Starting phenix.real_space_refine on Sat Jul 4 22:57:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dxg_30908/07_2026/7dxg_30908.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dxg_30908/07_2026/7dxg_30908.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/7dxg_30908/07_2026/7dxg_30908.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dxg_30908/07_2026/7dxg_30908.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dxg_30908/07_2026/7dxg_30908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dxg_30908/07_2026/7dxg_30908.map" model { file = "/net/cci-nas-00/data/ceres_data/7dxg_30908/07_2026/7dxg_30908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dxg_30908/07_2026/7dxg_30908.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= 0.001 sd= 0.239 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 8 9.91 5 Zn 4 6.06 5 P 4 5.49 5 S 144 5.16 5 Cl 4 4.86 5 C 15420 2.51 5 N 3704 2.21 5 O 4144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 136 residue(s): 0.03s 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: 23432 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 698, 5603 Classifications: {'peptide': 698} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 678} Chain breaks: 5 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 5603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 698, 5603 Classifications: {'peptide': 698} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 678} Chain breaks: 5 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 295 Unusual residues: {' CA': 2, ' ZN': 1, '98R': 2, 'HOR': 1, 'POV': 1, 'Y01': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "C" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 215 Unusual residues: {' CA': 2, ' ZN': 1, 'HOR': 1, 'POV': 1, 'Y01': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1193 SG CYS A 255 34.684 99.698 78.727 1.00155.21 S ATOM 1215 SG CYS A 258 35.706 95.758 79.266 1.00152.03 S ATOM 12399 SG CYS C 255 19.432 34.683 78.732 1.00155.21 S ATOM 12421 SG CYS C 258 23.372 35.706 79.270 1.00152.03 S Restraints were copied for chains: B, D Time building chain proxies: 9.35, per 1000 atoms: 0.40 Number of scatterers: 23432 At special positions: 0 Unit cell: (120.175, 120.175, 166.155, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 Ca 8 19.99 Cl 4 17.00 S 144 16.00 P 4 15.00 O 4144 8.00 N 3704 7.00 C 15420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 121 " distance=0.00 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 128 " distance=0.00 Simple disulfide: pdb=" SG CYS B 229 " - pdb=" SG CYS B 229 " distance=0.00 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 253 " distance=0.00 Simple disulfide: pdb=" SG CYS B 325 " - pdb=" SG CYS B 325 " distance=0.00 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 336 " distance=0.00 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 383 " distance=0.00 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 429 " distance=0.00 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 490 " distance=0.00 Simple disulfide: pdb=" SG CYS B 510 " - pdb=" SG CYS B 510 " distance=0.00 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: 1.91 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 255 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 249 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 258 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 255 " pdb="ZN ZN B1001 " - pdb=" ND1 HIS B 249 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 258 " pdb=" ZN C1002 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 255 " pdb="ZN ZN C1002 " - pdb=" ND1 HIS C 249 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 258 " pdb=" ZN D1002 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 255 " pdb="ZN ZN D1002 " - pdb=" ND1 HIS D 249 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 258 " 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5328 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 0 sheets defined 81.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 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 154 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 229 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 255 through 265 Processing helix chain 'A' and resid 265 through 281 Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.517A pdb=" N LEU A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 311 removed outlier: 3.662A pdb=" N ASN A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 335 removed outlier: 3.547A pdb=" N LEU A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 356 through 360 removed outlier: 3.513A pdb=" N GLY A 359 " --> pdb=" O GLY A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 Processing helix chain 'A' and resid 380 through 392 removed outlier: 3.678A pdb=" N GLN A 386 " --> pdb=" O ASN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 removed outlier: 4.479A pdb=" N GLN A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN A 401 " --> pdb=" O GLY A 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 401' Processing helix chain 'A' and resid 402 through 416 Processing helix chain 'A' and resid 416 through 427 Processing helix chain 'A' and resid 430 through 437 Processing helix chain 'A' and resid 438 through 461 removed outlier: 4.151A pdb=" N ALA A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 490 removed outlier: 3.710A pdb=" N THR A 488 " --> pdb=" O PHE A 484 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N CYS A 490 " --> pdb=" O MET A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 517 Processing helix chain 'A' and resid 517 through 524 removed outlier: 3.820A pdb=" N GLU A 524 " --> pdb=" O GLU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 558 removed outlier: 3.786A pdb=" N MET A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 558 " --> pdb=" O ALA A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.843A pdb=" N TYR A 578 " --> pdb=" O ASN A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 586 Processing helix chain 'A' and resid 590 through 607 removed outlier: 3.578A pdb=" N ILE A 601 " --> pdb=" O GLY A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 617 removed outlier: 4.406A pdb=" N LEU A 614 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Proline residue: A 615 - end of helix Processing helix chain 'A' and resid 620 through 657 removed outlier: 4.208A pdb=" N VAL A 639 " --> pdb=" O PHE A 635 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE A 640 " --> pdb=" O LYS A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 683 removed outlier: 3.666A pdb=" N ILE A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE A 683 " --> pdb=" O PHE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 691 removed outlier: 3.755A pdb=" N SER A 690 " --> pdb=" O GLU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 732 Processing helix chain 'A' and resid 738 through 755 removed outlier: 3.850A pdb=" N TYR A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU A 755 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 765 removed outlier: 3.566A pdb=" N ASN A 765 " --> pdb=" O VAL A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 876 Processing helix chain 'A' and resid 880 through 920 removed outlier: 3.515A pdb=" N TYR A 896 " --> pdb=" O SER A 892 " (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 154 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 229 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 255 through 265 Processing helix chain 'B' and resid 265 through 281 Processing helix chain 'B' and resid 282 through 290 removed outlier: 3.517A pdb=" N LEU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 311 removed outlier: 3.662A pdb=" N ASN B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 335 removed outlier: 3.547A pdb=" N LEU B 335 " --> pdb=" O GLY B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 347 Processing helix chain 'B' and resid 356 through 360 removed outlier: 3.513A pdb=" N GLY B 359 " --> pdb=" O GLY B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 380 through 392 removed outlier: 3.678A pdb=" N GLN B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 4.478A pdb=" N GLN B 400 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN B 401 " --> pdb=" O GLY B 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 401' Processing helix chain 'B' and resid 402 through 416 Processing helix chain 'B' and resid 416 through 427 Processing helix chain 'B' and resid 430 through 437 Processing helix chain 'B' and resid 438 through 461 removed outlier: 4.151A pdb=" N ALA B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 490 removed outlier: 3.710A pdb=" N THR B 488 " --> pdb=" O PHE B 484 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N CYS B 490 " --> pdb=" O MET B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 517 Processing helix chain 'B' and resid 517 through 524 removed outlier: 3.820A pdb=" N GLU B 524 " --> pdb=" O GLU B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 558 removed outlier: 3.786A pdb=" N MET B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 534 " --> pdb=" O ASP B 530 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 558 " --> pdb=" O ALA B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 581 removed outlier: 3.843A pdb=" N TYR B 578 " --> pdb=" O ASN B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 586 Processing helix chain 'B' and resid 590 through 607 removed outlier: 3.578A pdb=" N ILE B 601 " --> pdb=" O GLY B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 4.406A pdb=" N LEU B 614 " --> pdb=" O ALA B 611 " (cutoff:3.500A) Proline residue: B 615 - end of helix Processing helix chain 'B' and resid 620 through 657 removed outlier: 4.209A pdb=" N VAL B 639 " --> pdb=" O PHE B 635 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 683 removed outlier: 3.666A pdb=" N ILE B 682 " --> pdb=" O LEU B 678 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE B 683 " --> pdb=" O PHE B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 691 removed outlier: 3.755A pdb=" N SER B 690 " --> pdb=" O GLU B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 732 Processing helix chain 'B' and resid 738 through 755 removed outlier: 3.850A pdb=" N TYR B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU B 755 " --> pdb=" O PHE B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.566A pdb=" N ASN B 765 " --> pdb=" O VAL B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 876 Processing helix chain 'B' and resid 880 through 920 removed outlier: 3.515A pdb=" N TYR B 896 " --> pdb=" O SER B 892 " (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 154 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 229 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 255 through 265 Processing helix chain 'C' and resid 265 through 281 Processing helix chain 'C' and resid 282 through 290 removed outlier: 3.517A pdb=" N LEU C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 311 removed outlier: 3.663A pdb=" N ASN C 309 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 335 removed outlier: 3.547A pdb=" N LEU C 335 " --> pdb=" O GLY C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 356 through 360 removed outlier: 3.513A pdb=" N GLY C 359 " --> pdb=" O GLY C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 372 Processing helix chain 'C' and resid 380 through 392 removed outlier: 3.678A pdb=" N GLN C 386 " --> pdb=" O ASN C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 401 removed outlier: 4.479A pdb=" N GLN C 400 " --> pdb=" O SER C 396 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN C 401 " --> pdb=" O GLY C 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 396 through 401' Processing helix chain 'C' and resid 402 through 416 Processing helix chain 'C' and resid 416 through 427 Processing helix chain 'C' and resid 430 through 437 Processing helix chain 'C' and resid 438 through 461 removed outlier: 4.151A pdb=" N ALA C 461 " --> pdb=" O LEU C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 490 removed outlier: 3.710A pdb=" N THR C 488 " --> pdb=" O PHE C 484 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N CYS C 490 " --> pdb=" O MET C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 517 Processing helix chain 'C' and resid 517 through 524 removed outlier: 3.820A pdb=" N GLU C 524 " --> pdb=" O GLU C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 558 removed outlier: 3.786A pdb=" N MET C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 