Starting phenix.real_space_refine on Thu Mar 5 00:24:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vxk_21442/03_2026/6vxk_21442.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vxk_21442/03_2026/6vxk_21442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vxk_21442/03_2026/6vxk_21442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vxk_21442/03_2026/6vxk_21442.map" model { file = "/net/cci-nas-00/data/ceres_data/6vxk_21442/03_2026/6vxk_21442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vxk_21442/03_2026/6vxk_21442.cif" } resolution = 3.1 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 10988 2.51 5 N 2960 2.21 5 O 3372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17418 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3022 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 361} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5561 Classifications: {'peptide': 747} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 714} Chain breaks: 12 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 5, 'HIS:plan': 3, 'GLU:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 4, 'TYR:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 132 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Restraints were copied for chains: C, D Time building chain proxies: 5.38, per 1000 atoms: 0.31 Number of scatterers: 17418 At special positions: 0 Unit cell: (202.86, 101.844, 141.588, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 3372 8.00 N 2960 7.00 C 10988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 85 " distance=2.03 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 286 " distance=2.02 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 255 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 87 " distance=2.04 Simple disulfide: pdb=" SG CYS B 156 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 354 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 412 " - pdb=" SG CYS B 703 " distance=2.04 Simple disulfide: pdb=" SG CYS B 455 " - pdb=" SG CYS B 472 " distance=2.03 Simple disulfide: pdb=" SG CYS B 461 " - pdb=" SG CYS B 506 " distance=2.02 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 481 " distance=2.03 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 487 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 756 " - pdb=" SG CYS B 835 " distance=2.03 Simple disulfide: pdb=" SG CYS B 801 " - pdb=" SG CYS B 806 " distance=2.04 Simple disulfide: pdb=" SG CYS B 891 " - pdb=" SG CYS B 907 " distance=2.03 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 85 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 286 " distance=2.02 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 255 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 87 " distance=2.04 Simple disulfide: pdb=" SG CYS D 156 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 226 " - pdb=" SG CYS D 354 " distance=2.03 Simple disulfide: pdb=" SG CYS D 283 " - pdb=" SG CYS D 329 " distance=2.03 Simple disulfide: pdb=" SG CYS D 412 " - pdb=" SG CYS D 703 " distance=2.04 Simple disulfide: pdb=" SG CYS D 455 " - pdb=" SG CYS D 472 " distance=2.03 Simple disulfide: pdb=" SG CYS D 461 " - pdb=" SG CYS D 506 " distance=2.02 Simple disulfide: pdb=" SG CYS D 464 " - pdb=" SG CYS D 481 " distance=2.03 Simple disulfide: pdb=" SG CYS D 475 " - pdb=" SG CYS D 487 " distance=2.03 Simple disulfide: pdb=" SG CYS D 734 " - pdb=" SG CYS D 742 " distance=2.03 Simple disulfide: pdb=" SG CYS D 756 " - pdb=" SG CYS D 835 " distance=2.03 Simple disulfide: pdb=" SG CYS D 801 " - pdb=" SG CYS D 806 " distance=2.04 Simple disulfide: pdb=" SG CYS D 891 " - pdb=" SG CYS D 907 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 53 " " NAG B1601 " - " ASN B 141 " " NAG B1602 " - " ASN B 241 " " NAG B1603 " - " ASN B 149 " " NAG B1604 " - " ASN B 252 " " NAG B1605 " - " ASN B 86 " " NAG B1606 " - " ASN B 715 " " NAG B1607 " - " ASN B 771 " " NAG B1608 " - " ASN B 871 " " NAG C 501 " - " ASN C 53 " " NAG D1601 " - " ASN D 141 " " NAG D1602 " - " ASN D 241 " " NAG D1603 " - " ASN D 149 " " NAG D1604 " - " ASN D 252 " " NAG D1605 " - " ASN D 86 " " NAG D1606 " - " ASN D 715 " " NAG D1607 " - " ASN D 771 " " NAG D1608 " - " ASN D 871 " Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 802.3 milliseconds 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4180 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 50 sheets defined 5.2% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.715A pdb=" N SER A 204 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N HIS A 205 " --> pdb=" O LEU A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 201 through 205' Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 333 through 340 Processing helix chain 'B' and resid 460 through 466 removed outlier: 3.547A pdb=" N CYS B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 494 No H-bonds generated for 'chain 'B' and resid 492 through 494' Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.747A pdb=" N CYS B 506 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 875 No H-bonds generated for 'chain 'B' and resid 873 through 875' Processing helix chain 'C' and resid 201 through 205 removed outlier: 3.716A pdb=" N SER C 204 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N HIS C 205 " --> pdb=" O LEU C 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 201 through 205' Processing helix chain 'C' and resid 259 through 269 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'D' and resid 333 through 340 Processing helix chain 'D' and resid 460 through 466 removed outlier: 3.547A pdb=" N CYS D 464 " --> pdb=" O SER D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 494 No H-bonds generated for 'chain 'D' and resid 492 through 494' Processing helix chain 'D' and resid 502 through 506 removed outlier: 3.747A pdb=" N CYS D 506 " --> pdb=" O ALA D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 873 through 875 No H-bonds generated for 'chain 'D' and resid 873 through 875' Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 32 Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 removed outlier: 6.365A pdb=" N ILE A 64 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR A 78 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 111 through 113 Processing sheet with id=AA5, first strand: chain 'A' and resid 157 through 162 removed outlier: 7.148A pdb=" N LYS A 212 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASP A 309 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU A 214 " --> pdb=" O ASP A 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 217 through 218 removed outlier: 4.356A pdb=" N CYS A 217 " --> pdb=" O TYR A 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 234 removed outlier: 6.765A pdb=" N PHE A 244 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER A 230 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR A 242 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA A 232 