Starting phenix.real_space_refine on Sat Jul 4 21:14:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dxf_30907/07_2026/7dxf_30907.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dxf_30907/07_2026/7dxf_30907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7dxf_30907/07_2026/7dxf_30907.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dxf_30907/07_2026/7dxf_30907.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dxf_30907/07_2026/7dxf_30907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dxf_30907/07_2026/7dxf_30907.map" model { file = "/net/cci-nas-00/data/ceres_data/7dxf_30907/07_2026/7dxf_30907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dxf_30907/07_2026/7dxf_30907.cif" } resolution = 2.9 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= 0.006 sd= 0.194 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: 7 Type Number sf(0) Gaussians Ca 12 9.91 5 Zn 4 6.06 5 P 4 5.49 5 S 148 5.16 5 C 15060 2.51 5 N 3636 2.21 5 O 4076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22940 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5514 Classifications: {'peptide': 685} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 19, 'TRANS': 665} Chain breaks: 4 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 5514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5514 Classifications: {'peptide': 685} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 19, 'TRANS': 665} Chain breaks: 4 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 5514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5514 Classifications: {'peptide': 685} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 19, 'TRANS': 665} Chain breaks: 4 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 5514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5514 Classifications: {'peptide': 685} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 19, 'TRANS': 665} Chain breaks: 4 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Unusual residues: {' CA': 3, ' ZN': 1, '98R': 1, 'POV': 1, 'W99': 1, 'Y01': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Unusual residues: {' CA': 3, ' ZN': 1, '98R': 1, 'POV': 1, 'W99': 1, 'Y01': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "C" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Unusual residues: {' CA': 3, ' ZN': 1, '98R': 1, 'POV': 1, 'W99': 1, 'Y01': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "D" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Unusual residues: {' CA': 3, ' ZN': 1, '98R': 1, 'POV': 1, 'W99': 1, 'Y01': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1182 SG CYS A 253 24.529 35.531 59.613 1.00128.26 S ATOM 1197 SG CYS A 255 24.056 33.257 56.601 1.00138.81 S ATOM 1219 SG CYS A 258 27.452 34.827 57.218 1.00147.21 S ATOM 6696 SG CYS B 253 87.775 24.534 59.615 1.00128.26 S ATOM 6711 SG CYS B 255 90.050 24.061 56.603 1.00138.81 S ATOM 6733 SG CYS B 258 88.480 27.456 57.220 1.00147.21 S ATOM 12210 SG CYS C 253 98.773 87.780 59.615 1.00128.26 S ATOM 12225 SG CYS C 255 99.246 90.055 56.603 1.00138.81 S ATOM 12247 SG CYS C 258 95.850 88.485 57.220 1.00147.21 S ATOM 17724 SG CYS D 253 35.526 98.778 59.613 1.00128.26 S ATOM 17739 SG CYS D 255 33.252 99.250 56.601 1.00138.81 S ATOM 17761 SG CYS D 258 34.822 95.855 57.218 1.00147.21 S Time building chain proxies: 4.50, per 1000 atoms: 0.20 Number of scatterers: 22940 At special positions: 0 Unit cell: (124.355, 124.355, 143.165, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 12 19.99 S 148 16.00 P 4 15.00 O 4076 8.00 N 3636 7.00 C 15060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 789.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 249 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 255 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 258 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 253 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" ND1 HIS B 249 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 255 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 258 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 253 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" ND1 HIS C 249 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 255 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 258 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 253 " pdb=" ZN D1003 " pdb="ZN ZN D1003 " - pdb=" ND1 HIS D 249 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 255 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 258 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 253 " Number of angles added : 12 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5232 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 0 sheets defined 80.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 96 through 108 Processing helix chain 'A' and resid 110 through 121 Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 145 through 155 Processing helix chain 'A' and resid 160 through 171 Processing helix chain 'A' and resid 173 through 182 Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 255 through 265 Processing helix chain 'A' and resid 267 through 281 Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.973A pdb=" N SER A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 311 removed outlier: 3.823A pdb=" N ASN A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 335 Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 363 through 372 Processing helix chain 'A' and resid 380 through 392 removed outlier: 3.755A pdb=" N GLN A 386 " --> pdb=" O ASN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 removed outlier: 3.800A pdb=" N ARG A 399 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 400 " --> pdb=" O GLY A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 427 Proline residue: A 418 - end of helix removed outlier: 3.758A pdb=" N TRP A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 437 removed outlier: 3.773A pdb=" N ILE A 435 " --> pdb=" O LYS A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 460 Processing helix chain 'A' and resid 461 through 465 removed outlier: 4.045A pdb=" N PHE A 465 " --> pdb=" O ALA A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 490 Processing helix chain 'A' and resid 492 through 517 Processing helix chain 'A' and resid 517 through 523 Processing helix chain 'A' and resid 524 through 558 Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 582 through 586 Processing helix chain 'A' and resid 590 through 609 Processing helix chain 'A' and resid 610 through 617 removed outlier: 3.875A pdb=" N ILE A 613 " --> pdb=" O ILE A 610 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 614 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Proline residue: A 615 - end of helix No H-bonds generated for 'chain 'A' and resid 610 through 617' Processing helix chain 'A' and resid 620 through 629 Processing helix chain 'A' and resid 630 through 656 removed outlier: 3.914A pdb=" N ILE A 640 " --> pdb=" O LYS A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 683 removed outlier: 3.654A pdb=" N ILE A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE A 683 " --> pdb=" O PHE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 697 through 717 removed outlier: 4.025A pdb=" N GLU A 701 " --> pdb=" O HIS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 737 removed outlier: 3.896A pdb=" N GLU A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP A 737 " --> pdb=" O GLU A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 755 removed outlier: 3.631A pdb=" N TYR A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU A 755 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 876 Processing helix chain 'A' and resid 880 through 904 removed outlier: 3.572A pdb=" N ILE A 887 " --> pdb=" O GLU A 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 108 Processing helix chain 'B' and resid 110 through 121 Processing helix chain 'B' and resid 135 through 143 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 160 through 171 Processing helix chain 'B' and resid 173 through 182 Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 221 through 230 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 255 through 265 Processing helix chain 'B' and resid 267 through 281 Processing helix chain 'B' and resid 282 through 290 removed outlier: 3.973A pdb=" N SER B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 311 removed outlier: 3.823A pdb=" N ASN B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 310 " --> pdb=" O VAL B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 335 Processing helix chain 'B' and resid 338 through 347 Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 380 through 392 removed outlier: 3.755A pdb=" N GLN B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.801A pdb=" N ARG B 399 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN B 400 " --> pdb=" O GLY B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 427 Proline residue: B 418 - end of helix removed outlier: 3.758A pdb=" N TRP B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 437 removed outlier: 3.774A pdb=" N ILE B 435 " --> pdb=" O LYS B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 460 Processing helix chain 'B' and resid 461 through 465 removed outlier: 4.046A pdb=" N PHE B 465 " --> pdb=" O ALA B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 490 Processing helix chain 'B' and resid 492 through 517 Processing helix chain 'B' and resid 517 through 523 Processing helix chain 'B' and resid 524 through 558 Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'B' and resid 582 through 586 Processing helix chain 'B' and resid 590 through 609 Processing helix chain 'B' and resid 610 through 617 removed outlier: 3.875A pdb=" N ILE B 613 " --> pdb=" O ILE B 610 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 614 " --> pdb=" O ALA B 611 " (cutoff:3.500A) Proline residue: B 615 - end of helix No H-bonds generated for 'chain 'B' and resid 610 through 617' Processing helix chain 'B' and resid 620 through 629 Processing helix chain 'B' and resid 630 through 656 removed outlier: 3.914A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 683 removed outlier: 3.654A pdb=" N ILE B 682 " --> pdb=" O LEU B 678 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE B 683 " --> pdb=" O PHE B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 692 Processing helix chain 'B' and resid 697 through 717 removed outlier: 4.026A pdb=" N GLU B 701 " --> pdb=" O HIS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 737 removed outlier: 3.896A pdb=" N GLU B 733 " --> pdb=" O SER B 729 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP B 737 " --> pdb=" O GLU B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 755 removed outlier: 3.631A pdb=" N TYR B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU B 755 " --> pdb=" O PHE B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 876 Processing helix chain 'B' and resid 880 through 904 removed outlier: 3.572A pdb=" N ILE B 887 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 108 Processing helix chain 'C' and resid 110 through 121 Processing helix chain 'C' and resid 135 through 143 Processing helix chain 'C' and resid 145 through 155 Processing helix chain 'C' and resid 160 through 171 Processing helix chain 'C' and resid 173 through 182 Processing helix chain 'C' and resid 183 through 187 Processing helix chain 'C' and resid 221 through 230 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 255 through 265 Processing helix chain 'C' and resid 267 through 281 Processing helix chain 'C' and resid 282 through 290 removed outlier: 3.973A pdb=" N SER C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 311 removed outlier: 3.823A pdb=" N ASN