Starting phenix.real_space_refine on Tue Aug 26 18:04:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gfa_29983/08_2025/8gfa_29983_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gfa_29983/08_2025/8gfa_29983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gfa_29983/08_2025/8gfa_29983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gfa_29983/08_2025/8gfa_29983.map" model { file = "/net/cci-nas-00/data/ceres_data/8gfa_29983/08_2025/8gfa_29983_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gfa_29983/08_2025/8gfa_29983_neut_trim.cif" } resolution = 2.29 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= 0.017 sd= 0.093 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: 8 Type Number sf(0) Gaussians P 32 5.49 5 S 120 5.16 5 Cl 4 4.86 5 Na 2 4.78 5 C 12888 2.51 5 N 2812 2.21 5 O 3441 1.98 5 H 17380 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36679 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 8657 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 517} Chain breaks: 1 Chain: "B" Number of atoms: 8657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 8657 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 517} Chain breaks: 1 Chain: "D" Number of atoms: 8657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 8657 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 517} Chain breaks: 1 Chain: "A" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 487 Unusual residues: {' NA': 1, 'DU0': 1, 'POV': 9, 'ZEI': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 538 Unusual residues: {'DU0': 1, 'POV': 10, 'ZEI': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 486 Unusual residues: {'DU0': 1, 'POV': 9, 'ZEI': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Restraints were copied for chains: C Time building chain proxies: 13.76, per 1000 atoms: 0.38 Number of scatterers: 36679 At special positions: 0 Unit cell: (118.035, 118.68, 110.295, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 4 17.00 S 120 16.00 P 32 15.00 Na 2 11.00 O 3441 8.00 N 2812 7.00 C 12888 6.00 H 17380 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 391 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 391 " distance=2.03 Simple disulfide: pdb=" SG CYS C 258 " - pdb=" SG CYS C 258 " distance=0.00 Simple disulfide: pdb=" SG CYS C 363 " - pdb=" SG CYS C 363 " distance=0.00 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 391 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 387 " distance=0.00 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 391 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 387 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 391 " distance=0.00 Simple disulfide: pdb=" SG CYS C 443 " - pdb=" SG CYS C 443 " distance=0.00 Simple disulfide: pdb=" SG CYS C 578 " - pdb=" SG CYS C 578 " distance=0.00 Simple disulfide: pdb=" SG CYS C 635 " - pdb=" SG CYS C 635 " distance=0.00 Simple disulfide: pdb=" SG CYS C 716 " - pdb=" SG CYS C 716 " distance=0.00 Simple disulfide: pdb=" SG CYS C 742 " - pdb=" SG CYS C 742 " distance=0.00 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 391 " distance=2.03 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: 2.87 Conformation dependent library (CDL) restraints added in 801.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4008 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 4 sheets defined 65.5% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 214 through 224 removed outlier: 3.597A pdb=" N LEU A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 261 through 271 removed outlier: 3.798A pdb=" N LEU A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 299 through 321 removed outlier: 3.707A pdb=" N PHE A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 314 " --> pdb=" O TYR A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 345 Processing helix chain 'A' and resid 346 through 355 removed outlier: 3.651A pdb=" N GLN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 409 through 414 removed outlier: 4.049A pdb=" N LEU A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 430 Processing helix chain 'A' and resid 430 through 455 removed outlier: 3.637A pdb=" N ILE A 434 " --> pdb=" O PHE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 499 removed outlier: 3.707A pdb=" N TYR A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY A 477 " --> pdb=" O PHE A 473 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 510 removed outlier: 4.322A pdb=" N VAL A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 532 Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.571A pdb=" N SER A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 558 Processing helix chain 'A' and resid 559 through 575 Processing helix chain 'A' and resid 575 through 599 Processing helix chain 'A' and resid 630 through 641 removed outlier: 3.569A pdb=" N LYS A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 656 through 672 Processing helix chain 'A' and resid 674 through 715 removed outlier: 3.563A pdb=" N ALA A 691 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLN A 692 " --> pdb=" O ASN A 688 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU A 693 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 Processing helix chain 'B' and resid 214 through 224 removed outlier: 3.596A pdb=" N LEU B 220 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 261 through 271 removed outlier: 3.798A pdb=" N LEU B 269 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 299 through 321 removed outlier: 3.707A pdb=" N PHE B 305 " --> pdb=" O ASP B 301 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU B 312 " --> pdb=" O SER B 308 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 314 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 345 Processing helix chain 'B' and resid 346 through 355 removed outlier: 3.651A pdb=" N GLN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 409 through 414 removed outlier: 4.049A pdb=" N LEU B 414 " --> pdb=" O ARG B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 430 Processing helix chain 'B' and resid 430 through 455 removed outlier: 3.636A pdb=" N ILE B 434 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 499 removed outlier: 3.707A pdb=" N TYR B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 477 " --> pdb=" O PHE B 473 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 510 removed outlier: 4.323A pdb=" N VAL B 508 " --> pdb=" O LYS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 532 Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.571A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 558 Processing helix chain 'B' and resid 559 through 575 Processing helix chain 'B' and resid 575 through 599 Processing helix chain 'B' and resid 630 through 641 removed outlier: 3.570A pdb=" N LYS B 640 " --> pdb=" O LEU B 636 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 644 No H-bonds generated for 'chain 'B' and resid 642 through 644' Processing helix chain 'B' and resid 656 through 672 Processing helix chain 'B' and resid 674 through 715 removed outlier: 3.564A pdb=" N ALA B 691 " --> pdb=" O VAL B 687 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLN B 692 " --> pdb=" O ASN B 688 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU B 693 " --> pdb=" O LYS B 689 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 212 