Starting phenix.real_space_refine on Fri Jul 3 05:09:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zj7_14743/07_2026/7zj7_14743.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zj7_14743/07_2026/7zj7_14743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7zj7_14743/07_2026/7zj7_14743.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zj7_14743/07_2026/7zj7_14743.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zj7_14743/07_2026/7zj7_14743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zj7_14743/07_2026/7zj7_14743.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zj7_14743/07_2026/7zj7_14743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zj7_14743/07_2026/7zj7_14743.map" } resolution = 3.95 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= 0.002 sd= 0.028 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 57 5.16 5 C 7431 2.51 5 N 2055 2.21 5 O 2415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11958 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3828 Classifications: {'peptide': 486} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 466} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 Restraints were copied for chains: B, C, I, L, K, O Time building chain proxies: 2.94, per 1000 atoms: 0.25 Number of scatterers: 11958 At special positions: 0 Unit cell: (106.92, 111.24, 145.8, 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 57 16.00 O 2415 8.00 N 2055 7.00 C 7431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.01 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.04 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.01 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.04 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.04 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.02 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.02 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.01 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.00 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.04 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.04 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.04 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.04 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.04 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.04 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " BETA1-6 " NAG E 1 " - " FUC E 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 4 " " NAG L 1 " - " FUC L 4 " NAG-ASN " NAG A 601 " - " ASN A 22 " " NAG B 601 " - " ASN B 22 " " NAG C 601 " - " ASN C 22 " " NAG D 1 " - " ASN A 38 " " NAG E 1 " - " ASN A 81 " " NAG F 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 285 " " NAG H 1 " - " ASN B 38 " " NAG I 1 " - " ASN B 81 " " NAG J 1 " - " ASN B 165 " " NAG K 1 " - " ASN B 285 " " NAG L 1 " - " ASN C 81 " " NAG M 1 " - " ASN C 38 " " NAG N 1 " - " ASN C 165 " " NAG O 1 " - " ASN C 285 " Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 458.7 milliseconds 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2682 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 33 sheets defined 33.3% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 removed outlier: 4.135A pdb=" N ALA A 19 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL A 20 " --> pdb=" O HIS A 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 16 through 20' Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.909A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.763A pdb=" N LEU A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 338 through 351 removed outlier: 4.369A pdb=" N GLY A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 347 " --> pdb=" O TRP A 343 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP A 350 " --> pdb=" O MET A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 378 removed outlier: 3.701A pdb=" N ASN A 378 " --> pdb=" O ILE A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 456 removed outlier: 3.608A pdb=" N ASN A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 483 removed outlier: 3.895A pdb=" N ILE A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 490 No H-bonds generated for 'chain 'A' and resid 488 through 490' Processing helix chain 'A' and resid 491 through 499 Processing helix chain 'B' and resid 16 through 20 removed outlier: 4.135A pdb=" N ALA B 19 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL B 20 " --> pdb=" O HIS B 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 16 through 20' Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.910A pdb=" N GLN B 80 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.762A pdb=" N LEU B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 338 through 351 removed outlier: 4.372A pdb=" N GLY B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE B 347 " --> pdb=" O TRP B 343 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP B 350 " --> pdb=" O MET B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 378 removed outlier: 3.701A pdb=" N ASN B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 456 removed outlier: 3.607A pdb=" N ASN B 382 " --> pdb=" O ASN B 378 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 456 " --> pdb=" O ARG B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 removed outlier: 3.894A pdb=" N ILE B 478 " --> pdb=" O ASP B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 490 No H-bonds generated for 'chain 'B' and resid 488 through 490' Processing helix chain 'B' and resid 491 through 499 Processing helix chain 'C' and resid 16 through 20 removed outlier: 4.135A pdb=" N ALA C 19 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL C 20 " --> pdb=" O HIS