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE A 240 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 327 through 332 Processing sheet with id=AA9, first strand: chain 'B' and resid 39 through 41 removed outlier: 3.857A pdb=" N VAL B 430 " --> pdb=" O TYR B 440 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.605A pdb=" N SER B 77 " --> pdb=" O GLN B 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 108 through 112 Processing sheet with id=AB3, first strand: chain 'B' and resid 162 through 169 removed outlier: 4.957A pdb=" N ALA B 204 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLY B 221 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 11.957A pdb=" N ASP B 209 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 12.127A pdb=" N GLU B 219 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 231 through 234 Processing sheet with id=AB5, first strand: chain 'B' and resid 231 through 234 removed outlier: 6.290A pdb=" N ALA B 268 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE B 275 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL B 363 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER B 280 " --> pdb=" O VAL B 363 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 293 through 300 removed outlier: 6.511A pdb=" N VAL B 309 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER B 297 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA B 307 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU B 299 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL B 305 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 378 through 383 removed outlier: 6.435A pdb=" N LYS B 401 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N VAL B 415 " --> pdb=" O LYS B 401 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 480 through 482 Processing sheet with id=AB9, first strand: chain 'B' and resid 508 through 510 Processing sheet with id=AC1, first strand: chain 'B' and resid 546 through 548 Processing sheet with id=AC2, first strand: chain 'B' and resid 663 through 668 removed outlier: 3.729A pdb=" N TYR B 663 " --> pdb=" O ALA B 685 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR B 683 " --> pdb=" O LYS B 665 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE B 667 " --> pdb=" O ILE B 681 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE B 681 " --> pdb=" O ILE B 667 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N PHE B 721 " --> pdb=" O ASN B 679 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE B 681 " --> pdb=" O MET B 719 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N MET B 719 " --> pdb=" O ILE B 681 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 671 through 673 removed outlier: 6.909A pdb=" N VAL B 672 " --> pdb=" O ILE B 751 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER B 744 " --> pdb=" O ILE B 735 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE B 735 " --> pdb=" O SER B 744 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 746 " --> pdb=" O VAL B 733 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 756 through 759 removed outlier: 3.630A pdb=" N GLY B 807 " --> pdb=" O TYR B 800 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 763 through 765 removed outlier: 5.140A pdb=" N TYR B 832 " --> pdb=" O VAL B 828 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL B 828 " --> pdb=" O TYR B 832 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP B 834 " --> pdb=" O LEU B 826 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU B 826 " --> pdb=" O ASP B 834 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLY B 836 " --> pdb=" O VAL B 824 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N VAL B 824 " --> pdb=" O GLY B 836 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 846 through 849 Processing sheet with id=AC7, first strand: chain 'B' and resid 877 through 880 Processing sheet with id=AC8, first strand: chain 'C' and resid 14 through 19 Processing sheet with id=AC9, first strand: chain 'C' and resid 26 through 32 Processing sheet with id=AD1, first strand: chain 'C' and resid 63 through 66 removed outlier: 6.365A pdb=" N ILE C 64 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR C 78 " --> pdb=" O ILE C 64 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 111 through 113 Processing sheet with id=AD3, first strand: chain 'C' and resid 157 through 162 removed outlier: 7.148A pdb=" N LYS C 212 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP C 309 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU C 214 " --> pdb=" O ASP C 309 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 217 through 218 removed outlier: 4.357A pdb=" N CYS C 217 " --> pdb=" O TYR C 224 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 226 through 234 removed outlier: 6.766A pdb=" N PHE C 244 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER C 230 " --> pdb=" O TYR C 242 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR C 242 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA C 232 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE C 240 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 327 through 332 Processing sheet with id=AD7, first strand: chain 'D' and resid 39 through 41 removed outlier: 3.857A pdb=" N VAL D 430 " --> pdb=" O TYR D 440 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 48 through 51 removed outlier: 3.605A pdb=" N SER D 77 " --> pdb=" O GLN D 67 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 108 through 112 Processing sheet with id=AE1, first strand: chain 'D' and resid 162 through 169 removed outlier: 4.957A pdb=" N ALA D 204 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLY D 221 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 11.957A pdb=" N ASP D 209 " --> pdb=" O GLU D 219 " (cutoff:3.500A) removed outlier: 12.127A pdb=" N GLU D 219 " --> pdb=" O ASP D 209 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 231 through 234 Processing sheet with id=AE3, first strand: chain 'D' and resid 231 through 234 removed outlier: 6.290A pdb=" N ALA D 268 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE D 275 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL D 363 " --> pdb=" O GLN D 278 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER D 280 " --> pdb=" O VAL D 363 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 293 through 300 removed outlier: 6.512A pdb=" N VAL D 309 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER D 297 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA D 307 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU D 299 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL D 305 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 378 through 383 removed outlier: 6.435A pdb=" N LYS D 401 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL D 415 " --> pdb=" O LYS D 401 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 480 through 482 Processing sheet with id=AE7, first strand: chain 'D' and resid 508 through 510 Processing sheet