C 309 " --> pdb=" O ALA C 305 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE C 310 " --> pdb=" O VAL C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 335 Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 363 through 372 Processing helix chain 'C' and resid 380 through 392 removed outlier: 3.755A pdb=" N GLN C 386 " --> pdb=" O ASN C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 401 removed outlier: 3.801A pdb=" N ARG C 399 " --> pdb=" O SER C 396 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN C 400 " --> pdb=" O GLY C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 427 Proline residue: C 418 - end of helix removed outlier: 3.758A pdb=" N TRP C 425 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE C 426 " --> pdb=" O LEU C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 437 removed outlier: 3.773A pdb=" N ILE C 435 " --> pdb=" O LYS C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 460 Processing helix chain 'C' and resid 461 through 465 removed outlier: 4.045A pdb=" N PHE C 465 " --> pdb=" O ALA C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 490 Processing helix chain 'C' and resid 492 through 517 Processing helix chain 'C' and resid 517 through 523 Processing helix chain 'C' and resid 524 through 558 Processing helix chain 'C' and resid 577 through 581 Processing helix chain 'C' and resid 582 through 586 Processing helix chain 'C' and resid 590 through 609 Processing helix chain 'C' and resid 610 through 617 removed outlier: 3.875A pdb=" N ILE C 613 " --> pdb=" O ILE C 610 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 614 " --> pdb=" O ALA C 611 " (cutoff:3.500A) Proline residue: C 615 - end of helix No H-bonds generated for 'chain 'C' and resid 610 through 617' Processing helix chain 'C' and resid 620 through 629 Processing helix chain 'C' and resid 630 through 656 removed outlier: 3.914A pdb=" N ILE C 640 " --> pdb=" O LYS C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 683 removed outlier: 3.654A pdb=" N ILE C 682 " --> pdb=" O LEU C 678 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE C 683 " --> pdb=" O PHE C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 692 Processing helix chain 'C' and resid 697 through 717 removed outlier: 4.026A pdb=" N GLU C 701 " --> pdb=" O HIS C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 737 removed outlier: 3.896A pdb=" N GLU C 733 " --> pdb=" O SER C 729 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP C 737 " --> pdb=" O GLU C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 755 removed outlier: 3.631A pdb=" N TYR C 753 " --> pdb=" O LEU C 749 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU C 755 " --> pdb=" O PHE C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 876 Processing helix chain 'C' and resid 880 through 904 removed outlier: 3.572A pdb=" N ILE C 887 " --> pdb=" O GLU C 883 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 108 Processing helix chain 'D' and resid 110 through 121 Processing helix chain 'D' and resid 135 through 143 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 160 through 171 Processing helix chain 'D' and resid 173 through 182 Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'D' and resid 221 through 230 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 255 through 265 Processing helix chain 'D' and resid 267 through 281 Processing helix chain 'D' and resid 282 through 290 removed outlier: 3.973A pdb=" N SER D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 311 removed outlier: 3.823A pdb=" N ASN D 309 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE D 310 " --> pdb=" O VAL D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 335 Processing helix chain 'D' and resid 338 through 347 Processing helix chain 'D' and resid 363 through 372 Processing helix chain 'D' and resid 380 through 392 removed outlier: 3.755A pdb=" N GLN D 386 " --> pdb=" O ASN D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 401 removed outlier: 3.801A pdb=" N ARG D 399 " --> pdb=" O SER D 396 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN D 400 " --> pdb=" O GLY D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 427 Proline residue: D 418 - end of helix removed outlier: 3.758A pdb=" N TRP D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE D 426 " --> pdb=" O LEU D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 437 removed outlier: 3.773A pdb=" N ILE D 435 " --> pdb=" O LYS D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 460 Processing helix chain 'D' and resid 461 through 465 removed outlier: 4.045A pdb=" N PHE D 465 " --> pdb=" O ALA D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 490 Processing helix chain 'D' and resid 492 through 517 Processing helix chain 'D' and resid 517 through 523 Processing helix chain 'D' and resid 524 through 558 Processing helix chain 'D' and resid 577 through 581 Processing helix chain 'D' and resid 582 through 586 Processing helix chain 'D' and resid 590 through 609 Processing helix chain 'D' and resid 610 through 617 removed outlier: 3.875A pdb=" N ILE D 613 " --> pdb=" O ILE D 610 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU D 614 " --> pdb=" O ALA D 611 " (cutoff:3.500A) Proline residue: D 615 - end of helix No H-bonds generated for 'chain 'D' and resid 610 through 617' Processing helix chain 'D' and resid 620 through 629 Processing helix chain 'D' and resid 630 through 656 removed outlier: 3.914A pdb=" N ILE D 640 " --> pdb=" O LYS D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 683 removed outlier: 3.655A pdb=" N ILE D 682 " --> pdb=" O LEU D 678 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE D 683 " --> pdb=" O PHE D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 692 Processing helix chain 'D' and resid 697 through 717 removed outlier: 4.025A pdb=" N GLU D 701 " --> pdb=" O HIS D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 737 removed outlier: 3.896A pdb=" N GLU D 733 " --> pdb=" O SER D 729 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP D 737 " --> pdb=" O GLU D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 755 removed outlier: 3.631A pdb=" N TYR D 753 " --> pdb=" O LEU D 749 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU D 755 " --> pdb=" O PHE D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 876 Processing helix chain 'D' and resid 880 through 904 removed outlier: 3.572A pdb=" N ILE D 887 " --> pdb=" O GLU D 883 " (cutoff:3.500A) 1488 hydrogen bonds defined for protein. 4344 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: 3.42 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4843 1.33 - 1.45: 5139 1.45 - 1.57: 13214 1.57 - 1.69: 8 1.69 - 1.81: 248 Bond restraints: 23452 Sorted by residual: bond pdb=" CAY Y01 C1007 " pdb=" OAW Y01 C1007 " ideal model delta sigma weight residual 1.332 1.457 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" CAY Y01 D1005 " pdb=" OAW Y01 D1005 " ideal model delta sigma weight residual 1.332 1.457 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" CAY Y01 C1003 " pdb=" OAW Y01 C1003 " ideal model delta sigma weight residual 1.332 1.457 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" CAY Y01 B1003 " pdb=" OAW Y01 B1003 " ideal model delta sigma weight residual 1.332 1.457 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" CAY Y01 A1007 " pdb=" OAW Y01 A1007 " ideal model delta sigma weight residual 1.332 1.456 -0.124 2.00e-02 2.50e+03 3.87e+01 ... (remaining 23447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 30753 1.89 - 3.78: 609 3.78 - 5.68: 202 5.68 - 7.57: 58 7.57 - 9.46: 54 Bond angle restraints: 31676 Sorted by residual: angle pdb=" O ASP D 890 " pdb=" C ASP D 890 " pdb=" N ILE D 891 " ideal model delta sigma weight residual 122.07 128.65 -6.58 1.03e+00 9.43e-01 4.08e+01 angle pdb=" O ASP C 890 " pdb=" C ASP C 890 " pdb=" N ILE C 891 " ideal model delta sigma weight residual 122.07 128.63 -6.56 1.03e+00 9.43e-01 4.06e+01 angle pdb=" O ASP B 890 " pdb=" C ASP B 890 " pdb=" N ILE B 891 " ideal model delta sigma weight residual 122.07 128.63 -6.56 1.03e+00 9.43e-01 4.06e+01 angle pdb=" O ASP A 890 " pdb=" C ASP A 890 " pdb=" N ILE A 891 " ideal model delta sigma weight residual 122.07 128.59 -6.52 1.03e+00 9.43e-01 4.01e+01 angle pdb=" CA ASP C 890 " pdb=" C ASP C 890 " pdb=" N ILE C 891 " ideal model delta sigma weight residual 117.07 110.32 6.75 1.14e+00 7.69e-01 3.50e+01 ... (remaining 31671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.07: 13396 28.07 - 56.15: 436 56.15 - 84.22: 96 84.22 - 112.29: 36 112.29 - 140.36: 16 Dihedral angle restraints: 13980 sinusoidal: 5912 harmonic: 8068 Sorted by residual: dihedral pdb=" C12 98R A1008 " pdb=" C11 98R A1008 " pdb=" O3 98R A1008 " pdb=" C3 98R A1008 " ideal model delta sinusoidal sigma weight residual -178.27 -37.91 -140.36 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" C3 98R C1008 " pdb=" C11 98R C1008 " pdb=" O3 98R C1008 " pdb=" O11 98R C1008 " ideal model delta sinusoidal sigma weight residual -1.73 -142.09 140.36 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" C3 98R A1008 " pdb=" C11 98R A1008 " pdb=" O3 98R A1008 " pdb=" O11 98R A1008 " ideal model delta sinusoidal sigma weight residual -1.73 -142.07 140.34 1 3.00e+01 1.11e-03 1.89e+01 ... (remaining 13977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3083 0.060 - 0.119: 345 0.119 - 0.179: 37 0.179 - 0.238: 11 0.238 - 0.298: 12 Chirality restraints: 3488 Sorted by residual: chirality pdb=" C2 98R D1010 " pdb=" C1 98R D1010 " pdb=" C3 98R D1010 " pdb=" O2 98R D1010 " both_signs ideal model delta sigma weight residual False -2.31 -2.61 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C2 98R C1008 " pdb=" C1 98R C1008 " pdb=" C3 98R C1008 " pdb=" O2 98R C1008 " both_signs ideal model delta sigma weight residual False -2.31 -2.61 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C2 98R A1008 " pdb=" C1 98R A1008 " pdb=" C3 98R A1008 " pdb=" O2 98R A1008 " both_signs ideal model delta sigma weight residual False -2.31 -2.61 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 3485 not shown) Planarity restraints: 3896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 W99 C1002 " -0.045 2.00e-02 2.50e+03 3.92e-01 2.30e+03 pdb=" C11 W99 C1002 " -0.427 2.00e-02 2.50e+03 pdb=" C15 W99 C1002 " 0.474 2.00e-02 2.50e+03 pdb=" C8 W99 C1002 " 0.505 2.00e-02 2.50e+03 pdb=" N2 W99 C1002 " 0.001 2.00e-02 2.50e+03 pdb=" O1 W99 C1002 " -0.507 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 W99 B1002 " 0.045 2.00e-02 2.50e+03 3.92e-01 2.30e+03 pdb=" C11 W99 B1002 " 0.427 2.00e-02 2.50e+03 pdb=" C15 W99 B1002 " -0.474 2.00e-02 2.50e+03 pdb=" C8 W99 B1002 " -0.505 2.00e-02 2.50e+03 pdb=" N2 W99 B1002 " -0.001 2.00e-02 2.50e+03 pdb=" O1 W99 B1002 " 0.507 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 W99 A1002 " 0.045 2.00e-02 2.50e+03 3.92e-01 2.30e+03 pdb=" C11 W99 A1002 " 0.427 2.00e-02 2.50e+03 pdb=" C15 W99 A1002 " -0.474 2.00e-02 2.50e+03 pdb=" C8 W99 A1002 " -0.505 2.00e-02 2.50e+03 pdb=" N2 W99 A1002 " -0.001 2.00e-02 2.50e+03 pdb=" O1 W99 A1002 " 0.507 2.00e-02 2.50e+03 ... (remaining 3893 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3003 2.76 - 3.29: 23225 3.29 - 3.83: 38832 3.83 - 4.36: 44585 4.36 - 4.90: 77068 Nonbonded interactions: 186713 Sorted by model distance: nonbonded pdb=" CG GLU A 881 " pdb=" OE2 GLU B 883 " model vdw 2.221 3.440 nonbonded pdb=" CG GLU C 881 " pdb=" OE2 GLU D 883 " model vdw 2.221 3.440 nonbonded pdb=" CG GLU B 881 " pdb=" OE2 GLU C 883 " model vdw 2.221 3.440 nonbonded pdb=" OE2 GLU A 883 " pdb=" CG GLU D 881 " model vdw 2.222 3.440 nonbonded pdb=" CE LYS A 888 " pdb=" OE2 GLU B 886 " model vdw 2.247 3.440 ... (remaining 186708 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: 0.06 Found NCS groups: ncs_group { reference = (chain 'A' and resid 95 through 904) selection = (chain 'B' and resid 95 through 904) selection = (chain 'C' and resid 95 through 904) selection = (chain 'D' and resid 95 through 904) } 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 21.530 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 23468 Z= 0.318 Angle : 0.800 9.459 31688 Z= 0.377 Chirality : 0.043 0.298 3488 Planarity : 0.013 0.392 3896 Dihedral : 16.032 140.364 8748 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.56 % Favored : 96.30 % Rotamer: Outliers : 3.38 % Allowed : 4.91 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.16), residues: 2700 helix: 2.41 (0.12), residues: 1984 sheet: None (None), residues: 0 loop : -1.42 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 865 TYR 0.008 0.001 TYR B 866 PHE 0.015 0.001 PHE D 377 TRP 0.011 0.001 TRP C 526 HIS 0.002 0.000 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.32 (23452) covalent geometry : angle 0.79934 / 0.38 (31676) hydrogen bonds : bond 0.14599 / 10.04 ( 1488) hydrogen bonds : angle 5.07660 / 3.61 ( 4344) metal coordination : bond 0.02044 / 1.48 ( 16) metal coordination : angle 1.98829 / 1.