Processing helix chain 'C' and resid 214 through 224 removed outlier: 3.596A pdb=" N LEU C 220 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 261 through 271 removed outlier: 3.797A pdb=" N LEU C 269 " --> pdb=" O VAL C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 299 through 321 removed outlier: 3.707A pdb=" N PHE C 305 " --> pdb=" O ASP C 301 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU C 312 " --> pdb=" O SER C 308 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 314 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 345 Processing helix chain 'C' and resid 346 through 355 removed outlier: 3.652A pdb=" N GLN C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 409 through 414 removed outlier: 4.049A pdb=" N LEU C 414 " --> pdb=" O ARG C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 430 Processing helix chain 'C' and resid 430 through 455 removed outlier: 3.637A pdb=" N ILE C 434 " --> pdb=" O PHE C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 499 removed outlier: 3.707A pdb=" N TYR C 472 " --> pdb=" O LYS C 468 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY C 477 " --> pdb=" O PHE C 473 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 510 removed outlier: 4.322A pdb=" N VAL C 508 " --> pdb=" O LYS C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.571A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 558 Processing helix chain 'C' and resid 559 through 575 Processing helix chain 'C' and resid 575 through 599 Processing helix chain 'C' and resid 630 through 641 removed outlier: 3.570A pdb=" N LYS C 640 " --> pdb=" O LEU C 636 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 644 No H-bonds generated for 'chain 'C' and resid 642 through 644' Processing helix chain 'C' and resid 656 through 672 Processing helix chain 'C' and resid 674 through 715 removed outlier: 3.563A pdb=" N ALA C 691 " --> pdb=" O VAL C 687 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLN C 692 " --> pdb=" O ASN C 688 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU C 693 " --> pdb=" O LYS C 689 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 Processing helix chain 'D' and resid 214 through 224 removed outlier: 3.596A pdb=" N LEU D 220 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 238 Processing helix chain 'D' and resid 251 through 258 Processing helix chain 'D' and resid 261 through 271 removed outlier: 3.798A pdb=" N LEU D 269 " --> pdb=" O VAL D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 299 through 321 removed outlier: 3.707A pdb=" N PHE D 305 " --> pdb=" O ASP D 301 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU D 312 " --> pdb=" O SER D 308 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 314 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 345 Processing helix chain 'D' and resid 346 through 355 removed outlier: 3.652A pdb=" N GLN D 355 " --> pdb=" O ALA D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 409 through 414 removed outlier: 4.049A pdb=" N LEU D 414 " --> pdb=" O ARG D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 430 Processing helix chain 'D' and resid 430 through 455 removed outlier: 3.637A pdb=" N ILE D 434 " --> pdb=" O PHE D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 499 removed outlier: 3.707A pdb=" N TYR D 472 " --> pdb=" O LYS D 468 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY D 477 " --> pdb=" O PHE D 473 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR D 495 " --> pdb=" O ARG D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 510 removed outlier: 4.322A pdb=" N VAL D 508 " --> pdb=" O LYS D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.570A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 558 Processing helix chain 'D' and resid 559 through 575 Processing helix chain 'D' and resid 575 through 599 Processing helix chain 'D' and resid 630 through 641 removed outlier: 3.570A pdb=" N LYS D 640 " --> pdb=" O LEU D 636 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 644 No H-bonds generated for 'chain 'D' and resid 642 through 644' Processing helix chain 'D' and resid 656 through 672 Processing helix chain 'D' and resid 674 through 715 removed outlier: 3.564A pdb=" N ALA D 691 " --> pdb=" O VAL D 687 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLN D 692 " --> pdb=" O ASN D 688 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU D 693 " --> pdb=" O LYS D 689 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 370 through 375 removed outlier: 7.202A pdb=" N SER A 380 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ALA A 374 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASP A 738 " --> pdb=" O VAL A 729 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 370 through 375 removed outlier: 7.202A pdb=" N SER B 380 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ALA B 374 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASP B 738 " --> pdb=" O VAL B 729 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 370 through 375 removed outlier: 7.203A pdb=" N SER C 380 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ALA C 374 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASP C 738 " --> pdb=" O VAL C 729 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 370 through 375 removed outlier: 7.202A pdb=" N SER D 380 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ALA D 374 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASP D 738 " --> pdb=" O VAL D 729 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2892 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: 7.82 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 17352 1.01 - 1.22: 98 1.22 - 1.43: 7831 1.43 - 1.63: 11483 1.63 - 1.84: 208 Bond restraints: 36972 Sorted by residual: bond pdb=" CG LEU A 638 " pdb=" CD2 LEU A 638 " ideal model delta sigma weight residual 1.521 1.379 0.142 3.30e-02 9.18e+02 1.85e+01 bond pdb=" CG LEU B 638 " pdb=" CD2 LEU B 638 " ideal model delta sigma weight residual 1.521 1.379 0.142 3.30e-02 9.18e+02 1.84e+01 bond pdb=" CG LEU D 638 " pdb=" CD2 LEU D 638 " ideal model delta sigma weight residual 1.521 1.379 0.142 3.30e-02 9.18e+02 1.84e+01 bond pdb=" CG LEU C 638 " pdb=" CD2 LEU C 638 " ideal model delta sigma weight residual 1.521 1.380 0.141 3.30e-02 9.18e+02 1.84e+01 bond pdb="C315 POV D1207 " pdb="C316 POV D1207 " ideal model delta sigma weight residual 1.522 1.437 0.085 2.00e-02 2.50e+03 1.80e+01 ... (remaining 36967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.24: 65295 5.24 - 10.49: 197 10.49 - 15.73: 8 15.73 - 20.98: 0 20.98 - 26.22: 12 Bond angle restraints: 65512 Sorted by residual: angle pdb=" CG1 VAL A 295 " pdb=" CB VAL A 295 " pdb=" HB VAL A 295 " ideal model delta sigma weight residual 108.00 81.78 26.22 3.00e+00 1.11e-01 7.64e+01 angle pdb=" CG1 VAL D 295 " pdb=" CB VAL D 295 " pdb=" HB VAL D 295 " ideal model delta sigma weight residual 108.00 81.80 26.20 3.00e+00 1.11e-01 7.63e+01 angle pdb=" CG1 VAL B 295 " pdb=" CB VAL B 295 " pdb=" HB VAL B 295 " ideal model delta sigma weight residual 108.00 81.80 26.20 3.00e+00 1.11e-01 7.63e+01 angle pdb=" CG1 VAL C 295 " pdb=" CB VAL C 295 " pdb=" HB VAL C 295 " ideal model delta sigma weight residual 108.00 81.83 26.17 3.00e+00 1.11e-01 7.61e+01 angle pdb=" CG2 VAL B 295 " pdb=" CB VAL B 295 " pdb=" HB VAL B 295 " ideal model delta sigma