Starting phenix.real_space_refine on Wed Mar 4 08:45:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zj7_14743/03_2026/7zj7_14743.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zj7_14743/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zj7_14743/03_2026/7zj7_14743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zj7_14743/03_2026/7zj7_14743.map" model { file = "/net/cci-nas-00/data/ceres_data/7zj7_14743/03_2026/7zj7_14743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zj7_14743/03_2026/7zj7_14743.cif" } 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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, I, L, K, O Time building chain proxies: 3.13, per 1000 atoms: 0.26 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: 1.09 Conformation dependent library (CDL) restraints added in 494.0 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: 0.39 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: 1.90 Time building geometry restraints manager: 1.36 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 - 21.00: 7073 21.00 - 42.00: 547 42.00 - 62.99: 87 62.99 - 83.99: 54 83.99 - 104.99: 30 Dihedral angle restraints: 7791 sinusoidal: 3606 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 7788 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.990 Find NCS groups from input model: 0.240 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 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 : 17.474 104.989 5055 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 covalent geometry : bond 0.01343 (12198) covalent geometry : angle 1.89524 (16539) SS BOND : bond 0.01455 ( 18) SS BOND : angle 2.01678 ( 36) hydrogen bonds : bond 0.18730 ( 474) hydrogen bonds : angle 7.57323 ( 1404) link_BETA1-4 : bond 0.00696 ( 18) link_BETA1-4 : angle 2.91893 ( 54) link_BETA1-6 : bond 0.00576 ( 3) link_BETA1-6 : angle 1.56370 ( 9) link_NAG-ASN : bond 0.00636 ( 15) link_NAG-ASN : angle 3.90323 ( 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 : 0.451 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: 0.0922 time to fit residues: 31.0292 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 : 0.435 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS B 54 ASN 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 = 0.142448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.099685 restraints weight = 30039.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.100857 restraints weight = 19534.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.100765 restraints weight = 15542.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.100902 restraints weight = 16088.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.101169 restraints weight = 14621.630| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12252 Z= 0.147 Angle : 0.784 11.910 16683 Z= 0.379 Chirality : 0.050 0.577 1917 Planarity : 0.004 0.036 2118 Dihedral : 11.432 66.439 2316 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.04 % Allowed : 14.86 % 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: -0.19 (0.37), residues: 168 loop : -2.52 (0.15), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 405 TYR 0.019 0.002 TYR B 105 PHE 0.010 0.001 PHE A 258 TRP 0.019 0.001 TRP A 343 HIS 0.009 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00304 (12198) covalent geometry : angle 0.73438 (16539) SS BOND : bond 0.00923 ( 18) SS BOND : angle 1.27686 ( 36) hydrogen bonds : bond 0.04161 ( 474) hydrogen bonds : angle 5.29790 ( 1404) link_BETA1-4 : bond 0.00776 ( 18) link_BETA1-4 : angle 2.67516 ( 54) link_BETA1-6 : bond 0.00247 ( 3) link_BETA1-6 : angle 1.34370 ( 9) link_NAG-ASN : bond 0.00563 ( 15) link_NAG-ASN : angle 4.42640 ( 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 169 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.405 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: 0.8848 (mtmm) cc_final: 0.8620 (mtmm) REVERT: A 222 TRP cc_start: 0.8718 (m100) cc_final: 0.7999 (m-90) REVERT: A 383 ARG cc_start: 0.8870 (mtt180) cc_final: 0.8509 (mpt-90) REVERT: A 452 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7924 (tpm170) REVERT: B 222 TRP cc_start: 0.8627 (m100) cc_final: 0.7659 (t-100) REVERT: B 236 ILE cc_start: 0.9309 (mt) cc_final: 0.8923 (tt) REVERT: B 399 PHE cc_start: 0.9260 (OUTLIER) cc_final: 0.8492 (t80) REVERT: C 85 ASP cc_start: 0.8252 (m-30) cc_final: 0.7857 (t70) REVERT: C 222 TRP cc_start: 0.8708 (m100) cc_final: 0.8224 (m-90) REVERT: C 383 ARG cc_start: 0.8758 (mtt180) cc_final: 0.8363 (mpt-90) REVERT: C 399 PHE cc_start: 0.9342 (OUTLIER) cc_final: 0.8681 (t80) REVERT: C 452 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8024 (tpm170) outliers start: 26 outliers final: 10 residues processed: 163 average time/residue: 0.1051 time to fit residues: 25.0290 Evaluate side-chains 98 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU 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: 2.9990 chunk 46 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 131 optimal weight: 30.0000 chunk 77 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4096 r_free = 0.4096 target = 0.138604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.092651 restraints weight = 30145.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.094948 restraints weight = 19988.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.096273 restraints weight = 16011.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.096713 restraints weight = 14308.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.096713 restraints weight = 13580.691| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 12252 Z= 0.245 Angle : 0.830 13.162 16683 Z= 0.407 Chirality : 0.050 0.372 1917 Planarity : 0.004 0.070 2118 Dihedral : 8.884 55.361 2314 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.83 % Allowed : 16.59 % Favored : 80.58 % 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: -1.08 (0.20), residues: 1452 helix: 2.31 (0.25), residues: 414 sheet: -0.30 (0.34), residues: 207 loop : -2.62 (0.16), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 405 TYR 0.019 0.002 TYR B 423 PHE 0.016 0.002 PHE C 332 TRP 0.017 0.002 TRP A 343 HIS 0.005 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00568 (12198) covalent geometry : angle 0.79388 (16539) SS BOND : bond 0.01041 ( 18) SS BOND : angle 2.53926 ( 36) hydrogen bonds : bond 0.04323 ( 474) hydrogen bonds : angle 5.21559 ( 1404) link_BETA1-4 : bond 0.00525 ( 18) link_BETA1-4 : angle 1.84046 ( 54) link_BETA1-6 : bond 0.00188 ( 3) link_BETA1-6 : angle 1.28813 ( 9) link_NAG-ASN : bond 0.00615 ( 15) link_NAG-ASN : angle 3.72971 ( 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 136 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.547 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: 0.8892 (mtmm) cc_final: 0.8655 (mtmm) REVERT: A 85 ASP cc_start: 0.8163 (m-30) cc_final: 0.7947 (t70) REVERT: A 383 ARG cc_start: 0.8912 (mtt180) cc_final: 0.8385 (mpt-90) REVERT: A 462 MET cc_start: 0.7250 (ptp) cc_final: 0.6989 (pmm) REVERT: B 382 ASN cc_start: 0.6931 (OUTLIER) cc_final: 0.6724 (t0) REVERT: B 399 PHE cc_start: 0.9365 (OUTLIER) cc_final: 0.8529 (t80) REVERT: B 462 MET cc_start: 0.7356 (ptp) cc_final: 0.7052 (pmm) REVERT: C 85 ASP cc_start: 0.8335 (m-30) cc_final: 0.8001 (t70) REVERT: C 383 ARG cc_start: 0.8813 (mtt180) cc_final: 0.8417 (mpt-90) REVERT: C 399 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.8767 (t80) outliers start: 36 outliers final: 13 residues processed: 130 average time/residue: 0.1137 time to fit residues: 21.0247 Evaluate side-chains 97 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 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 166 VAL 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 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: 10.0000 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 137 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4108 r_free = 0.4108 target = 0.139704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.094120 restraints weight = 29677.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.095981 restraints weight = 20028.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.096659 restraints weight = 15400.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.096740 restraints weight = 15490.