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 475 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7759 (tt0) cc_final: 0.6962 (tp30) REVERT: A 116 LYS cc_start: 0.8200 (tttt) cc_final: 0.7875 (ttpp) REVERT: A 156 GLU cc_start: 0.8148 (tt0) cc_final: 0.7848 (mp0) REVERT: A 171 LYS cc_start: 0.7987 (mttm) cc_final: 0.7766 (mtmt) REVERT: A 432 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.6005 (ttp) REVERT: A 434 LYS cc_start: 0.7816 (mtpp) cc_final: 0.7336 (mtmm) REVERT: A 436 MET cc_start: 0.7003 (mtm) cc_final: 0.6745 (mmm) REVERT: A 459 MET cc_start: 0.7572 (mmm) cc_final: 0.7292 (mmm) REVERT: A 511 LYS cc_start: 0.5592 (OUTLIER) cc_final: 0.5029 (mmmt) REVERT: A 541 PHE cc_start: 0.7394 (m-10) cc_final: 0.7171 (m-80) REVERT: A 548 PHE cc_start: 0.7756 (t80) cc_final: 0.7480 (t80) REVERT: A 585 LYS cc_start: 0.7898 (mmpt) cc_final: 0.7589 (mptt) REVERT: A 587 ASP cc_start: 0.7451 (t0) cc_final: 0.7051 (t0) REVERT: A 612 TYR cc_start: 0.7565 (t80) cc_final: 0.6392 (t80) REVERT: A 633 ASP cc_start: 0.6876 (m-30) cc_final: 0.6325 (t0) REVERT: A 669 THR cc_start: 0.8228 (m) cc_final: 0.7925 (p) REVERT: A 673 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6736 (mm-30) REVERT: A 726 MET cc_start: 0.8113 (ttm) cc_final: 0.7828 (ttm) REVERT: A 875 GLU cc_start: 0.6528 (mt-10) cc_final: 0.6075 (mm-30) REVERT: A 900 GLU cc_start: 0.7019 (tp30) cc_final: 0.6669 (tm-30) REVERT: B 100 GLU cc_start: 0.7758 (tt0) cc_final: 0.6958 (tp30) REVERT: B 116 LYS cc_start: 0.8202 (tttt) cc_final: 0.7875 (ttpp) REVERT: B 156 GLU cc_start: 0.8144 (tt0) cc_final: 0.7842 (mp0) REVERT: B 171 LYS cc_start: 0.7990 (mttm) cc_final: 0.7772 (mtmt) REVERT: B 432 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.6008 (ttp) REVERT: B 434 LYS cc_start: 0.7816 (mtpp) cc_final: 0.7277 (mtmm) REVERT: B 436 MET cc_start: 0.7062 (mtm) cc_final: 0.6772 (mmm) REVERT: B 459 MET cc_start: 0.7573 (mmm) cc_final: 0.7292 (mmm) REVERT: B 511 LYS cc_start: 0.5591 (OUTLIER) cc_final: 0.5028 (mmmt) REVERT: B 541 PHE cc_start: 0.7400 (m-10) cc_final: 0.7148 (m-80) REVERT: B 548 PHE cc_start: 0.7756 (t80) cc_final: 0.7480 (t80) REVERT: B 585 LYS cc_start: 0.7939 (mmpt) cc_final: 0.7618 (mptt) REVERT: B 587 ASP cc_start: 0.7442 (t0) cc_final: 0.7047 (t0) REVERT: B 612 TYR cc_start: 0.7533 (t80) cc_final: 0.6347 (t80) REVERT: B 633 ASP cc_start: 0.6886 (m-30) cc_final: 0.6333 (t0) REVERT: B 669 THR cc_start: 0.8236 (m) cc_final: 0.7929 (p) REVERT: B 673 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6731 (mm-30) REVERT: B 726 MET cc_start: 0.8134 (ttm) cc_final: 0.7802 (ttm) REVERT: B 875 GLU cc_start: 0.6471 (mt-10) cc_final: 0.6019 (mm-30) REVERT: B 900 GLU cc_start: 0.7021 (tp30) cc_final: 0.6670 (tm-30) REVERT: C 100 GLU cc_start: 0.7758 (tt0) cc_final: 0.6961 (tp30) REVERT: C 116 LYS cc_start: 0.8202 (tttt) cc_final: 0.7876 (ttpp) REVERT: C 156 GLU cc_start: 0.8144 (tt0) cc_final: 0.7843 (mp0) REVERT: C 171 LYS cc_start: 0.7985 (mttm) cc_final: 0.7767 (mtmt) REVERT: C 432 MET cc_start: 0.6765 (OUTLIER) cc_final: 0.5996 (ttp) REVERT: C 434 LYS cc_start: 0.7819 (mtpp) cc_final: 0.7281 (mtmm) REVERT: C 436 MET cc_start: 0.7078 (mtm) cc_final: 0.6775 (mmm) REVERT: C 459 MET cc_start: 0.7574 (mmm) cc_final: 0.7292 (mmm) REVERT: C 541 PHE cc_start: 0.7398 (m-10) cc_final: 0.7173 (m-80) REVERT: C 548 PHE cc_start: 0.7763 (t80) cc_final: 0.7490 (t80) REVERT: C 585 LYS cc_start: 0.7935 (mmpt) cc_final: 0.7617 (mptt) REVERT: C 587 ASP cc_start: 0.7445 (t0) cc_final: 0.7052 (t0) REVERT: C 612 TYR cc_start: 0.7536 (t80) cc_final: 0.6300 (t80) REVERT: C 633 ASP cc_start: 0.6881 (m-30) cc_final: 0.6321 (t0) REVERT: C 669 THR cc_start: 0.8244 (m) cc_final: 0.7941 (p) REVERT: C 673 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6739 (mm-30) REVERT: C 715 MET cc_start: 0.7915 (mmt) cc_final: 0.7706 (mmt) REVERT: C 726 MET cc_start: 0.8124 (ttm) cc_final: 0.7820 (ttm) REVERT: C 875 GLU cc_start: 0.6534 (mt-10) cc_final: 0.6074 (mm-30) REVERT: C 900 GLU cc_start: 0.7021 (tp30) cc_final: 0.6674 (tm-30) REVERT: D 100 GLU cc_start: 0.7759 (tt0) cc_final: 0.6964 (tp30) REVERT: D 116 LYS cc_start: 0.8197 (tttt) cc_final: 0.7871 (ttpp) REVERT: D 156 GLU cc_start: 0.8149 (tt0) cc_final: 0.7849 (mp0) REVERT: D 171 LYS cc_start: 0.7985 (mttm) cc_final: 0.7762 (mtmt) REVERT: D 432 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.5996 (ttp) REVERT: D 434 LYS cc_start: 0.7816 (mtpp) cc_final: 0.7338 (mtmm) REVERT: D 436 MET cc_start: 0.7014 (mtm) cc_final: 0.6746 (mmm) REVERT: D 459 MET cc_start: 0.7576 (mmm) cc_final: 0.7294 (mmm) REVERT: D 541 PHE cc_start: 0.7390 (m-10) cc_final: 0.7165 (m-80) REVERT: D 548 PHE cc_start: 0.7760 (t80) cc_final: 0.7480 (t80) REVERT: D 585 LYS cc_start: 0.7896 (mmpt) cc_final: 0.7589 (mptt) REVERT: D 587 ASP cc_start: 0.7453 (t0) cc_final: 0.7054 (t0) REVERT: D 612 TYR cc_start: 0.7539 (t80) cc_final: 0.6304 (t80) REVERT: D 633 ASP cc_start: 0.6868 (m-30) cc_final: 0.6320 (t0) REVERT: D 669 THR cc_start: 0.8236 (m) cc_final: 0.7936 (p) REVERT: D 673 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6743 (mm-30) REVERT: D 726 MET cc_start: 0.8072 (ttm) cc_final: 0.7768 (ttm) REVERT: D 875 GLU cc_start: 0.6531 (mt-10) cc_final: 0.6074 (mm-30) REVERT: D 900 GLU cc_start: 0.7022 (tp30) cc_final: 0.6674 (tm-30) outliers start: 80 outliers final: 24 residues processed: 539 average time/residue: 0.6344 time to fit residues: 387.3966 Evaluate side-chains 360 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 330 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain D residue 209 TYR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 577 LYS Chi-restraints excluded: chain D residue 760 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 20.0000 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN A 384 GLN A 702 ASN A 889 GLN B 157 ASN B 384 GLN B 702 ASN B 889 GLN C 157 ASN C 384 GLN C 592 GLN C 702 ASN C 889 GLN D 157 ASN D 384 GLN D 702 ASN D 889 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.155029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.111452 restraints weight = 27763.163| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.24 r_work: 0.3144 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23468 Z= 0.137 Angle : 0.553 7.377 31688 Z= 0.278 Chirality : 0.037 0.150 3488 Planarity : 0.004 0.037 3896 Dihedral : 15.180 148.399 3528 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.81 % Allowed : 10.79 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.16), residues: 2700 helix: 2.44 (0.11), residues: 2008 sheet: None (None), residues: 0 loop : -1.25 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 360 TYR 0.011 0.001 TYR D 578 PHE 0.021 0.001 PHE D 545 TRP 0.010 0.001 TRP A 526 HIS 0.003 0.001 HIS D 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (23452) covalent geometry : angle 0.55232 / 0.28 (31676) hydrogen bonds : bond 0.04441 / 3.02 ( 1488) hydrogen bonds : angle 3.79373 / 2.72 ( 4344) metal coordination : bond 0.00621 / 0.44 ( 16) metal coordination : angle 1.73528 / 0.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 346 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8204 (tt0) cc_final: 0.7442 (tp30) REVERT: A 116 LYS cc_start: 0.8483 (tttt) cc_final: 0.8214 (ttpp) REVERT: A 171 LYS cc_start: 0.8460 (mttm) cc_final: 0.8170 (mtmt) REVERT: A 334 ASP cc_start: 0.8427 (t70) cc_final: 0.8002 (t0) REVERT: A 432 MET cc_start: 0.6394 (OUTLIER) cc_final: 0.5780 (ttp) REVERT: A 434 LYS cc_start: 0.8070 (mtpp) cc_final: 0.7630 (mtmm) REVERT: A 459 MET cc_start: 0.7964 (mmm) cc_final: 0.7726 (mmm) REVERT: A 496 MET cc_start: 0.8294 (mmt) cc_final: 0.7941 (mpt) REVERT: A 511 LYS cc_start: 0.6362 (OUTLIER) cc_final: 0.5911 (mmpt) REVERT: A 548 PHE cc_start: 0.8053 (t80) cc_final: 0.7767 (t80) REVERT: A 585 LYS cc_start: 0.8060 (mmpt) cc_final: 0.7753 (mptt) REVERT: A 587 ASP cc_start: 0.7793 (t0) cc_final: 0.7466 (t0) REVERT: A 612 TYR cc_start: 0.7545 (t80) cc_final: 0.6515 (t80) REVERT: A 633 ASP cc_start: 0.7171 (m-30) cc_final: 0.6698 (t0) REVERT: A 666 GLU cc_start: 0.7358 (pm20) cc_final: 0.6884 (mm-30) REVERT: A 669 THR cc_start: 0.8460 (m) cc_final: 0.8004 (p) REVERT: A 673 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7485 (mm-30) REVERT: A 875 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6636 (mm-30) REVERT: A 885 LYS cc_start: 0.8447 (tttp) cc_final: 0.8186 (tppt) REVERT: A 900 GLU cc_start: 0.7385 (tp30) cc_final: 0.7139 (tm-30) REVERT: B 100 GLU cc_start: 0.8207 (tt0) cc_final: 0.7441 (tp30) REVERT: B 116 LYS cc_start: 0.8487 (tttt) cc_final: 0.8215 (ttpp) REVERT: B 171 LYS cc_start: 0.8468 (mttm) cc_final: 0.8177 (mtmt) REVERT: B 334 ASP cc_start: 0.8445 (t70) cc_final: 0.8014 (t0) REVERT: B 432 MET cc_start: 0.6404 (OUTLIER) cc_final: 0.5795 (ttp) REVERT: B 434 LYS cc_start: 0.8086 (mtpp) cc_final: 0.7628 (mtmm) REVERT: B 459 MET cc_start: 0.7964 (mmm) cc_final: 0.7726 (mmm) REVERT: B 496 MET cc_start: 0.8273 (mmt) cc_final: 0.7922 (mpt) REVERT: B 511 LYS cc_start: 0.6385 (OUTLIER) cc_final: 0.5942 (mmpt) REVERT: B 541 PHE cc_start: 0.7770 (m-10) cc_final: 0.7567 (m-80) REVERT: B 548 PHE cc_start: 0.8050 (t80) cc_final: 0.7770 (t80) REVERT: B 585 LYS cc_start: 0.8062 (mmpt) cc_final: 0.7752 (mptt) REVERT: B 587 ASP cc_start: 0.7727 (t0) cc_final: 0.7415 (t0) REVERT: B 612 TYR cc_start: 0.7505 (t80) cc_final: 0.6445 (t80) REVERT: B 633 ASP cc_start: 0.7157 (m-30) cc_final: 0.6669 (t0) REVERT: B 666 GLU cc_start: 0.7365 (pm20) cc_final: 0.6909 (mm-30) REVERT: B 669 THR cc_start: 0.8471 (m) cc_final: 0.8010 (p) REVERT: B 673 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7490 (mm-30) REVERT: B 875 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6700 (mm-30) REVERT: B 885 LYS cc_start: 0.8453 (tttp) cc_final: 0.8195 (tppt) REVERT: B 900 GLU cc_start: 0.7369 (tp30) cc_final: 0.7127 (tm-30) REVERT: C 100 GLU cc_start: 0.8199 (tt0) cc_final: 0.7431 (tp30) REVERT: C 116 LYS cc_start: 0.8489 (tttt) cc_final: 0.8216 (ttpp) REVERT: C 171 LYS cc_start: 0.8465 (mttm) cc_final: 0.8172 (mtmt) REVERT: C 334 ASP cc_start: 0.8425 (t70) cc_final: 0.8002 (t0) REVERT: C 432 MET cc_start: 0.6400 (OUTLIER) cc_final: 0.5795 (ttp) REVERT: C 434 LYS cc_start: 0.8085 (mtpp) cc_final: 0.7630 (mtmm) REVERT: C 459 MET cc_start: 0.7959 (mmm) cc_final: 0.7698 (mmm) REVERT: C 496 MET cc_start: 0.8282 (mmt) cc_final: 0.7931 (mpt) REVERT: C 548 PHE cc_start: 0.8063 (t80) cc_final: 0.7790 (t80) REVERT: C 585 LYS cc_start: 0.8063 (mmpt) cc_final: 0.7753 (mptt) REVERT: C 587 ASP cc_start: 