C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 16 through 20' Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.910A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.763A pdb=" N LEU C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 338 through 351 removed outlier: 4.369A pdb=" N GLY C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET C 346 " --> pdb=" O GLY C 342 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE C 347 " --> pdb=" O TRP C 343 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP C 350 " --> pdb=" O MET C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 378 removed outlier: 3.700A pdb=" N ASN C 378 " --> pdb=" O ILE C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 456 removed outlier: 3.607A pdb=" N ASN C 382 " --> pdb=" O ASN C 378 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG C 456 " --> pdb=" O ARG C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 483 removed outlier: 3.895A pdb=" N ILE C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 490 No H-bonds generated for 'chain 'C' and resid 488 through 490' Processing helix chain 'C' and resid 491 through 499 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26 removed outlier: 3.738A pdb=" N ILE A 34 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 58 through 61 removed outlier: 6.397A pdb=" N PHE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 100 through 101 removed outlier: 6.877A pdb=" N ASP A 101 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 177 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 100 through 101 removed outlier: 6.877A pdb=" N ASP A 101 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 141 removed outlier: 8.085A pdb=" N ALA A 138 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 11.130A pdb=" N GLY A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB1, first strand: chain 'A' and resid 286 through 287 removed outlier: 3.614A pdb=" N ILE A 282 " --> pdb=" O TYR A 302 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 459 through 461 Processing sheet with id=AB3, first strand: chain 'B' and resid 24 through 26 removed outlier: 3.739A pdb=" N ILE B 34 " --> pdb=" O VAL B 26 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB5, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB6, first strand: chain 'B' and resid 58 through 61 removed outlier: 6.395A pdb=" N PHE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 100 through 101 removed outlier: 6.877A pdb=" N ASP B 101 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N TRP B 234 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 177 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ILE B 179 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 100 through 101 removed outlier: 6.877A pdb=" N ASP B 101 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N TRP B 234 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AC1, first strand: chain 'B' and resid 136 through 141 removed outlier: 8.084A pdb=" N ALA B 138 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 11.131A pdb=" N GLY B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AC3, first strand: chain 'B' and resid 286 through 287 removed outlier: 3.613A pdb=" N ILE B 282 " --> pdb=" O TYR B 302 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 459 through 461 Processing sheet with id=AC5, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.738A pdb=" N ILE C 34 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC7, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC8, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.398A pdb=" N PHE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.877A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 177 " --> pdb=" O PHE C 258 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.877A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AD3, first strand: chain 'C' and resid 136 through 141 removed outlier: 8.084A pdb=" N ALA C 138 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 11.130A pdb=" N GLY C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD5, first strand: chain 'C' and resid 286 through 287 removed outlier: 3.614A pdb=" N ILE C 282 " --> pdb=" O TYR C 302 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 459 through 461 504 hydrogen bonds defined for protein. 1404 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: 1.78 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2001 1.31 - 1.43: 3302 1.43 - 1.56: 6817 1.56 - 1.69: 0 1.69 - 1.82: 78 Bond restraints: 12198 Sorted by residual: bond pdb=" N ILE C 335 " pdb=" CA ILE C 335 " ideal model delta sigma weight residual 1.456 1.500 -0.044 1.11e-02 8.12e+03 1.56e+01 bond pdb=" N ILE A 335 " pdb=" CA ILE A 335 " ideal model delta sigma weight residual 1.456 1.499 -0.044 1.11e-02 8.12e+03 1.56e+01 bond pdb=" N ARG B 220 " pdb=" CA ARG B 220 " ideal model delta sigma weight residual 1.453 1.489 -0.035 9.20e-03 1.18e+04 1.47e+01 bond pdb=" N ILE B 335 " pdb=" CA ILE B 335 " ideal model delta sigma weight residual 1.456 1.500 -0.043 1.14e-02 7.69e+03 1.43e+01 bond pdb=" N ARG A 220 " pdb=" CA ARG A 220 " ideal model delta sigma weight residual 1.453 1.488 -0.035 9.20e-03 1.18e+04 1.42e+01 ... (remaining 12193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 14396 2.89 - 5.79: 2078 5.79 - 8.68: 53 8.68 - 11.57: 6 11.57 - 14.47: 6 Bond angle restraints: 16539 Sorted by residual: angle pdb=" CA GLU A 340 " pdb=" C GLU A 340 " pdb=" N ASN A 341 " ideal model delta sigma weight residual 116.97 123.63 -6.66 1.20e+00 6.94e-01 3.08e+01 angle pdb=" CA GLU C 340 " pdb=" C GLU C 340 " pdb=" N ASN C 341 " ideal model delta sigma