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.096895 restraints weight = 14523.951| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12252 Z= 0.132 Angle : 0.716 11.217 16683 Z= 0.350 Chirality : 0.045 0.303 1917 Planarity : 0.004 0.054 2118 Dihedral : 7.610 54.758 2314 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.12 % Allowed : 17.77 % Favored : 80.11 % 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: -0.76 (0.21), residues: 1452 helix: 2.63 (0.26), residues: 414 sheet: -0.07 (0.33), residues: 213 loop : -2.49 (0.17), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 329 TYR 0.014 0.001 TYR B 195 PHE 0.014 0.001 PHE C 467 TRP 0.016 0.001 TRP B 343 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00292 (12198) covalent geometry : angle 0.68440 (16539) SS BOND : bond 0.00789 ( 18) SS BOND : angle 2.31812 ( 36) hydrogen bonds : bond 0.03622 ( 474) hydrogen bonds : angle 4.71191 ( 1404) link_BETA1-4 : bond 0.00594 ( 18) link_BETA1-4 : angle 1.65906 ( 54) link_BETA1-6 : bond 0.00298 ( 3) link_BETA1-6 : angle 1.11536 ( 9) link_NAG-ASN : bond 0.00365 ( 15) link_NAG-ASN : angle 3.13457 ( 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 122 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.538 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: 0.8809 (mtmm) cc_final: 0.8506 (mtmm) REVERT: A 85 ASP cc_start: 0.8042 (m-30) cc_final: 0.7650 (t70) REVERT: A 383 ARG cc_start: 0.8911 (mtt180) cc_final: 0.8377 (mpt-90) REVERT: A 462 MET cc_start: 0.7365 (ptp) cc_final: 0.7036 (pmm) REVERT: B 399 PHE cc_start: 0.9366 (OUTLIER) cc_final: 0.9087 (m-80) REVERT: C 85 ASP cc_start: 0.8280 (m-30) cc_final: 0.7885 (t70) REVERT: C 383 ARG cc_start: 0.8822 (mtt180) cc_final: 0.8411 (mpt-90) REVERT: C 399 PHE cc_start: 0.9322 (OUTLIER) cc_final: 0.8574 (t80) outliers start: 27 outliers final: 16 residues processed: 116 average time/residue: 0.0860 time to fit residues: 15.7508 Evaluate side-chains 97 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 167 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 167 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 102 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 HIS B 133 ASN 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 = 0.4081 r_free = 0.4081 target = 0.137724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.091712 restraints weight = 29468.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.092602 restraints weight = 23503.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.092962 restraints weight = 18076.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.093120 restraints weight = 16345.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.093227 restraints weight = 16969.197| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12252 Z= 0.202 Angle : 0.721 11.043 16683 Z= 0.353 Chirality : 0.045 0.308 1917 Planarity : 0.004 0.064 2118 Dihedral : 7.422 54.619 2314 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.86 % Favored : 96.07 % Rotamer: Outliers : 2.67 % Allowed : 18.24 % Favored : 79.09 % 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: -0.79 (0.21), residues: 1452 helix: 2.46 (0.26), residues: 414 sheet: -0.04 (0.33), residues: 213 loop : -2.42 (0.17), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 405 TYR 0.016 0.002 TYR B 423 PHE 0.021 0.002 PHE C 467 TRP 0.013 0.001 TRP B 343 HIS 0.011 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00467 (12198) covalent geometry : angle 0.69065 (16539) SS BOND : bond 0.00723 ( 18) SS BOND : angle 2.26555 ( 36) hydrogen bonds : bond 0.03760 ( 474) hydrogen bonds : angle 4.78379 ( 1404) link_BETA1-4 : bond 0.00572 ( 18) link_BETA1-4 : angle 1.63276 ( 54) link_BETA1-6 : bond 0.00237 ( 3) link_BETA1-6 : angle 1.18413 ( 9) link_NAG-ASN : bond 0.00466 ( 15) link_NAG-ASN : angle 3.12630 ( 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 124 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 TRP cc_start: 0.8687 (m100) cc_final: 0.8167 (m100) REVERT: A 383 ARG cc_start: 0.8922 (mtt180) cc_final: 0.8375 (mpt-90) REVERT: B 222 TRP cc_start: 0.8593 (m100) cc_final: 0.8167 (m100) REVERT: B 399 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.9098 (m-80) REVERT: C 85 ASP cc_start: 0.8304 (m-30) cc_final: 0.8082 (t70) REVERT: C 222 TRP cc_start: 0.8730 (m100) cc_final: 0.8310 (m100) REVERT: C 226 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.6937 (tp) REVERT: C 246 ASN cc_start: 0.8162 (m110) cc_final: 0.7894 (m110) REVERT: C 383 ARG cc_start: 0.8847 (mtt180) cc_final: 0.8435 (mpt-90) REVERT: C 399 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.8629 (t80) REVERT: C 462 MET cc_start: 0.6620 (pmm) cc_final: 0.6328 (pmm) outliers start: 34 outliers final: 20 residues processed: 120 average time/residue: 0.0869 time to fit residues: 16.3163 Evaluate side-chains 97 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 126 THR Chi-restraints excluded: chain B residue 167 THR 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 167 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 19 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 25 optimal weight: 0.4980 chunk 85 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4076 r_free = 0.4076 target = 0.137491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.091878 restraints weight = 30167.