with id=AE8, first strand: chain 'D' and resid 546 through 548 Processing sheet with id=AE9, first strand: chain 'D' and resid 663 through 668 removed outlier: 3.729A pdb=" N TYR D 663 " --> pdb=" O ALA D 685 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR D 683 " --> pdb=" O LYS D 665 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE D 667 " --> pdb=" O ILE D 681 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE D 681 " --> pdb=" O ILE D 667 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N PHE D 721 " --> pdb=" O ASN D 679 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE D 681 " --> pdb=" O MET D 719 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N MET D 719 " --> pdb=" O ILE D 681 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 671 through 673 removed outlier: 6.909A pdb=" N VAL D 672 " --> pdb=" O ILE D 751 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER D 744 " --> pdb=" O ILE D 735 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE D 735 " --> pdb=" O SER D 744 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY D 746 " --> pdb=" O VAL D 733 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 756 through 759 removed outlier: 3.630A pdb=" N GLY D 807 " --> pdb=" O TYR D 800 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 763 through 765 removed outlier: 5.140A pdb=" N TYR D 832 " --> pdb=" O VAL D 828 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL D 828 " --> pdb=" O TYR D 832 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ASP D 834 " --> pdb=" O LEU D 826 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU D 826 " --> pdb=" O ASP D 834 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLY D 836 " --> pdb=" O VAL D 824 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL D 824 " --> pdb=" O GLY D 836 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 846 through 849 Processing sheet with id=AF5, first strand: chain 'D' and resid 877 through 880 568 hydrogen bonds defined for protein. 1440 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.42 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5558 1.33 - 1.45: 3598 1.45 - 1.58: 8484 1.58 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 17764 Sorted by residual: bond pdb=" C ILE A 311 " pdb=" N LYS A 312 " ideal model delta sigma weight residual 1.331 1.243 0.088 2.07e-02 2.33e+03 1.81e+01 bond pdb=" C ILE C 311 " pdb=" N LYS C 312 " ideal model delta sigma weight residual 1.331 1.243 0.088 2.07e-02 2.33e+03 1.79e+01 bond pdb=" CA ARG C 368 " pdb=" CB ARG C 368 " ideal model delta sigma weight residual 1.526 1.480 0.046 1.76e-02 3.23e+03 6.73e+00 bond pdb=" CA ARG A 368 " pdb=" CB ARG A 368 " ideal model delta sigma weight residual 1.526 1.481 0.045 1.76e-02 3.23e+03 6.62e+00 bond pdb=" CA SER C 252 " pdb=" CB SER C 252 " ideal model delta sigma weight residual 1.536 1.488 0.047 2.08e-02 2.31e+03 5.18e+00 ... (remaining 17759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 23607 2.35 - 4.71: 453 4.71 - 7.06: 42 7.06 - 9.42: 6 9.42 - 11.77: 2 Bond angle restraints: 24110 Sorted by residual: angle pdb=" C ASN B 411 " pdb=" N CYS B 412 " pdb=" CA CYS B 412 " ideal model delta sigma weight residual 120.67 112.83 7.84 1.34e+00 5.57e-01 3.43e+01 angle pdb=" C ASN D 411 " pdb=" N CYS D 412 " pdb=" CA CYS D 412 " ideal model delta sigma weight residual 120.67 112.83 7.84 1.34e+00 5.57e-01 3.43e+01 angle pdb=" CA CYS D 806 " pdb=" CB CYS D 806 " pdb=" SG CYS D 806 " ideal model delta sigma weight residual 114.40 126.17 -11.77 2.30e+00 1.89e-01 2.62e+01 angle pdb=" CA CYS B 806 " pdb=" CB CYS B 806 " pdb=" SG CYS B 806 " ideal model delta sigma weight residual 114.40 126.13 -11.73 2.30e+00 1.89e-01 2.60e+01 angle pdb=" N CYS D 801 " pdb=" CA CYS D 801 " pdb=" C CYS D 801 " ideal model delta sigma weight residual 109.52 117.32 -7.80 1.55e+00 4.16e-01 2.53e+01 ... (remaining 24105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 9612 17.70 - 35.39: 1032 35.39 - 53.09: 216 53.09 - 70.79: 46 70.79 - 88.49: 16 Dihedral angle restraints: 10922 sinusoidal: 4430 harmonic: 6492 Sorted by residual: dihedral pdb=" CB CYS D 801 " pdb=" SG CYS D 801 " pdb=" SG CYS D 806 " pdb=" CB CYS D 806 " ideal model delta sinusoidal sigma weight residual 93.00 4.51 88.49 1 1.00e+01 1.00e-02 9.35e+01 dihedral pdb=" CB CYS B 801 " pdb=" SG CYS B 801 " pdb=" SG CYS B 806 " pdb=" CB CYS B 806 " ideal model delta sinusoidal sigma weight residual 93.00 4.53 88.47 1 1.00e+01 1.00e-02 9.34e+01 dihedral pdb=" CB CYS B 156 " pdb=" SG CYS B 156 " pdb=" SG CYS B 194 " pdb=" CB CYS B 194 " ideal model delta sinusoidal sigma weight residual -86.00 -169.90 83.90 1 1.00e+01 1.00e-02 8.58e+01 ... (remaining 10919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2372 0.076 - 0.152: 411 0.152 - 0.228: 11 0.228 - 0.304: 4 0.304 - 0.380: 2 Chirality restraints: 2800 Sorted by residual: chirality pdb=" C1 NAG D1608 " pdb=" ND2 ASN D 871 " pdb=" C2 NAG D1608 " pdb=" O5 NAG D1608 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C1 NAG B1608 " pdb=" ND2 ASN B 871 " pdb=" C2 NAG B1608 " pdb=" O5 NAG B1608 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C1 NAG B1603 " pdb=" ND2 ASN B 149 " pdb=" C2 NAG B1603 " pdb=" O5 NAG B1603 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 2797 not shown) Planarity restraints: 3086 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 246 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO D 247 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 247 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 247 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 246 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO B 247 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 247 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 247 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 322 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO D 323 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 323 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 323 " -0.024 5.00e-02 4.00e+02 ... (remaining 3083 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 814 2.68 - 3.23: 16847 3.23 - 3.79: 27515 3.79 - 4.34: 36152 4.34 - 4.90: 62003 Nonbonded interactions: 143331 Sorted by model distance: nonbonded pdb=" O TRP B 175 " pdb=" OG1 THR B 210 " model vdw 2.122 3.040 nonbonded pdb=" O TRP D 175 " pdb=" OG1 THR D 210 " model vdw 2.122 3.040 nonbonded pdb=" O THR A 73 " pdb=" OG1 THR A 73 " model vdw 2.139 3.040 nonbonded pdb=" O THR C 73 " pdb=" OG1 THR C 73 " model vdw 2.139 3.040 nonbonded pdb=" OE2 GLU A 24 " pdb=" OH TYR A 45 " model vdw 2.160 3.040 ... (remaining 143326 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 'C' } ncs_group { reference = chain 'B' 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: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.450 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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 : 0.011 0.088 17816 