weight residual 116.97 123.62 -6.65 1.20e+00 6.94e-01 3.07e+01 angle pdb=" CA GLU B 340 " pdb=" C GLU B 340 " pdb=" N ASN B 341 " ideal model delta sigma weight residual 116.97 123.58 -6.61 1.20e+00 6.94e-01 3.03e+01 angle pdb=" C THR A 361 " pdb=" N GLY A 362 " pdb=" CA GLY A 362 " ideal model delta sigma weight residual 119.94 125.50 -5.56 1.09e+00 8.42e-01 2.60e+01 angle pdb=" C THR C 361 " pdb=" N GLY C 362 " pdb=" CA GLY C 362 " ideal model delta sigma weight residual 119.94 125.50 -5.56 1.09e+00 8.42e-01 2.60e+01 ... (remaining 16534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6292 17.88 - 35.77: 566 35.77 - 53.65: 155 53.65 - 71.53: 37 71.53 - 89.41: 9 Dihedral angle restraints: 7059 sinusoidal: 2874 harmonic: 4185 Sorted by residual: dihedral pdb=" CA VAL B 323 " pdb=" C VAL B 323 " pdb=" N PRO B 324 " pdb=" CA PRO B 324 " ideal model delta harmonic sigma weight residual -180.00 -151.41 -28.59 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA VAL A 323 " pdb=" C VAL A 323 " pdb=" N PRO A 324 " pdb=" CA PRO A 324 " ideal model delta harmonic sigma weight residual -180.00 -151.41 -28.59 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA VAL C 323 " pdb=" C VAL C 323 " pdb=" N PRO C 324 " pdb=" CA PRO C 324 " ideal model delta harmonic sigma weight residual -180.00 -151.41 -28.59 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 7056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1202 0.087 - 0.173: 625 0.173 - 0.259: 76 0.259 - 0.346: 7 0.346 - 0.432: 7 Chirality restraints: 1917 Sorted by residual: chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.55e+01 chirality pdb=" C1 BMA L 3 " pdb=" O4 NAG L 2 " pdb=" C2 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.50e+01 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.25e+01 ... (remaining 1914 not shown) Planarity restraints: 2133 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " 0.319 2.00e-02 2.50e+03 2.76e-01 9.55e+02 pdb=" C7 NAG I 2 " -0.136 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " 0.001 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " -0.442 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " 0.258 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 2 " -0.319 2.00e-02 2.50e+03 2.76e-01 9.55e+02 pdb=" C7 NAG L 2 " 0.136 2.00e-02 2.50e+03 pdb=" C8 NAG L 2 " -0.001 2.00e-02 2.50e+03 pdb=" N2 NAG L 2 " 0.442 2.00e-02 2.50e+03 pdb=" O7 NAG L 2 " -0.258 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.319 2.00e-02 2.50e+03 2.76e-01 9.55e+02 pdb=" C7 NAG E 2 " 0.136 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.001 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.442 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.258 2.00e-02 2.50e+03 ... (remaining 2130 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2403 2.84 - 3.36: 11621 3.36 - 3.87: 18611 3.87 - 4.39: 20879 4.39 - 4.90: 34171 Nonbonded interactions: 87685 Sorted by model distance: nonbonded pdb=" O HIS A 184 " pdb=" OG SER A 228 " model vdw 2.329 3.040 nonbonded pdb=" O HIS B 184 " pdb=" OG SER B 228 " model vdw 2.329 3.040 nonbonded pdb=" O HIS C 184 " pdb=" OG SER C 228 " model vdw 2.330 3.040 nonbonded pdb=" OG1 THR B 28 " pdb=" O ASP B 31 " model vdw 2.369 3.040 nonbonded pdb=" OG1 THR A 28 " pdb=" O ASP A 31 " model vdw 2.369 3.040 ... (remaining 87680 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.930 Find NCS groups from input model: 0.330 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: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.013 0.046 12252 Z= 1.013 Angle : 1.908 14.465 16683 Z= 1.334 Chirality : 0.093 0.432 1917 Planarity : 0.017 0.276 2118 Dihedral : 15.368 89.414 4323 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.55 % Allowed : 10.46 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -3.03 (0.16), residues: 1452 helix: -0.97 (0.21), residues: 408 sheet: -0.99 (0.31), residues: 192 loop : -2.95 (0.15), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 255 TYR 0.044 0.004 TYR C 423 PHE 0.023 0.004 PHE C 294 TRP 0.022 0.004 TRP A 350 HIS 0.013 0.003 HIS C 56 Details of bonding type rmsd/Z covalent geometry : bond 0.01343 / 1.02 (12198) covalent geometry : angle 1.89524 / 1.34 (16539) SS BOND : bond 0.01455 / 0.88 ( 18) SS BOND : angle 2.01678 / 1.20 ( 36) hydrogen bonds : bond 0.18730 / 12.71 ( 474) hydrogen bonds : angle 7.57323 / 5.41 ( 1404) link_BETA1-4 : bond 0.00696 / 0.37 ( 18) link_BETA1-4 : angle 2.91893 / 1.88 ( 54) link_BETA1-6 : bond 0.00576 / 0.29 ( 3) link_BETA1-6 : angle 1.56370 / 0.88 ( 9) link_NAG-ASN : bond 0.00636 / 0.35 ( 15) link_NAG-ASN : angle 3.90323 / 2.51 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 220 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8714 (t0) cc_final: 0.8417 (t0) REVERT: A 204 VAL cc_start: 0.9609 (t) cc_final: 0.9257 (m) REVERT: A 244 VAL cc_start: 0.9158 (t) cc_final: 0.8952 (t) REVERT: A 344 GLU cc_start: 0.8753 (tt0) cc_final: 0.8163 (tt0) REVERT: A 383 ARG cc_start: 0.8866 (mtt180) cc_final: 0.8653 (mmt90) REVERT: A 399 PHE cc_start: 0.9193 (OUTLIER) cc_final: 0.8620 (t80) REVERT: B 104 ASP cc_start: 0.8527 (t0) cc_final: 0.8289 (t0) REVERT: B 204 VAL cc_start: 0.9651 (t) cc_final: 0.9292 (m) REVERT: B 236 ILE cc_start: 0.9127 (mt) cc_final: 0.8783 (tt) REVERT: B 244 VAL cc_start: 0.9178 (t) cc_final: 0.8778 (t) REVERT: B 264 LYS cc_start: 0.8551 (mmtt) cc_final: 0.7973 (pptt) REVERT: B 399 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8530 (t80) REVERT: C 85 ASP cc_start: 0.8851 (m-30) cc_final: 0.7987 (t70) REVERT: C 104 ASP cc_start: 0.8523 (t0) cc_final: 0.8241 (t0) REVERT: C 222 TRP cc_start: 0.8968 (m100) cc_final: 0.8546 (m100) REVERT: C 244 VAL cc_start: 0.9195 (t) cc_final: 0.8841 (t) REVERT: C 252 ILE cc_start: 0.8529 (mm) cc_final: 0.8246 (mm) REVERT: C 383 ARG cc_start: 0.8700 (mtt180) cc_final: 0.8447 (mmt90) REVERT: C 399 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.8667 (t80) REVERT: C 433 ASN cc_start: 0.8743 (m-40) cc_final: 0.8334 (m110) outliers start: 7 outliers final: 0 residues processed: 226 average time/residue: 0.0890 time to fit residues: 29.9120 Evaluate side-chains 118 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain B residue 399 PHE Chi-restraints excluded: chain C residue 399 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS B 54 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 HIS C 54 ASN C 216 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.142444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.100823 restraints weight = 30043.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.101355 restraints weight = 20259.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.101275 restraints weight = 15465.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.101935 restraints weight = 16682.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.101929 restraints weight = 14695.413| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12252 Z= 0.152 Angle : 0.776 12.616 16683 Z= 0.378 Chirality : 0.048 0.469 1917 Planarity : 0.004 0.035 2118 Dihedral : 6.249 47.305 1584 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.12 % Allowed : 14.78 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.23 (0.19), residues: 1452 helix: 1.81 (0.24), residues: 426 sheet: -0.20 (0.37), residues: 168 loop : -2.52 (0.15), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 321 TYR 0.020 0.002 TYR C 105 PHE 0.010 0.001 PHE B 467 TRP 0.019 0.002 TRP A 343 HIS 0.009 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (12198) covalent geometry : angle 0.72964 / 0.37 (16539) SS BOND : bond 0.01267 / 0.66 ( 18) SS BOND : angle 1.23309 / 0.92 ( 36) hydrogen bonds : bond 0.04137 / 2.85 ( 474) hydrogen bonds : angle 5.30006 / 3.79 ( 1404) link_BETA1-4 : bond 0.00683 / 0.39 ( 18) link_BETA1-4 : angle 2.39244 / 1.56 ( 54) link_BETA1-6 : bond 0.00359 / 0.18 ( 3) link_BETA1-6 : angle 1.48112 / 0.84 ( 9) link_NAG-ASN : bond 0.00718 / 0.47 ( 15) link_NAG-ASN : angle 4.37201 / 2.93 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8815 (mtmm) cc_final: 0.8597 (mtmm) REVERT: A 222 TRP cc_start: 0.8620 (m100) cc_final: 0.7847 (m-90) REVERT: A 383 ARG cc_start: 0.8859 (mtt180) cc_final: 0.8505 (mpt-90) REVERT: A 452 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7939 (tpm170) REVERT: B 222 TRP cc_start: 0.8516 (m100) cc_final: 0.7618 (t-100) REVERT: B 236 ILE cc_start: 0.9320 (mt) cc_final: 0.8927 (tt) REVERT: B 399 PHE cc_start: 0.9245 (OUTLIER) cc_final: 0.8482 (t80) REVERT: C 85 ASP cc_start: 0.8213 (m-30) cc_final: 0.7850 (t70) REVERT: C 222 TRP cc_start: 0.8612 (m100) cc_final: 0.8107 (m-90) REVERT: C 383 ARG cc_start: 0.8742 (mtt180) cc_final: 0.8352 (mpt-90) REVERT: C 399 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.8665 (t80) REVERT: C 452 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8052 (tpm170) outliers start: 27 outliers final: 11 residues processed: 164 average time/residue: 0.0912 time to fit residues: 22.1877 Evaluate side-chains 100 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 399 PHE Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 382 ASN Chi-restraints excluded: chain C residue 399 PHE Chi-restraints excluded: chain C residue 452 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 102 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN C 433 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.139557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.093903 restraints weight = 30047.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.096387 restraints weight = 20908.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.096230 restraints weight = 17033.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.096473 restraints weight = 16188.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.096732 restraints weight = 15661.797| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 12252 Z= 0.212 Angle : 0.787 14.181 16683 Z= 0.386 Chirality : 0.047 0.325 1917 Planarity : 0.004 0.061 2118 Dihedral : 5.814 46.411 1582 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.44 % Allowed : 17.22 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.99 (0.20), residues: 1452 helix: 2.42 (0.25), residues: 414 sheet: -0.21 (0.35), residues: 192 loop : -2.56 (0.16), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 405 TYR 0.017 0.002 TYR B 423 PHE 0.015 0.002 PHE C 332 TRP 0.015 0.002 TRP A 343 HIS 0.014 0.001 HIS A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (12198) covalent geometry : angle 0.75118 / 0.38 (16539) SS BOND : bond 0.00837 / 0.48 ( 18) SS BOND : angle 2.53557 / 1.50 ( 36) hydrogen bonds : bond 0.04152 / 2.86 ( 474) hydrogen bonds : angle 5.06907 / 3.57 ( 1404) link_BETA1-4 : bond 0.00564 / 0.31 ( 18) link_BETA1-4 : angle 1.68900 / 1.16 ( 54) link_BETA1-6 : bond 0.00177 / 0.09 ( 3) link_BETA1-6 : angle 1.22413 / 0.69 ( 9) link_NAG-ASN : bond 0.00555 / 0.30 ( 15) link_NAG-ASN : angle 3.67521 / 2.45 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8903 (mtmm) cc_final: 0.8639 (mtmm) REVERT: A 85 ASP cc_start: 0.8160 (m-30) cc_final: 0.7913 (t70) REVERT: A 383 ARG cc_start: 0.8916 (mtt180) cc_final: 0.8384 (mpt-90) REVERT: A 462 MET cc_start: 0.7176 (ptp) cc_final: 0.6943 (pmm) REVERT: B 399 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.8512 (t80) REVERT: