D 678 MET cc_start: 0.7140 (ptp) cc_final: 0.6361 (ptt) REVERT: D 690 ILE cc_start: 0.8824 (mm) cc_final: 0.8309 (mm) REVERT: D 700 ARG cc_start: 0.8260 (ttp80) cc_final: 0.7886 (ttm170) REVERT: D 757 MET cc_start: 0.7358 (ppp) cc_final: 0.7150 (ppp) REVERT: E 218 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8260 (tm-30) REVERT: E 219 MET cc_start: 0.8588 (tpp) cc_final: 0.7569 (tpp) REVERT: E 304 ASP cc_start: 0.8656 (t0) cc_final: 0.8441 (t70) REVERT: E 312 LYS cc_start: 0.9410 (ptpt) cc_final: 0.9167 (ptpp) REVERT: E 411 LEU cc_start: 0.9043 (mp) cc_final: 0.8609 (mm) REVERT: E 529 LYS cc_start: 0.8374 (mmmt) cc_final: 0.7872 (tptt) REVERT: E 543 LYS cc_start: 0.9161 (mmtp) cc_final: 0.8635 (mmmt) REVERT: E 546 GLU cc_start: 0.8730 (mp0) cc_final: 0.8429 (mp0) REVERT: E 560 ARG cc_start: 0.8464 (mtp-110) cc_final: 0.8092 (mtp180) REVERT: E 601 ILE cc_start: 0.9023 (mt) cc_final: 0.8808 (mt) REVERT: E 651 LYS cc_start: 0.9135 (ptpt) cc_final: 0.8257 (pttp) REVERT: E 757 MET cc_start: 0.6975 (ppp) cc_final: 0.6694 (ppp) REVERT: F 205 ASP cc_start: 0.8473 (m-30) cc_final: 0.7854 (t0) REVERT: F 273 GLU cc_start: 0.8290 (tm-30) cc_final: 0.8006 (tm-30) REVERT: F 288 LYS cc_start: 0.8839 (mmmt) cc_final: 0.8529 (mmtm) REVERT: F 312 LYS cc_start: 0.9193 (ptpt) cc_final: 0.8899 (ptpp) REVERT: F 450 ASP cc_start: 0.7648 (m-30) cc_final: 0.7207 (t0) REVERT: F 484 ASP cc_start: 0.8602 (p0) cc_final: 0.8185 (p0) REVERT: F 499 HIS cc_start: 0.7912 (m90) cc_final: 0.7615 (m-70) REVERT: F 542 ILE cc_start: 0.8739 (tp) cc_final: 0.8492 (tp) REVERT: F 543 LYS cc_start: 0.9169 (mmtp) cc_final: 0.7950 (mmtm) REVERT: F 546 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8232 (mp0) REVERT: F 550 MET cc_start: 0.5826 (mmp) cc_final: 0.5227 (mmp) REVERT: F 560 ARG cc_start: 0.8381 (mtp-110) cc_final: 0.8175 (mtp-110) REVERT: F 561 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7999 (tp30) REVERT: F 565 LYS cc_start: 0.9267 (pttp) cc_final: 0.9015 (pttp) REVERT: F 662 ARG cc_start: 0.8320 (ttt90) cc_final: 0.7862 (ttt90) REVERT: F 689 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7787 (tm-30) outliers start: 1 outliers final: 0 residues processed: 639 average time/residue: 0.1693 time to fit residues: 166.2587 Evaluate side-chains 514 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 514 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 219 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 55 optimal weight: 0.0040 chunk 54 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 232 optimal weight: 0.9980 chunk 193 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 137 optimal weight: 0.0070 chunk 102 optimal weight: 7.9990 overall best weight: 0.5210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN B 602 ASN C 382 GLN C 602 ASN D 602 ASN E 602 ASN F 327 GLN F 494 GLN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.119281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.099625 restraints weight = 75877.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.102403 restraints weight = 48198.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.104333 restraints weight = 34053.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.105678 restraints weight = 26050.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.106623 restraints weight = 21304.499| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 25518 Z= 0.136 Angle : 0.751 15.628 34482 Z= 0.372 Chirality : 0.047 0.181 3894 Planarity : 0.005 0.064 4524 Dihedral : 8.320 110.041 3480 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.07 % Allowed : 0.41 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.16), residues: 3150 helix: -0.25 (0.13), residues: 1614 sheet: -1.37 (0.45), residues: 102 loop : -0.27 (0.18), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 638 TYR 0.023 0.002 TYR F 495 PHE 0.027 0.001 PHE C 267 TRP 0.014 0.002 TRP C 476 HIS 0.009 0.001 HIS D 735 Details of bonding type rmsd covalent geometry : bond 0.00312 (25518) covalent geometry : angle 0.75111 (34482) hydrogen bonds : bond 0.03632 ( 1017) hydrogen bonds : angle 5.24460 ( 3039) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4846.58 seconds wall clock time: 84 minutes 21.36 seconds (5061.36 seconds total)