weight residual 108.00 83.22 24.78 3.00e+00 1.11e-01 6.82e+01 ... (remaining 65507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 17570 35.57 - 71.14: 629 71.14 - 106.71: 64 106.71 - 142.27: 28 142.27 - 177.84: 16 Dihedral angle restraints: 18307 sinusoidal: 10535 harmonic: 7772 Sorted by residual: dihedral pdb=" CB CYS C 387 " pdb=" SG CYS C 387 " pdb=" SG CYS C 387 " pdb=" CB CYS C 387 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 391 " pdb=" CB CYS C 391 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CB CYS C 443 " pdb=" SG CYS C 443 " pdb=" SG CYS C 443 " pdb=" CB CYS C 443 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 ... (remaining 18304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.337: 2756 0.337 - 0.675: 0 0.675 - 1.012: 0 1.012 - 1.349: 0 1.349 - 1.687: 4 Chirality restraints: 2760 Sorted by residual: chirality pdb=" CB VAL C 295 " pdb=" CA VAL C 295 " pdb=" CG1 VAL C 295 " pdb=" CG2 VAL C 295 " both_signs ideal model delta sigma weight residual False -2.63 -0.94 -1.69 2.00e-01 2.50e+01 7.11e+01 chirality pdb=" CB VAL A 295 " pdb=" CA VAL A 295 " pdb=" CG1 VAL A 295 " pdb=" CG2 VAL A 295 " both_signs ideal model delta sigma weight residual False -2.63 -0.94 -1.68 2.00e-01 2.50e+01 7.09e+01 chirality pdb=" CB VAL D 295 " pdb=" CA VAL D 295 " pdb=" CG1 VAL D 295 " pdb=" CG2 VAL D 295 " both_signs ideal model delta sigma weight residual False -2.63 -0.95 -1.68 2.00e-01 2.50e+01 7.06e+01 ... (remaining 2757 not shown) Planarity restraints: 5128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 298 " -0.185 2.00e-02 2.50e+03 1.99e-01 5.94e+02 pdb=" CG ASN A 298 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 298 " 0.155 2.00e-02 2.50e+03 pdb=" ND2 ASN A 298 " 0.011 2.00e-02 2.50e+03 pdb="HD21 ASN A 298 " 0.290 2.00e-02 2.50e+03 pdb="HD22 ASN A 298 " -0.306 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 298 " 0.185 2.00e-02 2.50e+03 1.99e-01 5.92e+02 pdb=" CG ASN B 298 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN B 298 " -0.154 2.00e-02 2.50e+03 pdb=" ND2 ASN B 298 " -0.011 2.00e-02 2.50e+03 pdb="HD21 ASN B 298 " -0.289 2.00e-02 2.50e+03 pdb="HD22 ASN B 298 " 0.306 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 298 " 0.184 2.00e-02 2.50e+03 1.98e-01 5.88e+02 pdb=" CG ASN D 298 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN D 298 " -0.154 2.00e-02 2.50e+03 pdb=" ND2 ASN D 298 " -0.012 2.00e-02 2.50e+03 pdb="HD21 ASN D 298 " -0.288 2.00e-02 2.50e+03 pdb="HD22 ASN D 298 " 0.305 2.00e-02 2.50e+03 ... (remaining 5125 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 3875 2.24 - 2.83: 79411 2.83 - 3.42: 97247 3.42 - 4.01: 138959 4.01 - 4.60: 214984 Nonbonded interactions: 534476 Sorted by model distance: nonbonded pdb=" O HIS C 365 " pdb="HH22 ARG C 740 " model vdw 1.647 2.450 nonbonded pdb=" O HIS B 365 " pdb="HH22 ARG B 740 " model vdw 1.647 2.450 nonbonded pdb=" O HIS D 365 " pdb="HH22 ARG D 740 " model vdw 1.647 2.450 nonbonded pdb=" O HIS A 365 " pdb="HH22 ARG A 740 " model vdw 1.648 2.450 nonbonded pdb=" O ARG D 356 " pdb=" H ARG D 368 " model vdw 1.648 2.450 ... (remaining 534471 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 199 through 1201 or (resid 1205 through 1207 and (name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C310 or nam \ e C311 or name C312 or name C313 or name C314 or name C315 or name C316)) or res \ id 1208 through 1209)) selection = (chain 'B' and (resid 199 through 1201 or (resid 1205 through 1207 and (name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C310 or nam \ e C311 or name C312 or name C313 or name C314 or name C315 or name C316)) or res \ id 1208 through 1209)) selection = (chain 'C' and (resid 199 through 1201 or (resid 1205 through 1207 and (name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C310 or nam \ e C311 or name C312 or name C313 or name C314 or name C315 or name C316)) or res \ id 1208 through 1209)) selection = (chain 'D' and (resid 199 through 1201 or (resid 1205 through 1207 and (name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C310 or nam \ e C311 or name C312 or name C313 or name C314 or name C315 or name C316)) or res \ id 1208 through 1209)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 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: 0.200 Extract box with map and model: 0.470 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 37.560 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 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 : 0.018 0.142 19595 Z= 0.731 Angle : 1.233 14.613 26211 Z= 0.585 Chirality : 0.097 1.687 2760 Planarity : 0.006 0.045 3064 Dihedral : 20.024 177.844 8192 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.31 % Favored : 94.50 % Rotamer: Outliers : 0.05 % Allowed : 3.80 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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 aren not related in a simple way. whole: -3.88 (0.15), residues: 2108 helix: -2.54 (0.11), residues: 1260 sheet: -1.97 (0.48), residues: 56 loop : -2.39 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.004 ARG D 499 TYR 0.026 0.004 TYR B 584 PHE 0.053 0.005 PHE A 449 TRP 0.033 0.004 TRP D 698 HIS 0.012 0.003 HIS D 411 Details of bonding type rmsd covalent geometry : bond 0.01776 (19592) covalent geometry : angle 1.23323 (26196) SS BOND : bond 0.00053 ( 3) SS BOND : angle 1.43369 ( 15) hydrogen bonds : bond 0.25803 ( 996) hydrogen bonds : angle 8.81716 ( 2892) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 370 time to evaluate : 0.683 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: A 308 SER cc_start: 0.7731 (m) cc_final: 0.7356 (p) REVERT: A 335 MET cc_start: 0.7448 (mmm) cc_final: 0.6852 (mmt) REVERT: B 308 SER cc_start: 0.7742 (m) cc_final: 0.7340 (p) REVERT: B 507 PHE cc_start: 0.7752 (m-80) cc_final: 0.7477 (m-10) REVERT: C 363 CYS cc_start: 0.6231 (m) cc_final: 0.5978 (m) REVERT: C 379 HIS cc_start: 0.7354 (p90) cc_final: 0.7141 (p-80) REVERT: D 363 CYS cc_start: 0.6292 (m) cc_final: 0.6079 (m) outliers start: 1 outliers final: 0 residues processed: 371 average time/residue: 1.3236 time to fit residues: 548.6543 Evaluate side-chains 220 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN A 298 ASN A 629 ASN B 274 GLN B 298 ASN B 420 ASN B 629 ASN C 274 GLN C 298 ASN C 394 ASN C 629 ASN C 692 GLN D 274 GLN D 298 ASN D 394 ASN D 629 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.191346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.135591 restraints weight = 60183.576| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.87 r_work: 0.3502 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19595 Z= 0.139 Angle : 0.615 11.250 26211 Z= 0.317 Chirality : 0.067 1.480 2760 Planarity : 0.005 0.051 3064 Dihedral : 21.904 170.035 4144 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.32 % Favored : 96.49 % Rotamer: Outliers : 1.28 % Allowed : 11.83 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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 aren not related in a simple way. whole: -1.44 (0.17), residues: 2108 helix: -0.28 (0.13), residues: 1280 sheet: -2.12 (0.42), residues: 76 loop : -1.88 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 364 TYR 0.017 0.002 TYR A 632 PHE 0.012 0.002 PHE C 580 TRP 0.021 0.002 TRP A 698 HIS 0.002 0.001 HIS D 321 Details of bonding type rmsd covalent