534 " --> pdb=" O ASP C 530 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE C 558 " --> pdb=" O ALA C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 581 removed outlier: 3.843A pdb=" N TYR C 578 " --> pdb=" O ASN C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 586 Processing helix chain 'C' and resid 590 through 607 removed outlier: 3.578A pdb=" N ILE C 601 " --> pdb=" O GLY C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 617 removed outlier: 4.406A pdb=" N LEU C 614 " --> pdb=" O ALA C 611 " (cutoff:3.500A) Proline residue: C 615 - end of helix Processing helix chain 'C' and resid 620 through 657 removed outlier: 4.208A pdb=" N VAL C 639 " --> pdb=" O PHE C 635 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE C 640 " --> pdb=" O LYS C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 683 removed outlier: 3.666A pdb=" N ILE C 682 " --> pdb=" O LEU C 678 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE C 683 " --> pdb=" O PHE C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 691 removed outlier: 3.755A pdb=" N SER C 690 " --> pdb=" O GLU C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 732 Processing helix chain 'C' and resid 738 through 755 removed outlier: 3.850A pdb=" N TYR C 753 " --> pdb=" O LEU C 749 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU C 755 " --> pdb=" O PHE C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 765 removed outlier: 3.567A pdb=" N ASN C 765 " --> pdb=" O VAL C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 876 Processing helix chain 'C' and resid 880 through 920 removed outlier: 3.515A pdb=" N TYR C 896 " --> pdb=" O SER C 892 " (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 154 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 229 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 255 through 265 Processing helix chain 'D' and resid 265 through 281 Processing helix chain 'D' and resid 282 through 290 removed outlier: 3.517A pdb=" N LEU D 288 " --> pdb=" O ALA D 284 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 311 removed outlier: 3.662A pdb=" N ASN D 309 " --> pdb=" O ALA D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 335 removed outlier: 3.547A pdb=" N LEU D 335 " --> pdb=" O GLY D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 347 Processing helix chain 'D' and resid 356 through 360 removed outlier: 3.513A pdb=" N GLY D 359 " --> pdb=" O GLY D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 372 Processing helix chain 'D' and resid 380 through 392 removed outlier: 3.678A pdb=" N GLN D 386 " --> pdb=" O ASN D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 401 removed outlier: 4.479A pdb=" N GLN D 400 " --> pdb=" O SER D 396 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN D 401 " --> pdb=" O GLY D 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 396 through 401' Processing helix chain 'D' and resid 402 through 416 Processing helix chain 'D' and resid 416 through 427 Processing helix chain 'D' and resid 430 through 437 Processing helix chain 'D' and resid 438 through 461 removed outlier: 4.151A pdb=" N ALA D 461 " --> pdb=" O LEU D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 490 removed outlier: 3.710A pdb=" N THR D 488 " --> pdb=" O PHE D 484 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N CYS D 490 " --> pdb=" O MET D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 517 Processing helix chain 'D' and resid 517 through 524 removed outlier: 3.820A pdb=" N GLU D 524 " --> pdb=" O GLU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 558 removed outlier: 3.786A pdb=" N MET D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 534 " --> pdb=" O ASP D 530 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE D 558 " --> pdb=" O ALA D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.843A pdb=" N TYR D 578 " --> pdb=" O ASN D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 586 Processing helix chain 'D' and resid 590 through 607 removed outlier: 3.578A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 617 removed outlier: 4.406A pdb=" N LEU D 614 " --> pdb=" O ALA D 611 " (cutoff:3.500A) Proline residue: D 615 - end of helix Processing helix chain 'D' and resid 620 through 657 removed outlier: 4.208A pdb=" N VAL D 639 " --> pdb=" O PHE D 635 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE D 640 " --> pdb=" O LYS D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 683 removed outlier: 3.666A pdb=" N ILE D 682 " --> pdb=" O LEU D 678 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE D 683 " --> pdb=" O PHE D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 691 removed outlier: 3.755A pdb=" N SER D 690 " --> pdb=" O GLU D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 732 Processing helix chain 'D' and resid 738 through 755 removed outlier: 3.850A pdb=" N TYR D 753 " --> pdb=" O LEU D 749 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU D 755 " --> pdb=" O PHE D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 765 removed outlier: 3.566A pdb=" N ASN D 765 " --> pdb=" O VAL D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 876 Processing helix chain 'D' and resid 880 through 920 removed outlier: 3.515A pdb=" N TYR D 896 " --> pdb=" O SER D 892 " (cutoff:3.500A) 1564 hydrogen bonds defined for protein. 4524 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: 3.98 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3708 1.29 - 1.42: 6156 1.42 - 1.55: 13848 1.55 - 1.68: 8 1.68 - 1.81: 244 Bond restraints: 23964 Sorted by residual: bond pdb=" C19 HOR C1005 " pdb=" C20 HOR C1005 " ideal model delta sigma weight residual 1.424 1.284 0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C19 HOR A1004 " pdb=" C20 HOR A1004 " ideal model delta sigma weight residual 1.424 1.285 0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C19 HOR B1004 " pdb=" C20 HOR B1004 " ideal model delta sigma weight residual 1.424 1.285 0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C19 HOR D1005 " pdb=" C20 HOR D1005 " ideal model delta sigma weight residual 1.424 1.285 0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C31 POV A1007 " pdb=" O31 POV A1007 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.95e+01 ... (remaining 23959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 31447 1.99 - 3.97: 609 3.97 - 5.96: 212 5.96 - 7.95: 88 7.95 - 9.93: 36 Bond angle restraints: 32392 Sorted by residual: angle pdb=" C GLU D 881 " pdb=" N GLY D 882 " pdb=" CA GLY D 882 " ideal model delta sigma weight residual 120.00 124.27 -4.27 1.10e+00 8.26e-01 1.51e+01 angle pdb=" C GLU C 881 " pdb=" N GLY C 882 " pdb=" CA GLY C 882 " ideal model delta sigma weight residual 120.00 124.23 -4.23 1.10e+00 8.26e-01 1.48e+01 angle pdb=" C GLU B 881 " pdb=" N GLY B 882 " pdb=" CA GLY B 882 " ideal model delta sigma weight residual 120.00 124.23 -4.23 1.10e+00 8.26e-01 1.48e+01 angle pdb=" C GLU A 881 " pdb=" N GLY A 882 " pdb=" CA GLY A 882 " ideal model delta sigma weight residual 120.00 124.23 -4.23 1.10e+00 8.26e-01 1.48e+01 angle pdb=" N GLU B 886 " pdb=" CA GLU B 886 " pdb=" C GLU B 886 " ideal model delta sigma weight residual 111.82 107.53 4.29 1.16e+00 7.43e-01 1.36e+01 ... (remaining 32387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.05: 13680 31.05 - 62.11: 436 62.11 - 93.16: 68 93.16 - 124.22: 20 124.22 - 155.27: 8 Dihedral angle restraints: 14212 sinusoidal: 6000 harmonic: 8212 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 121 " pdb=" CB CYS B 121 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CB CYS B 128 " pdb=" SG CYS B 128 " pdb=" SG CYS B 128 " pdb=" CB CYS B 128 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CB CYS B 229 " pdb=" SG CYS B 229 " pdb=" SG CYS B 229 " pdb=" CB CYS B 229 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 ... (remaining 14209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2942 0.054 - 0.108: 546 0.108 - 0.161: 40 0.161 - 0.215: 36 0.215 - 0.269: 24 Chirality restraints: 3588 Sorted by residual: chirality pdb=" CBI Y01 C1009 " pdb=" CAU Y01 C1009 " pdb=" CBE Y01 C1009 " pdb=" CBG Y01 C1009 " both_signs ideal model delta sigma weight residual False 2.94 2.67 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CBI Y01 A1008 " pdb=" CAU Y01 A1008 " pdb=" CBE Y01 A1008 " pdb=" CBG Y01 A1008 " both_signs ideal model delta sigma weight residual False 2.94 2.67 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CBI Y01 D1009 " pdb=" CAU Y01 D1009 " pdb=" CBE Y01 D1009 " pdb=" CBG Y01 D1009 " both_signs ideal model delta sigma weight residual False 2.94 2.67 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 3585 not shown) Planarity restraints: 3960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 360 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO D 361 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 361 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 361 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 360 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO C 361 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 361 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 361 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 360 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO A 361 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " 0.030 5.00e-02 4.00e+02 ... (remaining 3957 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 7167 2.82 - 3.34: 23204 3.34 - 3.86: 38806 3.86 - 4.38: 46302 4.38 - 4.90: 78124 Nonbonded interactions: 193603 Sorted by model distance: nonbonded pdb=" OE1 GLU D 98 " pdb=" NH2 ARG D 101 " model vdw 2.306 3.120 nonbonded pdb=" OE1 GLU A 98 " pdb=" NH2 ARG A 101 " model vdw 2.306 3.120 nonbonded pdb=" OE1 GLU C 98 " pdb=" NH2 ARG C 101 " model vdw 2.306 3.120 nonbonded pdb=" OE1 GLU B 98 " pdb=" NH2 ARG B 101 " model vdw 2.307 3.120 nonbonded pdb=" N ASP C 463 " pdb=" OD1 ASP C 463 " model vdw 2.330 3.120 ... (remaining 193598 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.700 Find NCS groups from input model: 0.360 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:7.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 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 : 0.007 0.140 23976 Z= 0.353 Angle : 0.823 9.932 32402 Z= 0.358 Chirality : 0.047 0.269 3588 Planarity : 0.004 0.055 3960 Dihedral : 16.275 155.274 8864 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.01 % Allowed : 7.18 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.16 (0.15), residues: 2744 helix: 1.47 (0.11), residues: 2004 sheet: None (None), residues: 0 loop : -1.13 (0.19), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 583 TYR 0.007 0.001 TYR C 579 PHE 0.013 0.001 PHE A 377 TRP 0.008 0.001 TRP B 425 HIS 0.002 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.35 (23964) covalent geometry : angle 0.82341 / 0.36 (32392) SS BOND : angle 0.00000 / 0.00 ( 10) hydrogen bonds : bond 0.19324 / 13.09 ( 1564) hydrogen bonds : angle 5.57918 / 4.05 ( 4524) metal coordination : bond 0.00121 / 0.