Starting phenix.real_space_refine on Sat Sep 12 18:35:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vxk_21442/09_2026/6vxk_21442.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vxk_21442/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6vxk_21442/09_2026/6vxk_21442.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vxk_21442/09_2026/6vxk_21442.cif" model { file = "/net/cci-nas-00/data/ceres_data/6vxk_21442/09_2026/6vxk_21442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vxk_21442/09_2026/6vxk_21442.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vxk_21442/09_2026/6vxk_21442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vxk_21442/09_2026/6vxk_21442.map" } 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-2.2.1-6174/lib/python3.11/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 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 chiralities: 8 Restraints were copied for chains: C, D Time building chain proxies: 7.58, per 1000 atoms: 0.44 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: 1.69 Conformation dependent library (CDL) restraints added in 784.7 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: 0.75 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: 3.82 Time building geometry restraints manager: 2.25 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: 9290 17.70 - 35.39: 1008 35.39 - 53.09: 194 53.09 - 70.79: 36 70.79 - 88.49: 16 Dihedral angle restraints: 10544 sinusoidal: 4052 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 10541 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: 0.02 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: 4.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 21.810 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 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 : 14.735 87.569 6262 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/Z covalent geometry : bond 0.01131 / 0.51 (17764) covalent geometry : angle 0.84119 / 0.46 (24110) SS BOND : bond 0.00451 / 0.30 ( 34) SS BOND : angle 2.85444 / 2.00 ( 68) hydrogen bonds : bond 0.10870 / 7.45 ( 560) hydrogen bonds : angle 8.03152 / 5.53 ( 1440) link_NAG-ASN : bond 0.00722 / 0.46 ( 18) link_NAG-ASN : angle 4.24179 / 2.77 ( 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 : 0.672 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: 0.1004 time to fit residues: 34.5880 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 : 0.713 ------------------------------------------------------------------------------- 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... 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 = 0.3650 r_free = 0.3650 target = 0.078132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.052371 restraints weight = 53331.433| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.20 r_work: 0.2856 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17816 Z= 0.143 Angle : 0.649 10.841 24232 Z= 0.326 Chirality : 0.047 0.335 2800 Planarity : 0.004 0.041 3068 Dihedral : 7.844 56.502 2556 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.00 % Allowed : 19.65 % Favored : 76.35 % 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: -1.76 (0.53), residues: 110 sheet: -1.15 (0.18), residues: 794 loop : -2.49 (0.15), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 98 TYR 0.014 0.001 TYR C 351 PHE 0.016 0.001 PHE A 344 TRP 0.006 0.001 TRP D 240 HIS 0.003 0.001 HIS C 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (17764) covalent geometry : angle 0.61408 / 0.32 (24110) SS BOND : bond 0.00435 / 0.27 ( 34) SS BOND : angle 2.39342 / 1.70 ( 68) hydrogen bonds : bond 0.03496 / 2.38 ( 560) hydrogen bonds : angle 6.75614 / 4.63 ( 1440) link_NAG-ASN : bond 0.00736 / 0.48 ( 18) link_NAG-ASN : angle 3.68010 / 2.46 ( 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 138 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 64 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLN cc_start: 0.8956 (pm20) cc_final: 0.8695 (pm20) REVERT: A 244 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8236 (t80) REVERT: A 316 GLN cc_start: 0.8443 (pp30) cc_final: 0.8184 (pp30) REVERT: A 337 HIS cc_start: 0.7918 (m-70) cc_final: 0.7674 (m-70) REVERT: A 359 GLN cc_start: 0.8112 (pt0) cc_final: 0.7758 (pp30) REVERT: B 65 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8772 (tp) REVERT: B 523 MET cc_start: 0.7652 (mmp) cc_final: 0.7444 (mmp) REVERT: B 730 MET cc_start: 0.8469 (ttm) cc_final: 0.8182 (ttp) REVERT: B 760 PHE cc_start: 0.7470 (m-80) cc_final: 