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.093956 restraints weight = 21688.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.093943 restraints weight = 16794.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.094392 restraints weight = 16273.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.094565 restraints weight = 16478.194| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12252 Z= 0.235 Angle : 0.759 12.593 16683 Z= 0.373 Chirality : 0.046 0.327 1917 Planarity : 0.005 0.067 2118 Dihedral : 7.577 58.121 2314 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.48 % Favored : 95.39 % Rotamer: Outliers : 2.83 % Allowed : 18.63 % Favored : 78.54 % 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: -0.82 (0.20), residues: 1452 helix: 2.35 (0.25), residues: 411 sheet: -0.09 (0.34), residues: 207 loop : -2.35 (0.17), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 405 TYR 0.018 0.002 TYR C 423 PHE 0.016 0.002 PHE A 467 TRP 0.013 0.002 TRP B 343 HIS 0.005 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00546 (12198) covalent geometry : angle 0.72484 (16539) SS BOND : bond 0.00866 ( 18) SS BOND : angle 3.05001 ( 36) hydrogen bonds : bond 0.03955 ( 474) hydrogen bonds : angle 4.81612 ( 1404) link_BETA1-4 : bond 0.00552 ( 18) link_BETA1-4 : angle 1.64376 ( 54) link_BETA1-6 : bond 0.00183 ( 3) link_BETA1-6 : angle 1.23712 ( 9) link_NAG-ASN : bond 0.00562 ( 15) link_NAG-ASN : angle 3.07847 ( 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 118 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 82 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8821 (mtmm) cc_final: 0.8501 (mtmm) REVERT: A 222 TRP cc_start: 0.8671 (m100) cc_final: 0.8215 (m100) REVERT: A 383 ARG cc_start: 0.8942 (mtt180) cc_final: 0.8511 (mmt90) REVERT: B 217 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8832 (tp) REVERT: B 222 TRP cc_start: 0.8594 (m100) cc_final: 0.8299 (m100) REVERT: B 390 GLU cc_start: 0.8682 (pp20) cc_final: 0.8457 (pp20) REVERT: B 399 PHE cc_start: 0.9390 (OUTLIER) cc_final: 0.9102 (m-80) REVERT: C 217 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8769 (tp) REVERT: C 222 TRP cc_start: 0.8692 (m100) cc_final: 0.8357 (m100) REVERT: C 226 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.6987 (tp) REVERT: C 246 ASN cc_start: 0.8218 (m110) cc_final: 0.7944 (m110) REVERT: C 383 ARG cc_start: 0.8863 (mtt180) cc_final: 0.8446 (mpt-90) REVERT: C 462 MET cc_start: 0.6828 (pmm) cc_final: 0.6560 (pmm) outliers start: 36 outliers final: 20 residues processed: 114 average time/residue: 0.0902 time to fit residues: 15.8388 Evaluate side-chains 98 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 166 VAL 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 B residue 399 PHE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 29 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 140 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 127 optimal weight: 0.3980 chunk 50 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 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 = 0.4097 r_free = 0.4097 target = 0.138921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.093876 restraints weight = 29825.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.096276 restraints weight = 19096.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.097711 restraints weight = 15180.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.098346 restraints weight = 13503.