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 541 time to evaluate : 0.801 Fit side-chains REVERT: A 116 LYS cc_start: 0.7951 (tttt) cc_final: 0.7720 (tttp) REVERT: A 144 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7440 (tm-30) REVERT: A 230 GLN cc_start: 0.7807 (pt0) cc_final: 0.7539 (mt0) REVERT: A 259 ASN cc_start: 0.7111 (t0) cc_final: 0.6849 (m-40) REVERT: A 260 GLN cc_start: 0.8072 (tp40) cc_final: 0.7850 (tm-30) REVERT: A 299 GLU cc_start: 0.7902 (tt0) cc_final: 0.7557 (mm-30) REVERT: A 312 LYS cc_start: 0.7963 (mmtt) cc_final: 0.7559 (mppt) REVERT: A 351 GLU cc_start: 0.7958 (tp30) cc_final: 0.7525 (mt-10) REVERT: A 354 GLN cc_start: 0.8181 (mt0) cc_final: 0.7960 (tm130) REVERT: A 389 SER cc_start: 0.8130 (t) cc_final: 0.7758 (p) REVERT: A 437 ARG cc_start: 0.7796 (mtm110) cc_final: 0.7477 (mtm110) REVERT: A 441 MET cc_start: 0.7473 (mmm) cc_final: 0.7081 (mmm) REVERT: A 463 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7366 (p0) REVERT: A 468 THR cc_start: 0.4726 (OUTLIER) cc_final: 0.4269 (p) REVERT: A 505 MET cc_start: 0.7457 (mtt) cc_final: 0.7001 (mtm) REVERT: A 520 GLU cc_start: 0.7808 (tp30) cc_final: 0.7605 (tp30) REVERT: A 585 LYS cc_start: 0.8777 (mmpt) cc_final: 0.8120 (mtmt) REVERT: A 691 VAL cc_start: 0.8350 (t) cc_final: 0.8107 (m) REVERT: A 739 ASP cc_start: 0.7446 (t70) cc_final: 0.7156 (t70) REVERT: A 741 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7383 (mm-30) REVERT: A 758 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6607 (pmt-80) REVERT: A 856 GLN cc_start: 0.7838 (mt0) cc_final: 0.7266 (mm-40) REVERT: A 874 LYS cc_start: 0.6884 (ttpt) cc_final: 0.6574 (ttmt) REVERT: A 878 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7136 (mm-30) REVERT: A 881 GLU cc_start: 0.7231 (tt0) cc_final: 0.6912 (mt-10) REVERT: A 885 LYS cc_start: 0.7449 (tttp) cc_final: 0.6907 (tppt) REVERT: A 890 ASP cc_start: 0.7435 (m-30) cc_final: 0.7104 (m-30) REVERT: A 900 GLU cc_start: 0.7314 (tp30) cc_final: 0.6782 (tm-30) REVERT: B 116 LYS cc_start: 0.7958 (tttt) cc_final: 0.7725 (tttp) REVERT: B 144 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7443 (tm-30) REVERT: B 230 GLN cc_start: 0.7791 (pt0) cc_final: 0.7519 (mt0) REVERT: B 259 ASN cc_start: 0.7107 (t0) cc_final: 0.6846 (m-40) REVERT: B 260 GLN cc_start: 0.8071 (tp40) cc_final: 0.7852 (tm-30) REVERT: B 299 GLU cc_start: 0.7906 (tt0) cc_final: 0.7559 (mm-30) REVERT: B 312 LYS cc_start: 0.7965 (mmtt) cc_final: 0.7557 (mppt) REVERT: B 351 GLU cc_start: 0.7948 (tp30) cc_final: 0.7523 (mt-10) REVERT: B 354 GLN cc_start: 0.8184 (mt0) cc_final: 0.7961 (tm130) REVERT: B 389 SER cc_start: 0.8130 (t) cc_final: 0.7760 (p) REVERT: B 437 ARG cc_start: 0.7812 (mtm110) cc_final: 0.7198 (mtm110) REVERT: B 441 MET cc_start: 0.7481 (mmm) cc_final: 0.7088 (mmm) REVERT: B 463 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7363 (p0) REVERT: B 468 THR cc_start: 0.4720 (OUTLIER) cc_final: 0.4261 (p) REVERT: B 495 GLU cc_start: 0.6677 (mm-30) cc_final: 0.6442 (mm-30) REVERT: B 505 MET cc_start: 0.7443 (mtt) cc_final: 0.7003 (mtm) REVERT: B 520 GLU cc_start: 0.7803 (tp30) cc_final: 0.7601 (tp30) REVERT: B 585 LYS cc_start: 0.8776 (mmpt) cc_final: 0.8115 (mtmt) REVERT: B 691 VAL cc_start: 0.8344 (t) cc_final: 0.8094 (m) REVERT: B 739 ASP cc_start: 0.7443 (t70) cc_final: 0.7156 (t70) REVERT: B 741 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7395 (mm-30) REVERT: B 758 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6613 (pmt-80) REVERT: B 856 GLN cc_start: 0.7836 (mt0) cc_final: 0.7263 (mm-40) REVERT: B 874 LYS cc_start: 0.6897 (ttpt) cc_final: 0.6590 (ttmt) REVERT: B 878 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7137 (mm-30) REVERT: B 881 GLU cc_start: 0.7228 (tt0) cc_final: 0.6910 (mt-10) REVERT: B 885 LYS cc_start: 0.7451 (tttp) cc_final: 0.6903 (tppt) REVERT: B 890 ASP cc_start: 0.7447 (m-30) cc_final: 0.7115 (m-30) REVERT: B 900 GLU cc_start: 0.7264 (tp30) cc_final: 0.6730 (tm-30) REVERT: C 116 LYS cc_start: 0.7950 (tttt) cc_final: 0.7719 (tttp) REVERT: C 144 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7444 (tm-30) REVERT: C 230 GLN cc_start: 0.7792 (pt0) cc_final: 0.7518 (mt0) REVERT: C 233 GLU cc_start: 0.8242 (tp30) cc_final: 0.8042 (tt0) REVERT: C 259 ASN cc_start: 0.7110 (t0) cc_final: 0.6848 (m-40) REVERT: C 260 GLN cc_start: 0.8070 (tp40) cc_final: 0.7851 (tm-30) REVERT: C 299 GLU cc_start: 0.7906 (tt0) cc_final: 0.7560 (mm-30) REVERT: C 312 LYS cc_start: 0.7962 (mmtt) cc_final: 0.7556 (mppt) REVERT: C 351 GLU cc_start: 0.7958 (tp30) cc_final: 0.7526 (mt-10) REVERT: C 354 GLN cc_start: 0.8183 (mt0) cc_final: 0.7961 (tm130) REVERT: C 389 SER cc_start: 0.8132 (t) cc_final: 0.7761 (p) REVERT: C 437 ARG cc_start: 0.7798 (mtm110) cc_final: 0.7218 (mtm110) REVERT: C 441 MET cc_start: 0.7477 (mmm) cc_final: 0.7084 (mmm) REVERT: C 463 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7366 (p0) REVERT: C 468 THR cc_start: 0.4708 (OUTLIER) cc_final: 0.4259 (p) REVERT: C 495 GLU cc_start: 0.6680 (mm-30) cc_final: 0.6445 (mm-30) REVERT: C 505 MET cc_start: 0.7445 (mtt) cc_final: 0.7007 (mtm) REVERT: C 520 GLU cc_start: 0.7805 (tp30) cc_final: 0.7602 (tp30) REVERT: C 585 LYS cc_start: 0.8773 (mmpt) cc_final: 0.8111 (mtmt) REVERT: C 691 VAL cc_start: 0.8346 (t) cc_final: 0.8091 (m) REVERT: C 739 ASP cc_start: 0.7495 (t70) cc_final: 0.7219 (t70) REVERT: C 741 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7384 (mm-30) REVERT: C 758 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6578 (pmt-80) REVERT: C 856 GLN cc_start: 0.7836 (mt0) cc_final: 0.7263 (mm-40) REVERT: C 874 LYS cc_start: 0.6887 (ttpt) cc_final: 0.6577 (ttmt) REVERT: C 878 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7137 (mm-30) REVERT: C 881 GLU cc_start: 0.7225 (tt0) cc_final: 0.6907 (mt-10) REVERT: C 885 LYS cc_start: 0.7447 (tttp) cc_final: 0.6899 (tppt) REVERT: C 890 ASP cc_start: 0.7431 (m-30) cc_final: 0.7100 (m-30) REVERT: C 900 GLU cc_start: 0.7314 (tp30) cc_final: 0.6780 (tm-30) REVERT: D 116 LYS cc_start: 0.7956 (tttt) cc_final: 0.7724 (tttp) REVERT: D 144 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7441 (tm-30) REVERT: D 230 GLN cc_start: 0.7790 (pt0) cc_final: 0.7519 (mt0) REVERT: D 233 GLU cc_start: 0.8246 (tp30) cc_final: 0.8044 (tt0) REVERT: D 259 ASN cc_start: 0.7109 (t0) cc_final: 0.6849 (m-40) REVERT: D 260 GLN cc_start: 0.8073 (tp40) cc_final: 0.7851 (tm-30) REVERT: D 299 GLU cc_start: 0.7902 (tt0) cc_final: 0.7557 (mm-30) REVERT: D 312 LYS cc_start: 0.7965 (mmtt) cc_final: 0.7559 (mppt) REVERT: D 351 GLU cc_start: 0.7960 (tp30) cc_final: 0.7526 (mt-10) REVERT: D 354 GLN cc_start: 0.8183 (mt0) cc_final: 0.7960 (tm130) REVERT: D 389 SER cc_start: 0.8131 (t) cc_final: 0.7760 (p) REVERT: D 437 ARG cc_start: 0.7809 (mtm110) cc_final: 0.7198 (mtm110) REVERT: D 441 MET cc_start: 0.7478 (mmm) cc_final: 0.7086 (mmm) REVERT: D 463 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7363 (p0) REVERT: D 468 THR cc_start: 0.4721 (OUTLIER) cc_final: 0.4263 (p) REVERT: D 495 GLU cc_start: 0.6678 (mm-30) cc_final: 0.6438 (mm-30) REVERT: D 505 MET cc_start: 0.7442 (mtt) cc_final: 0.6987 (mtm) REVERT: D 520 GLU cc_start: 0.7805 (tp30) cc_final: 0.7604 (tp30) REVERT: D 585 LYS cc_start: 0.8778 (mmpt) cc_final: 0.8125 (mtmt) REVERT: D 691 VAL cc_start: 0.8357 (t) cc_final: 0.8110 (m) REVERT: D 739 ASP cc_start: 0.7445 (t70) cc_final: 0.7158 (t70) REVERT: D 741 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7383 (mm-30) REVERT: D 758 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6612 (pmt-80) REVERT: D 856 GLN cc_start: 0.7840 (mt0) cc_final: 0.7268 (mm-40) REVERT: D 874 LYS cc_start: 0.6895 (ttpt) cc_final: 0.6586 (ttmt) REVERT: D 878 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7136 (mm-30) REVERT: D 881 GLU cc_start: 0.7230 (tt0) cc_final: 0.6912 (mt-10) REVERT: D 885 LYS cc_start: 0.7538 (tttp) cc_final: 0.6998 (tppt) REVERT: D 890 ASP cc_start: 0.7440 (m-30) cc_final: 0.7111 (m-30) REVERT: D 900 GLU cc_start: 0.7270 (tp30) cc_final: 0.6644 (tm-30) outliers start: 72 outliers final: 8 residues processed: 593 average time/residue: 0.6194 time to fit residues: 416.3643 Evaluate side-chains 419 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 399 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 758 ARG Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 463 ASP Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain D residue 209 TYR Chi-restraints excluded: chain D residue 463 ASP Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 758 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.142693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.109727 restraints weight = 26282.479| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.02 r_work: 0.3115 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 23976 Z= 0.176 Angle : 0.595 6.764 32402 Z= 0.296 Chirality : 0.041 0.268 3588 Planarity : 0.005 0.058 3960 Dihedral : 14.111 91.563 3568 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.05 % Allowed : 14.48 % Favored : 81.47 % 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: 2.25 (0.15), residues: 2744 helix: 2.31 (0.11), residues: 2016 sheet: None (None), residues: 0 loop : -0.93 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 191 TYR 0.010 0.001 TYR D 705 PHE 0.016 0.001 PHE A 465 TRP 0.012 0.002 TRP C 391 HIS 0.003 0.001 HIS B 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (23964) covalent geometry : angle 0.59494 / 0.30 (32392) SS BOND : angle 0.00000 / 0.00 ( 10) hydrogen bonds : bond 0.05530 / 3.78 ( 1564) hydrogen bonds : angle 3.69410 / 2.66 ( 4524) metal coordination : bond 0.00673 / 0.39 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 419 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8637 (tttt) cc_final: 0.8358 (tttp) REVERT: A 259 ASN cc_start: 0.7251 (t0) cc_final: 0.7009 (m110) REVERT: A 260 GLN cc_start: 0.8133 (tp40) cc_final: 0.7932 (tm-30) REVERT: A 312 LYS cc_start: 0.8087 (mmtt) cc_final: 0.7648 (mppt) REVERT: A 351 GLU cc_start: 0.8219 (tp30) cc_final: 0.7955 (mt-10) REVERT: A 389 SER cc_start: 0.8628 (t) cc_final: 0.8270 (p) REVERT: A 437 ARG cc_start: 0.8221 (mtm110) cc_final: 0.7695 (mtm110) REVERT: A 441 MET cc_start: 0.8389 (mmm) cc_final: 0.8077 (mmm) REVERT: A 528 MET cc_start: 0.7574 (mmm) cc_final: 0.6744 (pp-130) REVERT: A 585 LYS cc_start: 0.9010 (mmpt) cc_final: 0.8385 (mtmt) REVERT: A 856 GLN cc_start: 0.8241 (mt0) cc_final: 0.7805 (mm-40) REVERT: A 874 LYS cc_start: 0.7950 (ttpt) cc_final: 0.7573 (ttmt) REVERT: A 878 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7845 (mm-30) REVERT: A 885 LYS cc_start: 0.8074 (tttp) cc_final: 0.7562 (tppt) REVERT: A 900 GLU cc_start: 0.7919 (tp30) cc_final: 0.7291 (tp30) REVERT: B 116 LYS cc_start: 0.8644 (tttt) cc_final: 0.8365 (tttp) REVERT: B 259 ASN cc_start: 0.7252 (t0) cc_final: 0.7011 (m110) REVERT: B 312 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7648 (mppt) REVERT: B 351 GLU cc_start: 0.8209 (tp30) cc_final: 0.7945 (mt-10) REVERT: B 389 SER cc_start: 0.8629 (t) cc_final: 0.8272 (p) REVERT: B 437 ARG cc_start: 0.8220 (mtm110) cc_final: 0.7694 (mtm110) REVERT: B 441 MET cc_start: 0.8388 (mmm) cc_final: 0.8073 (mmm) REVERT: B 528 MET cc_start: 0.7589 (mmm) cc_final: 0.6747 (pp-130) REVERT: B 585 LYS cc_start: 0.9020 (mmpt) cc_final: 0.8415 (mtmt) REVERT: B 856 GLN cc_start: 0.8229 (mt0) cc_final: 0.7788 (mm-40) REVERT: B 874 LYS cc_start: 0.7949 (ttpt) cc_final: 0.7574 (ttmt) REVERT: B 878 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7850 (mm-30) REVERT: B 885 LYS cc_start: 0.8083 (tttp) cc_final: 0.7574 (tppt) REVERT: B 900 GLU cc_start: 0.7927 (tp30) cc_final: 0.7301 (tp30) REVERT: C 116 LYS cc_start: 0.8627 (tttt) cc_final: 0.8347 (tttp) REVERT: C 259 ASN cc_start: 0.7258 (t0) cc_final: 0.7017 (m110) REVERT: C 260 GLN cc_start: 0.8137 (tp40) cc_final: 0.7937 (tm-30) REVERT: C 312 LYS cc_start: 0.8079 (mmtt) cc_final: 0.7638 (mppt) REVERT: C 351 GLU cc_start: 0.8230 (tp30) cc_final: 0.7944 (mt-10) REVERT: C 389 SER cc_start: 0.8629 (t) cc_final: 0.8270 (p) REVERT: C 437 ARG cc_start: 0.8211 (mtm110) cc_final: 0.7691 (mtm110) REVERT: C 441 MET cc_start: 0.8394 (mmm) cc_final: 0.8081 (mmm) REVERT: C 528 MET cc_start: 0.7574 (mmm) cc_final: 0.6743 (pp-130) REVERT: C 585 LYS cc_start: 0.9000 (mmpt) cc_final: 0.8361 (mtmt) REVERT: C 856 GLN cc_start: 0.8226 (mt0) cc_final: 0.7797 (mm-40) REVERT: C 874 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7581 (ttmt) REVERT: C 878 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7853 (mm-30) REVERT: C 885 LYS cc_start: 0.8082 (tttp) cc_final: 0.7573 (tppt) REVERT: C 900 GLU cc_start: 0.7926 (tp30) cc_final: 0.7301 (tp30) REVERT: D 116 LYS cc_start: 0.8639 (tttt) cc_final: 0.8362 (tttp) REVERT: D 161 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8444 (t) REVERT: D 259 ASN cc_start: 0.7253 (t0) cc_final: 0.7011 (m110) REVERT: D 312 LYS cc_start: 0.8086 (mmtt) cc_final: 0.7646 (mppt) REVERT: D 351 GLU cc_start: 0.8223 (tp30) cc_final: 0.7946 (mt-10) REVERT: D 389 SER cc_start: 0.8628 (t) cc_final: 0.8270 (p) REVERT: D 437 ARG cc_start: 0.8221 (mtm110) cc_final: 0.7693 (mtm110) REVERT: D 441 MET cc_start: 0.8383 (mmm) cc_final: 0.8068 (mmm) REVERT: D 528 MET cc_start: 0.7578 (mmm) cc_final: 0.6743 (pp-130) REVERT: D 585 LYS cc_start: 0.9007 (mmpt) cc_final: 0.8382 (mtmt) REVERT: D 856 GLN cc_start: 0.8237 (mt0) cc_final: 0.7802 (mm-40) REVERT: D 874 LYS cc_start: 0.7947 (ttpt) cc_final: 0.7571 (ttmt) REVERT: D 878 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7837 (mm-30) REVERT: D 885 LYS cc_start: 0.8080 (tttp) cc_final: 0.7569 (tppt) REVERT: D 900 GLU cc_start: 0.7920 (tp30) cc_final: 0.7296 (tp30) outliers start: 97 outliers final: 38 residues processed: 484 average time/residue: 0.6703 time to fit residues: 366.5906 Evaluate side-chains 389 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 350 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 758 ARG Chi-restraints excluded: chain B residue 887 ILE Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 385 