0.7732 (t0) cc_final: 0.7451 (t0) REVERT: C 612 TYR cc_start: 0.7491 (t80) cc_final: 0.6457 (t80) REVERT: C 633 ASP cc_start: 0.7152 (m-30) cc_final: 0.6664 (t0) REVERT: C 666 GLU cc_start: 0.7360 (pm20) cc_final: 0.6930 (mm-30) REVERT: C 669 THR cc_start: 0.8478 (m) cc_final: 0.8041 (p) REVERT: C 673 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7493 (mm-30) REVERT: C 875 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6641 (mm-30) REVERT: C 885 LYS cc_start: 0.8452 (tttp) cc_final: 0.8196 (tppt) REVERT: C 900 GLU cc_start: 0.7385 (tp30) cc_final: 0.7152 (tm-30) REVERT: D 100 GLU cc_start: 0.8188 (tt0) cc_final: 0.7426 (tp30) REVERT: D 116 LYS cc_start: 0.8482 (tttt) cc_final: 0.8213 (ttpp) REVERT: D 171 LYS cc_start: 0.8458 (mttm) cc_final: 0.8165 (mtmt) REVERT: D 334 ASP cc_start: 0.8422 (t70) cc_final: 0.7997 (t0) REVERT: D 432 MET cc_start: 0.6363 (OUTLIER) cc_final: 0.5751 (ttp) REVERT: D 434 LYS cc_start: 0.8078 (mtpp) cc_final: 0.7633 (mtmm) REVERT: D 459 MET cc_start: 0.7965 (mmm) cc_final: 0.7728 (mmm) REVERT: D 496 MET cc_start: 0.8300 (mmt) cc_final: 0.7963 (mpt) REVERT: D 548 PHE cc_start: 0.8060 (t80) cc_final: 0.7783 (t80) REVERT: D 585 LYS cc_start: 0.8060 (mmpt) cc_final: 0.7748 (mptt) REVERT: D 587 ASP cc_start: 0.7774 (t0) cc_final: 0.7477 (t0) REVERT: D 612 TYR cc_start: 0.7500 (t80) cc_final: 0.6462 (t80) REVERT: D 629 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8281 (mtp-110) REVERT: D 633 ASP cc_start: 0.7149 (m-30) cc_final: 0.6662 (t0) REVERT: D 641 PHE cc_start: 0.7749 (t80) cc_final: 0.7500 (t80) REVERT: D 666 GLU cc_start: 0.7356 (pm20) cc_final: 0.6919 (mm-30) REVERT: D 669 THR cc_start: 0.8496 (m) cc_final: 0.8070 (p) REVERT: D 673 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7500 (mm-30) REVERT: D 875 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6703 (mm-30) REVERT: D 885 LYS cc_start: 0.8449 (tttp) cc_final: 0.8190 (tppt) REVERT: D 900 GLU cc_start: 0.7382 (tp30) cc_final: 0.7142 (tm-30) outliers start: 90 outliers final: 36 residues processed: 412 average time/residue: 0.6138 time to fit residues: 288.5829 Evaluate side-chains 351 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 308 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain D residue 209 TYR Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 558 ILE Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 577 LYS Chi-restraints excluded: chain D residue 629 ARG Chi-restraints excluded: chain D residue 657 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 211 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 239 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 592 GLN A 721 ASN B 592 GLN B 721 ASN C 721 ASN D 157 ASN D 592 GLN D 721 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.155318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.112512 restraints weight = 27479.097| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.21 r_work: 0.3160 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23468 Z= 0.127 Angle : 0.527 10.139 31688 Z= 0.266 Chirality : 0.036 0.187 3488 Planarity : 0.004 0.043 3896 Dihedral : 13.497 141.463 3508 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.23 % Allowed : 11.68 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.16), residues: 2700 helix: 2.49 (0.11), residues: 2008 sheet: None (None), residues: 0 loop : -1.27 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 360 TYR 0.018 0.001 TYR B 251 PHE 0.013 0.001 PHE D 641 TRP 0.009 0.001 TRP D 391 HIS 0.003 0.000 HIS D 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (23452) covalent geometry : angle 0.52696 / 0.27 (31676) hydrogen bonds : bond 0.04133 / 2.80 ( 1488) hydrogen bonds : angle 3.64156 / 2.61 ( 4344) metal coordination : bond 0.00521 / 0.37 ( 16) metal coordination : angle 1.31897 / 0.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 348 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8200 (tt0) cc_final: 0.7437 (tp30) REVERT: A 116 LYS cc_start: 0.8488 (tttt) cc_final: 0.8235 (ttpp) REVERT: A 171 LYS cc_start: 0.8599 (mttm) cc_final: 0.8335 (mtmt) REVERT: A 334 ASP cc_start: 0.8484 (t70) cc_final: 0.8168 (t0) REVERT: A 432 MET cc_start: 0.6220 (OUTLIER) cc_final: 0.5776 (ttp) REVERT: A 434 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7717 (mtmm) REVERT: A 459 MET cc_start: 0.7949 (mmm) cc_final: 0.7723 (mpp) REVERT: A 496 MET cc_start: 0.8254 (mmt) cc_final: 0.7969 (mpt) REVERT: A 501 TRP cc_start: 0.8162 (OUTLIER) cc_final: 0.7927 (m-90) REVERT: A 511 LYS cc_start: 0.6396 (OUTLIER) cc_final: 0.5865 (mmmt) REVERT: A 548 PHE cc_start: 0.8087 (t80) cc_final: 0.7839 (t80) REVERT: A 585 LYS cc_start: 0.8092 (mmpt) cc_final: 0.7788 (mptt) REVERT: A 587 ASP cc_start: 0.7822 (t0) cc_final: 0.7566 (t0) REVERT: A 612 TYR cc_start: 0.7483 (t80) cc_final: 0.6472 (t80) REVERT: A 673 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7426 (mm-30) REVERT: A 859 MET cc_start: 0.9060 (mmp) cc_final: 0.8852 (mmm) REVERT: A 875 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6695 (mm-30) REVERT: A 885 LYS cc_start: 0.8454 (tttp) cc_final: 0.8169 (tppt) REVERT: A 900 GLU cc_start: 0.7319 (tp30) cc_final: 0.7096 (tm-30) REVERT: B 100 GLU cc_start: 0.8265 (tt0) cc_final: 0.7506 (tp30) REVERT: B 116 LYS cc_start: 0.8511 (tttt) cc_final: 0.8239 (ttpp) REVERT: B 171 LYS cc_start: 0.8603 (mttm) cc_final: 0.8342 (mtmt) REVERT: B 334 ASP cc_start: 0.8489 (t70) cc_final: 0.8170 (t0) REVERT: B 432 MET cc_start: 0.6234 (OUTLIER) cc_final: 0.5790 (ttp) REVERT: B 434 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7715 (mtmm) REVERT: B 459 MET cc_start: 0.7923 (mmm) cc_final: 0.7695 (mpp) REVERT: B 496 MET cc_start: 0.8262 (mmt) cc_final: 0.7970 (mpt) REVERT: B 511 LYS cc_start: 0.6384 (OUTLIER) cc_final: 0.5904 (mmmt) REVERT: B 548 PHE cc_start: 0.8090 (t80) cc_final: 0.7846 (t80) REVERT: B 585 LYS cc_start: 0.8131 (mmpt) cc_final: 0.7823 (mptt) REVERT: B 587 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7475 (t0) REVERT: B 612 TYR cc_start: 0.7478 (t80) cc_final: 0.6460 (t80) REVERT: B 673 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7432 (mm-30) REVERT: B 875 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6693 (mm-30) REVERT: B 885 LYS cc_start: 0.8443 (tttp) cc_final: 0.8157 (tppt) REVERT: B 900 GLU cc_start: 0.7325 (tp30) cc_final: 0.7108 (tm-30) REVERT: C 100 GLU cc_start: 0.8256 (tt0) cc_final: 0.7493 (tp30) REVERT: C 116 LYS cc_start: 0.8481 (tttt) cc_final: 0.8231 (ttpp) REVERT: C 171 LYS cc_start: 0.8608 (mttm) cc_final: 0.8345 (mtmt) REVERT: C 334 ASP cc_start: 0.8483 (t70) cc_final: 0.8165 (t0) REVERT: C 432 MET cc_start: 0.6239 (OUTLIER) cc_final: 0.5806 (ttp) REVERT: C 434 LYS cc_start: 0.8168 (mtpp) cc_final: 0.7712 (mtmm) REVERT: C 459 MET cc_start: 0.8079 (mmm) cc_final: 0.7837 (mpp) REVERT: C 496 MET cc_start: 0.8312 (mmt) cc_final: 0.8017 (mpt) REVERT: C 548 PHE cc_start: 0.8094 (t80) cc_final: 0.7851 (t80) REVERT: C 585 LYS cc_start: 0.8130 (mmpt) cc_final: 0.7818 (mptt) REVERT: C 587 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7474 (t0) REVERT: C 612 TYR cc_start: 0.7435 (t80) cc_final: 0.6423 (t80) REVERT: C 641 PHE cc_start: 0.7728 (t80) cc_final: 0.7497 (t80) REVERT: C 673 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7491 (mm-30) REVERT: C 875 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6686 (mm-30) REVERT: C 885 LYS cc_start: 0.8452 (tttp) cc_final: 0.8167 (tppt) REVERT: C 900 GLU cc_start: 0.7306 (tp30) cc_final: 0.7103 (tm-30) REVERT: D 100 GLU cc_start: 0.8192 (tt0) cc_final: 0.7420 (tp30) REVERT: D 116 LYS cc_start: 0.8485 (tttt) cc_final: 0.8236 (ttpp) REVERT: D 171 LYS cc_start: 0.8594 (mttm) cc_final: 0.8330 (mtmt) REVERT: D 334 ASP cc_start: 0.8481 (t70) cc_final: 0.8165 (t0) REVERT: D 432 MET cc_start: 0.6221 (OUTLIER) cc_final: 0.5789 (ttp) REVERT: D 434 LYS cc_start: 0.8187 (mtpp) cc_final: 0.7722 (mtmm) REVERT: D 459 MET cc_start: 0.7957 (mmm) cc_final: 0.7747 (mpp) REVERT: D 496 MET cc_start: 0.8272 (mmt) cc_final: 0.8022 (mpt) REVERT: D 501 TRP cc_start: 0.8157 (OUTLIER) cc_final: 0.7924 (m-90) REVERT: D 548 PHE cc_start: 0.8087 (t80) cc_final: 0.7844 (t80) REVERT: D 585 LYS cc_start: 0.8233 (mmpt) cc_final: 0.7813 (mptt) REVERT: D 587 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7466 (t0) REVERT: D 612 TYR cc_start: 0.7430 (t80) cc_final: 0.6422 (t80) REVERT: D 666 GLU cc_start: 0.7440 (pm20) cc_final: 0.7234 (pm20) REVERT: D 673 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7466 (mm-30) REVERT: D 875 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6687 (mm-30) REVERT: D 885 LYS cc_start: 0.8457 (tttp) cc_final: 0.8169 (tppt) REVERT: D 900 GLU cc_start: 0.7332 (tp30) cc_final: 0.7125 (tm-30) outliers start: 100 outliers final: 39 residues processed: 415 average time/residue: 0.5936 time to fit residues: 282.4781 Evaluate side-chains 375 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 325 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 501 TRP Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 209 TYR Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 501 TRP Chi-restraints excluded: chain D residue 558 ILE Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 577 LYS Chi-restraints excluded: chain D residue 587 ASP Chi-restraints excluded: chain D residue 657 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 105 optimal weight: 5.9990 chunk 262 optimal weight: 0.9990 chunk 178 optimal weight: 10.0000 chunk 224 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 231 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 211 optimal weight: 1.9990 chunk 179 optimal weight: 8.9990 chunk 269 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN C 157 ASN ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 721 ASN D 721 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.153708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.111161 restraints weight = 27588.956| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.21 r_work: 0.3138 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23468 Z= 0.144 Angle : 0.535 8.914 31688 Z= 0.274 Chirality : 0.037 0.190 3488 Planarity : 0.004 0.044 3896 Dihedral : 12.947 137.838 3508 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.27 % Allowed : 12.52 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.16), residues: 2700 helix: 2.35 (0.11), residues: 2008 sheet: None (None), residues: 0 loop : -1.32 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 629 TYR 0.017 0.001 TYR C 251 PHE 0.011 0.001 PHE D 377 TRP 0.009 0.001 TRP C 391 HIS 0.003 0.001 HIS D 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (23452) covalent geometry : angle 0.53511 / 0.27 (31676) hydrogen bonds : bond 0.04252 / 2.87 ( 1488) hydrogen bonds : angle 3.64889 / 2.61 ( 4344) metal coordination : bond 0.00615 / 0.44 ( 16) metal coordination : angle 0.81398 / 0.41 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 335 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8196 (tt0) cc_final: 0.7432 (tp30) REVERT: A 116 LYS cc_start: 0.8522 (tttt) cc_final: 0.8262 (ttpp) REVERT: A 171 LYS cc_start: 0.8640 (mttm) cc_final: 0.8317 (mttt) REVERT: A 271 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.6755 (mmt180) REVERT: A 314 PHE cc_start: 0.6473 (m-10) cc_final: 0.6041 (m-10) REVERT: A 334 ASP cc_start: 0.8593 (t70) cc_final: 0.8321 (t0) REVERT: A 432 MET cc_start: 0.6274 (OUTLIER) cc_final: 0.5779 (ttp) REVERT: A 434 LYS cc_start: 0.8217 (mtpp) cc_final: 0.7748 (mtmm) REVERT: A 459 MET cc_start: 0.7835 (mmm) cc_final: 0.7575 (mpp) REVERT: A 496 MET cc_start: 0.8312 (mmt) cc_final: 0.8087 (mpt) REVERT: A 501 TRP cc_start: 0.8181 (OUTLIER) cc_final: 0.7962 (m-90) REVERT: A 511 LYS cc_start: 0.6402 (OUTLIER) cc_final: 0.5870 (mmmt) REVERT: A 548 PHE cc_start: 0.8134 (t80) cc_final: 0.7898 (t80) REVERT: A 585 LYS cc_start: 0.8227 (mmpt) cc_final: 0.7804 (mptt) REVERT: A 587 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7667 (t0) REVERT: A 673 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7703 (mm-30) REVERT: A 875 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6789 (mm-30) REVERT: A 885 LYS cc_start: 0.8451 (tttp) cc_final: 0.8164 (tppt) REVERT: B 100 GLU cc_start: 0.8179 (tt0) cc_final: 0.7429 (tp30) REVERT: B 116 LYS cc_start: 0.8564 (tttt) cc_final: 0.8273 (ttpp) REVERT: B 171 LYS cc_start: 0.8645 (mttm) cc_final: 0.8327 (mttt) REVERT: B 271 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6770 (mmt180) REVERT: B 314 PHE cc_start: 0.6396 (m-10) cc_final: 0.5972 (m-10) REVERT: B 334 ASP cc_start: 0.8550 (t70) cc_final: 0.8273 (t0) REVERT: B 432 MET cc_start: 0.6297 (OUTLIER) cc_final: 0.5801 (ttp) REVERT: B 434 LYS cc_start: 0.8218 (mtpp) cc_final: 0.7749 (mtmm) REVERT: B 459 MET cc_start: 0.7841 (mmm) cc_final: 0.7573 (mpp) REVERT: B 496 MET cc_start: 0.8347 (mmt) cc_final: 0.8111 (mpt) REVERT: B 511 LYS cc_start: 0.6400 (OUTLIER) cc_final: 0.5869 (mmmt) REVERT: B 548 PHE cc_start: 0.8111 (t80) cc_final: 0.7875 (t80) REVERT: B 585 LYS cc_start: 0.8230 (mmpt) cc_final: 0.7810 (mptt) REVERT: B 587 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7624 (t0) REVERT: B 673 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7635 (mm-30) REVERT: B 875 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6798 (mm-30) REVERT: B 885 LYS cc_start: 0.8450 (tttp) cc_final: 0.8165 (tppt) REVERT: C 100 GLU cc_start: 0.8213 (tt0) cc_final: 0.7432 (tp30) REVERT: C 116 LYS cc_start: 0.8521 (tttt) cc_final: 0.8258 (ttpp) REVERT: C 171 LYS cc_start: 0.8643 (mttm) cc_final: 0.8322 (mttt) REVERT: C 271 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6761 (mmt180) REVERT: C 314 PHE cc_start: 0.6435 (m-10) cc_final: 0.6013 (m-10) REVERT: C 334 ASP cc_start: 0.8491 (t70) cc_final: 0.8217 (t0) REVERT: C 432 MET cc_start: 0.6421 (OUTLIER) cc_final: 0.5936 (ttp) REVERT: C 434 LYS cc_start: 0.8214 (mtpp) cc_final: 0.7740 (mtmm) REVERT: C 459 MET cc_start: 0.7933 (mmm) cc_final: 0.7678 (mpp) REVERT: C 496 MET cc_start: 0.8356 (mmt) cc_final: 0.8119 (mpt) REVERT: C 548 PHE cc_start: 0.8111 (t80) cc_final: 0.7877 (t80) REVERT: C 585 LYS cc_start: 0.8232 (mmpt) cc_final: 0.7806 (mptt) REVERT: C 587 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7627 (t70) REVERT: C 641 PHE cc_start: 0.7918 (t80) cc_final: 0.7665 (t80) REVERT: C 673 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7718 (mm-30) REVERT: C 859 MET cc_start: 0.9120 (mmp) cc_final: 0.8818 (mmm) REVERT: C 875 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6792 (mm-30) REVERT: C 885 LYS cc_start: 0.8462 (tttp) cc_final: 0.8176 (tppt) REVERT: D 100 GLU cc_start: 0.8189 (tt0) cc_final: 0.7423 (tp30) REVERT: D 116 LYS cc_start: 0.8515 (tttt) cc_final: 0.8255 (ttpp) REVERT: D 171 LYS cc_start: 0.8636 (mttm) cc_final: 0.8312 (mttt) REVERT: D 271 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6743 (mmt180) REVERT: D 314 PHE cc_start: 0.6413 (m-10) cc_final: 0.5993 (m-10) REVERT: D 334 ASP cc_start: 0.8532 (t70) cc_final: 0.8258 (t0) REVERT: D 432 MET cc_start: 0.6404 (OUTLIER) cc_final: 0.5918 (ttp) REVERT: D 434 LYS cc_start: 0.8209 (mtpp) cc_final: 0.7734 (mtmm) REVERT: D 459 MET cc_start: 0.7822 (mmm) cc_final: 0.7562 (mpp) REVERT: D 496 MET cc_start: 0.8311 (mmt) cc_final: 0.8088 (mpt) REVERT: D 501 TRP cc_start: 0.8175 (OUTLIER) cc_final: 0.7945 (m-90) REVERT: D 548 PHE cc_start: 0.8129 (t80) cc_final: 0.7894 (t80) REVERT: D 585 LYS cc_start: 0.8227 (mmpt) cc_final: 0.7807 (mptt) REVERT: D 587 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7628 (t70) REVERT: D 641 PHE cc_start: 0.7861 (t80) cc_final: 0.7612 (t80) REVERT: D 673 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7609 (mm-30) REVERT: D 875 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6788 (mm-30) REVERT: D 885 LYS cc_start: 0.8465 (tttp) cc_final: 0.8180 (tppt) REVERT: D 900 GLU cc_start: 0.7304 (tp30) cc_final: 0.7097 (tm-30) outliers start: 101 outliers final: 41 residues processed: 401 average time/residue: 0.6119 time to fit residues: 280.4400 Evaluate side-chains 369 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 312 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 501 TRP Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain D residue 209 TYR Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 271 ARG Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 501 TRP Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain D residue 558 ILE Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 577 LYS Chi-restraints excluded: chain D residue 587 ASP Chi-restraints excluded: chain D residue 657 SER Chi-restraints excluded: chain D residue 669 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 90 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 178 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 266 optimal weight: 0.4980 chunk 204 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 ASN ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 721 ASN D 721 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.151723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.109001 restraints weight = 27642.322| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.22 r_work: 0.3090 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23468 Z= 0.172 Angle : 0.556 8.697 31688 Z= 0.282 Chirality : 0.038 0.189 3488 Planarity : 0.004 0.043 3896 Dihedral : 12.692 132.958 3508 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.98 % Allowed : 14.00 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.16), residues: 2700 helix: 2.19 (0.11), residues: 2008 sheet: None (None), residues: 0 loop : -1.31 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 360 TYR 0.018 0.002 TYR D 251 PHE 0.018 0.001 PHE B 541 TRP 0.010 0.001 TRP B 391 HIS 0.003 0.001 HIS D 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (23452) covalent geometry : angle 0.55583 / 0.28 (31676) hydrogen bonds : bond 0.04577 / 3.08 ( 1488) hydrogen bonds : angle 3.71952 / 2.66 ( 4344) metal coordination : bond 0.00742 / 0.54 ( 16) metal coordination : angle 0.87772 / 0.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 333 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 98 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7589 (tm-30) REVERT: A 100 GLU cc_start: 0.8147 (tt0) cc_final: 0.7370 (tp30) REVERT: A 116 LYS cc_start: 0.8463 (tttt) cc_final: 0.8211 (ttpp) REVERT: A 124 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8717 (tp) REVERT: A 171 LYS cc_start: 0.8723 (mttm) cc_final: 0.8416 (mttt) REVERT: A 271 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6693 (mmt180) REVERT: A 314 PHE cc_start: 0.6274 (m-10) cc_final: 0.5866 (m-10) REVERT: A 334 ASP cc_start: 0.8615 (t70) cc_final: 0.8356 (t0) REVERT: A 432 MET cc_start: 0.6326 (OUTLIER) cc_final: 0.5813 (ttp) REVERT: A 434 LYS cc_start: 0.8237 (mtpp) cc_final: 0.7767 (mtmm) REVERT: A 459 MET cc_start: 0.7821 (mmm) cc_final: 0.7548 (mpp) REVERT: A 496 MET cc_start: 0.8286 (mmt) cc_final: 0.8060 (mpt) REVERT: A 501 TRP cc_start: 0.8223 (OUTLIER) cc_final: 0.8014 (m-90) REVERT: A 511 LYS cc_start: 0.6400 (OUTLIER) cc_final: 0.5843 (mmmt) REVERT: A 548 PHE cc_start: 0.8106 (t80) cc_final: 0.7880 (t80) REVERT: A 577 LYS cc_start: 0.5966 (OUTLIER) cc_final: 0.4240 (mptm) REVERT: A 585 LYS cc_start: 0.8282 (mmpt) cc_final: 0.7850 (mptt) REVERT: A 587 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7589 (t70) REVERT: A 610 ILE cc_start: 0.8083 (tt) cc_final: 0.7874 (tt) REVERT: A 660 ILE cc_start: 0.8248 (mm) cc_final: 0.7777 (tp) REVERT: A 673 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7802 (mm-30) REVERT: A 875 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6716 (mm-30) REVERT: A 885 LYS cc_start: 0.8492 (tttp) cc_final: 0.8191 (tppt) REVERT: B 98 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7582 (tm-30) REVERT: B 100 GLU cc_start: 0.8141 (tt0) cc_final: 0.7362 (tp30) REVERT: B 116 LYS cc_start: 0.8541 (tttt) cc_final: 0.8249 (ttpp) REVERT: B 124 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8717 (tp) REVERT: B 171 LYS cc_start: 0.8725 (mttm) cc_final: 0.8410 (mttt) REVERT: B 271 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6692 (mmt180) REVERT: B 314 PHE cc_start: 0.6279 (m-10) cc_final: 0.5894 (m-10) REVERT: B 334 ASP cc_start: 0.8616 (t70) cc_final: 0.8364 (t0) REVERT: B 432 MET cc_start: 0.6326 (OUTLIER) cc_final: 0.5814 (ttp) REVERT: B 434 LYS cc_start: 0.8240 (mtpp) cc_final: 0.7771 (mtmm) REVERT: B 459 MET cc_start: 0.7803 (mmm) cc_final: 0.7526 (mpp) REVERT: B 496 MET cc_start: 0.8267 (mmt) cc_final: 0.8033 (mpt) REVERT: B 511 LYS cc_start: 0.6407 (OUTLIER) cc_final: 0.5844 (mmmt) REVERT: B 548 PHE cc_start: 0.8104 (t80) cc_final: 0.7886 (t80) REVERT: B 577 LYS cc_start: 0.6077 (OUTLIER) cc_final: 0.4336 (mptm) REVERT: B 585 LYS cc_start: 0.8302 (mmpt) cc_final: 0.7874 (mptt) REVERT: B 587 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7555 (t70) REVERT: B 610 ILE cc_start: 0.8080 (tt) cc_final: 0.7872 (tt) REVERT: B 660 ILE cc_start: 0.8264 (mm) cc_final: 0.7768 (tp) REVERT: B 673 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7927 (mm-30) REVERT: B 875 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6702 (mm-30) REVERT: B 885 LYS cc_start: 0.8464 (tttp) cc_final: 0.8160 (tppt) REVERT: C 98 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7582 (tm-30) REVERT: C 100 GLU cc_start: 0.8146 (tt0) cc_final: 0.7367 (tp30) REVERT: C 116 LYS cc_start: 0.8474 (tttt) cc_final: 0.8222 (ttpp) REVERT: C 124 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8719 (tp) REVERT: C 171 LYS cc_start: 0.8716 (mttm) cc_final: 0.8408 (mttt) REVERT: C 271 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6695 (mmt180) REVERT: C 314 PHE cc_start: 0.6272 (m-10) cc_final: 0.5896 (m-10) REVERT: C 334 ASP cc_start: 0.8613 (t70) cc_final: 0.8360 (t0) REVERT: C 432 MET cc_start: 0.6457 (OUTLIER) cc_final: 0.5986 (ttp) REVERT: C 434 LYS cc_start: 0.8236 (mtpp) cc_final: 0.7838 (mtmm) REVERT: C 459 MET cc_start: 0.7892 (mmm) cc_final: 0.7614 (mpp) REVERT: C 496 MET cc_start: 0.8294 (mmt) cc_final: 0.8056 (mpt) REVERT: C 548 PHE cc_start: 0.8118 (t80) cc_final: 0.7904 (t80) REVERT: C 577 LYS cc_start: 0.5949 (OUTLIER) cc_final: 0.4229 (mptm) REVERT: C 585 LYS cc_start: 0.8325 (mmpt) cc_final: 0.7862 (mptt) REVERT: C 587 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7598 (t70) REVERT: C 610 ILE cc_start: 0.8061 (tt) cc_final: 0.7851 (tt) REVERT: C 660 ILE cc_start: 0.8238 (mm) cc_final: 0.7765 (tp) REVERT: C 673 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7919 (mm-30) REVERT: C 875 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6719 (mm-30) REVERT: C 885 LYS cc_start: 0.8468 (tttp) cc_final: 0.8174 (tppt) REVERT: D 98 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7582 (tm-30) REVERT: D 100 GLU cc_start: 0.8161 (tt0) cc_final: 0.7390 (tp30) REVERT: D 116 LYS cc_start: 0.8476 (tttt) cc_final: 0.8216 (ttpp) REVERT: D 124 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8714 (tp) REVERT: D 171 LYS cc_start: 0.8733 (mttm) cc_final: 0.8427 (mttt) REVERT: D 271 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6694 (mmt180) REVERT: D 314 PHE cc_start: 0.6265 (m-10) cc_final: 0.5872 (m-10) REVERT: D 334 ASP cc_start: 0.8611 (t70) cc_final: 0.8351 (t0) REVERT: D 432 MET cc_start: 0.6474 (OUTLIER) cc_final: 0.6011 (ttp) REVERT: D 434 LYS cc_start: 0.8228 (mtpp) cc_final: 0.7828 (mtmm) REVERT: D 459 MET cc_start: 0.7809 (mmm) cc_final: 0.7537 (mpp) REVERT: D 496 MET cc_start: 0.8283 (mmt) cc_final: 0.8056 (mpt) REVERT: D 501 TRP cc_start: 0.8241 (OUTLIER) cc_final: 0.8031 (m-90) REVERT: D 548 PHE cc_start: 0.8116 (t80) cc_final: 0.7899 (t80) REVERT: D 585 LYS cc_start: 0.8278 (mmpt) cc_final: 0.7844 (mptt) REVERT: D 587 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7594 (t70) REVERT: D 610 ILE cc_start: 0.8057 (tt) cc_final: 0.7847 (tt) REVERT: D 660 ILE cc_start: 0.8291 (mm) cc_final: 0.7797 (tp) REVERT: D 673 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7921 (mm-30) REVERT: D 875 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6713 (mm-30) REVERT: D 885 LYS cc_start: 0.8473 (tttp) cc_final: 0.8169 (tppt) outliers start: 94 outliers final: 36 residues processed: 407 average time/residue: 0.6434 time to fit residues: 298.7363 Evaluate side-chains 375 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 316 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 501 TRP Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 209 TYR Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 271 ARG Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 501 TRP Chi-restraints excluded: chain D residue 558 ILE Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 577 LYS Chi-restraints excluded: chain D residue 587 ASP Chi-restraints excluded: chain D residue 657 SER Chi-restraints excluded: chain D residue 669 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 143 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 205 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 chunk 263 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 chunk 227 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 721 ASN B 721 ASN C 721 ASN ** D 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.154614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.112173 restraints weight = 27776.243| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.23 r_work: 0.3142 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23468 Z= 0.113 Angle : 0.517 9.232 31688 Z= 0.262 Chirality : 0.036 0.184 3488 Planarity : 0.004 0.043 3896 Dihedral : 12.342 126.880 3508 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.09 % Allowed : 15.61 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.16), residues: 2700 helix: 2.32 (0.11), residues: 2016 sheet: None (None), residues: 0 loop : -1.30 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 360 TYR 0.016 0.001 TYR D 251 PHE 0.018 0.001 PHE D 641 TRP 0.010 0.001 TRP B 391 HIS 0.002 0.000 HIS D 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (23452) covalent geometry : angle 0.51714 / 0.26 (31676) hydrogen bonds : bond 0.03969 / 2.67 ( 1488) hydrogen bonds : angle 3.63091 / 2.59 ( 4344) metal coordination : bond 0.00644 / 0.47 ( 16) metal coordination : angle 0.91566 / 0.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 339 time to evaluate : 1.005 Fit side-chains REVERT: A 100 GLU cc_start: 0.8110 (tt0) cc_final: 0.7316 (tp30) REVERT: A 116 LYS cc_start: 0.8475 (tttt) cc_final: 0.8221 (ttpp) REVERT: A 334 ASP cc_start: 0.8564 (t70) cc_final: 0.8340 (t0) REVERT: A 432 MET cc_start: 0.6380 (OUTLIER) cc_final: 0.6095 (tpt) REVERT: A 434 LYS cc_start: 0.8202 (mtpp) cc_final: 0.7809 (mtmm) REVERT: A 501 TRP cc_start: 0.8201 (OUTLIER) cc_final: 0.7993 (m-90) REVERT: A 511 LYS cc_start: 0.6288 (OUTLIER) cc_final: 0.5845 (mmmt) REVERT: A 548 PHE cc_start: 0.8103 (t80) cc_final: 0.7901 (t80) REVERT: A 577 LYS cc_start: 0.6061 (OUTLIER) cc_final: 0.4325 (mptm) REVERT: A 585 LYS cc_start: 0.8295 (mmpt) cc_final: 0.7871 (mptt) REVERT: A 587 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7568 (t70) REVERT: A 673 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7559 (mm-30) REVERT: A 875 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6728 (mm-30) REVERT: A 885 LYS cc_start: 0.8413 (tttp) cc_final: 0.8116 (tppt) REVERT: B 100 GLU cc_start: 0.8173 (tt0) cc_final: 0.7384 (tp30) REVERT: B 116 LYS cc_start: 0.8466 (tttt) cc_final: 0.8216 (ttpp) REVERT: B 334 ASP cc_start: 0.8560 (t70) cc_final: 0.8336 (t0) REVERT: B 432 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.6126 (tpt) REVERT: B 434 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7813 (mtmm) REVERT: B 511 LYS cc_start: 0.6351 (OUTLIER) cc_final: 0.5851 (mmmt) REVERT: B 577 LYS cc_start: 0.6051 (OUTLIER) cc_final: 0.4317 (mptm) REVERT: B 585 LYS cc_start: 0.8294 (mmpt) cc_final: 0.7871 (mptt) REVERT: B 587 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7547 (t70) REVERT: B 610 ILE cc_start: 0.8010 (tt) cc_final: 0.7800 (tt) REVERT: B 633 ASP cc_start: 0.7392 (m-30) cc_final: 0.6587 (t0) REVERT: B 673 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7615 (mm-30) REVERT: B 726 MET cc_start: 0.7888 (ttm) cc_final: 0.7659 (ptp) REVERT: B 875 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6713 (mm-30) REVERT: B 885 LYS cc_start: 0.8384 (tttp) cc_final: 0.8086 (tppt) REVERT: C 100 GLU cc_start: 0.8173 (tt0) cc_final: 0.7391 (tp30) REVERT: C 116 LYS cc_start: 0.8481 (tttt) cc_final: 0.8224 (ttpp) REVERT: C 334 ASP cc_start: 0.8562 (t70) cc_final: 0.8335 (t0) REVERT: C 432 MET cc_start: 0.6446 (OUTLIER) cc_final: 0.5884 (ttp) REVERT: C 434 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7810 (mtmm) REVERT: C 577 LYS cc_start: 0.6039 (OUTLIER) cc_final: 0.4309 (mptm) REVERT: C 585 LYS cc_start: 0.8296 (mmpt) cc_final: 0.7867 (mptt) REVERT: C 587 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7541 (t70) REVERT: C 610 ILE cc_start: 0.8014 (tt) cc_final: 0.7803 (tt) REVERT: C 633 ASP cc_start: 0.7383 (m-30) cc_final: 0.6577 (t0) REVERT: C 641 PHE cc_start: 0.7839 (t80) cc_final: 0.7524 (t80) REVERT: C 673 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7571 (mm-30) REVERT: C 875 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6712 (mm-30) REVERT: C 885 LYS cc_start: 0.8407 (tttp) cc_final: 0.8112 (tppt) REVERT: D 100 GLU cc_start: 0.8102 (tt0) cc_final: 0.7309 (tp30) REVERT: D 116 LYS cc_start: 0.8470 (tttt) cc_final: 0.8217 (ttpp) REVERT: D 334 ASP cc_start: 0.8557 (t70) cc_final: 0.8325 (t0) REVERT: D 432 MET cc_start: 0.6430 (OUTLIER) cc_final: 0.5895 (ttp) REVERT: D 434 LYS cc_start: 0.8201 (mtpp) cc_final: 0.7804 (mtmm) REVERT: D 501 TRP cc_start: 0.8214 (OUTLIER) cc_final: 0.8002 (m-90) REVERT: D 577 LYS cc_start: 0.6042 (OUTLIER) cc_final: 0.4313 (mptm) REVERT: D 585 LYS cc_start: 0.8297 (mmpt) cc_final: 0.7868 (mptt) REVERT: D 587 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7548 (t70) REVERT: D 610 ILE cc_start: 0.8007 (tt) cc_final: 0.7794 (tt) REVERT: D 633 ASP cc_start: 0.7365 (m-30) cc_final: 0.6575 (t0) REVERT: D 641 PHE cc_start: 0.7930 (t80) cc_final: 0.7611 (t80) REVERT: D 673 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7618 (mm-30) REVERT: D 726 MET cc_start: 0.8000 (ttm) cc_final: 0.7737 (ptp) REVERT: D 875 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6711 (mm-30) REVERT: D 885 LYS cc_start: 0.8419 (tttp) cc_final: 0.8122 (tppt) outliers start: 73 outliers final: 28 residues processed: 390 average time/residue: 0.6367 time to fit residues: 284.6884 Evaluate side-chains 363 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 319 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 501 TRP Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain D residue 209 TYR Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 501 TRP Chi-restraints excluded: chain D residue 558 ILE Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 577 LYS Chi-restraints excluded: chain D residue 587 ASP Chi-restraints excluded: chain D residue 657 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 95 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.150783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.107953 restraints weight = 27729.678| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.23 r_work: 0.3074 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23468 Z= 0.218 Angle : 0.616 11.441 31688 Z= 0.312 Chirality : 0.039 0.185 3488 Planarity : 0.004 0.045 3896 Dihedral : 12.444 121.828 3508 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.68 % Allowed : 15.36 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.16), residues: 2700 helix: 1.99 (0.11), residues: 1988 sheet: None (None), residues: 0 loop : -1.42 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 160 TYR 0.019 0.002 TYR B 251 PHE 0.020 0.002 PHE D 641 TRP 0.011 0.001 TRP C 501 HIS 0.003 0.001 HIS C 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 (23452) covalent geometry : angle 0.61603 / 0.31 (31676) hydrogen bonds : bond 0.05049 / 3.39 ( 1488) hydrogen bonds : angle 3.86980 / 2.77 ( 4344) metal coordination : bond 0.00901 / 0.65 ( 16) metal coordination : angle 1.02432 / 0.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 324 time to evaluate : 0.852 Fit side-chains REVERT: A 100 GLU cc_start: 0.8138 (tt0) cc_final: 0.7365 (tp30) REVERT: A 116 LYS cc_start: 0.8476 (tttt) cc_final: 0.8219 (ttpp) REVERT: A 271 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6570 (mmt180) REVERT: A 314 PHE cc_start: 0.6367 (m-10) cc_final: 0.5965 (m-10) REVERT: A 334 ASP cc_start: 0.8615 (t70) cc_final: 0.8355 (t0) REVERT: A 432 MET cc_start: 0.6562 (OUTLIER) cc_final: 0.6296 (tpt) REVERT: A 434 LYS cc_start: 0.8203 (mtpp) cc_final: 0.7795 (mtmm) REVERT: A 496 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7697 (mpt) REVERT: A 501 TRP cc_start: 0.8233 (OUTLIER) cc_final: 0.7950 (m-90) REVERT: A 577 LYS cc_start: 0.6092 (OUTLIER) cc_final: 0.4407 (mptm) REVERT: A 585 LYS cc_start: 0.8325 (mmpt) cc_final: 0.7826 (mptt) REVERT: A 587 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7673 (t70) REVERT: A 610 ILE cc_start: 0.8152 (tt) cc_final: 0.7933 (tt) REVERT: A 673 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7948 (mm-30) REVERT: A 859 MET cc_start: 0.9197 (mmp) cc_final: 0.8845 (mmm) REVERT: A 875 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6754 (mm-30) REVERT: A 885 LYS cc_start: 0.8476 (tttp) cc_final: 0.8158 (tppt) REVERT: B 100 GLU cc_start: 0.8139 (tt0) cc_final: 0.7366 (tp30) REVERT: B 116 LYS cc_start: 0.8514 (tttt) cc_final: 0.8230 (ttpp) REVERT: B 271 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.6565 (mmt180) REVERT: B 314 PHE cc_start: 0.6326 (m-10) cc_final: 0.5957 (m-10) REVERT: B 334 ASP cc_start: 0.8620 (t70) cc_final: 0.8362 (t0) REVERT: B 432 MET cc_start: 0.6565 (OUTLIER) cc_final: 0.5912 (ttp) REVERT: B 434 LYS cc_start: 0.8206 (mtpp) cc_final: 0.7800 (mtmm) REVERT: B 496 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7705 (mpt) REVERT: B 549 TRP cc_start: 0.7167 (t-100) cc_final: 0.6566 (t60) REVERT: B 577 LYS cc_start: 0.6145 (OUTLIER) cc_final: 0.4413 (mptm) REVERT: B 585 LYS cc_start: 0.8330 (mmpt) cc_final: 0.7830 (mptt) REVERT: B 587 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7663 (t70) REVERT: B 610 ILE cc_start: 0.8147 (tt) cc_final: 0.7928 (tt) REVERT: B 673 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7966 (mm-30) REVERT: B 875 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6747 (mm-30) REVERT: B 885 LYS cc_start: 0.8476 (tttp) cc_final: 0.8156 (tppt) REVERT: C 100 GLU cc_start: 0.8144 (tt0) cc_final: 0.7363 (tp30) REVERT: C 116 LYS cc_start: 0.8473 (tttt) cc_final: 0.8213 (ttpp) REVERT: C 271 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6695 (mmt180) REVERT: C 314 PHE cc_start: 0.6319 (m-10) cc_final: 0.5955 (m-10) REVERT: C 334 ASP cc_start: 0.8622 (t70) cc_final: 0.8361 (t0) REVERT: C 432 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.5852 (ttp) REVERT: C 434 LYS cc_start: 0.8219 (mtpp) cc_final: 0.7756 (mtmm) REVERT: C 496 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7725 (mpt) REVERT: C 501 TRP cc_start: 0.8252 (OUTLIER) cc_final: 0.7965 (m-90) REVERT: C 577 LYS cc_start: 