geometry : bond 0.00298 (19592) covalent geometry : angle 0.61480 (26196) SS BOND : bond 0.00125 ( 3) SS BOND : angle 0.59960 ( 15) hydrogen bonds : bond 0.05025 ( 996) hydrogen bonds : angle 4.91556 ( 2892) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 285 time to evaluate : 0.926 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: A 379 HIS cc_start: 0.7284 (p-80) cc_final: 0.6992 (p-80) REVERT: A 398 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7574 (tt0) REVERT: A 502 SER cc_start: 0.7407 (t) cc_final: 0.7024 (p) REVERT: A 688 ASN cc_start: 0.8382 (t160) cc_final: 0.8172 (m110) REVERT: A 692 GLN cc_start: 0.7565 (mm110) cc_final: 0.7210 (tp40) REVERT: A 728 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6827 (tt0) REVERT: B 311 ASN cc_start: 0.6979 (t0) cc_final: 0.6576 (t0) REVERT: B 312 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7186 (mm-30) REVERT: B 315 MET cc_start: 0.6949 (mtt) cc_final: 0.6252 (mtt) REVERT: B 379 HIS cc_start: 0.6879 (p90) cc_final: 0.6537 (p-80) REVERT: B 398 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7471 (tt0) REVERT: B 502 SER cc_start: 0.7297 (t) cc_final: 0.6943 (p) REVERT: B 507 PHE cc_start: 0.8082 (m-80) cc_final: 0.7689 (m-80) REVERT: B 747 GLU cc_start: 0.6445 (tm-30) cc_final: 0.6197 (tm-30) REVERT: C 379 HIS cc_start: 0.6908 (p90) cc_final: 0.6609 (p-80) REVERT: C 398 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7439 (tt0) REVERT: C 507 PHE cc_start: 0.8117 (m-80) cc_final: 0.7646 (m-80) REVERT: C 692 GLN cc_start: 0.7636 (tp-100) cc_final: 0.7276 (mm110) REVERT: C 747 GLU cc_start: 0.6611 (tm-30) cc_final: 0.6394 (tm-30) REVERT: D 311 ASN cc_start: 0.6921 (t0) cc_final: 0.6496 (t0) REVERT: D 312 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7268 (mm-30) REVERT: D 315 MET cc_start: 0.6923 (mtt) cc_final: 0.6098 (mtt) REVERT: D 379 HIS cc_start: 0.6894 (p90) cc_final: 0.6549 (p-80) REVERT: D 398 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7441 (tt0) REVERT: D 433 ARG cc_start: 0.7610 (mmm160) cc_final: 0.7185 (tpt170) REVERT: D 507 PHE cc_start: 0.8168 (m-80) cc_final: 0.7687 (m-80) REVERT: D 692 GLN cc_start: 0.7389 (mm110) cc_final: 0.7057 (tp40) REVERT: D 747 GLU cc_start: 0.6490 (tm-30) cc_final: 0.6230 (tm-30) outliers start: 24 outliers final: 9 residues processed: 305 average time/residue: 0.9897 time to fit residues: 349.0839 Evaluate side-chains 250 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 240 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 651 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 63 optimal weight: 4.9990 chunk 15 optimal weight: 0.0870 chunk 175 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 193 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 728 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.183548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.125672 restraints weight = 60032.380| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.83 r_work: 0.3365 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19595 Z= 0.242 Angle : 0.659 11.418 26211 Z= 0.338 Chirality : 0.071 1.565 2760 Planarity : 0.005 0.061 3064 Dihedral : 21.328 178.662 4144 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.27 % Favored : 96.54 % Rotamer: Outliers : 1.93 % Allowed : 13.70 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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 aren not related in a simple way. whole: -0.77 (0.17), residues: 2108 helix: 0.38 (0.14), residues: 1272 sheet: -2.45 (0.46), residues: 76 loop : -1.77 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 499 TYR 0.020 0.002 TYR B 632 PHE 0.021 0.002 PHE A 650 TRP 0.016 0.002 TRP A 698 HIS 0.003 0.001 HIS C 411 Details of bonding type rmsd covalent geometry : bond 0.00535 (19592) covalent geometry : angle 0.65899 (26196) SS BOND : bond 0.00057 ( 3) SS BOND : angle 0.42510 ( 15) hydrogen bonds : bond 0.05182 ( 996) hydrogen bonds : angle 4.74974 ( 2892) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 247 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ASN cc_start: 0.7187 (t0) cc_final: 0.6703 (t0) REVERT: A 500 ARG cc_start: 0.7710 (mmm160) cc_final: 0.7311 (mmm160) REVERT: A 692 GLN cc_start: 0.7746 (mm110) cc_final: 0.7196 (tp-100) REVERT: A 717 MET cc_start: 0.5194 (ttt) cc_final: 0.4695 (mtt) REVERT: A 728 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6840 (tt0) REVERT: B 305 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6811 (t80) REVERT: B 311 ASN cc_start: 0.7082 (t0) cc_final: 0.6683 (t0) REVERT: B 315 MET cc_start: 0.7048 (mtt) cc_final: 0.6376 (mtt) REVERT: B 636 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8341 (tm) REVERT: B 688 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.8104 (t0) REVERT: B 692 GLN cc_start: 0.7763 (mm110) cc_final: 0.7187 (tp-100) REVERT: B 717 MET cc_start: 0.5164 (ttt) cc_final: 0.4601 (mtt) REVERT: C 398 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7731 (tt0) REVERT: C 499 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7574 (mtt180) REVERT: C 688 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.8026 (t0) REVERT: C 692 GLN cc_start: 0.8005 (tp-100) cc_final: 0.7170 (tp-100) REVERT: D 309 MET cc_start: 0.8102 (tpp) cc_final: 0.7881 (tpp) REVERT: D 311 ASN cc_start: 0.7053 (t0) cc_final: 0.6720 (t0) REVERT: D 398 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7747 (tt0) REVERT: D 433 ARG cc_start: 0.7698 (mmm160) cc_final: 0.7307 (tpt170) REVERT: D 499 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7553 (mtt180) REVERT: D 500 ARG cc_start: 0.7774 (mmm160) cc_final: 0.7369 (mmm160) REVERT: D 636 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8330 (tm) REVERT: D 688 ASN cc_start: 0.8366 (OUTLIER) cc_final: 0.8112 (t0) REVERT: D 692 GLN cc_start: 0.7689 (mm110) cc_final: 0.7164 (tp-100) REVERT: D 717 MET cc_start: 0.5132 (ttt) cc_final: 0.4581 (mtt) REVERT: D 737 ASP cc_start: 0.6821 (OUTLIER) cc_final: 0.6571 (m-30) outliers start: 36 outliers final: 5 residues processed: 272 average time/residue: 1.0929 time to fit residues: 340.7649 Evaluate side-chains 228 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 688 ASN Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 688 ASN Chi-restraints excluded: chain D residue 499 ARG Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 688 ASN Chi-restraints excluded: chain D residue 737 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 107 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 chunk 53 optimal weight: 20.0000 chunk 156 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 162 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 ASN A 561 GLN B 394 ASN B 728 GLN C 438 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.182428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.124808 restraints weight = 60259.085| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.85 r_work: 0.3347 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19595 Z= 0.232 Angle : 0.631 11.542 26211 Z= 0.324 Chirality : 0.072 1.600 2760 Planarity : 0.004 0.057 3064 Dihedral : 20.026 174.432 4144 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.13 % Favored : 95.68 % Rotamer: Outliers : 2.78 % Allowed : 14.40 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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 aren not