B 462 MET cc_start: 0.7308 (ptp) cc_final: 0.7047 (pmm) REVERT: C 85 ASP cc_start: 0.8359 (m-30) cc_final: 0.7981 (t70) REVERT: C 383 ARG cc_start: 0.8806 (mtt180) cc_final: 0.8412 (mpt-90) REVERT: C 399 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.8685 (t80) outliers start: 31 outliers final: 13 residues processed: 123 average time/residue: 0.0988 time to fit residues: 17.4014 Evaluate side-chains 94 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 399 PHE Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 382 ASN Chi-restraints excluded: chain C residue 399 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 69 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 20.0000 chunk 128 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.140726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.098422 restraints weight = 29872.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.098325 restraints weight = 20395.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.098217 restraints weight = 16927.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.098968 restraints weight = 17950.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.098974 restraints weight = 15479.735| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12252 Z= 0.133 Angle : 0.710 10.378 16683 Z= 0.350 Chirality : 0.045 0.308 1917 Planarity : 0.004 0.050 2118 Dihedral : 5.499 44.631 1582 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.20 % Allowed : 18.40 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.77 (0.21), residues: 1452 helix: 2.62 (0.26), residues: 414 sheet: -0.06 (0.33), residues: 213 loop : -2.50 (0.17), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 456 TYR 0.014 0.001 TYR C 195 PHE 0.011 0.001 PHE C 467 TRP 0.016 0.001 TRP B 343 HIS 0.007 0.001 HIS C 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (12198) covalent geometry : angle 0.67987 / 0.34 (16539) SS BOND : bond 0.00825 / 0.46 ( 18) SS BOND : angle 2.27800 / 1.06 ( 36) hydrogen bonds : bond 0.03638 / 2.48 ( 474) hydrogen bonds : angle 4.67886 / 3.28 ( 1404) link_BETA1-4 : bond 0.00542 / 0.31 ( 18) link_BETA1-4 : angle 1.48683 / 1.03 ( 54) link_BETA1-6 : bond 0.00342 / 0.17 ( 3) link_BETA1-6 : angle 1.10262 / 0.61 ( 9) link_NAG-ASN : bond 0.00374 / 0.19 ( 15) link_NAG-ASN : angle 3.12618 / 2.12 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8811 (mtmm) cc_final: 0.8536 (mtmm) REVERT: A 85 ASP cc_start: 0.7957 (m-30) cc_final: 0.7600 (t70) REVERT: A 383 ARG cc_start: 0.8907 (mtt180) cc_final: 0.8370 (mpt-90) REVERT: B 399 PHE cc_start: 0.9340 (OUTLIER) cc_final: 0.9038 (m-80) REVERT: C 85 ASP cc_start: 0.8207 (m-30) cc_final: 0.7860 (t70) REVERT: C 383 ARG cc_start: 0.8808 (mtt180) cc_final: 0.8395 (mpt-90) REVERT: C 399 PHE cc_start: 0.9309 (OUTLIER) cc_final: 0.8572 (t80) outliers start: 28 outliers final: 16 residues processed: 119 average time/residue: 0.0803 time to fit residues: 15.0420 Evaluate side-chains 95 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 399 PHE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 382 ASN Chi-restraints excluded: chain C residue 399 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 102 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN C 17 HIS C 133 ASN C 327 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.139218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.093898 restraints weight = 29800.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.096279 restraints weight = 19441.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.097762 restraints weight = 15575.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.098482 restraints weight = 13827.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.098482 restraints weight = 13028.399| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12252 Z= 0.169 Angle : 0.695 12.198 16683 Z= 0.342 Chirality : 0.044 0.302 1917 Planarity : 0.004 0.061 2118 Dihedral : 5.343 43.945 1582 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.65 % Favored : 96.28 % Rotamer: Outliers : 2.59 % Allowed : 18.63 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.71 (0.21), residues: 1452 helix: 2.48 (0.26), residues: 414 sheet: -0.10 (0.34), residues: 207 loop : -2.30 (0.17), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 269 TYR 0.014 0.002 TYR B 423 PHE 0.017 0.001 PHE C 467 TRP 0.013 0.001 TRP B 343 HIS 0.005 0.001 HIS A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (12198) covalent geometry : angle 0.66698 / 0.34 (16539) SS BOND : bond 0.00635 / 0.35 ( 18) SS BOND : angle 2.08230 / 1.32 ( 36) hydrogen bonds : bond 0.03642 / 2.48 ( 474) hydrogen bonds : angle 4.70888 / 3.29 ( 1404) link_BETA1-4 : bond 0.00497 / 0.27 ( 18) link_BETA1-4 : angle 1.48369 / 1.03 ( 54) link_BETA1-6 : bond 0.00248 / 0.12 ( 3) link_BETA1-6 : angle 1.12021 / 0.64 ( 9) link_NAG-ASN : bond 0.00412 / 0.22 ( 15) link_NAG-ASN : angle 3.04435 / 2.07 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 TRP cc_start: 0.8345 (m100) cc_final: 0.7969 (m100) REVERT: A 383 ARG cc_start: 0.8910 (mtt180) cc_final: 0.8368 (mpt-90) REVERT: B 222 TRP cc_start: 0.8308 (m100) cc_final: 0.8010 (m100) REVERT: B 399 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.9062 (m-80) REVERT: C 60 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8302 (t0) REVERT: C 85 ASP cc_start: 0.8160 (m-30) cc_final: 0.7929 (t70) REVERT: C 222 TRP cc_start: 0.8433 (m100) cc_final: 0.8179 (m100) REVERT: C 246 ASN cc_start: 0.8261 (m110) cc_final: 0.8021 (m110) REVERT: C 383 ARG cc_start: 0.8828 (mtt180) cc_final: 0.8426 (mpt-90) REVERT: C 462 MET cc_start: 0.6563 (pmm) cc_final: 0.6260 (pmm) outliers start: 33 outliers final: 18 residues processed: 117 average time/residue: 0.0997 time to fit residues: 17.9780 Evaluate side-chains 96 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 399 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 382 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 19 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 31 optimal weight: 0.0070 chunk 107 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 GLN B 17 HIS B 246 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.139093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.093946 restraints weight = 30135.