0.6136 (OUTLIER) cc_final: 0.4407 (mptm) REVERT: C 585 LYS cc_start: 0.8333 (mmpt) cc_final: 0.7833 (mptt) REVERT: C 587 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7661 (t70) REVERT: C 610 ILE cc_start: 0.8159 (tt) cc_final: 0.7940 (tt) REVERT: C 673 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7959 (mm-30) REVERT: C 875 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6744 (mm-30) REVERT: C 885 LYS cc_start: 0.8476 (tttp) cc_final: 0.8159 (tppt) REVERT: D 100 GLU cc_start: 0.8131 (tt0) cc_final: 0.7355 (tp30) REVERT: D 116 LYS cc_start: 0.8474 (tttt) cc_final: 0.8218 (ttpp) REVERT: D 271 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.6563 (mmt180) REVERT: D 314 PHE cc_start: 0.6426 (m-10) cc_final: 0.5983 (m-10) REVERT: D 334 ASP cc_start: 0.8613 (t70) cc_final: 0.8356 (t0) REVERT: D 432 MET cc_start: 0.6371 (OUTLIER) cc_final: 0.5844 (ttp) REVERT: D 434 LYS cc_start: 0.8214 (mtpp) cc_final: 0.7753 (mtmm) REVERT: D 496 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7692 (mpt) REVERT: D 501 TRP cc_start: 0.8239 (OUTLIER) cc_final: 0.7937 (m-90) REVERT: D 577 LYS cc_start: 0.6080 (OUTLIER) cc_final: 0.4400 (mptm) REVERT: D 585 LYS cc_start: 0.8330 (mmpt) cc_final: 0.7830 (mptt) REVERT: D 587 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7660 (t70) REVERT: D 610 ILE cc_start: 0.8153 (tt) cc_final: 0.7935 (tt) REVERT: D 673 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7959 (mm-30) REVERT: D 859 MET cc_start: 0.9196 (mmp) cc_final: 0.8833 (mmm) REVERT: D 875 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6746 (mm-30) REVERT: D 885 LYS cc_start: 0.8479 (tttp) cc_final: 0.8162 (tppt) outliers start: 87 outliers final: 36 residues processed: 384 average time/residue: 0.6218 time to fit residues: 273.1299 Evaluate side-chains 369 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 310 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 501 TRP Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 501 TRP Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain D residue 209 TYR Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 271 ARG Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 501 TRP Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 558 ILE Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 577 LYS Chi-restraints excluded: chain D residue 587 ASP Chi-restraints excluded: chain D residue 657 SER Chi-restraints excluded: chain D residue 669 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 13 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 269 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 267 optimal weight: 3.9990 chunk 108 optimal weight: 0.3980 chunk 130 optimal weight: 0.0870 chunk 223 optimal weight: 0.8980 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 721 ASN B 721 ASN C 721 ASN ** D 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.152700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.110095 restraints weight = 27770.167| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.24 r_work: 0.3120 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23468 Z= 0.131 Angle : 0.552 10.505 31688 Z= 0.276 Chirality : 0.036 0.179 3488 Planarity : 0.004 0.045 3896 Dihedral : 11.901 114.415 3500 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.96 % Allowed : 16.67 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.16), residues: 2700 helix: 2.16 (0.11), residues: 2012 sheet: None (None), residues: 0 loop : -1.40 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 629 TYR 0.017 0.001 TYR B 251 PHE 0.013 0.001 PHE A 548 TRP 0.010 0.001 TRP C 391 HIS 0.002 0.000 HIS D 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (23452) covalent geometry : angle 0.55208 / 0.28 (31676) hydrogen bonds : bond 0.04205 / 2.83 ( 1488) hydrogen bonds : angle 3.71204 / 2.66 ( 4344) metal coordination : bond 0.00725 / 0.53 ( 16) metal coordination : angle 1.08113 / 0.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 333 time to evaluate : 0.649 Fit side-chains REVERT: A 100 GLU cc_start: 0.8157 (tt0) cc_final: 0.7379 (tp30) REVERT: A 116 LYS cc_start: 0.8470 (tttt) cc_final: 0.8218 (ttpp) REVERT: A 334 ASP cc_start: 0.8558 (t70) cc_final: 0.8329 (t0) REVERT: A 434 LYS cc_start: 0.8177 (mtpp) cc_final: 0.7775 (mtmm) REVERT: A 496 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7660 (mpt) REVERT: A 501 TRP cc_start: 0.8241 (OUTLIER) cc_final: 0.7940 (m-90) REVERT: A 549 TRP cc_start: 0.7179 (t-100) cc_final: 0.6608 (t60) REVERT: A 577 LYS cc_start: 0.6156 (OUTLIER) cc_final: 0.4487 (mptm) REVERT: A 585 LYS cc_start: 0.8340 (mmpt) cc_final: 0.7813 (mptt) REVERT: A 587 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7626 (t70) REVERT: A 610 ILE cc_start: 0.8101 (tt) cc_final: 0.7886 (tt) REVERT: A 673 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7910 (mm-30) REVERT: A 726 MET cc_start: 0.8341 (ptp) cc_final: 0.7982 (ptt) REVERT: A 859 MET cc_start: 0.9141 (mmp) cc_final: 0.8937 (mmm) REVERT: A 875 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6760 (mm-30) REVERT: A 885 LYS cc_start: 0.8448 (tttp) cc_final: 0.8072 (tppt) REVERT: B 100 GLU cc_start: 0.8163 (tt0) cc_final: 0.7389 (tp30) REVERT: B 116 LYS cc_start: 0.8469 (tttt) cc_final: 0.8219 (ttpp) REVERT: B 313 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7210 (pm20) REVERT: B 334 ASP cc_start: 0.8563 (t70) cc_final: 0.8329 (t0) REVERT: B 434 LYS cc_start: 0.8177 (mtpp) cc_final: 0.7774 (mtmm) REVERT: B 496 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7646 (mpt) REVERT: B 549 TRP cc_start: 0.7183 (t-100) cc_final: 0.6623 (t60) REVERT: B 577 LYS cc_start: 0.6131 (OUTLIER) cc_final: 0.4435 (mptm) REVERT: B 585 LYS cc_start: 0.8344 (mmpt) cc_final: 0.7817 (mptt) REVERT: B 587 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7586 (t70) REVERT: B 610 ILE cc_start: 0.8102 (tt) cc_final: 0.7889 (tt) REVERT: B 673 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7923 (mm-30) REVERT: B 885 LYS cc_start: 0.8438 (tttp) cc_final: 0.8113 (tppt) REVERT: C 100 GLU cc_start: 0.8160 (tt0) cc_final: 0.7381 (tp30) REVERT: C 116 LYS cc_start: 0.8478 (tttt) cc_final: 0.8221 (ttpp) REVERT: C 313 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7210 (pm20) REVERT: C 334 ASP cc_start: 0.8547 (t70) cc_final: 0.8319 (t0) REVERT: C 432 MET cc_start: 0.6353 (OUTLIER) cc_final: 0.5556 (ttp) REVERT: C 434 LYS cc_start: 0.8181 (mtpp) cc_final: 0.7779 (mtmm) REVERT: C 436 MET cc_start: 0.7589 (mmt) cc_final: 0.7350 (mmm) REVERT: C 496 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7670 (mpt) REVERT: C 549 TRP cc_start: 0.7151 (t-100) cc_final: 0.6600 (t60) REVERT: C 577 LYS cc_start: 0.6129 (OUTLIER) cc_final: 0.4427 (mptm) REVERT: C 585 LYS cc_start: 0.8344 (mmpt) cc_final: 0.7815 (mptt) REVERT: C 587 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7590 (t70) REVERT: C 610 ILE cc_start: 0.8111 (tt) cc_final: 0.7899 (tt) REVERT: C 641 PHE cc_start: 0.7882 (t80) cc_final: 0.7609 (t80) REVERT: C 673 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7925 (mm-30) REVERT: C 875 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6746 (mm-30) REVERT: C 885 LYS cc_start: 0.8440 (tttp) cc_final: 0.8116 (tppt) REVERT: D 100 GLU cc_start: 0.8158 (tt0) cc_final: 0.7376 (tp30) REVERT: D 116 LYS cc_start: 0.8472 (tttt) cc_final: 0.8220 (ttpp) REVERT: D 271 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6576 (mmt180) REVERT: D 314 PHE cc_start: 0.6311 (m-10) cc_final: 0.5952 (m-10) REVERT: D 334 ASP cc_start: 0.8550 (t70) cc_final: 0.8317 (t0) REVERT: D 432 MET cc_start: 0.6343 (OUTLIER) cc_final: 0.5565 (ttp) REVERT: D 434 LYS cc_start: 0.8177 (mtpp) cc_final: 0.7775 (mtmm) REVERT: D 436 MET cc_start: 0.7604 (mmt) cc_final: 0.7367 (mmm) REVERT: D 496 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7668 (mpt) REVERT: D 501 TRP cc_start: 0.8238 (OUTLIER) cc_final: 0.8017 (m-90) REVERT: D 549 TRP cc_start: 0.7160 (t-100) cc_final: 0.6590 (t60) REVERT: D 577 LYS cc_start: 0.6177 (OUTLIER) cc_final: 0.4493 (mptm) REVERT: D 585 LYS cc_start: 0.8315 (mmpt) cc_final: 0.7810 (mptt) REVERT: D 587 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7583 (t70) REVERT: D 610 ILE cc_start: 0.8114 (tt) cc_final: 0.7899 (tt) REVERT: D 641 PHE cc_start: 0.7967 (t80) cc_final: 0.7668 (t80) REVERT: D 673 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7919 (mm-30) REVERT: D 859 MET cc_start: 0.9142 (mmp) cc_final: 0.8941 (mmm) REVERT: D 875 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6749 (mm-30) REVERT: D 885 LYS cc_start: 0.8451 (tttp) cc_final: 0.8125 (tppt) outliers start: 70 outliers final: 34 residues processed: 380 average time/residue: 0.5769 time to fit residues: 251.8976 Evaluate side-chains 380 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 329 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 501 TRP Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain D residue 209 TYR Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 271 ARG Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 501 TRP Chi-restraints excluded: chain D residue 558 ILE Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 577 LYS Chi-restraints excluded: chain D residue 587 ASP Chi-restraints excluded: chain D residue 657 SER Chi-restraints excluded: chain D residue 669 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 91 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 252 optimal weight: 0.0370 chunk 89 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 116 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 198 optimal weight: 0.0980 chunk 63 optimal weight: 0.7980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 696 ASN B 696 ASN C 696 ASN C 721 ASN D 721 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.156109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.113855 restraints weight = 27888.848| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.27 r_work: 0.3174 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23468 Z= 0.109 Angle : 0.533 10.268 31688 Z= 0.269 Chirality : 0.036 0.175 3488 Planarity : 0.004 0.044 3896 Dihedral : 11.026 103.516 3494 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.20 % Allowed : 18.19 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.16), residues: 2700 helix: 2.33 (0.11), residues: 2040 sheet: None (None), residues: 0 loop : -1.39 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 629 TYR 0.016 0.001 TYR C 251 PHE 0.019 0.001 PHE C 548 TRP 0.011 0.001 TRP B 391 HIS 0.001 0.000 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (23452) covalent geometry : angle 0.53230 / 0.27 (31676) hydrogen bonds : bond 0.03660 / 2.46 ( 1488) hydrogen bonds : angle 3.58130 / 2.56 ( 4344) metal coordination : bond 0.00614 / 0.45 ( 16) metal coordination : angle 1.12629 / 0.