0.7154 (t80) REVERT: B 800 TYR cc_start: 0.6160 (t80) cc_final: 0.5927 (t80) REVERT: C 105 GLN cc_start: 0.8885 (pm20) cc_final: 0.8528 (pm20) REVERT: C 244 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8199 (t80) REVERT: C 337 HIS cc_start: 0.8342 (m-70) cc_final: 0.7985 (m-70) REVERT: D 65 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8777 (tp) REVERT: D 523 MET cc_start: 0.7651 (mmp) cc_final: 0.7441 (mmp) REVERT: D 730 MET cc_start: 0.8438 (ttm) cc_final: 0.8150 (ttp) REVERT: D 760 PHE cc_start: 0.7464 (m-80) cc_final: 0.7147 (t80) REVERT: D 800 TYR cc_start: 0.6154 (t80) cc_final: 0.5924 (t80) outliers start: 74 outliers final: 43 residues processed: 130 average time/residue: 0.1310 time to fit residues: 26.5505 Evaluate side-chains 104 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 57 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 379 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 65 LEU 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 65 LEU 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: 0.9980 chunk 196 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 3 optimal weight: 0.0870 chunk 1 optimal weight: 1.9990 chunk 216 optimal weight: 7.9990 chunk 172 optimal weight: 8.9990 chunk 143 optimal weight: 0.9990 chunk 202 optimal weight: 10.0000 chunk 203 optimal weight: 0.8980 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3663 r_free = 0.3663 target = 0.078711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.053023 restraints weight = 54292.791| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.25 r_work: 0.2873 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17816 Z= 0.123 Angle : 0.610 10.492 24232 Z= 0.305 Chirality : 0.046 0.341 2800 Planarity : 0.003 0.038 3068 Dihedral : 6.160 47.568 2457 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 5.18 % Allowed : 18.57 % 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: -2.34 (0.17), residues: 2198 helix: -1.40 (0.55), residues: 110 sheet: -0.83 (0.18), residues: 778 loop : -2.11 (0.15), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 338 TYR 0.011 0.001 TYR A 351 PHE 0.015 0.001 PHE C 344 TRP 0.006 0.001 TRP D 261 HIS 0.002 0.000 HIS C 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (17764) covalent geometry : angle 0.57487 / 0.29 (24110) SS BOND : bond 0.00449 / 0.27 ( 34) SS BOND : angle 2.39062 / 1.70 ( 68) hydrogen bonds : bond 0.03237 / 2.17 ( 560) hydrogen bonds : angle 6.38979 / 4.38 ( 1440) link_NAG-ASN : bond 0.00719 / 0.46 ( 18) link_NAG-ASN : angle 3.49767 / 2.34 ( 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 161 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 65 time to evaluate : 0.766 Fit side-chains REVERT: A 79 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8637 (p0) REVERT: A 105 GLN cc_start: 0.8944 (pm20) cc_final: 0.8680 (pm20) REVERT: A 244 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8185 (t80) REVERT: A 316 GLN cc_start: 0.8371 (pp30) cc_final: 0.8112 (pp30) REVERT: A 338 ARG cc_start: 0.8365 (tpp80) cc_final: 0.7970 (tpp80) REVERT: A 359 GLN cc_start: 0.8136 (pt0) cc_final: 0.7738 (pp30) REVERT: B 137 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8280 (ptp-110) REVERT: B 730 MET cc_start: 0.8466 (ttm) cc_final: 0.8178 (ttp) REVERT: B 760 PHE cc_start: 0.7395 (m-80) cc_final: 0.7048 (t80) REVERT: B 800 TYR cc_start: 0.6285 (t80) cc_final: 0.6065 (t80) REVERT: C 105 GLN cc_start: 0.8867 (pm20) cc_final: 0.8539 (pm20) REVERT: C 219 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8852 (mm) REVERT: C 244 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8182 (t80) REVERT: C 316 GLN cc_start: 0.8391 (pp30) cc_final: 0.8146 (pp30) REVERT: D 137 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8241 (ptp-110) REVERT: D 351 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7561 (pm20) REVERT: D 730 MET cc_start: 0.8447 (ttm) cc_final: 0.8157 (ttp) REVERT: D 760 PHE cc_start: 0.7380 (m-80) cc_final: 0.7030 (t80) REVERT: D 800 TYR cc_start: 0.6291 (t80) cc_final: 0.6074 (t80) outliers start: 96 outliers final: 59 residues processed: 153 average time/residue: 0.1318 time to fit residues: 31.5398 Evaluate side-chains 128 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 62 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 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 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 522 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 826 LEU Chi-restraints excluded: chain B residue 837 THR 