Z= 0.507 Angle : 0.876 11.770 24232 Z= 0.472 Chirality : 0.053 0.380 2800 Planarity : 0.004 0.047 3068 Dihedral : 14.805 87.569 6640 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 8.05 % Allowed : 17.01 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -3.69 (0.15), residues: 2198 helix: -2.73 (0.43), residues: 96 sheet: -1.59 (0.17), residues: 762 loop : -3.11 (0.13), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 222 TYR 0.016 0.002 TYR A 351 PHE 0.020 0.002 PHE C 344 TRP 0.020 0.002 TRP D 765 HIS 0.006 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.01131 (17764) covalent geometry : angle 0.84119 (24110) SS BOND : bond 0.00451 ( 34) SS BOND : angle 2.85444 ( 68) hydrogen bonds : bond 0.10870 ( 560) hydrogen bonds : angle 8.03152 ( 1440) link_NAG-ASN : bond 0.00722 ( 18) link_NAG-ASN : angle 4.24179 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 69 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 GLN cc_start: 0.7858 (pt0) cc_final: 0.7623 (pp30) REVERT: B 113 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7947 (ttm-80) REVERT: B 730 MET cc_start: 0.8480 (ttm) cc_final: 0.8057 (ttm) REVERT: B 760 PHE cc_start: 0.7387 (m-80) cc_final: 0.7078 (t80) REVERT: D 113 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.7954 (ttm-80) REVERT: D 730 MET cc_start: 0.8484 (ttm) cc_final: 0.8060 (ttm) REVERT: D 760 PHE cc_start: 0.7394 (m-80) cc_final: 0.7080 (t80) outliers start: 149 outliers final: 95 residues processed: 208 average time/residue: 0.1088 time to fit residues: 37.5519 Evaluate side-chains 153 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 56 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 741 ASN Chi-restraints excluded: chain B residue 765 TRP Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 49 ASN Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 683 THR Chi-restraints excluded: chain D residue 741 ASN Chi-restraints excluded: chain D residue 765 TRP Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 929 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 30.0000 chunk 200 optimal weight: 7.9990 chunk 212 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 264 HIS A 295 HIS B 218 GLN B 458 HIS B 670 GLN B 709 GLN B 718 HIS ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN B 829 GLN C 80 ASN C 264 HIS C 295 HIS D 218 GLN D 458 HIS D 670 GLN D 709 GLN D 718 HIS ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 794 ASN D 829 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.078031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.052332 restraints weight = 53316.927| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.20 r_work: 0.2853 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17816 Z= 0.145 Angle : 0.652 10.660 24232 Z= 0.327 Chirality : 0.047 0.320 2800 Planarity : 0.004 0.040 3068 Dihedral : 8.406 57.686 2934 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.00 % Allowed : 19.76 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.85 (0.16), residues: 2198 helix: -1.74 (0.53), residues: 110 sheet: -1.08 (0.18), residues: 780 loop : -2.53 (0.15), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 291 TYR 0.014 0.001 TYR C 351 PHE 0.015 0.001 PHE A 344 TRP 0.006 0.001 TRP D 240 HIS 0.002 0.001 HIS C 114 Details of bonding type rmsd covalent geometry : bond 0.00328 (17764) covalent geometry : angle 0.61684 (24110) SS BOND : bond 0.00459 ( 34) SS BOND : angle 2.33335 ( 68) hydrogen bonds : bond 0.03518 ( 560) hydrogen bonds : angle 6.78838 ( 1440) link_NAG-ASN : bond 0.00748 ( 18) link_NAG-ASN : angle 3.73668 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 65 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLN cc_start: 0.8958 (pm20) cc_final: 0.8688 (pm20) REVERT: A 244 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8204 (t80) REVERT: A 316 GLN cc_start: 0.8446 (pp30) cc_final: 0.8186 (pp30) REVERT: A 337 HIS cc_start: 0.7930 (m-70) cc_final: 0.7684 (m-70) REVERT: A 359 GLN cc_start: 0.8129 (pt0) cc_final: 0.7771 (pp30) REVERT: B 523 MET cc_start: 0.7660 (mmp) cc_final: 0.7438 (mmp) REVERT: B 730 MET cc_start: 0.8476 (ttm) cc_final: 0.8187 (ttp) REVERT: B 760 PHE cc_start: 0.7466 (m-80) cc_final: 0.7152 (t80) REVERT: B 800 TYR cc_start: 0.6205 (t80) cc_final: 0.6002 (t80) REVERT: C 105 GLN cc_start: 0.8889 (pm20) cc_final: 0.8534 (pm20) REVERT: C 244 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8201 (t80) REVERT: C 337 HIS cc_start: 0.8345 (m-70) cc_final: 0.7982 (m-70) REVERT: C 359 GLN cc_start: 0.7890 (pp30) cc_final: 0.7534 (pp30) REVERT: D 523 MET cc_start: 0.7658 (mmp) cc_final: 0.7433 (mmp) REVERT: D 730 MET cc_start: 0.8443 (ttm) cc_final: 0.8154 (ttp) REVERT: D 760 PHE cc_start: 0.7460 (m-80) cc_final: 0.7150 (t80) REVERT: D 800 TYR cc_start: 0.6214 (t80) cc_final: 0.6011 (t80) outliers start: 74 outliers final: 44 residues processed: 131 average time/residue: 0.1325 time to fit residues: 26.9631 Evaluate side-chains 103 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 57 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 765 TRP Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 527 PHE Chi-restraints excluded: chain D residue 765 TRP Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 929 LEU Chi-restraints excluded: chain D residue 934 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 223 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 216 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 chunk 143 optimal weight: 0.9990 chunk 202 optimal weight: 9.9990 chunk 203 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 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 = 0.3641 r_free = 0.3641 target = 0.077738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.051947 restraints weight = 54421.896| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.24 r_work: 0.2839 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17816 Z= 0.180 Angle : 0.646 10.922 24232 Z= 0.321 Chirality : 0.047 0.316 2800 Planarity : 0.004 0.038 3068 Dihedral : 6.955 53.247 2835 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 5.18 % Allowed : 18.63 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.47 (0.17), residues: 2198 helix: -1.43 (0.56), residues: 110 sheet: -0.91 (0.18), residues: 794 loop : -2.21 (0.15), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 338 TYR 0.013 0.001 TYR A 351 PHE 0.018 0.001 PHE C 344 TRP 0.007 0.001 TRP C 207 HIS 0.003 0.001 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00412 (17764) covalent geometry : angle 0.61007 (24110) SS BOND : bond 0.00394 ( 34) SS BOND : angle 2.44882 ( 68) hydrogen bonds : bond 0.03506 ( 560) hydrogen bonds : angle 6.60645 ( 1440) link_NAG-ASN : bond 0.00694 ( 18) link_NAG-ASN : angle 3.64475 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 59 time to evaluate : 0.659 Fit side-chains REVERT: A 79 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8593 (p0) REVERT: A 244 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8197 (t80) REVERT: A 316 GLN cc_start: 0.8457 (pp30) cc_final: 0.8209 (pp30) REVERT: A 338 ARG cc_start: 0.8322 (tpp80) cc_final: 0.7932 (tpp80) REVERT: A 359 GLN cc_start: 0.8117 (pt0) cc_final: 0.7732 (pp30) REVERT: B 137 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8410 (ptp-110) REVERT: B 730 MET cc_start: 0.8512 (ttm) cc_final: 0.8223 (ttp) REVERT: B 760 PHE cc_start: 0.7442 (m-80) cc_final: 0.7119 (t80) REVERT: B 800 TYR cc_start: 0.6305 (t80) cc_final: 0.6060 (t80) REVERT: C 105 GLN cc_start: 0.8894 (pm20) cc_final: 0.8531 (pm20) REVERT: C 219 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8898 (mm) REVERT: C 244 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8221 (t80) REVERT: C 316 GLN cc_start: 0.8414 (pp30) cc_final: 0.8159 (pp30) REVERT: D 137 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8404 (ptp-110) REVERT: D 351 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7559 (pm20) REVERT: D 730 MET cc_start: 0.8494 (ttm) cc_final: 0.8208 (ttp) REVERT: D 760 PHE cc_start: 0.7431 (m-80) cc_final: 0.7109 (t80) REVERT: D 800 TYR cc_start: 0.6313 (t80) cc_final: 0.6070 (t80) outliers start: 96 outliers final: 67 residues processed: 146 average time/residue: 0.1345 time to fit residues: 30.4437 Evaluate side-chains 130 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 56 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 719 MET Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 765 TRP Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 527 PHE Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 719 MET Chi-restraints excluded: chain D residue 747 SER Chi-restraints excluded: chain D residue 765 TRP Chi-restraints excluded: chain D residue 806 CYS Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 929 LEU Chi-restraints excluded: chain D residue 934 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 7 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 176 optimal weight: 8.9990 chunk 100 optimal weight: 0.0870 chunk 59 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 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 = 0.3651 r_free = 0.3651 target = 0.078045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.052445 restraints weight = 54186.936| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.23 r_work: 0.2849 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17816 Z= 0.169 Angle : 0.660 11.483 24232 Z= 0.329 Chirality : 0.047 0.314 2800 Planarity : 0.004 0.036 3068 Dihedral : 6.605 53.647 2829 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 5.29 % Allowed : 18.79 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.24 (0.17), residues: 2198 helix: -1.34 (0.56), residues: 110 sheet: -0.78 (0.18), residues: 794 loop : -2.02 (0.16), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 338 TYR 0.017 0.001 TYR D 663 PHE 0.018 0.001 PHE A 344 TRP 0.007 0.001 TRP C 327 HIS 0.003 0.000 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00389 (17764) covalent geometry : angle 0.61525 (24110) SS BOND : bond 0.00387 ( 34) SS BOND : angle 3.29852 ( 68) hydrogen bonds : bond 0.03439 ( 560) hydrogen bonds : angle 6.53253 ( 1440) link_NAG-ASN : bond 0.00698 ( 18) link_NAG-ASN : angle 3.60732 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 59 time to evaluate : 0.690 Fit side-chains REVERT: A 79 ASN cc_start: 0.8934 (OUTLIER) cc_final: 0.8717 (p0) REVERT: A 244 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8175 (t80) REVERT: A 316 GLN cc_start: 0.8439 (pp30) cc_final: 0.7923 (pp30) REVERT: A 338 ARG cc_start: 0.8318 (tpp80) cc_final: 0.7978 (tpp80) REVERT: A 359 GLN cc_start: 0.8118 (pt0) cc_final: 0.7696 (pp30) REVERT: B 113 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8192 (ttm-80) REVERT: B 137 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8567 (ptp-110) REVERT: B 351 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7557 (pm20) REVERT: B 730 MET cc_start: 0.8521 (ttm) cc_final: 0.8237 (ttp) REVERT: B 760 PHE cc_start: 0.7405 (m-80) cc_final: 0.7087 (t80) REVERT: C 79 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8375 (p0) REVERT: C 219 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8853 (mm) REVERT: C 244 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8151 (t80) REVERT: C 316 GLN cc_start: 0.8418 (pp30) cc_final: 0.8180 (pp30) REVERT: C 338 ARG cc_start: 0.8499 (mmp80) cc_final: 0.8285 (mmp80) REVERT: C 359 GLN cc_start: 0.7875 (pp30) cc_final: 0.7548 (pp30) REVERT: D 113 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8186 (ttm-80) REVERT: D 137 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8557 (ptp-110) REVERT: D 351 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7548 (pm20) REVERT: D 730 MET cc_start: 0.8497 (ttm) cc_final: 0.8214 (ttp) REVERT: D 760 PHE cc_start: 0.7388 (m-80) cc_final: 0.7074 (t80) outliers start: 98 outliers final: 66 residues processed: 149 average time/residue: 0.1237 time to fit residues: 29.4696 Evaluate side-chains 135 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 58 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 719 MET Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 765 TRP Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 527 PHE Chi-restraints excluded: chain D residue 719 MET Chi-restraints excluded: chain D residue 747 SER Chi-restraints excluded: chain D residue 765 TRP Chi-restraints excluded: chain D residue 806 CYS Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 929 LEU Chi-restraints excluded: chain D residue 934 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 1 optimal weight: 7.9990 chunk 208 optimal weight: 0.0040 chunk 194 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 121 optimal weight: 0.0000 chunk 21 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 178 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 202 optimal weight: 9.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 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 = 0.3680 r_free = 0.3680 target = 0.079262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.053652 restraints weight = 54050.620| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.63 r_work: 0.2870 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17816 Z= 0.111 Angle : 0.605 10.417 24232 Z= 0.301 Chirality : 0.046 0.331 2800 Planarity : 0.003 0.035 3068 Dihedral : 6.042 54.169 2825 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 4.91 % Allowed : 19.28 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.03 (0.17), residues: 2198 helix: -1.25 (0.55), residues: 110 sheet: -0.65 (0.18), residues: 784 loop : -1.87 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 338 TYR 0.010 0.001 TYR C 351 PHE 0.015 0.001 PHE A 344 TRP 0.006 0.001 TRP C 86 HIS 0.003 0.000 HIS D 755 Details of bonding type rmsd covalent geometry : bond 0.00249 (17764) covalent geometry : angle 0.56863 (24110) SS BOND : bond 0.00344 ( 34) SS BOND : angle 2.49275 ( 68) hydrogen bonds : bond 0.03043 ( 560) hydrogen bonds : angle 6.21869 ( 1440) link_NAG-ASN : bond 0.00728 ( 18) link_NAG-ASN : angle 3.46523 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 64 time to evaluate : 0.687 Fit side-chains REVERT: A 316 GLN cc_start: 0.8415 (pp30) cc_final: 0.8158 (pp30) REVERT: A 338 ARG cc_start: 0.8328 (tpp80) cc_final: 0.8031 (tpp80) REVERT: A 359 GLN cc_start: 0.8143 (pt0) cc_final: 0.7690 (pp30) REVERT: B 113 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8220 (ttm-80) REVERT: B 137 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8341 (ptp-110) REVERT: B 351 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7571 (pm20) REVERT: B 730 MET cc_start: 0.8532 (ttm) cc_final: 0.8210 (ttp) REVERT: B 760 PHE cc_start: 0.7308 (m-80) cc_final: 0.7052 (t80) REVERT: C 79 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8284 (p0) REVERT: C 219 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8775 (mm) REVERT: C 316 GLN cc_start: 0.8409 (pp30) cc_final: 0.8185 (pp30) REVERT: C 359 GLN cc_start: 0.7936 (pp30) cc_final: 0.7594 (pp30) REVERT: D 113 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8223 (ttm-80) REVERT: D 137 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8379 (ptp-110) REVERT: D 351 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7549 (pm20) REVERT: D 730 MET cc_start: 0.8507 (ttm) cc_final: 0.8196 (ttp) REVERT: D 760 PHE cc_start: 0.7302 (m-80) cc_final: 0.7047 (t80) outliers start: 91 outliers final: 59 residues processed: 147 average time/residue: 0.1290 time to fit residues: 30.1982 Evaluate side-chains 127 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 60 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 765 TRP Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 527 PHE Chi-restraints excluded: chain D residue 747 SER Chi-restraints excluded: chain D residue 765 TRP Chi-restraints excluded: chain D residue 806 CYS Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 934 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 111 optimal weight: 7.9990 chunk 216 optimal weight: 20.0000 chunk 148 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 215 optimal weight: 0.7980 chunk 212 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN B 353 HIS ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN D 353 HIS ** D 784 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 = 0.3626 r_free = 0.3626 target = 0.077130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.051157 restraints weight = 53881.950| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.21 r_work: 0.2814 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 17816 Z= 0.302 Angle : 0.701 13.129 24232 Z= 0.350 Chirality : 0.049 0.339 2800 Planarity : 0.004 0.038 3068 Dihedral : 6.411 52.167 2816 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 5.29 % Allowed : 19.65 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.17), residues: 2198 helix: -1.32 (0.55), residues: 110 sheet: -0.60 (0.18), residues: 776 loop : -1.88 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 338 TYR 0.018 0.002 TYR B 663 PHE 0.022 0.002 PHE A 344 TRP 0.010 0.001 TRP C 327 HIS 0.004 0.001 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00698 (17764) covalent geometry : angle 0.66654 (24110) SS BOND : bond 0.00310 ( 34) SS BOND : angle 2.65505 ( 68) hydrogen bonds : bond 0.03792 ( 560) hydrogen bonds : angle 6.51823 ( 1440) link_NAG-ASN : bond 0.00672 ( 18) link_NAG-ASN : angle 3.60344 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 59 time to evaluate : 0.584 Fit side-chains REVERT: A 181 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8108 (ptp-170) REVERT: A 244 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8224 (t80) REVERT: A 338 ARG cc_start: 0.8309 (tpp80) cc_final: 0.8051 (tpp80) REVERT: A 359 GLN cc_start: 0.8105 (pt0) cc_final: 0.7645 (pp30) REVERT: B 113 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8203 (ttm-80) REVERT: B 137 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8547 (ptp-110) REVERT: B 351 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7527 (pm20) REVERT: B 730 MET cc_start: 0.8568 (ttm) cc_final: 0.8321 (ttp) REVERT: B 760 PHE cc_start: 0.7437 (m-80) cc_final: 0.7102 (t80) REVERT: C 79 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8466 (p0) REVERT: C 117 CYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7656 (m) REVERT: C 219 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8948 (mm) REVERT: C 244 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8224 (t80) REVERT: C 338 ARG cc_start: 0.8487 (mmp80) cc_final: 0.8226 (mmp80) REVERT: C 359 GLN cc_start: 0.7940 (pp30) cc_final: 0.7539 (pp30) REVERT: D 113 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8202 (ttm-80) REVERT: D 137 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8550 (ptp-110) REVERT: D 351 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7511 (pm20) REVERT: D 730 MET cc_start: 0.8553 (ttm) cc_final: 0.8308 (ttp) REVERT: D 760 PHE cc_start: 0.7427 (m-80) cc_final: 0.7136 (t80) outliers start: 98 outliers final: 74 residues processed: 151 average time/residue: 0.1187 time to fit residues: 28.4679 Evaluate side-chains 145 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 59 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 765 TRP Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 527 PHE Chi-restraints excluded: chain D residue 683 THR Chi-restraints excluded: chain D residue 695 MET Chi-restraints excluded: chain D residue 747 SER Chi-restraints excluded: chain D residue 765 TRP Chi-restraints excluded: chain D residue 806 CYS Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 934 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 41 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 129 optimal weight: 0.5980 chunk 154 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 216 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 173 optimal weight: 0.9990 chunk 80 optimal weight: 0.3980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.078652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.052914 restraints weight = 53488.054| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.22 r_work: 0.2864 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17816 Z= 0.142 Angle : 0.612 10.752 24232 Z= 0.305 Chirality : 0.046 0.337 2800 Planarity : 0.003 0.034 3068 Dihedral : 6.028 54.161 2816 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 5.13 % Allowed : 20.41 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.89 (0.17), residues: 2198 helix: -1.22 (0.54), residues: 110 sheet: -0.53 (0.18), residues: 776 loop : -1.76 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 338 TYR 0.012 0.001 TYR A 351 PHE 0.016 0.001 PHE A 344 TRP 0.007 0.001 TRP C 327 HIS 0.002 0.000 HIS B 718 Details of bonding type rmsd covalent geometry : bond 0.00322 (17764) covalent geometry : angle 0.57934 (24110) SS BOND : bond 0.00209 ( 34) SS BOND : angle 2.18597 ( 68) hydrogen bonds : bond 0.03244 ( 560) hydrogen bonds : angle 