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 352 time to evaluate : 0.781 Fit side-chains REVERT: A 100 GLU cc_start: 0.8158 (tt0) cc_final: 0.7323 (tp30) REVERT: A 116 LYS cc_start: 0.8486 (tttt) cc_final: 0.8222 (ttpp) REVERT: A 294 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7735 (t) REVERT: A 434 LYS cc_start: 0.8197 (mtpp) cc_final: 0.7804 (mtmm) REVERT: A 496 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7690 (mpt) REVERT: A 501 TRP cc_start: 0.8241 (OUTLIER) cc_final: 0.7989 (m-90) REVERT: A 549 TRP cc_start: 0.7190 (t-100) cc_final: 0.6619 (t60) REVERT: A 577 LYS cc_start: 0.6139 (OUTLIER) cc_final: 0.4397 (mptm) REVERT: A 585 LYS cc_start: 0.8317 (mmpt) cc_final: 0.7811 (mptt) REVERT: A 633 ASP cc_start: 0.7180 (m-30) cc_final: 0.6382 (t0) REVERT: A 641 PHE cc_start: 0.7779 (t80) cc_final: 0.7514 (t80) REVERT: A 673 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7568 (mm-30) REVERT: A 726 MET cc_start: 0.8402 (ptp) cc_final: 0.8134 (ptt) REVERT: A 859 MET cc_start: 0.9084 (mmp) cc_final: 0.8811 (mmm) REVERT: A 885 LYS cc_start: 0.8340 (tttp) cc_final: 0.8009 (tppt) REVERT: B 100 GLU cc_start: 0.8157 (tt0) cc_final: 0.7324 (tp30) REVERT: B 116 LYS cc_start: 0.8487 (tttt) cc_final: 0.8222 (ttpp) REVERT: B 294 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7740 (t) REVERT: B 434 LYS cc_start: 0.8201 (mtpp) cc_final: 0.7804 (mtmm) REVERT: B 496 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7657 (mpt) REVERT: B 549 TRP cc_start: 0.7217 (t-100) cc_final: 0.6666 (t60) REVERT: B 577 LYS cc_start: 0.6130 (OUTLIER) cc_final: 0.4388 (mptm) REVERT: B 585 LYS cc_start: 0.8295 (mmpt) cc_final: 0.7812 (mptt) REVERT: B 587 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7617 (t70) REVERT: B 630 THR cc_start: 0.7766 (m) cc_final: 0.7508 (p) REVERT: B 633 ASP cc_start: 0.7310 (m-30) cc_final: 0.6508 (t0) REVERT: B 641 PHE cc_start: 0.7866 (t80) cc_final: 0.7540 (t80) REVERT: B 673 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7716 (mm-30) REVERT: B 726 MET cc_start: 0.8181 (ptp) cc_final: 0.7843 (ptm) REVERT: B 885 LYS cc_start: 0.8397 (tttp) cc_final: 0.8020 (tppt) REVERT: C 100 GLU cc_start: 0.8159 (tt0) cc_final: 0.7312 (tp30) REVERT: C 116 LYS cc_start: 0.8476 (tttt) cc_final: 0.8211 (ttpp) REVERT: C 294 VAL cc_start: 0.8085 (OUTLIER) cc_final: 0.7776 (t) REVERT: C 432 MET cc_start: 0.6340 (OUTLIER) cc_final: 0.5585 (ttp) REVERT: C 434 LYS cc_start: 0.8168 (mtpp) cc_final: 0.7775 (mtmm) REVERT: C 436 MET cc_start: 0.7546 (mmt) cc_final: 0.7344 (mmm) REVERT: C 496 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7659 (mpt) REVERT: C 549 TRP cc_start: 0.7175 (t-100) cc_final: 0.6653 (t60) REVERT: C 577 LYS cc_start: 0.6132 (OUTLIER) cc_final: 0.4475 (mptp) REVERT: C 585 LYS cc_start: 0.8295 (mmpt) cc_final: 0.7810 (mptt) REVERT: C 587 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7678 (t70) REVERT: C 630 THR cc_start: 0.7758 (m) cc_final: 0.7490 (p) REVERT: C 633 ASP cc_start: 0.7280 (m-30) cc_final: 0.6545 (t0) REVERT: C 673 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7714 (mm-30) REVERT: C 726 MET cc_start: 0.8366 (ptp) cc_final: 0.8135 (ptm) REVERT: C 885 LYS cc_start: 0.8343 (tttp) cc_final: 0.8013 (tppt) REVERT: D 100 GLU cc_start: 0.8155 (tt0) cc_final: 0.7314 (tp30) REVERT: D 116 LYS cc_start: 0.8471 (tttt) cc_final: 0.8211 (ttpp) REVERT: D 294 VAL cc_start: 0.8050 (OUTLIER) cc_final: 0.7731 (t) REVERT: D 432 MET cc_start: 0.6336 (OUTLIER) cc_final: 0.5582 (ttp) REVERT: D 434 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7776 (mtmm) REVERT: D 436 MET cc_start: 0.7571 (mmt) cc_final: 0.7367 (mmm) REVERT: D 496 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7662 (mpt) REVERT: D 549 TRP cc_start: 0.7177 (t-100) cc_final: 0.6657 (t60) REVERT: D 577 LYS cc_start: 0.6136 (OUTLIER) cc_final: 0.4480 (mptp) REVERT: D 585 LYS cc_start: 0.8296 (mmpt) cc_final: 0.7813 (mptt) REVERT: D 587 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7678 (t70) REVERT: D 630 THR cc_start: 0.7769 (m) cc_final: 0.7496 (p) REVERT: D 633 ASP cc_start: 0.7299 (m-30) cc_final: 0.6560 (t0) REVERT: D 673 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7712 (mm-30) REVERT: D 885 LYS cc_start: 0.8351 (tttp) cc_final: 0.8021 (tppt) outliers start: 52 outliers final: 27 residues processed: 388 average time/residue: 0.6115 time to fit residues: 271.5046 Evaluate side-chains 363 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 318 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 501 TRP Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain D residue 209 TYR Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 558 ILE Chi-restraints excluded: chain D residue 577 LYS Chi-restraints excluded: chain D residue 587 ASP Chi-restraints excluded: chain D residue 657 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 129 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 245 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 256 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 696 ASN B 696 ASN C 696 ASN D 696 ASN D 721 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.152657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.110048 restraints weight = 27936.383| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.27 r_work: 0.3124 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23468 Z= 0.155 Angle : 0.598 10.343 31688 Z= 0.303 Chirality : 0.037 0.180 3488 Planarity : 0.004 0.045 3896 Dihedral : 11.035 101.176 3494 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.07 % Allowed : 19.42 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.16), residues: 2700 helix: 2.26 (0.11), residues: 2032 sheet: None (None), residues: 0 loop : -1.35 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 629 TYR 0.017 0.001 TYR D 251 PHE 0.019 0.001 PHE A 548 TRP 0.010 0.001 TRP C 501 HIS 0.007 0.001 HIS C 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (23452) covalent geometry : angle 0.59801 / 0.30 (31676) hydrogen bonds : bond 0.04151 / 2.78 ( 1488) hydrogen bonds : angle 3.63984 / 2.60 ( 4344) metal coordination : bond 0.00607 / 0.44 ( 16) metal coordination : angle 0.93587 / 0.46 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 323 time to evaluate : 0.895 Fit side-chains REVERT: A 100 GLU cc_start: 0.8152 (tt0) cc_final: 0.7348 (tp30) REVERT: A 116 LYS cc_start: 0.8473 (tttt) cc_final: 0.8217 (ttpp) REVERT: A 209 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.8304 (p90) REVERT: A 271 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.6730 (mmt180) REVERT: A 294 VAL cc_start: 0.8109 (OUTLIER) cc_final: 0.7786 (t) REVERT: A 314 PHE cc_start: 0.6249 (m-10) cc_final: 0.5805 (m-10) REVERT: A 434 LYS cc_start: 0.8189 (mtpp) cc_final: 0.7777 (mtmm) REVERT: A 436 MET cc_start: 0.7713 (mmm) cc_final: 0.7367 (pp-130) REVERT: A 496 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7689 (mpt) REVERT: A 501 TRP cc_start: 0.8217 (OUTLIER) cc_final: 0.7909 (m-90) REVERT: A 549 TRP cc_start: 0.7207 (t-100) cc_final: 0.6655 (t60) REVERT: A 577 LYS cc_start: 0.6155 (OUTLIER) cc_final: 0.4440 (mptm) REVERT: A 585 LYS cc_start: 0.8330 (mmpt) cc_final: 0.7824 (mptt) REVERT: A 587 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7658 (t0) REVERT: A 610 ILE cc_start: 0.8106 (tt) cc_final: 0.7893 (tt) REVERT: A 673 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7814 (mm-30) REVERT: A 859 MET cc_start: 0.9112 (mmp) cc_final: 0.8775 (mmm) REVERT: A 885 LYS cc_start: 0.8382 (tttp) cc_final: 0.8043 (tppt) REVERT: B 100 GLU cc_start: 0.8148 (tt0) cc_final: 0.7349 (tp30) REVERT: B 116 LYS cc_start: 0.8481 (tttt) cc_final: 0.8220 (ttpp) REVERT: B 294 VAL cc_start: 0.8103 (OUTLIER) cc_final: 0.7780 (t) REVERT: B 434 LYS cc_start: 0.8203 (mtpp) cc_final: 0.7785 (mtmm) REVERT: B 436 MET cc_start: 0.7698 (mmm) cc_final: 0.7365 (pp-130) REVERT: B 496 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7684 (mpt) REVERT: B 549 TRP cc_start: 0.7205 (t-100) cc_final: 0.6676 (t60) REVERT: B 577 LYS cc_start: 0.6144 (OUTLIER) cc_final: 0.4400 (mptm) REVERT: B 585 LYS cc_start: 0.8366 (mmpt) cc_final: 0.7829 (mptt) REVERT: B 587 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7643 (t70) REVERT: B 610 ILE cc_start: 0.8106 (tt) cc_final: 0.7895 (tt) REVERT: B 673 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7825 (mm-30) REVERT: B 885 LYS cc_start: 0.8420 (tttp) cc_final: 0.8086 (tppt) REVERT: C 100 GLU cc_start: 0.8161 (tt0) cc_final: 0.7356 (tp30) REVERT: C 116 LYS cc_start: 0.8480 (tttt) cc_final: 0.8213 (ttpp) REVERT: C 294 VAL cc_start: 0.8106 (OUTLIER) cc_final: 0.7784 (t) REVERT: C 432 MET cc_start: 0.6258 (OUTLIER) cc_final: 0.5513 (ttp) REVERT: C 434 LYS cc_start: 0.8162 (mtpp) cc_final: 0.7763 (mtmm) REVERT: C 436 MET cc_start: 0.7553 (mmt) cc_final: 0.7350 (mmm) REVERT: C 496 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7698 (mpt) REVERT: C 549 TRP cc_start: 0.7206 (t-100) cc_final: 0.6659 (t60) REVERT: C 577 LYS cc_start: 0.6155 (OUTLIER) cc_final: 0.4484 (mptp) REVERT: C 585 LYS cc_start: 0.8367 (mmpt) cc_final: 0.7829 (mptt) REVERT: C 587 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7648 (t70) REVERT: C 610 ILE cc_start: 0.8112 (tt) cc_final: 0.7900 (tt) REVERT: C 673 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7824 (mm-30) REVERT: C 726 MET cc_start: 0.8386 (ptp) cc_final: 0.8176 (ptm) REVERT: C 875 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6686 (mm-30) REVERT: C 885 LYS cc_start: 0.8370 (tttp) cc_final: 0.8025 (tppt) REVERT: D 100 GLU cc_start: 0.8146 (tt0) cc_final: 0.7339 (tp30) REVERT: D 116 LYS cc_start: 0.8472 (tttt) cc_final: 0.8207 (ttpp) REVERT: D 209 TYR cc_start: 0.8925 (OUTLIER) cc_final: 0.8311 (p90) REVERT: D 294 VAL cc_start: 0.8104 (OUTLIER) cc_final: 0.7784 (t) REVERT: D 432 MET cc_start: 0.6256 (OUTLIER) cc_final: 0.5542 (ttp) REVERT: D 434 LYS cc_start: 0.8158 (mtpp) cc_final: 0.7760 (mtmm) REVERT: D 496 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7700 (mpt) REVERT: D 549 TRP cc_start: 0.7183 (t-100) cc_final: 0.6637 (t60) REVERT: D 577 LYS cc_start: 0.6160 (OUTLIER) cc_final: 0.4495 (mptp) REVERT: D 585 LYS cc_start: 0.8369 (mmpt) cc_final: 0.7831 (mptt) REVERT: D 587 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7650 (t70) REVERT: D 610 ILE cc_start: 0.8118 (tt) cc_final: 0.7904 (tt) REVERT: D 673 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7823 (mm-30) REVERT: D 726 MET cc_start: 0.8391 (ptp) cc_final: 0.8158 (ptm) REVERT: D 885 LYS cc_start: 0.8419 (tttp) cc_final: 0.8035 (tppt) outliers start: 49 outliers final: 25 residues processed: 359 average time/residue: 0.6339 time to fit residues: 261.1439 Evaluate side-chains 368 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 321 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 501 TRP Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain D residue 209 TYR Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 558 ILE Chi-restraints excluded: chain D residue 577 LYS Chi-restraints excluded: chain D residue 587 ASP Chi-restraints excluded: chain D residue 657 SER Chi-restraints excluded: chain D residue 696 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 211 optimal weight: 0.9980 chunk 180 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 263 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 153 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 696 ASN B 696 ASN C 696 ASN ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 696 ASN D 721 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.153832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.111416 restraints weight = 27782.375| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.25 r_work: 0.3128 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23468 Z= 0.131 Angle : 0.574 10.175 31688 Z= 0.293 Chirality : 0.036 0.181 3488 Planarity : 0.004 0.044 3896 Dihedral : 10.909 97.704 3494 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.12 % Allowed : 19.54 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.16), residues: 2700 helix: 2.32 (0.11), residues: 2020 sheet: None (None), residues: 0 loop : -1.35 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 629 TYR 0.016 0.001 TYR C 251 PHE 0.020 0.001 PHE B 314 TRP 0.011 0.001 TRP B 391 HIS 0.004 0.000 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (23452) covalent geometry : angle 0.57362 / 0.29 (31676) hydrogen bonds : bond 0.03978 / 2.67 ( 1488) hydrogen bonds : angle 3.64177 / 2.60 ( 4344) metal coordination : bond 0.00677 / 0.49 ( 16) metal coordination : angle 0.86418 / 0.44 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7063.87 seconds wall clock time: 121 minutes 9.25 seconds (7269.25 seconds total)