GLN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain C residue 618 GLU Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 209 TYR Chi-restraints excluded: chain D residue 365 ARG Chi-restraints excluded: chain D residue 385 GLN Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 618 GLU Chi-restraints excluded: chain D residue 740 VAL Chi-restraints excluded: chain D residue 758 ARG Chi-restraints excluded: chain D residue 887 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 10 optimal weight: 4.9990 chunk 239 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 238 optimal weight: 7.9990 chunk 230 optimal weight: 2.9990 chunk 217 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 chunk 219 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 85 optimal weight: 0.6980 chunk 186 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.142525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.110026 restraints weight = 26235.748| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.00 r_work: 0.3118 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 23976 Z= 0.173 Angle : 0.560 6.730 32402 Z= 0.277 Chirality : 0.041 0.304 3588 Planarity : 0.004 0.056 3960 Dihedral : 12.744 89.489 3556 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.63 % Allowed : 15.11 % Favored : 80.26 % 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: 2.46 (0.16), residues: 2744 helix: 2.49 (0.11), residues: 2016 sheet: None (None), residues: 0 loop : -0.94 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 191 TYR 0.011 0.001 TYR C 579 PHE 0.029 0.002 PHE A 407 TRP 0.015 0.002 TRP C 391 HIS 0.002 0.001 HIS D 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (23964) covalent geometry : angle 0.55964 / 0.28 (32392) SS BOND : angle 0.00000 / 0.00 ( 10) hydrogen bonds : bond 0.05191 / 3.55 ( 1564) hydrogen bonds : angle 3.52515 / 2.54 ( 4524) metal coordination : bond 0.00579 / 0.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 387 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8626 (tttt) cc_final: 0.8381 (tttp) REVERT: A 144 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: A 260 GLN cc_start: 0.8156 (tp40) cc_final: 0.7904 (tm-30) REVERT: A 312 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7703 (mppt) REVERT: A 351 GLU cc_start: 0.8238 (tp30) cc_final: 0.7986 (mt-10) REVERT: A 389 SER cc_start: 0.8662 (t) cc_final: 0.8333 (p) REVERT: A 437 ARG cc_start: 0.8239 (mtm110) cc_final: 0.7750 (mtm110) REVERT: A 441 MET cc_start: 0.8402 (mmm) cc_final: 0.8049 (mmm) REVERT: A 521 TYR cc_start: 0.8231 (t80) cc_final: 0.7928 (t80) REVERT: A 528 MET cc_start: 0.7471 (mmm) cc_final: 0.6768 (pp-130) REVERT: A 549 TRP cc_start: 0.7459 (t-100) cc_final: 0.7163 (t60) REVERT: A 585 LYS cc_start: 0.9035 (mmpt) cc_final: 0.8437 (mtmt) REVERT: A 856 GLN cc_start: 0.8219 (mt0) cc_final: 0.7821 (mm-40) REVERT: A 857 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8412 (ttmm) REVERT: A 874 LYS cc_start: 0.7952 (ttpt) cc_final: 0.7140 (tmmt) REVERT: A 878 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7820 (mm-30) REVERT: A 881 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7381 (mt-10) REVERT: A 885 LYS cc_start: 0.8096 (tttp) cc_final: 0.7591 (tppt) REVERT: A 900 GLU cc_start: 0.8029 (tp30) cc_final: 0.7489 (tm-30) REVERT: B 116 LYS cc_start: 0.8625 (tttt) cc_final: 0.8381 (tttp) REVERT: B 144 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: B 312 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7704 (mppt) REVERT: B 351 GLU cc_start: 0.8236 (tp30) cc_final: 0.8004 (mt-10) REVERT: B 389 SER cc_start: 0.8661 (t) cc_final: 0.8332 (p) REVERT: B 437 ARG cc_start: 0.8239 (mtm110) cc_final: 0.7743 (mtm110) REVERT: B 441 MET cc_start: 0.8403 (mmm) cc_final: 0.8050 (mmm) REVERT: B 496 MET cc_start: 0.8252 (tpp) cc_final: 0.8028 (tpt) REVERT: B 521 TYR cc_start: 0.8220 (t80) cc_final: 0.7925 (t80) REVERT: B 528 MET cc_start: 0.7482 (mmm) cc_final: 0.6773 (pp-130) REVERT: B 549 TRP cc_start: 0.7564 (t-100) cc_final: 0.7204 (t60) REVERT: B 585 LYS cc_start: 0.9033 (mmpt) cc_final: 0.8441 (mtmt) REVERT: B 687 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8218 (mp0) REVERT: B 856 GLN cc_start: 0.8226 (mt0) cc_final: 0.7827 (mm-40) REVERT: B 857 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8432 (ttmm) REVERT: B 874 LYS cc_start: 0.7966 (ttpt) cc_final: 0.7150 (tmmt) REVERT: B 878 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7833 (mm-30) REVERT: B 881 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7386 (mt-10) REVERT: B 885 LYS cc_start: 0.8118 (tttp) cc_final: 0.7602 (tppt) REVERT: B 900 GLU cc_start: 0.7948 (tp30) cc_final: 0.7397 (tm-30) REVERT: C 116 LYS cc_start: 0.8629 (tttt) cc_final: 0.8383 (tttp) REVERT: C 144 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7921 (tm-30) REVERT: C 260 GLN cc_start: 0.8149 (tp40) cc_final: 0.7905 (tm-30) REVERT: C 312 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7694 (mppt) REVERT: C 351 GLU cc_start: 0.8242 (tp30) cc_final: 0.7987 (mt-10) REVERT: C 389 SER cc_start: 0.8661 (t) cc_final: 0.8334 (p) REVERT: C 437 ARG cc_start: 0.8237 (mtm110) cc_final: 0.7748 (mtm110) REVERT: C 441 MET cc_start: 0.8413 (mmm) cc_final: 0.8062 (mmm) REVERT: C 496 MET cc_start: 0.8293 (tpp) cc_final: 0.8066 (tpt) REVERT: C 521 TYR cc_start: 0.8224 (t80) cc_final: 0.7928 (t80) REVERT: C 528 MET cc_start: 0.7472 (mmm) cc_final: 0.6766 (pp-130) REVERT: C 549 TRP cc_start: 0.7549 (t-100) cc_final: 0.7194 (t60) REVERT: C 585 LYS cc_start: 0.9035 (mmpt) cc_final: 0.8442 (mtmt) REVERT: C 687 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8246 (mp0) REVERT: C 729 SER cc_start: 0.8467 (m) cc_final: 0.8239 (p) REVERT: C 856 GLN cc_start: 0.8222 (mt0) cc_final: 0.7828 (mm-40) REVERT: C 857 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8422 (ttmm) REVERT: C 874 LYS cc_start: 0.7958 (ttpt) cc_final: 0.7149 (tmmt) REVERT: C 878 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7833 (mm-30) REVERT: C 881 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7378 (mt-10) REVERT: C 885 LYS cc_start: 0.8099 (tttp) cc_final: 0.7595 (tppt) REVERT: C 900 GLU cc_start: 0.7949 (tp30) cc_final: 0.7403 (tm-30) REVERT: D 116 LYS cc_start: 0.8619 (tttt) cc_final: 0.8376 (tttp) REVERT: D 144 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: D 312 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7705 (mppt) REVERT: D 351 GLU cc_start: 0.8236 (tp30) cc_final: 0.7991 (mt-10) REVERT: D 389 SER cc_start: 0.8659 (t) cc_final: 0.8331 (p) REVERT: D 437 ARG cc_start: 0.8236 (mtm110) cc_final: 0.7737 (mtm110) REVERT: D 441 MET cc_start: 0.8400 (mmm) cc_final: 0.8046 (mmm) REVERT: D 468 THR cc_start: 0.4914 (OUTLIER) cc_final: 0.4518 (p) REVERT: D 496 MET cc_start: 0.8291 (tpp) cc_final: 0.8064 (tpt) REVERT: D 521 TYR cc_start: 0.8226 (t80) cc_final: 0.7927 (t80) REVERT: D 528 MET cc_start: 0.7476 (mmm) cc_final: 0.6771 (pp-130) REVERT: D 549 TRP cc_start: 0.7471 (t-100) cc_final: 0.7171 (t60) REVERT: D 585 LYS cc_start: 0.9029 (mmpt) cc_final: 0.8437 (mtmt) REVERT: D 687 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: D 856 GLN cc_start: 0.8219 (mt0) cc_final: 0.7817 (mm-40) REVERT: D 857 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8420 (ttmm) REVERT: D 874 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7144 (tmmt) REVERT: D 878 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7821 (mm-30) REVERT: D 881 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7391 (mt-10) REVERT: D 885 LYS cc_start: 0.8110 (tttp) cc_final: 0.7595 (tppt) REVERT: D 900 GLU cc_start: 0.8029 (tp30) cc_final: 0.7485 (tm-30) outliers start: 111 outliers final: 48 residues processed: 458 average time/residue: 0.6363 time to fit residues: 332.9737 Evaluate side-chains 423 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 363 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 758 ARG Chi-restraints excluded: chain B residue 857 LYS Chi-restraints excluded: chain B residue 887 ILE Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 385 GLN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 857 LYS Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 209 TYR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 365 ARG Chi-restraints excluded: chain D residue 385 GLN Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 558 ILE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 687 GLU Chi-restraints excluded: chain D residue 740 VAL Chi-restraints excluded: chain D residue 758 ARG Chi-restraints excluded: chain D residue 857 LYS Chi-restraints excluded: chain D residue 887 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 84 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 216 optimal weight: 0.0670 chunk 170 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 251 optimal weight: 9.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.143231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.110478 restraints weight = 26146.556| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.04 r_work: 0.3117 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 23976 Z= 0.164 Angle : 0.542 7.952 32402 Z= 0.270 Chirality : 0.040 0.284 3588 Planarity : 0.004 0.054 3960 Dihedral : 11.990 84.641 3556 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.22 % Allowed : 16.69 % Favored : 79.09 % 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: 2.51 (0.16), residues: 2744 helix: 2.54 (0.11), residues: 2016 sheet: None (None), residues: 0 loop : -0.97 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 191 TYR 0.010 0.001 TYR A 579 PHE 0.023 0.001 PHE B 465 TRP 0.015 0.001 TRP C 391 HIS 0.002 0.001 HIS D 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (23964) covalent geometry : angle 0.54203 / 0.27 (32392) SS BOND : angle 0.00000 / 0.00 ( 10) hydrogen bonds : bond 0.04785 / 3.27 ( 1564) hydrogen bonds : angle 3.42788 / 2.48 ( 4524) metal coordination : bond 0.00817 / 0.47 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 378 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8624 (tttt) cc_final: 0.8338 (tttp) REVERT: A 144 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7906 (tm-30) REVERT: A 312 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7615 (mppt) REVERT: A 351 GLU cc_start: 0.8195 (tp30) cc_final: 0.7947 (mt-10) REVERT: A 389 SER cc_start: 0.8618 (t) cc_final: 0.8290 (p) REVERT: A 437 ARG cc_start: 0.8176 (mtm110) cc_final: 0.7728 (mtm110) REVERT: A 441 MET cc_start: 0.8430 (mmm) cc_final: 0.8045 (mmm) REVERT: A 468 THR cc_start: 0.4937 (OUTLIER) cc_final: 0.4531 (p) REVERT: A 549 TRP cc_start: 0.7545 (t-100) cc_final: 0.7242 (t60) REVERT: A 585 LYS cc_start: 0.9041 (mmpt) cc_final: 0.8447 (mtmt) REVERT: A 731 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.6921 (t80) REVERT: A 856 GLN cc_start: 0.8228 (mt0) cc_final: 0.7834 (mm-40) REVERT: A 857 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8424 (ttmm) REVERT: A 874 LYS cc_start: 0.7901 (ttpt) cc_final: 0.7091 (tmmt) REVERT: A 878 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7773 (mm-30) REVERT: A 881 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7462 (mt-10) REVERT: A 885 LYS cc_start: 0.8137 (tttp) cc_final: 0.7606 (tppt) REVERT: B 116 LYS cc_start: 0.8615 (tttt) cc_final: 0.8326 (tttp) REVERT: B 144 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: B 312 LYS cc_start: 0.8122 (mmtt) cc_final: 0.7608 (mppt) REVERT: B 351 GLU cc_start: 0.8220 (tp30) cc_final: 0.7960 (mt-10) REVERT: B 389 SER cc_start: 0.8620 (t) cc_final: 0.8293 (p) REVERT: B 437 ARG cc_start: 0.8183 (mtm110) cc_final: 0.7736 (mtm110) REVERT: B 441 MET cc_start: 0.8424 (mmm) cc_final: 0.8039 (mmm) REVERT: B 468 THR cc_start: 0.4883 (OUTLIER) cc_final: 0.4483 (p) REVERT: B 496 MET cc_start: 0.8350 (tpp) cc_final: 0.8139 (tpt) REVERT: B 505 MET cc_start: 0.8037 (mtt) cc_final: 0.7605 (mtm) REVERT: B 549 TRP cc_start: 0.7563 (t-100) cc_final: 0.7262 (t60) REVERT: B 585 LYS cc_start: 0.9033 (mmpt) cc_final: 0.8448 (mtmt) REVERT: B 687 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8267 (mp0) REVERT: B 731 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7143 (t80) REVERT: B 856 GLN cc_start: 0.8227 (mt0) cc_final: 0.7838 (mm-40) REVERT: B 857 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8434 (ttmm) REVERT: B 874 LYS cc_start: 0.7899 (ttpt) cc_final: 0.7085 (tmmt) REVERT: B 878 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7765 (mm-30) REVERT: B 881 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7444 (mt-10) REVERT: B 885 LYS cc_start: 0.8120 (tttp) cc_final: 0.7605 (tppt) REVERT: C 116 LYS cc_start: 0.8642 (tttt) cc_final: 0.8349 (tttp) REVERT: C 144 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7884 (tm-30) REVERT: C 312 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7618 (mppt) REVERT: C 351 GLU cc_start: 0.8247 (tp30) cc_final: 0.7969 (mt-10) REVERT: C 389 SER cc_start: 0.8621 (t) cc_final: 0.8289 (p) REVERT: C 437 ARG cc_start: 0.8187 (mtm110) cc_final: 0.7738 (mtm110) REVERT: C 441 MET cc_start: 0.8420 (mmm) cc_final: 0.8033 (mmm) REVERT: C 468 THR cc_start: 0.4654 (OUTLIER) cc_final: 0.4303 (p) REVERT: C 496 MET cc_start: 0.8373 (tpp) cc_final: 0.8154 (tpt) REVERT: C 549 TRP cc_start: 0.7542 (t-100) cc_final: 0.7247 (t60) REVERT: C 585 LYS cc_start: 0.9041 (mmpt) cc_final: 0.8454 (mtmt) REVERT: C 638 MET cc_start: 0.7682 (mmp) cc_final: 0.7185 (tpp) REVERT: C 856 GLN cc_start: 0.8250 (mt0) cc_final: 0.7851 (mm-40) REVERT: C 874 LYS cc_start: 0.7924 (ttpt) cc_final: 0.7112 (tmmt) REVERT: C 878 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7783 (mm-30) REVERT: C 881 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7443 (mt-10) REVERT: C 885 LYS cc_start: 0.8098 (tttp) cc_final: 0.7580 (tppt) REVERT: D 116 LYS cc_start: 0.8622 (tttt) cc_final: 0.8329 (tttp) REVERT: D 144 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7892 (tm-30) REVERT: D 312 LYS cc_start: 0.8203 (mmtt) cc_final: 0.7706 (mppt) REVERT: D 351 GLU cc_start: 0.8244 (tp30) cc_final: 0.7971 (mt-10) REVERT: D 389 SER cc_start: 0.8615 (t) cc_final: 0.8284 (p) REVERT: D 437 ARG cc_start: 0.8203 (mtm110) cc_final: 0.7756 (mtm110) REVERT: D 441 MET cc_start: 0.8403 (mmm) cc_final: 0.8018 (mmm) REVERT: D 496 MET cc_start: 0.8371 (tpp) cc_final: 0.8150 (tpt) REVERT: D 549 TRP cc_start: 0.7547 (t-100) cc_final: 0.7244 (t60) REVERT: D 585 LYS cc_start: 0.9016 (mmpt) cc_final: 0.8438 (mtmt) REVERT: D 687 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: D 731 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7301 (t80) REVERT: D 856 GLN cc_start: 0.8243 (mt0) cc_final: 0.7841 (mm-40) REVERT: D 874 LYS cc_start: 0.7901 (ttpt) cc_final: 0.7094 (tmmt) REVERT: D 878 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7738 (mm-30) REVERT: D 881 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7502 (mt-10) REVERT: D 885 LYS cc_start: 0.8121 (tttp) cc_final: 0.7590 (tppt) outliers start: 101 outliers final: 45 residues processed: 448 average time/residue: 0.5738 time to fit residues: 293.9029 Evaluate side-chains 416 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 357 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 575 ASN Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 758 ARG Chi-restraints excluded: chain B residue 857 LYS Chi-restraints excluded: chain B residue 887 ILE Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 385 GLN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain C residue 575 ASN Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 209 TYR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 365 ARG Chi-restraints excluded: chain D residue 385 GLN Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 687 GLU Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 740 VAL Chi-restraints excluded: chain D residue 758 ARG Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 909 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 256 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 174 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 240 optimal weight: 0.0870 chunk 113 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 516 GLN ** A 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 GLN ** B 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 GLN ** C 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 GLN ** D 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.145835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.113826 restraints weight = 26072.595| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.99 r_work: 0.3168 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23976 Z= 0.117 Angle : 0.497 7.992 32402 Z= 0.247 Chirality : 0.038 0.277 3588 Planarity : 0.004 0.052 3960 Dihedral : 11.286 82.839 3556 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.55 % Allowed : 18.53 % Favored : 77.92 % 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: 2.80 (0.16), residues: 2744 helix: 2.76 (0.11), residues: 2024 sheet: None (None), residues: 0 loop : -0.93 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 191 TYR 0.008 0.001 TYR C 579 PHE 0.031 0.001 PHE A 407 TRP 0.011 0.001 TRP C 391 HIS 0.002 0.000 HIS D 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (23964) covalent geometry : angle 0.49675 / 0.25 (32392) SS BOND : angle 0.00000 / 0.00 ( 10) hydrogen bonds : bond 0.04171 / 2.86 ( 1564) hydrogen bonds : angle 3.23770 / 2.33 ( 4524) metal coordination : bond 0.00314 / 0.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 385 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8632 (tttt) cc_final: 0.8405 (tttm) REVERT: A 144 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7860 (tm-30) REVERT: A 312 LYS cc_start: 0.8054 (mmtt) cc_final: 0.7559 (mppt) REVERT: A 351 GLU cc_start: 0.8268 (tp30) cc_final: 0.8025 (mt-10) REVERT: A 395 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8714 (mp) REVERT: A 437 ARG cc_start: 0.8135 (mtm110) cc_final: 0.7757 (mtm110) REVERT: A 441 MET cc_start: 0.8408 (mmm) cc_final: 0.8095 (mmm) REVERT: A 468 THR cc_start: 0.4854 (OUTLIER) cc_final: 0.4493 (p) REVERT: A 528 MET cc_start: 0.7506 (mmm) cc_final: 0.6921 (pp-130) REVERT: A 549 TRP cc_start: 0.7593 (t-100) cc_final: 0.7288 (t60) REVERT: A 585 LYS cc_start: 0.9033 (mmpt) cc_final: 0.8443 (mtmt) REVERT: A 638 MET cc_start: 0.7649 (mmp) cc_final: 0.6622 (ttp) REVERT: A 731 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.6986 (t80) REVERT: A 856 GLN cc_start: 0.8195 (mt0) cc_final: 0.7832 (mm-40) REVERT: A 874 LYS cc_start: 0.7976 (ttpt) cc_final: 0.7204 (tmmt) REVERT: A 878 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7806 (mm-30) REVERT: A 881 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7504 (mt-10) REVERT: A 885 LYS cc_start: 0.8143 (tttp) cc_final: 0.7602 (tppt) REVERT: B 116 LYS cc_start: 0.8642 (tttt) cc_final: 0.8398 (tttp) REVERT: B 144 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: B 312 LYS cc_start: 0.8057 (mmtt) cc_final: 0.7561 (mppt) REVERT: B 351 GLU cc_start: 0.8249 (tp30) cc_final: 0.8030 (mt-10) REVERT: B 395 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8691 (mp) REVERT: B 437 ARG cc_start: 0.8132 (mtm110) cc_final: 0.7732 (mtm110) REVERT: B 441 MET cc_start: 0.8401 (mmm) cc_final: 0.8087 (mmm) REVERT: B 468 THR cc_start: 0.4811 (OUTLIER) cc_final: 0.4483 (p) REVERT: B 496 MET cc_start: 0.8372 (tpp) cc_final: 0.8157 (tpt) REVERT: B 528 MET cc_start: 0.7510 (mmm) cc_final: 0.6920 (pp-130) REVERT: B 549 TRP cc_start: 0.7597 (t-100) cc_final: 0.7301 (t60) REVERT: B 585 LYS cc_start: 0.9037 (mmpt) cc_final: 0.8444 (mtmt) REVERT: B 638 MET cc_start: 0.7657 (mmp) cc_final: 0.6633 (ttp) REVERT: B 856 GLN cc_start: 0.8195 (mt0) cc_final: 0.7831 (mm-40) REVERT: B 874 LYS cc_start: 0.7972 (ttpt) cc_final: 0.7196 (tmmt) REVERT: B 878 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7823 (mm-30) REVERT: B 881 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7499 (mt-10) REVERT: B 885 LYS cc_start: 0.8177 (tttp) cc_final: 0.7612 (tppt) REVERT: C 116 LYS cc_start: 0.8635 (tttt) cc_final: 0.8409 (tttm) REVERT: C 144 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7843 (tm-30) REVERT: C 312 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7549 (mppt) REVERT: C 351 GLU cc_start: 0.8259 (tp30) cc_final: 0.8030 (mt-10) REVERT: C 395 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8709 (mp) REVERT: C 437 ARG cc_start: 0.8129 (mtm110) cc_final: 0.7729 (mtm110) REVERT: C 441 MET cc_start: 0.8406 (mmm) cc_final: 0.8091 (mmm) REVERT: C 468 THR cc_start: 0.4538 (OUTLIER) cc_final: 0.4259 (p) REVERT: C 496 MET cc_start: 0.8385 (tpp) cc_final: 0.8169 (tpt) REVERT: C 528 MET cc_start: 0.7510 (mmm) cc_final: 0.6923 (pp-130) REVERT: C 549 TRP cc_start: 0.7590 (t-100) cc_final: 0.7278 (t60) REVERT: C 585 LYS cc_start: 0.9014 (mmpt) cc_final: 0.8440 (mtmt) REVERT: C 856 GLN cc_start: 0.8240 (mt0) cc_final: 0.7871 (mm-40) REVERT: C 874 LYS cc_start: 0.7969 (ttpt) cc_final: 0.7196 (tmmt) REVERT: C 878 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7829 (mm-30) REVERT: C 881 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7485 (mt-10) REVERT: C 885 LYS cc_start: 0.8168 (tttp) cc_final: 0.7598 (tppt) REVERT: D 116 LYS cc_start: 0.8642 (tttt) cc_final: 0.8398 (tttp) REVERT: D 144 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: D 312 LYS cc_start: 0.8000 (mmtt) cc_final: 0.7512 (mppt) REVERT: D 351 GLU cc_start: 0.8260 (tp30) cc_final: 0.8037 (mt-10) REVERT: D 395 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8691 (mp) REVERT: D 437 ARG cc_start: 0.8134 (mtm110) cc_final: 0.7751 (mtm110) REVERT: D 441 MET cc_start: 0.8403 (mmm) cc_final: 0.8087 (mmm) REVERT: D 496 MET cc_start: 0.8381 (tpp) cc_final: 0.8165 (tpt) REVERT: D 528 MET cc_start: 0.7503 (mmm) cc_final: 0.6913 (pp-130) REVERT: D 549 TRP cc_start: 0.7595 (t-100) cc_final: 0.7293 (t60) REVERT: D 585 LYS cc_start: 0.9029 (mmpt) cc_final: 0.8450 (mtmt) REVERT: D 638 MET cc_start: 0.7656 (mmp) cc_final: 0.7123 (tpp) REVERT: D 731 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7303 (t80) REVERT: D 856 GLN cc_start: 0.8232 (mt0) cc_final: 0.7861 (mm-40) REVERT: D 874 LYS cc_start: 0.7969 (ttpt) cc_final: 0.7195 (tmmt) REVERT: D 878 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7806 (mm-30) REVERT: D 881 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7482 (mt-10) REVERT: D 885 LYS cc_start: 0.8151 (tttp) cc_final: 0.7610 (tppt) outliers start: 85 outliers final: 42 residues processed: 442 average time/residue: 0.6017 time to fit residues: 303.0178 Evaluate side-chains 422 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 367 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 758 ARG Chi-restraints excluded: chain B residue 887 ILE Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 385 GLN Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 209 TYR Chi-restraints excluded: chain D residue 365 ARG Chi-restraints excluded: chain D residue 385 GLN Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 558 ILE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 740 VAL Chi-restraints excluded: chain D residue 758 ARG Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 909 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 186 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 235 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 516 GLN ** A 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 GLN ** B 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 GLN ** C 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 GLN ** D 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.141716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107194 restraints weight = 26241.156| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.16 r_work: 0.3041 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 23976 Z= 0.222 Angle : 0.577 8.243 32402 Z= 0.285 Chirality : 0.042 0.286 3588 Planarity : 0.004 0.055 3960 Dihedral : 11.451 80.721 3556 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.71 % Allowed : 18.61 % Favored : 77.67 % 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: 2.46 (0.16), residues: 2744 helix: 2.51 (0.11), residues: 2024 sheet: None (None), residues: 0 loop : -1.03 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 365 TYR 0.012 0.001 TYR B 579 PHE 0.020 0.002 PHE A 465 TRP 0.017 0.002 TRP C 391 HIS 0.003 0.001 HIS D 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.22 (23964) covalent geometry : angle 0.57741 / 0.29 (32392) SS BOND : angle 0.00000 / 0.00 ( 10) hydrogen bonds : bond 0.05101 / 3.49 ( 1564) hydrogen bonds : angle 3.46369 / 2.50 ( 4524) metal coordination : bond 0.00473 / 0.26 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 374 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8592 (tttt) cc_final: 0.8365 (tttp) REVERT: A 144 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7888 (tm-30) REVERT: A 312 LYS cc_start: 0.8039 (mmtt) cc_final: 0.7525 (mppt) REVERT: A 351 GLU cc_start: 0.8276 (tp30) cc_final: 0.7930 (mt-10) REVERT: A 385 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7471 (pp30) REVERT: A 437 ARG cc_start: 0.8104 (mtm110) cc_final: 0.7584 (mtm110) REVERT: A 441 MET cc_start: 0.8406 (mmm) cc_final: 0.8022 (mmm) REVERT: A 466 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6666 (mp0) REVERT: A 468 THR cc_start: 0.4593 (OUTLIER) cc_final: 0.4237 (p) REVERT: A 528 MET cc_start: 0.7436 (mmm) cc_final: 0.6744 (pp-130) REVERT: A 549 TRP cc_start: 0.7551 (t-100) cc_final: 0.7249 (t60) REVERT: A 585 LYS cc_start: 0.9003 (mmpt) cc_final: 0.8368 (mtmt) REVERT: A 856 GLN cc_start: 0.8220 (mt0) cc_final: 0.7805 (mm-40) REVERT: A 874 LYS cc_start: 0.7700 (ttpt) cc_final: 0.7045 (ttmt) REVERT: A 878 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7746 (mm-30) REVERT: A 881 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7377 (mt-10) REVERT: A 885 LYS cc_start: 0.8132 (tttp) cc_final: 0.7601 (tppt) REVERT: B 116 LYS cc_start: 0.8598 (tttt) cc_final: 0.8320 (tttp) REVERT: B 144 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: B 312 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7539 (mppt) REVERT: B 351 GLU cc_start: 0.8261 (tp30) cc_final: 0.7922 (mt-10) REVERT: B 385 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7475 (pp30) REVERT: B 395 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8653 (mp) REVERT: B 437 ARG cc_start: 0.8102 (mtm110) cc_final: 0.7581 (mtm110) REVERT: B 441 MET cc_start: 0.8404 (mmm) cc_final: 0.8023 (mmm) REVERT: B 466 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6668 (mp0) REVERT: B 468 THR cc_start: 0.4580 (OUTLIER) cc_final: 0.4221 (p) REVERT: B 496 MET cc_start: 0.8252 (tpp) cc_final: 0.8044 (tpt) REVERT: B 528 MET cc_start: 0.7444 (mmm) cc_final: 0.6745 (pp-130) REVERT: B 549 TRP cc_start: 0.7549 (t-100) cc_final: 0.7226 (t60) REVERT: B 585 LYS cc_start: 0.9002 (mmpt) cc_final: 0.8370 (mtmt) REVERT: B 731 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7051 (t80) REVERT: B 856 GLN cc_start: 0.8218 (mt0) cc_final: 0.7806 (mm-40) REVERT: B 874 LYS cc_start: 0.7714 (ttpt) cc_final: 0.7045 (ttmt) REVERT: B 878 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7740 (mm-30) REVERT: B 881 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7374 (mt-10) REVERT: B 885 LYS cc_start: 0.8104 (tttp) cc_final: 0.7577 (tppt) REVERT: C 116 LYS cc_start: 0.8591 (tttt) cc_final: 0.8363 (tttp) REVERT: C 144 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7909 (tm-30) REVERT: C 312 LYS cc_start: 0.8047 (mmtt) cc_final: 0.7533 (mppt) REVERT: C 351 GLU cc_start: 0.8268 (tp30) cc_final: 0.7931 (mt-10) REVERT: C 385 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7471 (pp30) REVERT: C 437 ARG cc_start: 0.8106 (mtm110) cc_final: 0.7589 (mtm110) REVERT: C 441 MET cc_start: 0.8411 (mmm) cc_final: 0.8026 (mmm) REVERT: C 466 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6664 (mp0) REVERT: C 468 THR cc_start: 0.4592 (OUTLIER) cc_final: 0.4245 (p) REVERT: C 496 MET cc_start: 0.8227 (tpp) cc_final: 0.8022 (tpt) REVERT: C 528 MET cc_start: 0.7436 (mmm) cc_final: 0.6740 (pp-130) REVERT: C 549 TRP cc_start: 0.7544 (t-100) cc_final: 0.7240 (t60) REVERT: C 585 LYS cc_start: 0.9019 (mmpt) cc_final: 0.8390 (mtmt) REVERT: C 856 GLN cc_start: 0.8224 (mt0) cc_final: 0.7792 (mm-40) REVERT: C 874 LYS cc_start: 0.7715 (ttpt) cc_final: 0.7046 (ttmt) REVERT: C 878 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7737 (mm-30) REVERT: C 881 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7360 (mt-10) REVERT: C 885 LYS cc_start: 0.8106 (tttp) cc_final: 0.7589 (tppt) REVERT: D 116 LYS cc_start: 0.8602 (tttt) cc_final: 0.8323 (tttp) REVERT: D 144 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7830 (tm-30) REVERT: D 312 LYS cc_start: 0.8013 (mmtt) cc_final: 0.7511 (mppt) REVERT: D 351 GLU cc_start: 0.8272 (tp30) cc_final: 0.7928 (mt-10) REVERT: D 385 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7467 (pp30) REVERT: D 437 ARG cc_start: 0.8104 (mtm110) cc_final: 0.7585 (mtm110) REVERT: D 441 MET cc_start: 0.8407 (mmm) cc_final: 0.8026 (mmm) REVERT: D 466 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6671 (mp0) REVERT: D 468 THR cc_start: 0.4596 (OUTLIER) cc_final: 0.4241 (p) REVERT: D 496 MET cc_start: 0.8263 (tpp) cc_final: 0.8053 (tpt) REVERT: D 528 MET cc_start: 0.7443 (mmm) cc_final: 0.6746 (pp-130) REVERT: D 549 TRP cc_start: 0.7558 (t-100) cc_final: 0.7246 (t60) REVERT: D 585 LYS cc_start: 0.9006 (mmpt) cc_final: 0.8375 (mtmt) REVERT: D 856 GLN cc_start: 0.8227 (mt0) cc_final: 0.7795 (mm-40) REVERT: D 874 LYS cc_start: 0.7707 (ttpt) cc_final: 0.7052 (ttmt) REVERT: D 878 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7752 (mm-30) REVERT: D 881 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7391 (mt-10) REVERT: D 885 LYS cc_start: 0.8132 (tttp) cc_final: 0.7603 (tppt) outliers start: 89 outliers final: 46 residues processed: 433 average time/residue: 0.5984 time to fit residues: 294.1126 Evaluate side-chains 414 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 354 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 575 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 758 ARG Chi-restraints excluded: chain B residue 887 ILE Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 385 GLN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain C residue 575 ASN Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 209 TYR Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 365 ARG Chi-restraints excluded: chain D residue 385 GLN Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 558 ILE Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 740 VAL Chi-restraints excluded: chain D residue 758 ARG Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 909 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 47 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 137 optimal weight: 30.0000 chunk 181 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 264 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 272 optimal weight: 0.0770 chunk 168 optimal weight: 0.8980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 516 GLN ** A 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 GLN ** B 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 GLN ** C 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 GLN D 905 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.144821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.111179 restraints weight = 26321.041| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.16 r_work: 0.3096 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23976 Z= 0.125 Angle : 0.508 8.662 32402 Z= 0.253 Chirality : 0.039 0.282 3588 Planarity : 0.004 0.051 3960 Dihedral : 10.907 83.049 3556 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.26 % Allowed : 18.99 % Favored : 77.75 % 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: 2.74 (0.16), residues: 2744 helix: 2.71 (0.11), residues: 2024 sheet: None (None), residues: 0 loop : -0.95 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 191 TYR 0.009 0.001 TYR B 579 PHE 0.031 0.001 PHE B 407 TRP 0.011 0.001 TRP C 391 HIS 0.002 0.001 HIS D 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (23964) covalent geometry : angle 0.50810 / 0.25 (32392) SS BOND : angle 0.00000 / 0.00 ( 10) hydrogen bonds : bond 0.04318 / 2.96 ( 1564) hydrogen bonds : angle 3.27761 / 2.37 ( 4524) metal coordination : bond 0.00256 / 0.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 369 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8567 (tttt) cc_final: 0.8317 (tttp) REVERT: A 144 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7763 (tm-30) REVERT: A 312 LYS cc_start: 0.8015 (mmtt) cc_final: 0.7487 (mppt) REVERT: A 351 GLU cc_start: 0.8282 (tp30) cc_final: 0.7943 (mt-10) REVERT: A 437 ARG cc_start: 0.8074 (mtm110) cc_final: 0.7699 (mtm110) REVERT: A 441 MET cc_start: 0.8370 (mmm) cc_final: 0.7982 (mmm) REVERT: A 466 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6575 (mp0) REVERT: A 468 THR cc_start: 0.4551 (OUTLIER) cc_final: 0.4227 (p) REVERT: A 549 TRP cc_start: 0.7562 (t-100) cc_final: 0.7249 (t60) REVERT: A 575 ASN cc_start: 0.7804 (OUTLIER) cc_final: 0.7293 (m110) REVERT: A 585 LYS cc_start: 0.9005 (mmpt) cc_final: 0.8473 (mtmt) REVERT: A 856 GLN cc_start: 0.8154 (mt0) cc_final: 0.7722 (mm-40) REVERT: A 874 LYS cc_start: 0.7772 (ttpt) cc_final: 0.6959 (tmmt) REVERT: A 878 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7648 (mm-30) REVERT: A 881 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7448 (mt-10) REVERT: A 885 LYS cc_start: 0.8077 (tttp) cc_final: 0.7495 (tppt) REVERT: B 116 LYS cc_start: 0.8556 (tttt) cc_final: 0.8303 (tttp) REVERT: B 144 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: B 312 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7476 (mppt) REVERT: B 351 GLU cc_start: 0.8271 (tp30) cc_final: 0.7940 (mt-10) REVERT: B 395 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8644 (mp) REVERT: B 437 ARG cc_start: 0.8063 (mtm110) cc_final: 0.7676 (mtm110) REVERT: B 441 MET cc_start: 0.8357 (mmm) cc_final: 0.7972 (mmm) REVERT: B 466 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6575 (mp0) REVERT: B 468 THR cc_start: 0.4539 (OUTLIER) cc_final: 0.4199 (p) REVERT: B 496 MET cc_start: 0.8277 (tpp) cc_final: 0.8066 (tpt) REVERT: B 549 TRP cc_start: 0.7568 (t-100) cc_final: 0.7247 (t60) REVERT: B 575 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7276 (m110) REVERT: B 585 LYS cc_start: 0.9032 (mmpt) cc_final: 0.8511 (mtmt) REVERT: B 728 ASN cc_start: 0.7720 (OUTLIER) cc_final: 0.7057 (m110) REVERT: B 731 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.7076 (t80) REVERT: B 856 GLN cc_start: 0.8138 (mt0) cc_final: 0.7714 (mm-40) REVERT: B 874 LYS cc_start: 0.7770 (ttpt) cc_final: 0.6966 (tmmt) REVERT: B 878 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7664 (mm-30) REVERT: B 881 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7464 (mt-10) REVERT: B 885 LYS cc_start: 0.8061 (tttp) cc_final: 0.7503 (tppt) REVERT: C 116 LYS cc_start: 0.8557 (tttt) cc_final: 0.8308 (tttp) REVERT: C 144 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7803 (tm-30) REVERT: C 312 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7475 (mppt) REVERT: C 351 GLU cc_start: 0.8285 (tp30) cc_final: 0.7934 (mt-10) REVERT: C 441 MET cc_start: 0.8361 (mmm) cc_final: 0.7975 (mmm) REVERT: C 466 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6538 (mp0) REVERT: C 468 THR cc_start: 0.4540 (OUTLIER) cc_final: 0.4208 (p) REVERT: C 496 MET cc_start: 0.8286 (tpp) cc_final: 0.8081 (tpt) REVERT: C 549 TRP cc_start: 0.7555 (t-100) cc_final: 0.7243 (t60) REVERT: C 575 ASN cc_start: 0.7800 (OUTLIER) cc_final: 0.7304 (m110) REVERT: C 585 LYS cc_start: 0.9039 (mmpt) cc_final: 0.8510 (mtmt) REVERT: C 856 GLN cc_start: 0.8138 (mt0) cc_final: 0.7722 (mm-40) REVERT: C 874 LYS cc_start: 0.7774 (ttpt) cc_final: 0.6966 (tmmt) REVERT: C 878 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7662 (mm-30) REVERT: C 881 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7451 (mt-10) REVERT: C 885 LYS cc_start: 0.8057 (tttp) cc_final: 0.7496 (tppt) REVERT: D 116 LYS cc_start: 0.8565 (tttt) cc_final: 0.8309 (tttp) REVERT: D 144 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: D 312 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7482 (mppt) REVERT: D 351 GLU cc_start: 0.8250 (tp30) cc_final: 0.7933 (mt-10) REVERT: D 437 ARG cc_start: 0.8073 (mtm110) cc_final: 0.7699 (mtm110) REVERT: D 441 MET cc_start: 0.8360 (mmm) cc_final: 0.7973 (mmm) REVERT: D 466 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6582 (mp0) REVERT: D 468 THR cc_start: 0.4545 (OUTLIER) cc_final: 0.4217 (p) REVERT: D 496 MET cc_start: 0.8270 (tpp) cc_final: 0.8060 (tpt) REVERT: D 549 TRP cc_start: 0.7561 (t-100) cc_final: 0.7240 (t60) REVERT: D 575 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7299 (m110) REVERT: D 585 LYS cc_start: 0.9009 (mmpt) cc_final: 0.8479 (mtmt) REVERT: D 728 ASN cc_start: 0.7734 (OUTLIER) cc_final: 0.7088 (m110) REVERT: D 731 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7234 (t80) REVERT: D 856 GLN cc_start: 0.8137 (mt0) cc_final: 0.7713 (mm-40) REVERT: D 874 LYS cc_start: 0.7764 (ttpt) cc_final: 0.6959 (tmmt) REVERT: D 878 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7658 (mm-30) REVERT: D 881 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7464 (mt-10) REVERT: D 885 LYS cc_start: 0.8082 (tttp) cc_final: 0.7501 (tppt) outliers start: 78 outliers final: 42 residues processed: 423 average time/residue: 0.6034 time to fit residues: 290.0458 Evaluate side-chains 419 