related in a simple way. whole: -0.39 (0.18), residues: 2108 helix: 0.70 (0.14), residues: 1292 sheet: -2.51 (0.45), residues: 76 loop : -1.69 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 368 TYR 0.020 0.002 TYR A 632 PHE 0.020 0.002 PHE C 721 TRP 0.018 0.002 TRP A 273 HIS 0.003 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00505 (19592) covalent geometry : angle 0.63084 (26196) SS BOND : bond 0.00058 ( 3) SS BOND : angle 0.64065 ( 15) hydrogen bonds : bond 0.04814 ( 996) hydrogen bonds : angle 4.51139 ( 2892) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 231 time to evaluate : 0.808 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: A 247 TYR cc_start: 0.7842 (t80) cc_final: 0.7623 (t80) REVERT: A 305 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.6790 (t80) REVERT: A 311 ASN cc_start: 0.7221 (t0) cc_final: 0.6657 (t0) REVERT: A 500 ARG cc_start: 0.7740 (mmm160) cc_final: 0.7328 (mmm160) REVERT: A 636 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8255 (tm) REVERT: B 305 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.6836 (t80) REVERT: B 311 ASN cc_start: 0.7210 (t0) cc_final: 0.6978 (t0) REVERT: B 315 MET cc_start: 0.7194 (mtt) cc_final: 0.6882 (mtt) REVERT: B 379 HIS cc_start: 0.7155 (p90) cc_final: 0.6950 (p-80) REVERT: B 433 ARG cc_start: 0.7900 (tpt170) cc_final: 0.7490 (tpt170) REVERT: B 500 ARG cc_start: 0.7722 (mmm160) cc_final: 0.7320 (mmm160) REVERT: B 561 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7903 (mp10) REVERT: B 636 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8251 (tm) REVERT: B 692 GLN cc_start: 0.7744 (mm110) cc_final: 0.7460 (tp40) REVERT: C 305 PHE cc_start: 0.7204 (OUTLIER) cc_final: 0.6726 (t80) REVERT: C 311 ASN cc_start: 0.7195 (t0) cc_final: 0.6736 (t0) REVERT: C 379 HIS cc_start: 0.7141 (p90) cc_final: 0.6925 (p-80) REVERT: C 398 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7844 (tt0) REVERT: C 433 ARG cc_start: 0.7920 (tpt170) cc_final: 0.7508 (tpt170) REVERT: C 500 ARG cc_start: 0.7777 (mmm160) cc_final: 0.7277 (mmm160) REVERT: C 561 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7914 (mp10) REVERT: D 305 PHE cc_start: 0.7221 (OUTLIER) cc_final: 0.6737 (t80) REVERT: D 311 ASN cc_start: 0.7160 (t0) cc_final: 0.6759 (t0) REVERT: D 433 ARG cc_start: 0.7706 (mmm160) cc_final: 0.7312 (tpt170) REVERT: D 500 ARG cc_start: 0.7750 (mmm160) cc_final: 0.7264 (mmm160) REVERT: D 561 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7913 (mp10) REVERT: D 636 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8276 (tm) REVERT: D 737 ASP cc_start: 0.6865 (OUTLIER) cc_final: 0.6542 (m-30) outliers start: 52 outliers final: 24 residues processed: 268 average time/residue: 1.1581 time to fit residues: 350.6461 Evaluate side-chains 247 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 689 LYS Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 561 GLN Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 689 LYS Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 689 LYS Chi-restraints excluded: chain D residue 737 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 92 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 182 optimal weight: 0.9980 chunk 175 optimal weight: 8.9990 chunk 171 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 210 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN B 728 GLN D 688 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.183186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.126093 restraints weight = 60434.888| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.87 r_work: 0.3368 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19595 Z= 0.156 Angle : 0.561 11.243 26211 Z= 0.290 Chirality : 0.068 1.519 2760 Planarity : 0.004 0.052 3064 Dihedral : 18.572 176.040 4144 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.23 % Favored : 96.58 % Rotamer: Outliers : 2.57 % Allowed : 15.74 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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 aren not related in a simple way. whole: 0.07 (0.18), residues: 2108 helix: 1.09 (0.14), residues: 1296 sheet: -2.44 (0.47), residues: 76 loop : -1.55 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 368 TYR 0.015 0.002 TYR A 632 PHE 0.016 0.002 PHE C 721 TRP 0.016 0.002 TRP C 273 HIS 0.002 0.000 HIS D 233 Details of bonding type rmsd covalent geometry : bond 0.00333 (19592) covalent geometry : angle 0.56101 (26196) SS BOND : bond 0.00076 ( 3) SS BOND : angle 0.47426 ( 15) hydrogen bonds : bond 0.04370 ( 996) hydrogen bonds : angle 4.30498 ( 2892) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 239 time to evaluate : 0.710 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: A 305 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.6842 (t80) REVERT: A 311 ASN cc_start: 0.7181 (t0) cc_final: 0.6664 (t0) REVERT: A 433 ARG cc_start: 0.7910 (tpt170) cc_final: 0.7510 (tpt170) REVERT: A 500 ARG cc_start: 0.7722 (mmm160) cc_final: 0.7431 (mmm160) REVERT: A 636 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8220 (tm) REVERT: B 305 PHE cc_start: 0.7428 (OUTLIER) cc_final: 0.6900 (t80) REVERT: B 433 ARG cc_start: 0.7903 (tpt170) cc_final: 0.7495 (tpt170) REVERT: B 500 ARG cc_start: 0.7725 (mmm160) cc_final: 0.7243 (mmm160) REVERT: B 636 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8254 (tm) REVERT: B 692 GLN cc_start: 0.7720 (mm110) cc_final: 0.7415 (tp40) REVERT: C 305 PHE cc_start: 0.7265 (OUTLIER) cc_final: 0.6780 (t80) REVERT: C 311 ASN cc_start: 0.7131 (t0) cc_final: 0.6650 (t0) REVERT: C 433 ARG cc_start: 0.7901 (tpt170) cc_final: 0.7487 (tpt170) REVERT: C 500 ARG cc_start: 0.7725 (mmm160) cc_final: 0.7251 (mmm160) REVERT: C 636 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8214 (tm) REVERT: C 717 MET cc_start: 0.5267 (tmt) cc_final: 0.4972 (tmt) REVERT: D 305 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.6710 (t80) REVERT: D 309 MET cc_start: 0.8071 (tpp) cc_final: 0.7529 (tpp) REVERT: D 311 ASN cc_start: 0.7099 (t0) cc_final: 0.6713 (t0) REVERT: D 379 HIS cc_start: 0.7324 (p-80) cc_final: 0.7028 (p-80) REVERT: D 433 ARG cc_start: 0.7699 (mmm160) cc_final: 0.7323 (tpt170) REVERT: D 500 ARG cc_start: 0.7725 (mmm160) cc_final: 0.7240 (mmm160) REVERT: D 636 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8253 (tm) outliers start: 48 outliers final: 18 residues processed: 270 average time/residue: 1.0698 time to fit residues: 330.9684 Evaluate side-chains 249 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 688 ASN Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 688 ASN Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 651 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 44 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 209 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN B 728 GLN C 261 GLN C 692 GLN D 261 GLN D 688 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.181728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.123916 restraints weight = 60514.034| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.87 r_work: 0.3340 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19595 Z= 0.230 Angle : 0.617 11.081 26211 Z= 0.316 Chirality : 0.067 1.447 2760 Planarity : 0.004 0.053 3064 Dihedral : 19.222 172.160 4144 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.13 % Favored : 95.68 % Rotamer: Outliers : 2.41 % Allowed : 16.97 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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 aren not related in a simple way. whole: -0.02 (0.18), residues: 2108 helix: 0.99 (0.14), residues: 1284 sheet: -2.51 (0.45), residues: 84 loop : -1.46 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 368 TYR 0.017 0.002 TYR B 632 PHE 0.019 0.002 PHE A 721 TRP 0.020 0.002 TRP D 273 HIS 0.003 0.001 HIS D 233 Details of bonding type rmsd covalent geometry : bond 0.00505 (19592) covalent geometry : angle 0.61664 (26196) SS BOND : bond 0.00041 ( 3) SS BOND : angle 0.48695 ( 15) hydrogen bonds : bond 0.04733 ( 996) hydrogen bonds : angle 4.41894 ( 2892) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 227 time to evaluate : 0.991 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: A 305 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.6821 (t80) REVERT: A 311 ASN cc_start: 0.7354 (t0) cc_final: 0.6972 (t0) REVERT: A 315 MET cc_start: 0.6968 (OUTLIER) cc_final: 0.6470 (mtt) REVERT: A 433 ARG cc_start: 0.7932 (tpt170) cc_final: 0.7523 (tpt170) REVERT: A 500 ARG cc_start: 0.7822 (mmm160) cc_final: 0.7468 (mmm160) REVERT: A 636 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8251 (tm) REVERT: A 728 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6849 (tt0) REVERT: B 305 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.6843 (t80) REVERT: B 433 ARG cc_start: 0.7895 (tpt170) cc_final: 0.7459 (tpt170) REVERT: B 500 ARG cc_start: 0.7789 (mmm160) cc_final: 0.7305 (mmm160) REVERT: B 636 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8264 (tm) REVERT: C 305 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.6763 (t80) REVERT: C 364 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.7081 (ttp-110) REVERT: C 433 ARG cc_start: 0.7895 (tpt170) cc_final: 0.7455 (tpt170) REVERT: C 500 ARG cc_start: 0.7796 (mmm160) cc_final: 0.7307 (mmm160) REVERT: C 636 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8230 (tm) REVERT: C 692 GLN cc_start: 0.8076 (tp-100) cc_final: 0.7353 (tp-100) REVERT: C 717 MET cc_start: 0.5415 (tmt) cc_final: 0.5156 (tmt) REVERT: C 737 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.6609 (m-30) REVERT: D 305 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.6732 (t80) REVERT: D 311 ASN cc_start: 0.7287 (t0) cc_final: 0.6853 (t0) REVERT: D 315 MET cc_start: 0.7095 (mtt) cc_final: 0.6608 (mtt) REVERT: D 433 ARG cc_start: 0.7684 (mmm160) cc_final: 0.7298 (tpt170) REVERT: D 500 ARG cc_start: 0.7798 (mmm160) cc_final: 0.7300 (mmm160) REVERT: D 636 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8276 (tm) REVERT: D 737 ASP cc_start: 0.6872 (OUTLIER) cc_final: 0.6522 (m-30) outliers start: 45 outliers final: 20 residues processed: 255 average time/residue: 1.1121 time to fit residues: 323.3404 Evaluate side-chains 254 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 688 ASN Chi-restraints excluded: chain B residue 689 LYS Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 688 ASN Chi-restraints excluded: chain C residue 689 LYS Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 689 LYS Chi-restraints excluded: chain D residue 737 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 202 optimal weight: 3.9990 chunk 34 optimal weight: 0.0870 chunk 174 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN B 728 GLN C 261 GLN D 261 GLN D 688 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.183024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.125735 restraints weight = 60640.222| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.87 r_work: 0.3366 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19595 Z= 0.155 Angle : 0.559 10.840 26211 Z= 0.288 Chirality : 0.066 1.464 2760 Planarity : 0.004 0.049 3064 Dihedral : 18.017 164.984 4144 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.23 % Favored : 96.68 % Rotamer: Outliers : 2.14 % Allowed : 16.54 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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 aren not related in a simple way. whole: 0.29 (0.18), residues: 2108 helix: 1.25 (0.14), residues: 1296 sheet: -2.33 (0.47), residues: 84 loop : -1.40 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 368 TYR 0.015 0.002 TYR A 375 PHE 0.016 0.002 PHE B 721 TRP 0.018 0.002 TRP B 273 HIS 0.001 0.000 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00334 (19592) covalent geometry : angle 0.55943 (26196) SS BOND : bond 0.00063 ( 3) SS BOND : angle 0.48419 ( 15) hydrogen bonds : bond 0.04302 ( 996) hydrogen bonds : angle 4.23556 ( 2892) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 233 time to evaluate : 0.990 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: A 235 ASP cc_start: 0.7031 (m-30) cc_final: 0.6368 (m-30) REVERT: A 305 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.6768 (t80) REVERT: A 309 MET cc_start: 0.8109 (tpp) cc_final: 0.7802 (tpp) REVERT: A 311 ASN cc_start: 0.7320 (t0) cc_final: 0.6724 (t0) REVERT: A 433 ARG cc_start: 0.7915 (tpt170) cc_final: 0.7508 (tpt170) REVERT: A 500 ARG cc_start: 0.7750 (mmm160) cc_final: 0.7405 (mmm160) REVERT: A 506 LEU cc_start: 0.7796 (mm) cc_final: 0.7566 (mt) REVERT: A 636 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8216 (tm) REVERT: A 717 MET cc_start: 0.5413 (tmt) cc_final: 0.5183 (tmt) REVERT: B 235 ASP cc_start: 0.6970 (m-30) cc_final: 0.6312 (m-30) REVERT: B 305 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.6814 (t80) REVERT: B 433 ARG cc_start: 0.7868 (tpt170) cc_final: 0.7445 (tpt170) REVERT: B 500 ARG cc_start: 0.7743 (mmm160) cc_final: 0.7244 (mmm160) REVERT: B 506 LEU cc_start: 0.7822 (mm) cc_final: 0.7578 (mt) REVERT: B 636 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8236 (tm) REVERT: B 692 GLN cc_start: 0.7723 (mm110) cc_final: 0.7436 (tp40) REVERT: C 235 ASP cc_start: 0.7006 (m-30) cc_final: 0.6359 (m-30) REVERT: C 305 PHE cc_start: 0.7367 (OUTLIER) cc_final: 0.6743 (t80) REVERT: C 364 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.7062 (ttp-170) REVERT: C 433 ARG cc_start: 0.7878 (tpt170) cc_final: 0.7453 (tpt170) REVERT: C 500 ARG cc_start: 0.7745 (mmm160) cc_final: 0.7372 (mmm160) REVERT: C 506 LEU cc_start: 0.7865 (mm) cc_final: 0.7638 (mt) REVERT: C 717 MET cc_start: 0.5328 (tmt) cc_final: 0.5046 (tmt) REVERT: D 235 ASP cc_start: 0.6988 (m-30) cc_final: 0.6344 (m-30) REVERT: D 305 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6688 (t80) REVERT: D 364 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.7039 (ttp-170) REVERT: D 433 ARG cc_start: 0.7709 (mmm160) cc_final: 0.7295 (tpt170) REVERT: D 500 ARG cc_start: 0.7732 (mmm160) cc_final: 0.7229 (mmm160) REVERT: D 506 LEU cc_start: 0.7849 (mm) cc_final: 0.7558 (mt) REVERT: D 636 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8257 (tm) REVERT: D 737 ASP cc_start: 0.6922 (OUTLIER) cc_final: 0.6572 (m-30) outliers start: 40 outliers final: 16 residues processed: 259 average time/residue: 1.1453 time to fit residues: 338.3911 Evaluate side-chains 249 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 688 ASN Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 688 ASN Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 737 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN B 438 ASN B 728 GLN C 261 GLN C 692 GLN D 261 GLN D 438 ASN D 688 