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 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 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 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 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: 2.9990 chunk 206 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 216 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN ** 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 = 0.3636 r_free = 0.3636 target = 0.077517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.051670 restraints weight = 54296.728| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.24 r_work: 0.2835 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17816 Z= 0.232 Angle : 0.690 12.658 24232 Z= 0.345 Chirality : 0.048 0.330 2800 Planarity : 0.004 0.036 3068 Dihedral : 6.263 46.148 2447 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 5.02 % Allowed : 18.84 % Favored : 76.13 % 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: -2.21 (0.17), residues: 2198 helix: -1.32 (0.56), residues: 110 sheet: -0.76 (0.18), residues: 794 loop : -2.01 (0.15), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 338 TYR 0.019 0.002 TYR B 663 PHE 0.021 0.002 PHE A 344 TRP 0.011 0.001 TRP C 327 HIS 0.004 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.23 (17764) covalent geometry : angle 0.64874 / 0.33 (24110) SS BOND : bond 0.00350 / 0.24 ( 34) SS BOND : angle 3.23654 / 2.30 ( 68) hydrogen bonds : bond 0.03691 / 2.50 ( 560) hydrogen bonds : angle 6.58283 / 4.56 ( 1440) link_NAG-ASN : bond 0.00662 / 0.43 ( 18) link_NAG-ASN : angle 3.57222 / 2.38 ( 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 150 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 57 time to evaluate : 0.499 Fit side-chains REVERT: A 79 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8723 (p0) REVERT: A 244 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.8177 (t80) REVERT: A 338 ARG cc_start: 0.8310 (tpp80) cc_final: 0.7979 (tpp80) REVERT: A 359 GLN cc_start: 0.8027 (pt0) cc_final: 0.7625 (pp30) REVERT: B 113 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8168 (ttm-80) REVERT: B 137 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8548 (ptp-110) REVERT: B 351 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: B 730 MET cc_start: 0.8570 (ttm) cc_final: 0.8297 (ttp) REVERT: B 760 PHE cc_start: 0.7383 (m-80) cc_final: 0.7003 (t80) REVERT: C 79 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8400 (p0) REVERT: C 219 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8927 (mm) REVERT: C 244 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.8177 (t80) REVERT: C 316 GLN cc_start: 0.8413 (pp30) cc_final: 0.8178 (pp30) REVERT: C 359 GLN cc_start: 0.7901 (pp30) cc_final: 0.7517 (pp30) REVERT: D 113 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8167 (ttm-80) REVERT: D 137 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8542 (ptp-110) REVERT: D 351 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7549 (pm20) REVERT: D 730 MET cc_start: 0.8540 (ttm) cc_final: 0.8270 (ttp) REVERT: D 760 PHE cc_start: 0.7374 (m-80) cc_final: 0.6995 (t80) outliers start: 93 outliers final: 62 residues processed: 146 average time/residue: 0.1227 time to fit residues: 28.6576 Evaluate side-chains 130 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 57 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 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 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: 6.9990 chunk 208 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 178 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 202 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3674 r_free = 0.3674 target = 0.078987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.053564 restraints weight = 54073.029| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.27 r_work: 0.2882 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2174 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= 0.121 Angle : 0.605 10.441 24232 Z= 0.302 Chirality : 0.046 0.333 2800 Planarity : 0.003 0.034 3068 Dihedral : 5.779 46.234 2447 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.75 % Allowed : 19.76 % Favored : 75.49 % 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: -2.00 (0.17), residues: 2198 helix: -1.23 (0.55), residues: 110 sheet: -0.60 (0.18), residues: 780 loop : -1.86 (0.16), residues: 1308 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 0.015 0.001 PHE A 344 TRP 0.007 0.001 TRP C 