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.098480 restraints weight = 12754.857| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12252 Z= 0.150 Angle : 0.724 12.997 16683 Z= 0.352 Chirality : 0.044 0.288 1917 Planarity : 0.004 0.061 2118 Dihedral : 7.419 59.865 2312 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.65 % Favored : 96.28 % Rotamer: Outliers : 2.59 % Allowed : 19.26 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.65 (0.21), residues: 1452 helix: 2.48 (0.26), residues: 414 sheet: -0.08 (0.34), residues: 207 loop : -2.23 (0.17), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 90 TYR 0.017 0.002 TYR C 302 PHE 0.012 0.001 PHE A 467 TRP 0.015 0.001 TRP B 343 HIS 0.006 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00342 (12198) covalent geometry : angle 0.67993 (16539) SS BOND : bond 0.01090 ( 18) SS BOND : angle 4.12381 ( 36) hydrogen bonds : bond 0.03622 ( 474) hydrogen bonds : angle 4.56948 ( 1404) link_BETA1-4 : bond 0.00551 ( 18) link_BETA1-4 : angle 1.51356 ( 54) link_BETA1-6 : bond 0.00249 ( 3) link_BETA1-6 : angle 1.15178 ( 9) link_NAG-ASN : bond 0.00383 ( 15) link_NAG-ASN : angle 2.82008 ( 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 119 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 86 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8863 (mtmm) cc_final: 0.8553 (mtmm) REVERT: A 217 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8803 (tp) REVERT: A 222 TRP cc_start: 0.8327 (m100) cc_final: 0.8100 (m100) REVERT: A 383 ARG cc_start: 0.8899 (mtt180) cc_final: 0.8370 (mpt-90) REVERT: A 462 MET cc_start: 0.6897 (pmm) cc_final: 0.6493 (pmm) REVERT: B 217 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8872 (tp) REVERT: C 217 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8760 (tp) REVERT: C 226 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.6796 (tp) REVERT: C 246 ASN cc_start: 0.8250 (m110) cc_final: 0.7951 (m110) REVERT: C 383 ARG cc_start: 0.8840 (mtt180) cc_final: 0.8417 (mpt-90) REVERT: C 462 MET cc_start: 0.6650 (pmm) cc_final: 0.6409 (pmm) outliers start: 33 outliers final: 20 residues processed: 115 average time/residue: 0.0990 time to fit residues: 17.0582 Evaluate side-chains 101 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 208 ARG 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 40 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 49 optimal weight: 0.0060 chunk 51 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 chunk 128 optimal weight: 0.0070 chunk 80 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN B 246 ASN ** 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 = 0.4107 r_free = 0.4107 target = 0.139654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.094188 restraints weight = 29555.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.095938 restraints weight = 19253.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.095974 restraints weight = 14196.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.096219 restraints weight = 15113.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.096332 restraints weight = 14180.106| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12252 Z= 0.119 Angle : 0.715 14.426 16683 Z= 0.348 Chirality : 0.044 0.284 1917 Planarity : 0.004 0.054 2118 Dihedral : 7.236 56.360 2310 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.89 % Allowed : 20.75 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.47 (0.21), residues: 1452 helix: 2.64 (0.26), residues: 414 sheet: -0.09 (0.35), residues: 207 loop : -2.09 (0.18), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 224 TYR 0.014 0.001 TYR B 105 PHE 0.010 0.001 PHE A 467 TRP 0.018 0.002 TRP B 222 HIS 0.009 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00264 (12198) covalent geometry : angle 0.66923 (16539) SS BOND : bond 0.00572 ( 18) SS BOND : angle 4.41698 ( 36) hydrogen bonds : bond 0.03389 ( 474) hydrogen bonds : angle 4.36672 ( 1404) link_BETA1-4 : bond 0.00554 ( 18) link_BETA1-4 : angle 1.43844 ( 54) link_BETA1-6 : bond 0.00399 ( 3) link_BETA1-6 : angle 1.10398 ( 9) link_NAG-ASN : bond 0.00302 ( 15) link_NAG-ASN : angle 2.59283 ( 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 114 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8864 (mtmm) cc_final: 0.8541 (mtmm) REVERT: A 139 CYS cc_start: 0.5089 (t) cc_final: 0.4587 (t) REVERT: A 217 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8812 (tp) REVERT: A 222 TRP cc_start: 0.8705 (m100) cc_final: 0.8291 (m100) REVERT: A 383 ARG cc_start: 0.8931 (mtt180) cc_final: 0.8452 (mmt90) REVERT: A 462 MET cc_start: 0.6841 (pmm) cc_final: 0.6450 (pmm) REVERT: B 217 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8905 (tp) REVERT: B 222 TRP cc_start: 0.8400 (m100) cc_final: 0.7294 (t-100) REVERT: C 217 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8796 (tp) REVERT: C 222 TRP cc_start: 0.8676 (m100) cc_final: 0.7373 (t-100) REVERT: C 246 ASN cc_start: 0.8210 (m110) cc_final: 0.7969 (m110) REVERT: C 383 ARG cc_start: 0.8883 (mtt180) cc_final: 0.8440 (mpt-90) REVERT: C 462 MET cc_start: 0.6683 (pmm) cc_final: 0.6410 (pmm) outliers start: 24 outliers final: 20 residues processed: 111 average time/residue: 0.0912 time to fit residues: 15.7691 Evaluate side-chains 104 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 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 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 223 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 382 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 104 optimal weight: 0.0370 chunk 99 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 31 optimal weight: 20.0000 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4109 r_free = 0.4109 target = 0.141849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.094195 restraints weight = 28758.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.097090 restraints weight = 19366.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.097229 restraints weight = 13914.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.097304 restraints weight = 13847.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.097599 restraints weight = 13586.196| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12252 Z= 0.127 Angle : 0.708 14.539 16683 Z= 0.345 Chirality : 0.044 0.281 1917 Planarity : 0.004 0.055 2118 Dihedral : 7.165 56.171 2310 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.04 % Allowed : 20.99 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.41 (0.21), residues: 1452 helix: 2.66 (0.26), residues: 414 sheet: -0.04 (0.35), residues: 207 loop : -2.03 (0.18), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 208 TYR 0.013 0.001 TYR B 105 PHE 0.009 0.001 PHE C 467 TRP 0.018 0.001 TRP A 180 HIS 0.008 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00288 (12198) covalent geometry : angle 0.66172 (16539) SS BOND : bond 0.00498 ( 18) SS BOND : angle 4.41319 ( 36) hydrogen bonds : bond 0.03379 ( 474) hydrogen bonds : angle 4.29719 ( 1404) link_BETA1-4 : bond 0.00535 ( 18) link_BETA1-4 : angle 1.43831 ( 54) link_BETA1-6 : bond 0.00336 ( 3) link_BETA1-6 : angle 1.12765 ( 9) link_NAG-ASN : bond 0.00286 ( 15) link_NAG-ASN : angle 2.54005 ( 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 115 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8864 (mtmm) cc_final: 0.8534 (mtmm) REVERT: A 139 CYS cc_start: 0.5114 (t) cc_final: 0.4606 (t) REVERT: A 217 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8804 (tp) REVERT: A 383 ARG cc_start: 0.8908 (mtt180) cc_final: 0.8447 (mmt90) REVERT: A 462 MET cc_start: 0.6680 (pmm) cc_final: 0.6311 (pmm) REVERT: B 217 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8895 (tp) REVERT: B 222 TRP cc_start: 0.8351 (m100) cc_final: 0.7250 (t-100) REVERT: B 390 GLU cc_start: 0.8624 (pp20) cc_final: 0.8405 (pp20) REVERT: C 217 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8751 (tp) REVERT: C 222 TRP cc_start: 0.8616 (m100) cc_final: 0.7310 (t-100) REVERT: C 246 ASN cc_start: 0.8314 (m110) cc_final: 0.8071 (m110) REVERT: C 383 ARG cc_start: 0.8792 (mtt180) cc_final: 0.8390 (mpt-90) REVERT: C 462 MET cc_start: 0.6484 (pmm) cc_final: 0.6210 (pmm) outliers start: 26 outliers final: 20 residues processed: 110 average time/residue: 0.0837 time to fit residues: 14.4232 Evaluate side-chains 110 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 43 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 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 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 223 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 28 optimal weight: 0.7980 chunk 68 optimal weight: 0.0470 chunk 55 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4109 r_free = 0.4109 target = 0.141975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.095434 restraints weight = 29099.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.096993 restraints weight = 19526.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.097172 restraints weight = 14564.