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 360 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 575 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 758 ARG Chi-restraints excluded: chain B residue 887 ILE Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 385 GLN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain C residue 575 ASN Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 209 TYR Chi-restraints excluded: chain D residue 365 ARG Chi-restraints excluded: chain D residue 385 GLN Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 687 GLU Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 740 VAL Chi-restraints excluded: chain D residue 758 ARG Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 909 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 37 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 252 optimal weight: 0.3980 chunk 126 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 516 GLN ** A 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 GLN ** B 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 GLN ** C 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.145353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.110969 restraints weight = 25881.989| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.16 r_work: 0.3092 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23976 Z= 0.132 Angle : 0.518 8.433 32402 Z= 0.256 Chirality : 0.039 0.276 3588 Planarity : 0.004 0.051 3960 Dihedral : 10.609 85.256 3556 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.42 % Allowed : 18.82 % Favored : 77.75 % 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: 2.79 (0.16), residues: 2744 helix: 2.75 (0.11), residues: 2024 sheet: None (None), residues: 0 loop : -0.93 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 609 TYR 0.009 0.001 TYR A 579 PHE 0.009 0.001 PHE C 548 TRP 0.013 0.001 TRP D 391 HIS 0.003 0.001 HIS D 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (23964) covalent geometry : angle 0.51848 / 0.26 (32392) SS BOND : angle 0.00000 / 0.00 ( 10) hydrogen bonds : bond 0.04310 / 2.96 ( 1564) hydrogen bonds : angle 3.24346 / 2.34 ( 4524) metal coordination : bond 0.00205 / 0.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 371 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8542 (tttt) cc_final: 0.8303 (tttp) REVERT: A 144 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: A 312 LYS cc_start: 0.8045 (mmtt) cc_final: 0.7519 (mppt) REVERT: A 351 GLU cc_start: 0.8223 (tp30) cc_final: 0.7870 (mt-10) REVERT: A 441 MET cc_start: 0.8371 (mmm) cc_final: 0.7982 (mmm) REVERT: A 465 PHE cc_start: 0.8004 (m-80) cc_final: 0.7803 (m-80) REVERT: A 466 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6537 (mp0) REVERT: A 549 TRP cc_start: 0.7566 (t-100) cc_final: 0.7244 (t60) REVERT: A 575 ASN cc_start: 0.7755 (OUTLIER) cc_final: 0.7244 (m110) REVERT: A 585 LYS cc_start: 0.8993 (mmpt) cc_final: 0.8452 (mtmt) REVERT: A 687 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8457 (mp0) REVERT: A 856 GLN cc_start: 0.8157 (mt0) cc_final: 0.7730 (mm-40) REVERT: A 874 LYS cc_start: 0.7730 (ttpt) cc_final: 0.6937 (tmmt) REVERT: A 878 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7739 (mm-30) REVERT: A 881 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7411 (mt-10) REVERT: A 885 LYS cc_start: 0.8077 (tttp) cc_final: 0.7551 (tppt) REVERT: B 116 LYS cc_start: 0.8596 (tttt) cc_final: 0.8336 (tttp) REVERT: B 144 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: B 312 LYS cc_start: 0.8005 (mmtt) cc_final: 0.7492 (mppt) REVERT: B 351 GLU cc_start: 0.8212 (tp30) cc_final: 0.7867 (mt-10) REVERT: B 395 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8607 (mp) REVERT: B 441 MET cc_start: 0.8366 (mmm) cc_final: 0.7978 (mmm) REVERT: B 466 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6536 (mp0) REVERT: B 496 MET cc_start: 0.8236 (tpp) cc_final: 0.8024 (tpt) REVERT: B 505 MET cc_start: 0.7972 (mtt) cc_final: 0.7586 (mtm) REVERT: B 549 TRP cc_start: 0.7565 (t-100) cc_final: 0.7243 (t60) REVERT: B 575 ASN cc_start: 0.7799 (OUTLIER) cc_final: 0.7214 (m110) REVERT: B 585 LYS cc_start: 0.8989 (mmpt) cc_final: 0.8451 (mtmt) REVERT: B 728 ASN cc_start: 0.7767 (OUTLIER) cc_final: 0.7134 (m110) REVERT: B 856 GLN cc_start: 0.8161 (mt0) cc_final: 0.7738 (mm-40) REVERT: B 874 LYS cc_start: 0.7734 (ttpt) cc_final: 0.6938 (tmmt) REVERT: B 878 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7699 (mm-30) REVERT: B 881 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7423 (mt-10) REVERT: B 885 LYS cc_start: 0.8092 (tttp) cc_final: 0.7567 (tppt) REVERT: C 116 LYS cc_start: 0.8552 (tttt) cc_final: 0.8315 (tttp) REVERT: C 144 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: C 312 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7483 (mppt) REVERT: C 351 GLU cc_start: 0.8200 (tp30) cc_final: 0.7866 (mt-10) REVERT: C 441 MET cc_start: 0.8363 (mmm) cc_final: 0.7974 (mmm) REVERT: C 466 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6531 (mp0) REVERT: C 496 MET cc_start: 0.8258 (tpp) cc_final: 0.8049 (tpt) REVERT: C 549 TRP cc_start: 0.7568 (t-100) cc_final: 0.7237 (t60) REVERT: C 575 ASN cc_start: 0.7786 (OUTLIER) cc_final: 0.7248 (m110) REVERT: C 585 LYS cc_start: 0.8997 (mmpt) cc_final: 0.8468 (mtmt) REVERT: C 856 GLN cc_start: 0.8168 (mt0) cc_final: 0.7724 (mm-40) REVERT: C 874 LYS cc_start: 0.7745 (ttpt) cc_final: 0.6946 (tmmt) REVERT: C 878 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7748 (mm-30) REVERT: C 881 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7427 (mt-10) REVERT: C 885 LYS cc_start: 0.8086 (tttp) cc_final: 0.7560 (tppt) REVERT: D 116 LYS cc_start: 0.8594 (tttt) cc_final: 0.8331 (tttp) REVERT: D 144 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7806 (tm-30) REVERT: D 312 LYS cc_start: 0.7971 (mmtt) cc_final: 0.7470 (mppt) REVERT: D 351 GLU cc_start: 0.8206 (tp30) cc_final: 0.7867 (mt-10) REVERT: D 441 MET cc_start: 0.8368 (mmm) cc_final: 0.7979 (mmm) REVERT: D 466 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6514 (mp0) REVERT: D 496 MET cc_start: 0.8228 (tpp) cc_final: 0.8014 (tpt) REVERT: D 528 MET cc_start: 0.7437 (mmm) cc_final: 0.6773 (pp-130) REVERT: D 549 TRP cc_start: 0.7571 (t-100) cc_final: 0.7244 (t60) REVERT: D 575 ASN cc_start: 0.7767 (OUTLIER) cc_final: 0.7249 (m110) REVERT: D 585 LYS cc_start: 0.8993 (mmpt) cc_final: 0.8456 (mtmt) REVERT: D 728 ASN cc_start: 0.7778 (OUTLIER) cc_final: 0.7128 (m110) REVERT: D 856 GLN cc_start: 0.8155 (mt0) cc_final: 0.7710 (mm-40) REVERT: D 874 LYS cc_start: 0.7733 (ttpt) cc_final: 0.6941 (tmmt) REVERT: D 878 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7676 (mm-30) REVERT: D 881 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7426 (mt-10) REVERT: D 885 LYS cc_start: 0.8081 (tttp) cc_final: 0.7543 (tppt) outliers start: 82 outliers final: 41 residues processed: 430 average time/residue: 0.5882 time to fit residues: 287.6222 Evaluate side-chains 420 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 367 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 575 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 758 ARG Chi-restraints excluded: chain B residue 887 ILE Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 385 GLN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain C residue 575 ASN Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 209 TYR Chi-restraints excluded: chain D residue 365 ARG Chi-restraints excluded: chain D residue 385 GLN Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 687 GLU Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 740 VAL Chi-restraints excluded: chain D residue 758 ARG Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 909 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 55 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 206 optimal weight: 8.9990 chunk 121 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 245 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 15 optimal weight: 0.4980 chunk 232 optimal weight: 0.9980 chunk 160 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 516 GLN A 905 ASN B 516 GLN ** B 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 GLN ** C 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.146840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112257 restraints weight = 26173.022| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.19 r_work: 0.3112 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23976 Z= 0.118 Angle : 0.511 9.322 32402 Z= 0.252 Chirality : 0.039 0.277 3588 Planarity : 0.004 0.049 3960 Dihedral : 10.260 87.995 3556 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.55 % Allowed : 19.70 % Favored : 77.75 % 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: 2.88 (0.16), residues: 2744 helix: 2.81 (0.11), residues: 2024 sheet: None (None), residues: 0 loop : -0.86 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 101 TYR 0.008 0.001 TYR C 579 PHE 0.032 0.001 PHE B 407 TRP 0.012 0.001 TRP C 391 HIS 0.002 0.000 HIS B 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (23964) covalent geometry : angle 0.51129 / 0.25 (32392) SS BOND : angle 0.00000 / 0.00 ( 10) hydrogen bonds : bond 0.04123 / 2.84 ( 1564) hydrogen bonds : angle 3.22914 / 2.33 ( 4524) metal coordination : bond 0.00145 / 0.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 376 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8514 (tttt) cc_final: 0.8256 (tttp) REVERT: A 144 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7506 (tm-30) REVERT: A 312 LYS cc_start: 0.8003 (mmtt) cc_final: 0.7513 (mppt) REVERT: A 351 GLU cc_start: 0.8189 (tp30) cc_final: 0.7982 (mt-10) REVERT: A 385 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7313 (pt0) REVERT: A 441 MET cc_start: 0.8186 (mmm) cc_final: 0.7829 (mmm) REVERT: A 466 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6600 (mp0) REVERT: A 528 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6617 (pp-130) REVERT: A 549 TRP cc_start: 0.7579 (t-100) cc_final: 0.7276 (t60) REVERT: A 575 ASN cc_start: 0.7738 (OUTLIER) cc_final: 0.7177 (m110) REVERT: A 585 LYS cc_start: 0.8989 (mmpt) cc_final: 0.8475 (mtmt) REVERT: A 687 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8245 (mp0) REVERT: A 856 GLN cc_start: 0.7952 (mt0) cc_final: 0.7593 (mm-40) REVERT: A 874 LYS cc_start: 0.7726 (ttpt) cc_final: 0.6923 (tmmt) REVERT: A 878 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7646 (mm-30) REVERT: A 881 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7125 (mt-10) REVERT: A 885 LYS cc_start: 0.7999 (tttp) cc_final: 0.7436 (tppt) REVERT: B 116 LYS cc_start: 0.8511 (tttt) cc_final: 0.8267 (tttp) REVERT: B 144 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7507 (tm-30) REVERT: B 312 LYS cc_start: 0.7959 (mmtt) cc_final: 0.7485 (mppt) REVERT: B 385 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7313 (pt0) REVERT: B 395 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8584 (mp) REVERT: B 441 MET cc_start: 0.8193 (mmm) cc_final: 0.7779 (mmm) REVERT: B 466 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6598 (mp0) REVERT: B 496 MET cc_start: 0.8088 (tpp) cc_final: 0.7870 (tpt) REVERT: B 505 MET cc_start: 0.7870 (mtt) cc_final: 0.7441 (mtm) REVERT: B 528 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6611 (pp-130) REVERT: B 549 TRP cc_start: 0.7569 (t-100) cc_final: 0.7267 (t60) REVERT: B 575 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7148 (m110) REVERT: B 585 LYS cc_start: 0.8987 (mmpt) cc_final: 0.8475 (mtmt) REVERT: B 728 ASN cc_start: 0.7709 (OUTLIER) cc_final: 0.7048 (m110) REVERT: B 756 GLU cc_start: 0.8187 (pt0) cc_final: 0.7903 (pt0) REVERT: B 856 GLN cc_start: 0.7950 (mt0) cc_final: 0.7593 (mm-40) REVERT: B 874 LYS cc_start: 0.7719 (ttpt) cc_final: 0.6915 (tmmt) REVERT: B 878 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7652 (mm-30) REVERT: B 881 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7158 (mt-10) REVERT: B 885 LYS cc_start: 0.8005 (tttp) cc_final: 0.7443 (tppt) REVERT: C 116 LYS cc_start: 0.8520 (tttt) cc_final: 0.8259 (tttp) REVERT: C 144 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7507 (tm-30) REVERT: C 312 LYS cc_start: 0.7955 (mmtt) cc_final: 0.7483 (mppt) REVERT: C 385 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7319 (pt0) REVERT: C 441 MET cc_start: 0.8182 (mmm) cc_final: 0.7823 (mmm) REVERT: C 466 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6595 (mp0) REVERT: C 496 MET cc_start: 0.8095 (tpp) cc_final: 0.7867 (tpt) REVERT: C 548 PHE cc_start: 0.7659 (t80) cc_final: 0.7315 (t80) REVERT: C 549 TRP cc_start: 0.7570 (t-100) cc_final: 0.7256 (t60) REVERT: C 575 ASN cc_start: 0.7733 (OUTLIER) cc_final: 0.7163 (m110) REVERT: C 585 LYS cc_start: 0.8988 (mmpt) cc_final: 0.8478 (mtmt) REVERT: C 856 GLN cc_start: 0.7960 (mt0) cc_final: 0.7581 (mm-40) REVERT: C 874 LYS cc_start: 0.7722 (ttpt) cc_final: 0.6919 (tmmt) REVERT: C 878 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7647 (mm-30) REVERT: C 881 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7151 (mt-10) REVERT: C 885 LYS cc_start: 0.8002 (tttp) cc_final: 0.7439 (tppt) REVERT: D 116 LYS cc_start: 0.8514 (tttt) cc_final: 0.8269 (tttp) REVERT: D 144 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: D 312 LYS cc_start: 0.7960 (mmtt) cc_final: 0.7491 (mppt) REVERT: D 351 GLU cc_start: 0.8191 (tp30) cc_final: 0.7984 (mt-10) REVERT: D 385 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7310 (pt0) REVERT: D 441 MET cc_start: 0.8189 (mmm) cc_final: 0.7830 (mmm) REVERT: D 466 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6598 (mp0) REVERT: D 496 MET cc_start: 0.8079 (tpp) cc_final: 0.7850 (tpt) REVERT: D 549 TRP cc_start: 0.7581 (t-100) cc_final: 0.7277 (t60) REVERT: D 575 ASN cc_start: 0.7745 (OUTLIER) cc_final: 0.7180 (m110) REVERT: D 585 LYS cc_start: 0.8990 (mmpt) cc_final: 0.8481 (mtmt) REVERT: D 728 ASN cc_start: 0.7704 (OUTLIER) cc_final: 0.7047 (m110) REVERT: D 756 GLU cc_start: 0.8190 (pt0) cc_final: 0.7909 (pt0) REVERT: D 856 GLN cc_start: 0.7946 (mt0) cc_final: 0.7569 (mm-40) REVERT: D 874 LYS cc_start: 0.7722 (ttpt) cc_final: 0.6920 (tmmt) REVERT: D 878 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7651 (mm-30) REVERT: D 881 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7168 (mt-10) REVERT: D 885 LYS cc_start: 0.8006 (tttp) cc_final: 0.7445 (tppt) outliers start: 61 outliers final: 37 residues processed: 419 average time/residue: 0.6213 time to fit residues: 295.9633 Evaluate side-chains 416 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 361 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 575 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 758 ARG Chi-restraints excluded: chain B residue 887 ILE Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 385 GLN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain C residue 575 ASN Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 209 TYR Chi-restraints excluded: chain D residue 365 ARG Chi-restraints excluded: chain D residue 385 GLN Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 687 GLU Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 740 VAL Chi-restraints excluded: chain D residue 758 ARG Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 909 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 159 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 224 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 147 optimal weight: 0.9990 chunk 266 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 210 optimal weight: 0.0050 chunk 29 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 516 GLN B 516 GLN B 905 ASN C 516 GLN C 905 ASN D 516 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.148503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.113979 restraints weight = 25995.013| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.18 r_work: 0.3128 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23976 Z= 0.113 Angle : 0.504 10.167 32402 Z= 0.251 Chirality : 0.038 0.271 3588 Planarity : 0.004 0.048 3960 Dihedral : 9.685 87.483 3556 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.38 % Allowed : 19.99 % Favored : 77.63 % 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: 2.93 (0.16), residues: 2744 helix: 2.85 (0.11), residues: 2032 sheet: None (None), residues: 0 loop : -0.91 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 609 TYR 0.008 0.001 TYR C 579 PHE 0.016 0.001 PHE C 465 TRP 0.013 0.001 TRP A 391 HIS 0.002 0.000 HIS C 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (23964) covalent geometry : angle 0.50399 / 0.25 (32392) SS BOND : angle 0.00000 / 0.00 ( 10) hydrogen bonds : bond 0.03963 / 2.73 ( 1564) hydrogen bonds : angle 3.17095 / 2.29 ( 4524) metal coordination : bond 0.00132 / 0.07 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 384 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8458 (tttt) cc_final: 0.8244 (tttp) REVERT: A 144 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: A 312 LYS cc_start: 0.7991 (mmtt) cc_final: 0.7501 (mppt) REVERT: A 385 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7328 (pt0) REVERT: A 415 ILE cc_start: 0.8162 (mt) cc_final: 0.7960 (mp) REVERT: A 441 MET cc_start: 0.8175 (mmm) cc_final: 0.7813 (mmm) REVERT: A 466 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6636 (mp0) REVERT: A 516 GLN cc_start: 0.8117 (tp40) cc_final: 0.7877 (tp-100) REVERT: A 528 MET cc_start: 0.7260 (tpt) cc_final: 0.6720 (pp-130) REVERT: A 549 TRP cc_start: 0.7549 (t-100) cc_final: 0.7238 (t60) REVERT: A 575 ASN cc_start: 0.7652 (OUTLIER) cc_final: 0.7072 (m110) REVERT: A 585 LYS cc_start: 0.8988 (mmpt) cc_final: 0.8488 (mtmt) REVERT: A 618 GLU cc_start: 0.8038 (tt0) cc_final: 0.7653 (mt-10) REVERT: A 687 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8309 (pm20) REVERT: A 696 ASN cc_start: 0.7979 (t0) cc_final: 0.7530 (p0) REVERT: A 856 GLN cc_start: 0.7932 (mt0) cc_final: 0.7584 (mm-40) REVERT: A 874 LYS cc_start: 0.7692 (ttpt) cc_final: 0.7068 (ttmt) REVERT: A 878 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7644 (mm-30) REVERT: A 881 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7118 (mt-10) REVERT: A 885 LYS cc_start: 0.8011 (tttp) cc_final: 0.7437 (tppt) REVERT: B 144 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7491 (tm-30) REVERT: B 312 LYS cc_start: 0.7936 (mmtt) cc_final: 0.7464 (mppt) REVERT: B 385 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7327 (pt0) REVERT: B 395 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8602 (mp) REVERT: B 415 ILE cc_start: 0.8157 (mt) cc_final: 0.7956 (mp) REVERT: B 441 MET cc_start: 0.8146 (mmm) cc_final: 0.7782 (mmm) REVERT: B 466 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6642 (mp0) REVERT: B 496 MET cc_start: 0.8081 (tpp) cc_final: 0.7852 (tpt) REVERT: B 505 MET cc_start: 0.7896 (mtt) cc_final: 0.7466 (mtm) REVERT: B 516 GLN cc_start: 0.8117 (tp40) cc_final: 0.7879 (tp-100) REVERT: B 528 MET cc_start: 0.7250 (tpt) cc_final: 0.6716 (pp-130) REVERT: B 548 PHE cc_start: 0.7647 (t80) cc_final: 0.7306 (t80) REVERT: B 549 TRP cc_start: 0.7596 (t-100) cc_final: 0.7267 (t60) REVERT: B 575 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.7034 (m110) REVERT: B 585 LYS cc_start: 0.8975 (mmpt) cc_final: 0.8484 (mtmt) REVERT: B 618 GLU cc_start: 0.8019 (tt0) cc_final: 0.7622 (mt-10) REVERT: B 687 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8233 (pm20) REVERT: B 696 ASN cc_start: 0.7981 (t0) cc_final: 0.7500 (p0) REVERT: B 756 GLU cc_start: 0.8070 (pt0) cc_final: 0.7786 (pt0) REVERT: B 856 GLN cc_start: 0.7911 (mt0) cc_final: 0.7558 (mm-40) REVERT: B 874 LYS cc_start: 0.7681 (ttpt) cc_final: 0.6879 (tmmt) REVERT: B 878 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7649 (mm-30) REVERT: B 881 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7120 (mt-10) REVERT: B 885 LYS cc_start: 0.7987 (tttp) cc_final: 0.7416 (tppt) REVERT: C 116 LYS cc_start: 0.8465 (tttt) cc_final: 0.8252 (tttp) REVERT: C 144 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7492 (tm-30) REVERT: C 312 LYS cc_start: 0.7934 (mmtt) cc_final: 0.7461 (mppt) REVERT: C 385 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7334 (pt0) REVERT: C 415 ILE cc_start: 0.8163 (mt) cc_final: 0.7962 (mp) REVERT: C 441 MET cc_start: 0.8169 (mmm) cc_final: 0.7811 (mmm) REVERT: C 466 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6632 (mp0) REVERT: C 496 MET cc_start: 0.8089 (tpp) cc_final: 0.7860 (tpt) REVERT: C 516 GLN cc_start: 0.8129 (tp40) cc_final: 0.7888 (tp-100) REVERT: C 528 MET cc_start: 0.7244 (tpt) cc_final: 0.6704 (pp-130) REVERT: C 549 TRP cc_start: 0.7588 (t-100) cc_final: 0.7283 (t60) REVERT: C 575 ASN cc_start: 0.7627 (OUTLIER) cc_final: 0.7077 (m110) REVERT: C 585 LYS cc_start: 0.8981 (mmpt) cc_final: 0.8489 (mtmt) REVERT: C 618 GLU cc_start: 0.8031 (tt0) cc_final: 0.7620 (mt-10) REVERT: C 638 MET cc_start: 0.7450 (mmp) cc_final: 0.6880 (OUTLIER) REVERT: C 696 ASN cc_start: 0.7980 (t0) cc_final: 0.7541 (p0) REVERT: C 856 GLN cc_start: 0.7909 (mt0) cc_final: 0.7542 (mm-40) REVERT: C 874 LYS cc_start: 0.7686 (ttpt) cc_final: 0.7053 (ttmt) REVERT: C 878 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7696 (mm-30) REVERT: C 881 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7150 (mt-10) REVERT: C 885 LYS cc_start: 0.7986 (tttp) cc_final: 0.7415 (tppt) REVERT: D 144 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7488 (tm-30) REVERT: D 312 LYS cc_start: 0.7903 (mmtt) cc_final: 0.7446 (mppt) REVERT: D 385 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7323 (pt0) REVERT: D 415 ILE cc_start: 0.8161 (mt) cc_final: 0.7960 (mp) REVERT: D 441 MET cc_start: 0.8173 (mmm) cc_final: 0.7814 (mmm) REVERT: D 466 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6629 (mp0) REVERT: D 496 MET cc_start: 0.8086 (tpp) cc_final: 0.7856 (tpt) REVERT: D 516 GLN cc_start: 0.8135 (tp40) cc_final: 0.7880 (tp-100) REVERT: D 528 MET cc_start: 0.7238 (tpt) cc_final: 0.6700 (pp-130) REVERT: D 548 PHE cc_start: 0.7565 (t80) cc_final: 0.7250 (t80) REVERT: D 549 TRP cc_start: 0.7608 (t-100) cc_final: 0.7276 (t60) REVERT: D 575 ASN cc_start: 0.7650 (OUTLIER) cc_final: 0.7071 (m110) REVERT: D 585 LYS cc_start: 0.8985 (mmpt) cc_final: 0.8488 (mtmt) REVERT: D 687 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8233 (pm20) REVERT: D 696 ASN cc_start: 0.7992 (t0) cc_final: 0.7548 (p0) REVERT: D 756 GLU cc_start: 0.8125 (pt0) cc_final: 0.7851 (pt0) REVERT: D 856 GLN cc_start: 0.7925 (mt0) cc_final: 0.7568 (mm-40) REVERT: D 874 LYS cc_start: 0.7690 (ttpt) cc_final: 0.7065 (ttmt) REVERT: D 878 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7649 (mm-30) REVERT: D 881 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7134 (mt-10) REVERT: D 885 LYS cc_start: 0.7992 (tttp) cc_final: 0.7425 (tppt) outliers start: 57 outliers final: 27 residues processed: 428 average time/residue: 0.6394 time to fit residues: 311.5929 Evaluate side-chains 407 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 365 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 575 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 887 ILE Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 385 GLN Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain C residue 575 ASN Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 209 TYR Chi-restraints excluded: chain D residue 365 ARG Chi-restraints excluded: chain D residue 385 GLN Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 687 GLU Chi-restraints excluded: chain D residue 740 VAL Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 909 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 261 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 267 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 214 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 234 optimal weight: 0.2980 chunk 262 optimal weight: 3.9990 chunk 203 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.148072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.113388 restraints weight = 25949.251| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.19 r_work: 0.3123 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23976 Z= 0.124 Angle : 0.527 10.065 32402 Z= 0.259 Chirality : 0.039 0.268 3588 Planarity : 0.004 0.049 3960 Dihedral : 9.336 83.521 3540 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.55 % Allowed : 20.53 % Favored : 76.92 % 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: 2.96 (0.16), residues: 2744 helix: 2.85 (0.11), residues: 2024 sheet: None (None), residues: 0 loop : -0.79 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 609 TYR 0.009 0.001 TYR D 579 PHE 0.036 0.001 PHE D 407 TRP 0.013 0.001 TRP A 391 HIS 0.002 0.000 HIS C 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (23964) covalent geometry : angle 0.52728 / 0.26 (32392) SS BOND : angle 0.00000 / 0.00 ( 10) hydrogen bonds : bond 0.04022 / 2.77 ( 1564) hydrogen bonds : angle 3.19391 / 2.31 ( 4524) metal coordination : bond 0.00141 / 0.08 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7959.40 seconds wall clock time: 136 minutes 11.36 seconds (8171.36 seconds total)