6.24274 ( 1440) link_NAG-ASN : bond 0.00702 ( 18) link_NAG-ASN : angle 3.51477 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 59 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7900 (t) REVERT: A 244 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8149 (t80) REVERT: A 316 GLN cc_start: 0.8343 (pp30) cc_final: 0.8091 (pp30) REVERT: A 338 ARG cc_start: 0.8244 (tpp80) cc_final: 0.7987 (tpp80) REVERT: A 359 GLN cc_start: 0.8107 (pt0) cc_final: 0.7686 (pp30) REVERT: B 113 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8205 (ttm-80) REVERT: B 137 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8518 (ptp-110) REVERT: B 351 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: B 730 MET cc_start: 0.8519 (ttm) cc_final: 0.8258 (ttp) REVERT: B 760 PHE cc_start: 0.7316 (m-80) cc_final: 0.7075 (t80) REVERT: C 79 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8320 (p0) REVERT: C 219 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8858 (mm) REVERT: C 244 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.8140 (t80) REVERT: C 316 GLN cc_start: 0.8369 (pp30) cc_final: 0.8117 (pp30) REVERT: C 359 GLN cc_start: 0.7894 (pp30) cc_final: 0.7562 (pp30) REVERT: D 113 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8201 (ttm-80) REVERT: D 137 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8516 (ptp-110) REVERT: D 351 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7501 (pm20) REVERT: D 730 MET cc_start: 0.8500 (ttm) cc_final: 0.8239 (ttp) REVERT: D 760 PHE cc_start: 0.7304 (m-80) cc_final: 0.7064 (t80) outliers start: 95 outliers final: 70 residues processed: 148 average time/residue: 0.1180 time to fit residues: 27.8608 Evaluate side-chains 138 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 57 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 765 TRP Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 527 PHE Chi-restraints excluded: chain D residue 747 SER Chi-restraints excluded: chain D residue 765 TRP Chi-restraints excluded: chain D residue 806 CYS Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 929 LEU Chi-restraints excluded: chain D residue 934 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 169 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 8 optimal weight: 0.0010 chunk 78 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 195 optimal weight: 20.0000 chunk 205 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 206 optimal weight: 0.9980 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 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 = 0.3655 r_free = 0.3655 target = 0.078425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.052542 restraints weight = 53541.600| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.22 r_work: 0.2855 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17816 Z= 0.167 Angle : 0.617 10.019 24232 Z= 0.308 Chirality : 0.047 0.339 2800 Planarity : 0.003 0.034 3068 Dihedral : 6.002 53.343 2816 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.91 % Allowed : 20.14 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.82 (0.17), residues: 2198 helix: -1.14 (0.54), residues: 110 sheet: -0.49 (0.18), residues: 776 loop : -1.72 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 338 TYR 0.019 0.001 TYR D 663 PHE 0.017 0.001 PHE A 344 TRP 0.007 0.001 TRP C 327 HIS 0.002 0.001 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00385 (17764) covalent geometry : angle 0.58623 (24110) SS BOND : bond 0.00207 ( 34) SS BOND : angle 2.12891 ( 68) hydrogen bonds : bond 0.03326 ( 560) hydrogen bonds : angle 6.25337 ( 1440) link_NAG-ASN : bond 0.00681 ( 18) link_NAG-ASN : angle 3.43048 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 57 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 THR cc_start: 0.8141 (OUTLIER) cc_final: 0.7890 (t) REVERT: A 244 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8154 (t80) REVERT: A 316 GLN cc_start: 0.8345 (pp30) cc_final: 0.8066 (pp30) REVERT: A 338 ARG cc_start: 0.8260 (tpp80) cc_final: 0.8015 (tpp80) REVERT: A 359 GLN cc_start: 0.8104 (pt0) cc_final: 0.7654 (pp30) REVERT: B 113 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8182 (ttm-80) REVERT: B 351 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7519 (pm20) REVERT: B 730 MET cc_start: 0.8561 (ttm) cc_final: 0.8303 (ttp) REVERT: B 760 PHE cc_start: 0.7411 (m-80) cc_final: 0.7171 (t80) REVERT: C 79 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8389 (p0) REVERT: C 181 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8060 (ptp-170) REVERT: C 219 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8860 (mm) REVERT: C 244 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.8140 (t80) REVERT: C 316 GLN cc_start: 0.8385 (pp30) cc_final: 0.8106 (pp30) REVERT: C 359 GLN cc_start: 0.7882 (pp30) cc_final: 0.7522 (pp30) REVERT: D 113 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8177 (ttm-80) REVERT: D 137 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8545 (ptp-110) REVERT: D 351 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7491 (pm20) REVERT: D 730 MET cc_start: 0.8537 (ttm) cc_final: 0.8288 (ttp) REVERT: D 760 PHE cc_start: 0.7399 (m-80) cc_final: 0.7158 (t80) outliers start: 91 outliers final: 76 residues processed: 140 average time/residue: 0.1273 time to fit residues: 28.0852 Evaluate side-chains 144 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 57 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 765 TRP Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 527 PHE Chi-restraints excluded: chain D residue 695 MET Chi-restraints excluded: chain D residue 747 SER Chi-restraints excluded: chain D residue 765 TRP Chi-restraints excluded: chain D residue 806 CYS Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 929 LEU Chi-restraints excluded: chain D residue 934 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 153 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 118 optimal weight: 8.9990 chunk 175 optimal weight: 0.9990 chunk 198 optimal weight: 50.0000 chunk 37 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 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 = 0.3612 r_free = 0.3612 target = 0.076609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.050730 restraints weight = 54857.009| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.20 r_work: 0.2805 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 17816 Z= 0.361 Angle : 0.719 9.793 24232 Z= 0.362 Chirality : 0.050 0.340 2800 Planarity : 0.004 0.039 3068 Dihedral : 6.732 52.024 2816 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 5.56 % Allowed : 19.49 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.95 (0.17), residues: 2198 helix: -1.35 (0.53), residues: 110 sheet: -0.59 (0.18), residues: 780 loop : -1.79 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 134 TYR 0.017 0.002 TYR A 351 PHE 0.026 0.002 PHE A 344 TRP 0.010 0.001 TRP A 207 HIS 0.005 0.001 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00841 (17764) covalent geometry : angle 0.68749 (24110) SS BOND : bond 0.00317 ( 34) SS BOND : angle 2.39542 ( 68) hydrogen bonds : bond 0.03968 ( 560) hydrogen bonds : angle 6.64958 ( 1440) link_NAG-ASN : bond 0.00648 ( 18) link_NAG-ASN : angle 3.73868 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 55 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8252 (ptp-170) REVERT: A 244 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8204 (t80) REVERT: A 316 GLN cc_start: 0.8449 (pp30) cc_final: 0.8156 (pp30) REVERT: A 338 ARG cc_start: 0.8283 (tpp80) cc_final: 0.8025 (tpp80) REVERT: A 359 GLN cc_start: 0.8076 (pt0) cc_final: 0.7587 (pp30) REVERT: B 113 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8132 (ttm-80) REVERT: B 351 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7300 (pp20) REVERT: B 730 MET cc_start: 0.8563 (ttm) cc_final: 0.8327 (ttp) REVERT: B 760 PHE cc_start: 0.7472 (m-80) cc_final: 0.7092 (t80) REVERT: C 79 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8509 (p0) REVERT: C 181 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8277 (ptp-170) REVERT: C 244 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8192 (t80) REVERT: C 316 GLN cc_start: 0.8457 (pp30) cc_final: 0.8160 (pp30) REVERT: C 359 GLN cc_start: 0.7911 (pp30) cc_final: 0.7507 (pp30) REVERT: D 113 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8124 (ttm-80) REVERT: D 351 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7438 (pp20) REVERT: D 730 MET cc_start: 0.8548 (ttm) cc_final: 0.8314 (ttp) REVERT: D 760 PHE cc_start: 0.7455 (m-80) cc_final: 0.7072 (t80) outliers start: 103 outliers final: 79 residues processed: 152 average time/residue: 0.1220 time to fit residues: 29.6551 Evaluate side-chains 143 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 55 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 765 TRP Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 527 PHE Chi-restraints excluded: chain D residue 683 THR Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 765 TRP Chi-restraints excluded: chain D residue 806 CYS Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 929 LEU Chi-restraints excluded: chain D residue 934 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 145 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 110 optimal weight: 40.0000 chunk 66 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 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 = 0.3659 r_free = 0.3659 target = 0.078682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.053002 restraints weight = 53375.213| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.23 r_work: 0.2866 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17816 Z= 0.122 Angle : 0.610 10.250 24232 Z= 0.304 Chirality : 0.047 0.340 2800 Planarity : 0.003 0.034 3068 Dihedral : 6.154 54.583 2815 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.21 % Allowed : 20.46 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.76 (0.17), residues: 2198 helix: -0.88 (0.58), residues: 98 sheet: -0.41 (0.19), residues: 756 loop : -1.71 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 338 TYR 0.011 0.001 TYR C 351 PHE 0.013 0.001 PHE A 344 TRP 0.009 0.001 TRP C 327 HIS 0.002 0.000 HIS D 755 Details of bonding type rmsd covalent geometry : bond 0.00277 (17764) covalent geometry : angle 0.57611 (24110) SS BOND : bond 0.00181 ( 34) SS BOND : angle 2.30140 ( 68) hydrogen bonds : bond 0.03217 ( 560) hydrogen bonds : angle 6.29091 ( 1440) link_NAG-ASN : bond 0.00706 ( 18) link_NAG-ASN : angle 3.49470 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 56 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8101 (ptp-170) REVERT: A 244 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8104 (t80) REVERT: A 316 GLN cc_start: 0.8392 (pp30) cc_final: 0.8087 (pp30) REVERT: A 338 ARG cc_start: 0.8200 (tpp80) cc_final: 0.7929 (tpp80) REVERT: A 359 GLN cc_start: 0.8127 (pt0) cc_final: 0.7674 (pp30) REVERT: B 113 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8192 (ttm-80) REVERT: B 351 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7490 (pm20) REVERT: B 730 MET cc_start: 0.8501 (ttm) cc_final: 0.8240 (ttp) REVERT: B 760 PHE cc_start: 0.7386 (m-80) cc_final: 0.7127 (t80) REVERT: C 79 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8304 (p0) REVERT: C 244 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8104 (t80) REVERT: C 316 GLN cc_start: 0.8400 (pp30) cc_final: 0.8088 (pp30) REVERT: C 359 GLN cc_start: 0.7904 (pp30) cc_final: 0.7585 (pp30) REVERT: D 113 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8185 (ttm-80) REVERT: D 351 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7503 (pm20) REVERT: D 730 MET cc_start: 0.8488 (ttm) cc_final: 0.8227 (ttp) REVERT: D 760 PHE cc_start: 0.7361 (m-80) cc_final: 0.7131 (t80) outliers start: 78 outliers final: 68 residues processed: 130 average time/residue: 0.1271 time to fit residues: 26.8470 Evaluate side-chains 131 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 55 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 765 TRP Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 527 PHE Chi-restraints excluded: chain D residue 683 THR Chi-restraints excluded: chain D residue 747 SER Chi-restraints excluded: chain D residue 765 TRP Chi-restraints excluded: chain D residue 806 CYS Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 929 LEU Chi-restraints excluded: chain D residue 934 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 203 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 105 optimal weight: 20.0000 chunk 162 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 188 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 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 = 0.3649 r_free = 0.3649 target = 0.078164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.052449 restraints weight = 54025.641| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.23 r_work: 0.2849 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17816 Z= 0.171 Angle : 0.615 10.021 24232 Z= 0.307 Chirality : 0.047 0.339 2800 Planarity : 0.003 0.033 3068 Dihedral : 6.096 53.584 2815 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 4.43 % Allowed : 20.63 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.69 (0.17), residues: 2198 helix: -0.80 (0.59), residues: 98 sheet: -0.37 (0.19), residues: 756 loop : -1.66 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.012 0.001 TYR A 351 PHE 0.017 0.001 PHE A 344 TRP 0.007 0.001 TRP C 207 HIS 0.002 0.001 HIS B 755 Details of bonding type rmsd covalent geometry : bond 0.00395 (17764) covalent geometry : angle 0.58272 (24110) SS BOND : bond 0.00199 ( 34) SS BOND : angle 2.23047 ( 68) hydrogen bonds : bond 0.03344 ( 560) hydrogen bonds : angle 6.26208 ( 1440) link_NAG-ASN : bond 0.00676 ( 18) link_NAG-ASN : angle 3.43695 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4269.84 seconds wall clock time: 73 minutes 59.52 seconds (4439.52 seconds total)