327 HIS 0.002 0.000 HIS C 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (17764) covalent geometry : angle 0.56913 / 0.29 (24110) SS BOND : bond 0.00288 / 0.19 ( 34) SS BOND : angle 2.45518 / 1.76 ( 68) hydrogen bonds : bond 0.03170 / 2.14 ( 560) hydrogen bonds : angle 6.25270 / 4.31 ( 1440) link_NAG-ASN : bond 0.00694 / 0.45 ( 18) link_NAG-ASN : angle 3.43181 / 2.30 ( 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 150 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 62 time to evaluate : 0.703 Fit side-chains REVERT: A 244 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8153 (t80) REVERT: A 316 GLN cc_start: 0.8330 (pp30) cc_final: 0.8038 (pp30) REVERT: A 338 ARG cc_start: 0.8298 (tpp80) cc_final: 0.8002 (tpp80) REVERT: A 359 GLN cc_start: 0.8096 (pt0) cc_final: 0.7664 (pp30) REVERT: B 113 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8203 (ttm-80) REVERT: B 137 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8372 (ptp-110) REVERT: B 351 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7521 (pm20) REVERT: B 730 MET cc_start: 0.8530 (ttm) cc_final: 0.8240 (ttp) REVERT: B 760 PHE cc_start: 0.7362 (m-80) cc_final: 0.7008 (t80) REVERT: C 79 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8290 (p0) REVERT: C 219 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8783 (mm) REVERT: C 244 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8199 (t80) REVERT: C 359 GLN cc_start: 0.7929 (pp30) cc_final: 0.7592 (pp30) REVERT: D 113 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8205 (ttm-80) REVERT: D 137 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8402 (ptp-110) REVERT: D 351 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7508 (pm20) REVERT: D 730 MET cc_start: 0.8501 (ttm) cc_final: 0.8215 (ttp) REVERT: D 760 PHE cc_start: 0.7357 (m-80) cc_final: 0.7002 (t80) outliers start: 88 outliers final: 61 residues processed: 146 average time/residue: 0.1202 time to fit residues: 28.1592 Evaluate side-chains 131 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 60 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 70 VAL 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 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 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 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 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 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 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 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 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 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 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: 1.9990 chunk 145 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 215 optimal weight: 0.8980 chunk 212 optimal weight: 8.9990 chunk 11 optimal weight: 0.1980 chunk 123 optimal weight: 0.0270 chunk 80 optimal weight: 9.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3686 r_free = 0.3686 target = 0.079578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.053959 restraints weight = 53899.743| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.62 r_work: 0.2880 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2461 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= 0.112 Angle : 0.581 10.396 24232 Z= 0.290 Chirality : 0.046 0.328 2800 Planarity : 0.003 0.033 3068 Dihedral : 5.290 45.422 2441 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 4.64 % Allowed : 20.14 % Favored : 75.22 % 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: -1.81 (0.17), residues: 2198 helix: -1.16 (0.54), residues: 110 sheet: -0.48 (0.19), residues: 784 loop : -1.71 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 338 TYR 0.014 0.001 TYR B 663 PHE 0.014 0.001 PHE C 344 TRP 0.007 0.001 TRP C 86 HIS 0.006 0.000 HIS C 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (17764) covalent geometry : angle 0.55058 / 0.28 (24110) SS BOND : bond 0.00377 / 0.25 ( 34) SS BOND : angle 2.12136 / 1.51 ( 68) hydrogen bonds : bond 0.03101 / 2.10 ( 560) hydrogen bonds : angle 6.00393 / 4.14 ( 1440) link_NAG-ASN : bond 0.00710 / 0.46 ( 18) link_NAG-ASN : angle 3.23385 / 2.16 ( 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 148 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 62 time to evaluate : 0.691 Fit side-chains REVERT: A 78 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7788 (t) REVERT: A 244 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8228 (t80) REVERT: A 338 ARG cc_start: 