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.181477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.123924 restraints weight = 60671.481| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.89 r_work: 0.3339 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 19595 Z= 0.219 Angle : 0.610 11.000 26211 Z= 0.313 Chirality : 0.067 1.472 2760 Planarity : 0.004 0.051 3064 Dihedral : 18.369 157.184 4144 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.22 % Favored : 95.73 % Rotamer: Outliers : 2.57 % Allowed : 16.22 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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 aren not related in a simple way. whole: 0.11 (0.18), residues: 2108 helix: 1.07 (0.14), residues: 1284 sheet: -2.32 (0.48), residues: 84 loop : -1.38 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 368 TYR 0.016 0.002 TYR B 632 PHE 0.019 0.002 PHE D 721 TRP 0.017 0.002 TRP D 273 HIS 0.001 0.000 HIS C 365 Details of bonding type rmsd covalent geometry : bond 0.00480 (19592) covalent geometry : angle 0.61052 (26196) SS BOND : bond 0.00044 ( 3) SS BOND : angle 0.48167 ( 15) hydrogen bonds : bond 0.04655 ( 996) hydrogen bonds : angle 4.36814 ( 2892) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 229 time to evaluate : 0.860 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: A 305 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.6820 (t80) REVERT: A 309 MET cc_start: 0.8113 (tpp) cc_final: 0.7842 (tpp) REVERT: A 311 ASN cc_start: 0.7415 (t0) cc_final: 0.6776 (t0) REVERT: A 433 ARG cc_start: 0.7904 (tpt170) cc_final: 0.7489 (tpt170) REVERT: A 500 ARG cc_start: 0.7774 (mmm160) cc_final: 0.7434 (mmm160) REVERT: A 636 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8236 (tm) REVERT: A 725 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7307 (pttm) REVERT: B 305 PHE cc_start: 0.7513 (OUTLIER) cc_final: 0.6877 (t80) REVERT: B 309 MET cc_start: 0.8045 (tpp) cc_final: 0.7828 (tpp) REVERT: B 311 ASN cc_start: 0.7441 (t0) cc_final: 0.7143 (t0) REVERT: B 315 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6729 (mtt) REVERT: B 500 ARG cc_start: 0.7756 (mmm160) cc_final: 0.7268 (mmm160) REVERT: B 636 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8259 (tm) REVERT: B 689 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8140 (mptp) REVERT: B 692 GLN cc_start: 0.7747 (mm110) cc_final: 0.7462 (tp40) REVERT: B 717 MET cc_start: 0.5455 (tmt) cc_final: 0.5218 (tmt) REVERT: B 725 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.7242 (pttm) REVERT: C 305 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.6749 (t80) REVERT: C 309 MET cc_start: 0.8046 (tpp) cc_final: 0.7828 (tpp) REVERT: C 364 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.7089 (ttp-110) REVERT: C 433 ARG cc_start: 0.7892 (tpt170) cc_final: 0.7452 (tpt170) REVERT: C 500 ARG cc_start: 0.7750 (mmm160) cc_final: 0.7387 (mmm160) REVERT: C 689 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8153 (mptp) REVERT: C 692 GLN cc_start: 0.8090 (tp-100) cc_final: 0.7595 (mm110) REVERT: C 725 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7250 (pttm) REVERT: C 737 ASP cc_start: 0.6970 (OUTLIER) cc_final: 0.6645 (m-30) REVERT: D 305 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.6660 (t80) REVERT: D 309 MET cc_start: 0.8105 (tpp) cc_final: 0.7832 (tpp) REVERT: D 311 ASN cc_start: 0.7435 (t0) cc_final: 0.6957 (t0) REVERT: D 364 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.7041 (ttp-110) REVERT: D 433 ARG cc_start: 0.7716 (mmm160) cc_final: 0.7308 (tpt170) REVERT: D 500 ARG cc_start: 0.7773 (mmm160) cc_final: 0.7401 (mmm160) REVERT: D 636 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8270 (tm) REVERT: D 725 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.7224 (pttm) REVERT: D 737 ASP cc_start: 0.6959 (OUTLIER) cc_final: 0.6603 (m-30) outliers start: 48 outliers final: 19 residues processed: 260 average time/residue: 1.1107 time to fit residues: 329.0901 Evaluate side-chains 261 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 725 LYS Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 688 ASN Chi-restraints excluded: chain B residue 689 LYS Chi-restraints excluded: chain B residue 725 LYS Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 688 ASN Chi-restraints excluded: chain C residue 689 LYS Chi-restraints excluded: chain C residue 725 LYS Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 725 LYS Chi-restraints excluded: chain D residue 737 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 171 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 80 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 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 261 GLN B 261 GLN B 728 GLN C 261 GLN D 261 GLN D 688 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.182677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.125628 restraints weight = 60930.010| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.88 r_work: 0.3361 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19595 Z= 0.155 Angle : 0.562 10.880 26211 Z= 0.289 Chirality : 0.066 1.464 2760 Planarity : 0.004 0.048 3064 Dihedral : 17.389 147.478 4144 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.98 % Allowed : 17.08 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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 aren not related in a simple way. whole: 0.38 (0.18), residues: 2108 helix: 1.29 (0.14), residues: 1296 sheet: -2.19 (0.52), residues: 76 loop : -1.35 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 368 TYR 0.014 0.002 TYR A 555 PHE 0.016 0.002 PHE A 721 TRP 0.023 0.002 TRP B 273 HIS 0.001 0.000 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00334 (19592) covalent geometry : angle 0.56163 (26196) SS BOND : bond 0.00053 ( 3) SS BOND : angle 0.46338 ( 15) hydrogen bonds : bond 0.04275 ( 996) hydrogen bonds : angle 4.21275 ( 2892) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 0.963 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: A 235 ASP cc_start: 0.7024 (m-30) cc_final: 0.6353 (m-30) REVERT: A 305 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.6802 (t80) REVERT: A 309 MET cc_start: 0.8120 (tpp) cc_final: 0.7852 (tpp) REVERT: A 311 ASN cc_start: 0.7389 (t0) cc_final: 0.6754 (t0) REVERT: A 433 ARG cc_start: 0.7877 (tpt170) cc_final: 0.7473 (tpt170) REVERT: A 500 ARG cc_start: 0.7763 (mmm160) cc_final: 0.7406 (mmm160) REVERT: A 506 LEU cc_start: 0.7760 (mm) cc_final: 0.7418 (mt) REVERT: A 692 GLN cc_start: 0.7721 (mm110) cc_final: 0.7423 (tp40) REVERT: B 235 ASP cc_start: 0.6945 (m-30) cc_final: 0.6293 (m-30) REVERT: B 305 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.6862 (t80) REVERT: B 309 MET cc_start: 0.8091 (tpp) cc_final: 0.7883 (tpp) REVERT: B 311 ASN cc_start: 0.7401 (t0) cc_final: 0.6917 (t0) REVERT: B 433 ARG cc_start: 0.7904 (tpt170) cc_final: 0.7542 (tpt170) REVERT: B 500 ARG cc_start: 0.7739 (mmm160) cc_final: 0.7364 (mmm160) REVERT: B 506 LEU cc_start: 0.7792 (mm) cc_final: 0.7450 (mt) REVERT: B 692 GLN cc_start: 0.7694 (mm110) cc_final: 0.7384 (tp40) REVERT: B 717 MET cc_start: 0.5328 (tmt) cc_final: 0.5081 (tmt) REVERT: C 235 ASP cc_start: 0.6991 (m-30) cc_final: 0.6349 (m-30) REVERT: C 305 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.6726 (t80) REVERT: C 311 ASN cc_start: 0.7370 (t0) cc_final: 0.6790 (t0) REVERT: C 433 