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.097554 restraints weight = 14393.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.097684 restraints weight = 13504.278| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12252 Z= 0.124 Angle : 0.660 11.731 16683 Z= 0.321 Chirality : 0.043 0.278 1917 Planarity : 0.004 0.054 2118 Dihedral : 6.988 59.681 2310 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.97 % Allowed : 20.75 % Favored : 77.28 % 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: -0.32 (0.21), residues: 1452 helix: 2.70 (0.26), residues: 414 sheet: 0.12 (0.35), residues: 201 loop : -1.97 (0.18), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 383 TYR 0.013 0.001 TYR B 105 PHE 0.009 0.001 PHE C 467 TRP 0.024 0.002 TRP C 343 HIS 0.007 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00282 (12198) covalent geometry : angle 0.63127 (16539) SS BOND : bond 0.00497 ( 18) SS BOND : angle 2.74108 ( 36) hydrogen bonds : bond 0.03334 ( 474) hydrogen bonds : angle 4.23966 ( 1404) link_BETA1-4 : bond 0.00536 ( 18) link_BETA1-4 : angle 1.42976 ( 54) link_BETA1-6 : bond 0.00322 ( 3) link_BETA1-6 : angle 1.15072 ( 9) link_NAG-ASN : bond 0.00290 ( 15) link_NAG-ASN : angle 2.47578 ( 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 112 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8852 (mtmm) cc_final: 0.8564 (mtmm) REVERT: A 217 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8813 (tp) REVERT: A 383 ARG cc_start: 0.8889 (mtt180) cc_final: 0.8424 (mmt90) REVERT: A 462 MET cc_start: 0.6572 (pmm) cc_final: 0.6180 (pmm) REVERT: B 180 TRP cc_start: 0.8162 (p-90) cc_final: 0.7768 (p-90) REVERT: B 217 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8900 (tp) REVERT: B 222 TRP cc_start: 0.8364 (m100) cc_final: 0.7289 (t-100) REVERT: B 390 GLU cc_start: 0.8662 (pp20) cc_final: 0.8441 (pp20) REVERT: C 217 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8758 (tp) REVERT: C 222 TRP cc_start: 0.8657 (m100) cc_final: 0.7333 (t-100) REVERT: C 383 ARG cc_start: 0.8852 (mtt180) cc_final: 0.8458 (mpt-90) REVERT: C 462 MET cc_start: 0.6547 (pmm) cc_final: 0.6279 (pmm) outliers start: 25 outliers final: 19 residues processed: 109 average time/residue: 0.0941 time to fit residues: 15.6407 Evaluate side-chains 103 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 43 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 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 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 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: 9.9990 chunk 117 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 80 optimal weight: 0.0670 chunk 50 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4079 r_free = 0.4079 target = 0.137722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.091450 restraints weight = 30111.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.093997 restraints weight = 18997.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.095422 restraints weight = 14918.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.095902 restraints weight = 13284.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.096610 restraints weight = 12601.015| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 12252 Z= 0.240 Angle : 0.739 13.089 16683 Z= 0.365 Chirality : 0.046 0.289 1917 Planarity : 0.005 0.068 2118 Dihedral : 7.180 59.503 2310 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.04 % Allowed : 20.99 % Favored : 76.97 % 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: -0.60 (0.21), residues: 1452 helix: 2.50 (0.25), residues: 411 sheet: -0.11 (0.35), residues: 207 loop : -2.15 (0.18), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 405 TYR 0.019 0.002 TYR B 423 PHE 0.014 0.002 PHE B 87 TRP 0.020 0.002 TRP A 180 HIS 0.008 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00562 (12198) covalent geometry : angle 0.70472 (16539) SS BOND : bond 0.00650 ( 18) SS BOND : angle 3.38170 ( 36) hydrogen bonds : bond 0.03846 ( 474) hydrogen bonds : angle 4.52548 ( 1404) link_BETA1-4 : bond 0.00508 ( 18) link_BETA1-4 : angle 1.58079 ( 54) link_BETA1-6 : bond 0.00264 ( 3) link_BETA1-6 : angle 1.34697 ( 9) link_NAG-ASN : bond 0.00543 ( 15) link_NAG-ASN : angle 2.73569 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1890.20 seconds wall clock time: 33 minutes 26.12 seconds (2006.12 seconds total)