0.8293 (tpp80) cc_final: 0.8027 (tpp80) REVERT: A 359 GLN cc_start: 0.8143 (pt0) cc_final: 0.7662 (pp30) REVERT: B 113 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8218 (ttm-80) REVERT: B 137 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8228 (ptp-110) REVERT: B 351 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7496 (pm20) REVERT: B 730 MET cc_start: 0.8560 (ttm) cc_final: 0.8250 (ttp) REVERT: B 760 PHE cc_start: 0.7362 (m-80) cc_final: 0.7063 (t80) REVERT: C 79 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8343 (p0) REVERT: C 219 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8811 (mm) REVERT: C 244 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.8226 (t80) REVERT: C 316 GLN cc_start: 0.8366 (pp30) cc_final: 0.8094 (pp30) REVERT: C 359 GLN cc_start: 0.7901 (pp30) cc_final: 0.7579 (pp30) REVERT: D 113 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8219 (ttm-80) REVERT: D 137 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8557 (ptp-110) REVERT: D 351 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7505 (pm20) REVERT: D 730 MET cc_start: 0.8544 (ttm) cc_final: 0.8237 (ttp) REVERT: D 760 PHE cc_start: 0.7363 (m-80) cc_final: 0.7064 (t80) outliers start: 86 outliers final: 56 residues processed: 146 average time/residue: 0.1246 time to fit residues: 29.3598 Evaluate side-chains 125 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 58 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 244 PHE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 376 SER 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 128 THR Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 LEU 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 879 ILE 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 74 LEU 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 244 PHE Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 376 SER 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 113 ARG Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 177 LEU 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 879 ILE 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: 9.9990 chunk 1 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 HIS B 353 HIS ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN C 295 HIS D 353 HIS ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.076335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.050689 restraints weight = 54487.935| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.14 r_work: 0.2799 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.090 17816 Z= 0.403 Angle : 0.743 10.145 24232 Z= 0.373 Chirality : 0.050 0.328 2800 Planarity : 0.004 0.037 3068 Dihedral : 5.724 48.653 2429 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 4.75 % Allowed : 20.30 % 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: -1.53 (0.52), residues: 110 sheet: -0.49 (0.18), residues: 752 loop : -1.82 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 225 TYR 0.018 0.002 TYR A 351 PHE 0.028 0.002 PHE A 344 TRP 0.011 0.001 TRP C 327 HIS 0.004 0.001 HIS D 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00936 / 0.40 (17764) covalent geometry : angle 0.71185 / 0.36 (24110) SS BOND : bond 0.00358 / 0.25 ( 34) SS BOND : angle 2.52923 / 1.76 ( 68) hydrogen bonds : bond 0.04078 / 2.77 ( 560) hydrogen bonds : angle 6.60025 / 4.55 ( 1440) link_NAG-ASN : bond 0.00660 / 0.44 ( 18) link_NAG-ASN : angle 3.65440 / 2.44 ( 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 145 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 57 time to evaluate : 0.659 Fit side-chains REVERT: A 181 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8363 (ptp-170) REVERT: A 244 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8196 (t80) REVERT: A 338 ARG cc_start: 0.8272 (tpp80) cc_final: 0.8018 (tpp80) REVERT: A 359 GLN cc_start: 0.8088 (pt0) cc_final: 0.7590 (pp30) REVERT: B 113 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8181 (ttm-80) REVERT: B 351 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7535 (pm20) REVERT: B 730 MET cc_start: 0.8568 (ttm) cc_final: 0.8325 (ttp) REVERT: B 760 PHE cc_start: 0.7479 (m-80) cc_final: 0.7102 (t80) REVERT: C 79 ASN cc_start: 0.8875 (OUTLIER) cc_final: 0.8526 (p0) REVERT: C 244 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8195 (t80) REVERT: C 359 GLN cc_start: 0.7890 (pp30) cc_final: 0.7477 (pp30) REVERT: D 113 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8173 (ttm-80) REVERT: D 351 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7339 (pp20) REVERT: D 730 MET cc_start: 0.8549 (ttm) cc_final: 0.8310 (ttp) REVERT: D 760 PHE cc_start: 0.7495 (m-80) cc_final: 0.7100 (t80) outliers start: 88 outliers final: 59 residues processed: 140 average time/residue: 0.1286 time to fit residues: 28.6205 Evaluate side-chains 124 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 57 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 129 ILE 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 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 79 LEU Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 177 LEU 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 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 74 LEU Chi-restraints excluded: chain C residue 79 ASN 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 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 113 ARG Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 177 LEU 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 523 MET 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 934 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 169 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 195 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 158 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 206 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 HIS ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.079019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.053334 restraints weight = 53708.863| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.55 r_work: 0.2862 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2376 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= 0.114 Angle : 0.595 10.212 24232 Z= 0.297 Chirality : 0.046 0.331 2800 Planarity : 0.003 0.034 3068 Dihedral : 5.211 48.018 2428 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.10 % Allowed : 20.63 % Favored : 75.27 % 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: -1.80 (0.17), residues: 2198 helix: -1.32 (0.51), residues: 110 sheet: -0.41 (0.18), residues: 776 loop : -1.74 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 338 TYR 0.016 0.001 TYR D 663 PHE 0.015 0.001 PHE A 344 TRP 0.008 0.001 TRP A 327 HIS 0.007 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (17764) covalent geometry : angle 0.56531 / 0.29 (24110) SS BOND : bond 0.00222 / 0.15 ( 34) SS BOND : angle 1.93576 / 1.37 ( 68) hydrogen bonds : bond 0.03144 / 2.13 ( 560) hydrogen bonds : angle 6.15218 / 4.22 ( 1440) link_NAG-ASN : bond 0.00694 / 0.45 ( 18) link_NAG-ASN : angle 3.40537 / 2.28 ( 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 134 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 58 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.8128 (t80) REVERT: A 316 GLN cc_start: 0.8334 (pp30) cc_final: 0.8094 (pp30) REVERT: A 338 ARG cc_start: 0.8236 (tpp80) cc_final: 0.7990 (tpp80) REVERT: A 359 GLN cc_start: 0.8143 (pt0) cc_final: 0.7667 (pp30) REVERT: B 113 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8207 (ttm-80) REVERT: B 351 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7509 (pm20) REVERT: B 730 MET cc_start: 0.8514 (ttm) cc_final: 0.8213 (ttp) REVERT: B 760 PHE cc_start: 0.7455 (m-80) cc_final: 0.7140 (t80) REVERT: C 79 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8250 (p0) REVERT: C 181 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.7940 (ptp-170) REVERT: C 244 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8123 (t80) REVERT: C 316 GLN cc_start: 0.8367 (pp30) cc_final: 0.8124 (pp30) REVERT: C 359 GLN cc_start: 0.7903 (pp30) cc_final: 0.7556 (pp30) REVERT: D 113 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8202 (ttm-80) REVERT: D 351 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7499 (pm20) REVERT: D 730 MET cc_start: 0.8508 (ttm) cc_final: 0.8208 (ttp) REVERT: D 760 PHE cc_start: 0.7408 (m-80) cc_final: 0.7107 (t80) outliers start: 76 outliers final: 61 residues processed: 128 average time/residue: 0.1248 time to fit residues: 26.0128 Evaluate side-chains 126 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 57 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 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 365 VAL Chi-restraints excluded: chain A residue 376 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 128 THR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 194 CYS 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 523 MET 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 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 376 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 113 ARG 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 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 523 MET 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 934 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 153 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 175 optimal weight: 0.0870 chunk 198 optimal weight: 50.0000 chunk 37 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 overall best weight: 2.