ARG cc_start: 0.7878 (tpt170) cc_final: 0.7450 (tpt170) REVERT: C 500 ARG cc_start: 0.7744 (mmm160) cc_final: 0.7376 (mmm160) REVERT: C 506 LEU cc_start: 0.7822 (mm) cc_final: 0.7495 (mt) REVERT: C 725 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7229 (pttm) REVERT: C 753 TRP cc_start: 0.6227 (m100) cc_final: 0.5902 (m100) REVERT: D 235 ASP cc_start: 0.7006 (m-30) cc_final: 0.6361 (m-30) REVERT: D 305 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.6645 (t80) REVERT: D 309 MET cc_start: 0.8111 (tpp) cc_final: 0.7867 (tpp) REVERT: D 311 ASN cc_start: 0.7426 (t0) cc_final: 0.6941 (t0) REVERT: D 364 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.7036 (ttp-170) REVERT: D 433 ARG cc_start: 0.7711 (mmm160) cc_final: 0.7299 (tpt170) REVERT: D 500 ARG cc_start: 0.7749 (mmm160) cc_final: 0.7365 (mmm160) REVERT: D 506 LEU cc_start: 0.7822 (mm) cc_final: 0.7491 (mt) REVERT: D 692 GLN cc_start: 0.7703 (mm110) cc_final: 0.7403 (tp40) REVERT: D 737 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6647 (m-30) outliers start: 37 outliers final: 16 residues processed: 255 average time/residue: 1.0940 time to fit residues: 318.4437 Evaluate side-chains 250 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 688 ASN Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 688 ASN Chi-restraints excluded: chain C residue 725 LYS Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 737 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 48 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 205 optimal weight: 0.4980 chunk 116 optimal weight: 0.3980 chunk 2 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN B 728 GLN C 261 GLN C 692 GLN D 261 GLN D 688 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.183339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.126760 restraints weight = 60950.208| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.89 r_work: 0.3375 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19595 Z= 0.131 Angle : 0.545 10.876 26211 Z= 0.281 Chirality : 0.065 1.460 2760 Planarity : 0.004 0.048 3064 Dihedral : 16.613 127.122 4144 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.45 % Allowed : 18.15 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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 aren not related in a simple way. whole: 0.58 (0.18), residues: 2108 helix: 1.47 (0.14), residues: 1292 sheet: -1.99 (0.53), residues: 76 loop : -1.30 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 213 TYR 0.012 0.001 TYR A 375 PHE 0.014 0.001 PHE A 721 TRP 0.026 0.002 TRP C 273 HIS 0.001 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00281 (19592) covalent geometry : angle 0.54473 (26196) SS BOND : bond 0.00057 ( 3) SS BOND : angle 0.49054 ( 15) hydrogen bonds : bond 0.04082 ( 996) hydrogen bonds : angle 4.14333 ( 2892) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 231 time to evaluate : 1.014 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: A 235 ASP cc_start: 0.6980 (m-30) cc_final: 0.6318 (m-30) REVERT: A 305 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6620 (t80) REVERT: A 309 MET cc_start: 0.8114 (tpp) cc_final: 0.7873 (tpp) REVERT: A 433 ARG cc_start: 0.7852 (tpt170) cc_final: 0.7448 (tpt170) REVERT: A 500 ARG cc_start: 0.7739 (mmm160) cc_final: 0.7390 (mmm160) REVERT: A 506 LEU cc_start: 0.7791 (mm) cc_final: 0.7452 (mt) REVERT: A 692 GLN cc_start: 0.7676 (mm110) cc_final: 0.7382 (tp40) REVERT: B 235 ASP cc_start: 0.6936 (m-30) cc_final: 0.6259 (m-30) REVERT: B 305 PHE cc_start: 0.7342 (OUTLIER) cc_final: 0.6814 (t80) REVERT: B 311 ASN cc_start: 0.7386 (t0) cc_final: 0.6901 (t0) REVERT: B 433 ARG cc_start: 0.7908 (tpt170) cc_final: 0.7533 (tpt170) REVERT: B 500 ARG cc_start: 0.7716 (mmm160) cc_final: 0.7362 (mmm160) REVERT: B 506 LEU cc_start: 0.7847 (mm) cc_final: 0.7540 (mt) REVERT: B 688 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.8073 (t0) REVERT: B 692 GLN cc_start: 0.7671 (mm110) cc_final: 0.7348 (tp40) REVERT: C 235 ASP cc_start: 0.6979 (m-30) cc_final: 0.6328 (m-30) REVERT: C 305 PHE cc_start: 0.7194 (OUTLIER) cc_final: 0.6462 (t80) REVERT: C 311 ASN cc_start: 0.7383 (t0) cc_final: 0.6802 (t0) REVERT: C 433 ARG cc_start: 0.7859 (tpt170) cc_final: 0.7436 (tpt170) REVERT: C 500 ARG cc_start: 0.7737 (mmm160) cc_final: 0.7384 (mmm160) REVERT: C 506 LEU cc_start: 0.7845 (mm) cc_final: 0.7503 (mt) REVERT: C 692 GLN cc_start: 0.8023 (tp-100) cc_final: 0.7263 (tp-100) REVERT: C 725 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.7210 (pttm) REVERT: C 753 TRP cc_start: 0.6259 (m100) cc_final: 0.5944 (m100) REVERT: D 235 ASP cc_start: 0.7006 (m-30) cc_final: 0.6365 (m-30) REVERT: D 305 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6518 (t80) REVERT: D 309 MET cc_start: 0.8094 (tpp) cc_final: 0.7870 (tpp) REVERT: D 364 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.7019 (ttp-170) REVERT: D 433 ARG cc_start: 0.7692 (mmm160) cc_final: 0.7287 (tpt170) REVERT: D 466 MET cc_start: 0.6959 (mmt) cc_final: 0.6750 (mmt) REVERT: D 500 ARG cc_start: 0.7737 (mmm160) cc_final: 0.7373 (mmm160) REVERT: D 506 LEU cc_start: 0.7850 (mm) cc_final: 0.7498 (mt) REVERT: D 688 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.8101 (t0) REVERT: D 692 GLN cc_start: 0.7653 (mm110) cc_final: 0.7358 (tp40) REVERT: D 725 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7221 (pttm) REVERT: D 753 TRP cc_start: 0.6231 (m100) cc_final: 0.5861 (m100) outliers start: 27 outliers final: 12 residues processed: 247 average time/residue: 1.3547 time to fit residues: 381.1919 Evaluate side-chains 244 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 688 ASN Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 688 ASN Chi-restraints excluded: chain C residue 725 LYS Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 688 ASN Chi-restraints excluded: chain D residue 725 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 96 optimal weight: 4.9990 chunk 18 optimal weight: 0.0040 chunk 183 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN B 728 GLN C 261 GLN D 261 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.181719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.124767 restraints weight = 60594.302| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.88 r_work: 0.3347 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19595 Z= 0.199 Angle : 0.593 10.986 26211 Z= 0.305 Chirality : 0.067 1.477 2760 Planarity : 0.004 0.050 3064 Dihedral : 16.926 106.742 4144 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.61 % Allowed : 18.52 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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 aren not related in a simple way. whole: 0.42 (0.18), residues: 2108 helix: 1.30 (0.14), residues: 1292 sheet: -2.05 (0.53), residues: 76 loop : -1.27 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 368 TYR 0.016 0.002 TYR A 375 PHE 0.017 0.002 PHE A 721 TRP 0.021 0.002 TRP D 273 HIS 0.001 0.000 HIS C 365 Details of bonding type rmsd covalent geometry : bond 0.00436 (19592) covalent geometry : angle 0.59297 (26196) SS BOND : bond 0.00035 ( 3) SS BOND : angle 0.47915 ( 15) hydrogen bonds : bond 0.04472 ( 996) hydrogen bonds : angle 4.25673 ( 2892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16200.95 seconds wall clock time: 273 minutes 53.11 seconds (16433.11 seconds total)