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.095541 restraints weight = 23694.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.096252 restraints weight = 16773.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.096263 restraints weight = 16232.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.096646 restraints weight = 15379.196| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12252 Z= 0.171 Angle : 0.708 11.731 16683 Z= 0.346 Chirality : 0.044 0.299 1917 Planarity : 0.005 0.062 2118 Dihedral : 5.215 42.292 1580 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.99 % Favored : 95.87 % Rotamer: Outliers : 2.75 % Allowed : 18.47 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.63 (0.21), residues: 1452 helix: 2.53 (0.25), residues: 411 sheet: -0.00 (0.34), residues: 207 loop : -2.24 (0.17), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 456 TYR 0.013 0.002 TYR B 423 PHE 0.041 0.002 PHE A 467 TRP 0.018 0.001 TRP C 343 HIS 0.009 0.001 HIS C 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (12198) covalent geometry : angle 0.67485 / 0.34 (16539) SS BOND : bond 0.00766 / 0.40 ( 18) SS BOND : angle 3.05674 / 1.41 ( 36) hydrogen bonds : bond 0.03672 / 2.51 ( 474) hydrogen bonds : angle 4.62711 / 3.23 ( 1404) link_BETA1-4 : bond 0.00494 / 0.27 ( 18) link_BETA1-4 : angle 1.44331 / 0.99 ( 54) link_BETA1-6 : bond 0.00255 / 0.13 ( 3) link_BETA1-6 : angle 1.11797 / 0.63 ( 9) link_NAG-ASN : bond 0.00417 / 0.22 ( 15) link_NAG-ASN : angle 2.90289 / 1.95 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 87 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8747 (mtmm) cc_final: 0.8489 (mtmm) REVERT: A 222 TRP cc_start: 0.8618 (m100) cc_final: 0.8147 (m100) REVERT: A 383 ARG cc_start: 0.8923 (mtt180) cc_final: 0.8421 (mmt90) REVERT: A 462 MET cc_start: 0.7455 (pmm) cc_final: 0.7104 (pmm) REVERT: B 217 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8887 (tp) REVERT: C 217 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8775 (tp) REVERT: C 222 TRP cc_start: 0.8658 (m100) cc_final: 0.8329 (m100) REVERT: C 226 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.6567 (tp) REVERT: C 246 ASN cc_start: 0.8204 (m110) cc_final: 0.7942 (m110) REVERT: C 383 ARG cc_start: 0.8837 (mtt180) cc_final: 0.8425 (mpt-90) REVERT: C 462 MET cc_start: 0.6734 (pmm) cc_final: 0.6455 (pmm) outliers start: 35 outliers final: 22 residues processed: 116 average time/residue: 0.0960 time to fit residues: 17.3727 Evaluate side-chains 98 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 382 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 29 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 140 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 246 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.137708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.092113 restraints weight = 30037.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.094449 restraints weight = 19788.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.095726 restraints weight = 15946.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.096562 restraints weight = 14212.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.096820 restraints weight = 13428.159| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12252 Z= 0.238 Angle : 0.783 13.006 16683 Z= 0.382 Chirality : 0.046 0.299 1917 Planarity : 0.005 0.065 2118 Dihedral : 5.207 32.939 1578 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.27 % Favored : 95.66 % Rotamer: Outliers : 2.52 % Allowed : 19.58 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.77 (0.21), residues: 1452 helix: 2.32 (0.25), residues: 414 sheet: -0.12 (0.34), residues: 207 loop : -2.28 (0.17), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 90 TYR 0.019 0.002 TYR B 423 PHE 0.024 0.002 PHE A 467 TRP 0.020 0.002 TRP A 180 HIS 0.009 0.001 HIS C 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.24 (12198) covalent geometry : angle 0.73978 / 0.37 (16539) SS BOND : bond 0.00945 / 0.50 ( 18) SS BOND : angle 4.12977 / 2.13 ( 36) hydrogen bonds : bond 0.03912 / 2.69 ( 474) hydrogen bonds : angle 4.76510 / 3.31 ( 1404) link_BETA1-4 : bond 0.00463 / 0.25 ( 18) link_BETA1-4 : angle 1.53830 / 1.06 ( 54) link_BETA1-6 : bond 0.00236 / 0.12 ( 3) link_BETA1-6 : angle 1.26205 / 0.71 ( 9) link_NAG-ASN : bond 0.00551 / 0.30 ( 15) link_NAG-ASN : angle 3.01506 / 2.00 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8814 (mtmm) cc_final: 0.8553 (mtmm) REVERT: A 60 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8431 (t0) REVERT: A 383 ARG cc_start: 0.8910 (mtt180) cc_final: 0.8500 (mmt90) REVERT: A 462 MET cc_start: 0.7418 (pmm) cc_final: 0.7043 (pmm) REVERT: B 217 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8865 (tp) REVERT: B 390 GLU cc_start: 0.8730 (pp20) cc_final: 0.8513 (pp20) REVERT: C 217 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8776 (tp) REVERT: C 226 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7415 (tp) REVERT: C 246 ASN cc_start: 0.8242 (m110) cc_final: 0.7986 (m110) REVERT: C 383 ARG cc_start: 0.8854 (mtt180) cc_final: 0.8435 (mpt-90) REVERT: C 399 PHE cc_start: 0.9363 (OUTLIER) cc_final: 0.8592 (t80) REVERT: C 462 MET cc_start: 0.6734 (pmm) cc_final: 0.6432 (pmm) outliers start: 32 outliers final: 20 residues processed: 114 average time/residue: 0.0887 time to fit residues: 16.1474 Evaluate side-chains 101 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 382 ASN Chi-restraints excluded: chain C residue 399 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 40 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 128 optimal weight: 0.0980 chunk 80 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 246 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.140001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.095379 restraints weight = 30159.