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 HIS ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.077671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.051898 restraints weight = 54476.561| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.24 r_work: 0.2835 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17816 Z= 0.232 Angle : 0.633 9.761 24232 Z= 0.317 Chirality : 0.047 0.327 2800 Planarity : 0.004 0.033 3068 Dihedral : 5.322 48.947 2428 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.64 % Allowed : 20.36 % Favored : 75.00 % 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: -1.18 (0.53), residues: 110 sheet: -0.38 (0.19), residues: 756 loop : -1.70 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 225 TYR 0.014 0.001 TYR C 351 PHE 0.020 0.002 PHE A 344 TRP 0.008 0.001 TRP C 207 HIS 0.003 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 (17764) covalent geometry : angle 0.60400 / 0.31 (24110) SS BOND : bond 0.00234 / 0.16 ( 34) SS BOND : angle 2.08788 / 1.46 ( 68) hydrogen bonds : bond 0.03502 / 2.37 ( 560) hydrogen bonds : angle 6.29462 / 4.32 ( 1440) link_NAG-ASN : bond 0.00657 / 0.43 ( 18) link_NAG-ASN : angle 3.40971 / 2.27 ( 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 143 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 57 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8073 (ptp-170) REVERT: A 244 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.8167 (t80) REVERT: A 316 GLN cc_start: 0.8359 (pp30) cc_final: 0.8109 (pp30) REVERT: A 338 ARG cc_start: 0.8248 (tpp80) cc_final: 0.8005 (tpp80) REVERT: A 359 GLN cc_start: 0.8089 (pt0) cc_final: 0.7620 (pp30) REVERT: B 113 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8168 (ttm-80) REVERT: B 351 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: B 730 MET cc_start: 0.8575 (ttm) cc_final: 0.8321 (ttp) REVERT: B 760 PHE cc_start: 0.7423 (m-80) cc_final: 0.7110 (t80) REVERT: C 79 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8417 (p0) REVERT: C 181 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8230 (ptp-170) REVERT: C 244 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.8151 (t80) REVERT: C 316 GLN cc_start: 0.8370 (pp30) cc_final: 0.8116 (pp30) REVERT: C 359 GLN cc_start: 0.7870 (pp30) cc_final: 0.7505 (pp30) REVERT: D 113 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8166 (ttm-80) REVERT: D 351 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7469 (pm20) REVERT: D 730 MET cc_start: 0.8556 (ttm) cc_final: 0.8306 (ttp) REVERT: D 760 PHE cc_start: 0.7413 (m-80) cc_final: 0.7097 (t80) outliers start: 86 outliers final: 65 residues processed: 137 average time/residue: 0.1234 time to fit residues: 27.4949 Evaluate side-chains 131 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 57 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 365 VAL Chi-restraints excluded: chain A residue 376 SER 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 177 LEU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 231 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 523 MET 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 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 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 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 113 ARG 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 231 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 523 MET 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 934 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 145 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 HIS ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.077489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.051717 restraints weight = 53944.904| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.22 r_work: 0.2831 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 17816 Z= 0.245 Angle : 0.649 9.744 24232 Z= 0.325 Chirality : 0.047 0.328 2800 Planarity : 0.004 0.031 3068 Dihedral : 5.502 50.500 