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.097918 restraints weight = 19306.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.099383 restraints weight = 15286.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.100020 restraints weight = 13542.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.100020 restraints weight = 12775.747| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12252 Z= 0.120 Angle : 0.708 14.453 16683 Z= 0.345 Chirality : 0.043 0.291 1917 Planarity : 0.004 0.055 2118 Dihedral : 4.996 42.245 1578 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.20 % Allowed : 20.28 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.38 (0.21), residues: 1452 helix: 2.74 (0.26), residues: 408 sheet: 0.12 (0.35), residues: 201 loop : -2.03 (0.18), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 141 TYR 0.015 0.001 TYR B 105 PHE 0.022 0.001 PHE A 467 TRP 0.018 0.001 TRP A 180 HIS 0.007 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (12198) covalent geometry : angle 0.66186 / 0.33 (16539) SS BOND : bond 0.00621 / 0.32 ( 18) SS BOND : angle 4.40835 / 2.33 ( 36) hydrogen bonds : bond 0.03448 / 2.34 ( 474) hydrogen bonds : angle 4.36233 / 3.06 ( 1404) link_BETA1-4 : bond 0.00532 / 0.31 ( 18) link_BETA1-4 : angle 1.38639 / 0.95 ( 54) link_BETA1-6 : bond 0.00359 / 0.18 ( 3) link_BETA1-6 : angle 1.09196 / 0.62 ( 9) link_NAG-ASN : bond 0.00307 / 0.16 ( 15) link_NAG-ASN : angle 2.64626 / 1.78 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8820 (mtmm) cc_final: 0.8532 (mtmm) REVERT: A 60 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8127 (t0) REVERT: A 217 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8782 (tp) REVERT: A 222 TRP cc_start: 0.8396 (m100) cc_final: 0.8102 (m100) REVERT: A 383 ARG cc_start: 0.8924 (mtt180) cc_final: 0.8447 (mmt90) REVERT: A 462 MET cc_start: 0.7415 (pmm) cc_final: 0.7055 (pmm) REVERT: B 217 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8888 (tp) REVERT: B 390 GLU cc_start: 0.8693 (pp20) cc_final: 0.8482 (pp20) REVERT: C 226 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7306 (tp) REVERT: C 246 ASN cc_start: 0.8310 (m110) cc_final: 0.8067 (m110) REVERT: C 383 ARG cc_start: 0.8868 (mtt180) cc_final: 0.8436 (mpt-90) REVERT: C 399 PHE cc_start: 0.9349 (OUTLIER) cc_final: 0.9142 (m-80) REVERT: C 462 MET cc_start: 0.6580 (pmm) cc_final: 0.6317 (pmm) outliers start: 28 outliers final: 20 residues processed: 116 average time/residue: 0.0834 time to fit residues: 15.3821 Evaluate side-chains 103 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 382 ASN Chi-restraints excluded: chain C residue 399 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 104 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 120 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 246 ASN ** C 80 GLN ** 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 = 0.4094 r_free = 0.4094 target = 0.138756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.094736 restraints weight = 29902.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.096227 restraints weight = 21885.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.096527 restraints weight = 16686.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.096599 restraints weight = 16858.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.096785 restraints weight = 16136.548| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12252 Z= 0.167 Angle : 0.719 14.465 16683 Z= 0.350 Chirality : 0.044 0.293 1917 Planarity : 0.005 0.063 2118 Dihedral : 5.012 45.838 1578 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.36 % Allowed : 20.83 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.37 (0.21), residues: 1452 helix: 2.64 (0.25), residues: 411 sheet: 0.15 (0.35), residues: 201 loop : -1.99 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 90 TYR 0.014 0.002 TYR B 423 PHE 0.020 0.001 PHE A 467 TRP 0.019 0.001 TRP A 180 HIS 0.007 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (12198) covalent geometry : angle 0.67722 / 0.34 (16539) SS BOND : bond 0.00548 / 0.30 ( 18) SS BOND : angle 4.06809 / 2.27 ( 36) hydrogen bonds : bond 0.03548 / 2.43 ( 474) hydrogen bonds : angle 4.39589 / 3.08 ( 1404) link_BETA1-4 : bond 0.00467 / 0.26 ( 18) link_BETA1-4 : angle 1.43219 / 0.98 ( 54) link_BETA1-6 : bond 0.00220 / 0.11 ( 3) link_BETA1-6 : angle 1.12388 / 0.63 ( 9) link_NAG-ASN : bond 0.00383 / 0.21 ( 15) link_NAG-ASN : angle 2.71907 / 1.82 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8806 (mtmm) cc_final: 0.8531 (mtmm) REVERT: A 60 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8208 (t0) REVERT: A 217 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8791 (tp) REVERT: A 383 ARG cc_start: 0.8893 (mtt180) cc_final: 0.8470 (mmt90) REVERT: A 462 MET cc_start: 0.7342 (pmm) cc_final: 0.6955 (pmm) REVERT: B 217 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8884 (tp) REVERT: B 390 GLU cc_start: 0.8625 (pp20) cc_final: 0.8386 (pp20) REVERT: C 217 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8755 (tp) REVERT: C 226 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7455 (tp) REVERT: C 383 ARG cc_start: 0.8787 (mtt180) cc_final: 0.8385 (mpt-90) REVERT: C 399 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.9133 (m-80) REVERT: C 462 MET cc_start: 0.6491 (pmm) cc_final: 0.6209 (pmm) outliers start: 30 outliers final: 23 residues processed: 116 average time/residue: 0.0872 time to fit residues: 16.1461 Evaluate side-chains 112 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 382 ASN Chi-restraints excluded: chain C residue 399 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 28 optimal weight: 0.6980 chunk 68 optimal weight: 0.0020 chunk 55 optimal weight: 0.4980 chunk 71 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 111 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN C 33 GLN ** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 GLN ** 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 = 0.4115 r_free = 0.4115 target = 0.140344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.099413 restraints weight = 30227.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.098550 restraints weight = 22943.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.099164 restraints weight = 17673.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.099736 restraints weight = 17533.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.099708 restraints weight = 16257.175| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12252 Z= 0.108 Angle : 0.649 9.714 16683 Z= 0.315 Chirality : 0.043 0.283 1917 Planarity : 0.004 0.054 2118 Dihedral : 4.686 36.428 1578 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.28 % Allowed : 21.07 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.26 (0.21), residues: 1452 helix: 2.77 (0.26), residues: 411 sheet: 0.16 (0.35), residues: 201 loop : -1.92 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 90 TYR 0.014 0.001 TYR B 105 PHE 0.020 0.001 PHE A 467 TRP 0.017 0.001 TRP C 343 HIS 0.006 0.001 HIS C 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (12198) covalent geometry : angle 0.61996 / 0.31 (16539) SS BOND : bond 0.00492 / 0.26 ( 18) SS BOND : angle 2.83280 / 1.55 ( 36) hydrogen bonds : bond 0.03293 / 2.23 ( 474) hydrogen bonds : angle 4.20649 / 2.96 ( 1404) link_BETA1-4 : bond 0.00512 / 0.30 ( 18) link_BETA1-4 : angle 1.33963 / 0.92 ( 54) link_BETA1-6 : bond 0.00327 / 0.17 ( 3) link_BETA1-6 : angle 1.06009 / 0.60 ( 9) link_NAG-ASN : bond 0.00250 / 0.13 ( 15) link_NAG-ASN : angle 2.47281 / 1.66 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8811 (mtmm) cc_final: 0.8552 (mtmm) REVERT: A 60 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8100 (t0) REVERT: A 217 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8783 (tp) REVERT: A 383 ARG cc_start: 0.8901 (mtt180) cc_final: 0.8438 (mmt90) REVERT: A 462 MET cc_start: 0.7248 (pmm) cc_final: 0.6910 (pmm) REVERT: B 180 TRP cc_start: 0.8016 (p-90) cc_final: 0.7650 (p-90) REVERT: B 217 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8876 (tp) REVERT: B 226 LEU cc_start: 0.7717 (tp) cc_final: 0.7408 (tp) REVERT: C 217 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8803 (tp) REVERT: C 226 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7376 (tp) REVERT: C 383 ARG cc_start: 0.8811 (mtt180) cc_final: 0.8430 (mpt-90) REVERT: C 462 MET cc_start: 0.6304 (pmm) cc_final: 0.6046 (pmm) outliers start: 29 outliers final: 23 residues processed: 115 average time/residue: 0.0909 time to fit residues: 16.4138 Evaluate side-chains 113 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 382 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 62 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 GLN ** 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 = 0.4074 r_free = 0.4074 target = 0.137295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093211 restraints weight = 30443.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.094784 restraints weight = 24228.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.095035 restraints weight = 18451.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.095070 restraints weight = 19178.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.095190 restraints weight = 17548.275| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 12252 Z= 0.255 Angle : 0.749 13.097 16683 Z= 0.368 Chirality : 0.045 0.291 1917 Planarity : 0.005 0.070 2118 Dihedral : 4.971 47.661 1578 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.44 % Allowed : 20.91 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.59 (0.21), residues: 1452 helix: 2.45 (0.25), residues: 414 sheet: -0.09 (0.35), residues: 207 loop : -2.12 (0.18), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 405 TYR 0.020 0.002 TYR B 423 PHE 0.020 0.002 PHE A 467 TRP 0.023 0.002 TRP A 180 HIS 0.010 0.001 HIS C 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.26 (12198) covalent geometry : angle 0.71207 / 0.36 (16539) SS BOND : bond 0.00698 / 0.38 ( 18) SS BOND : angle 3.55914 / 2.09 ( 36) hydrogen bonds : bond 0.03904 / 2.70 ( 474) hydrogen bonds : angle 4.55377 / 3.18 ( 1404) link_BETA1-4 : bond 0.00436 / 0.24 ( 18) link_BETA1-4 : angle 1.55716 / 1.06 ( 54) link_BETA1-6 : bond 0.00178 / 0.09 ( 3) link_BETA1-6 : angle 1.30865 / 0.73 ( 9) link_NAG-ASN : bond 0.00573 / 0.33 ( 15) link_NAG-ASN : angle 2.85338 / 1.90 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1917.09 seconds wall clock time: 34 minutes 1.93 seconds (2041.93 seconds total)