2428 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 4.32 % Allowed : 20.73 % 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: -1.78 (0.17), residues: 2198 helix: -1.21 (0.53), residues: 110 sheet: -0.39 (0.19), residues: 752 loop : -1.71 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 225 TYR 0.018 0.002 TYR B 663 PHE 0.021 0.002 PHE A 344 TRP 0.008 0.001 TRP A 327 HIS 0.003 0.001 HIS D 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.25 (17764) covalent geometry : angle 0.61897 / 0.32 (24110) SS BOND : bond 0.00254 / 0.18 ( 34) SS BOND : angle 2.16689 / 1.51 ( 68) hydrogen bonds : bond 0.03581 / 2.42 ( 560) hydrogen bonds : angle 6.39691 / 4.39 ( 1440) link_NAG-ASN : bond 0.00655 / 0.43 ( 18) link_NAG-ASN : angle 3.46650 / 2.30 ( 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 137 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 57 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8114 (ptp-170) REVERT: A 244 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8201 (t80) REVERT: A 316 GLN cc_start: 0.8412 (pp30) cc_final: 0.8151 (pp30) REVERT: A 338 ARG cc_start: 0.8243 (tpp80) cc_final: 0.7992 (tpp80) REVERT: A 359 GLN cc_start: 0.8081 (pt0) cc_final: 0.7614 (pp30) REVERT: B 113 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8163 (ttm-80) REVERT: B 351 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7504 (pm20) REVERT: B 730 MET cc_start: 0.8572 (ttm) cc_final: 0.8331 (ttp) REVERT: B 760 PHE cc_start: 0.7442 (m-80) cc_final: 0.7072 (t80) REVERT: C 79 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8413 (p0) REVERT: C 181 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8270 (ptp-170) REVERT: C 244 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8194 (t80) REVERT: C 316 GLN cc_start: 0.8412 (pp30) cc_final: 0.8148 (pp30) REVERT: C 359 GLN cc_start: 0.7882 (pp30) cc_final: 0.7532 (pp30) REVERT: D 113 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8162 (ttm-80) REVERT: D 351 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7478 (pm20) REVERT: D 730 MET cc_start: 0.8558 (ttm) cc_final: 0.8317 (ttp) REVERT: D 760 PHE cc_start: 0.7436 (m-80) cc_final: 0.7062 (t80) outliers start: 80 outliers final: 68 residues processed: 131 average time/residue: 0.1193 time to fit residues: 25.2805 Evaluate side-chains 134 residues out of total 1966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 57 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 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 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 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 523 MET 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 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 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 365 VAL 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 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 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 523 MET 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 934 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 162 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 chunk 145 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3665 r_free = 0.3665 target = 0.078716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.053290 restraints weight = 54420.682| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.29 r_work: 0.2874 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2417 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= 0.129 Angle : 0.596 9.957 24232 Z= 0.297 Chirality : 0.046 0.328 2800 Planarity : 0.003 0.033 3068 Dihedral : 5.222 50.139 2428 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.83 % Allowed : 21.33 % Favored : 74.84 % 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: -1.68 (0.17), residues: 2198 helix: -1.03 (0.54), residues: 110 sheet: -0.31 (0.19), residues: 756 loop : -1.66 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 338 TYR 0.011 0.001 TYR A 351 PHE 0.015 0.001 PHE A 344 TRP 0.007 0.001 TRP A 327 HIS 0.010 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (17764) covalent geometry : angle 0.56623 / 0.29 (24110) SS BOND : bond 0.00214 / 0.15 ( 34) SS BOND : angle 2.07581 / 1.50 ( 68) hydrogen bonds : bond 0.03220 / 2.17 ( 560) hydrogen bonds : angle 6.19335 / 4.24 ( 1440) link_NAG-ASN : bond 0.00690 / 0.45 ( 18) link_NAG-ASN : angle 3.32729 / 2.21 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4223.34 seconds wall clock time: 73 minutes 21.71 seconds (4401.71 seconds total)