Starting phenix.real_space_refine on Wed Jul 30 11:05:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zj7_14743/07_2025/7zj7_14743.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zj7_14743/07_2025/7zj7_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_14743/07_2025/7zj7_14743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zj7_14743/07_2025/7zj7_14743.map" model { file = "/net/cci-nas-00/data/ceres_data/7zj7_14743/07_2025/7zj7_14743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zj7_14743/07_2025/7zj7_14743.cif" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.94, per 1000 atoms: 0.75 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: 3.60 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.86 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: 4.42 Time building geometry restraints manager: 4.21 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: 0.09 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: 44.660 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: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 33.890 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 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:3.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.560 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.022 0.004 TRP A 350 HIS 0.013 0.003 HIS C 56 PHE 0.023 0.004 PHE C 294 TYR 0.044 0.004 TYR C 423 ARG 0.006 0.001 ARG C 255 Details of bonding type rmsd link_NAG-ASN : bond 0.00636 ( 15) link_NAG-ASN : angle 3.90323 ( 45) link_BETA1-4 : bond 0.00696 ( 18) link_BETA1-4 : angle 2.91893 ( 54) hydrogen bonds : bond 0.18730 ( 474) hydrogen bonds : angle 7.57323 ( 1404) link_BETA1-6 : bond 0.00576 ( 3) link_BETA1-6 : angle 1.56370 ( 9) SS BOND : bond 0.01455 ( 18) SS BOND : angle 2.01678 ( 36) covalent geometry : bond 0.01343 (12198) covalent geometry : angle 1.89524 (16539) *********************** 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 : 1.464 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: 0.8779 (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: 0.8531 (t80) REVERT: C 85 ASP cc_start: 0.8851 (m-30) cc_final: 0.7986 (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 344 GLU cc_start: 0.8733 (tt0) cc_final: 0.8410 (tt0) 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: 0.8335 (m110) outliers start: 7 outliers final: 0 residues processed: 226 average time/residue: 0.2428 time to fit residues: 80.4915 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 : 1.676 ------------------------------------------------------------------------------- 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 121 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 HIS C 54 ASN C 216 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.140319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.096675 restraints weight = 29699.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.097222 restraints weight = 21340.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.097259 restraints weight = 17226.763| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12252 Z= 0.227 Angle : 0.834 12.358 16683 Z= 0.407 Chirality : 0.049 0.464 1917 Planarity : 0.004 0.050 2118 Dihedral : 11.687 67.758 2316 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.36 % Allowed : 15.49 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.19), residues: 1452 helix: 1.84 (0.24), residues: 414 sheet: -0.16 (0.37), residues: 168 loop : -2.63 (0.15), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 343 HIS 0.009 0.001 HIS B 17 PHE 0.012 0.001 PHE B 294 TYR 0.020 0.002 TYR C 105 ARG 0.004 0.001 ARG A 405 Details of bonding type rmsd link_NAG-ASN : bond 0.00757 ( 15) link_NAG-ASN : angle 4.50925 ( 45) link_BETA1-4 : bond 0.00824 ( 18) link_BETA1-4 : angle 2.75078 ( 54) hydrogen bonds : bond 0.04388 ( 474) hydrogen bonds : angle 5.53306 ( 1404) link_BETA1-6 : bond 0.00129 ( 3) link_BETA1-6 : angle 1.51688 ( 9) SS BOND : bond 0.00892 ( 18) SS BOND : angle 1.29838 ( 36) covalent geometry : bond 0.00507 (12198) covalent geometry : angle 0.78572 (16539) *********************** 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: 30 poor density : 139 time to evaluate : 1.335 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: 0.8865 (mtmm) cc_final: 0.8632 (mtmm) REVERT: A 66 LEU cc_start: 0.8808 (tp) cc_final: 0.8582 (tp) REVERT: A 222 TRP cc_start: 0.8785 (m100) cc_final: 0.8146 (m-90) REVERT: A 383 ARG cc_start: 0.8889 (mtt180) cc_final: 0.8601 (mpt-90) REVERT: A 399 PHE cc_start: 0.9338 (OUTLIER) cc_final: 0.8664 (t80) REVERT: A 452 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7984 (tpm170) REVERT: B 222 TRP cc_start: 0.8693 (m100) cc_final: 0.7663 (t-100) REVERT: B 236 ILE cc_start: 0.9329 (mt) cc_final: 0.8927 (tt) REVERT: B 399 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8591 (t80) REVERT: C 85 ASP cc_start: 0.8388 (m-30) cc_final: 0.8038 (t70) REVERT: C 222 TRP cc_start: 0.8731 (m100) cc_final: 0.8269 (m-90) REVERT: C 383 ARG cc_start: 0.8763 (mtt180) cc_final: 0.8396 (mpt-90) REVERT: C 399 PHE cc_start: 0.9391 (OUTLIER) cc_final: 0.8714 (t80) REVERT: C 452 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7958 (tpm170) outliers start: 30 outliers final: 7 residues processed: 163 average time/residue: 0.2355 time to fit residues: 55.8208 Evaluate side-chains 98 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 399 PHE 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 399 PHE Chi-restraints excluded: chain C residue 166 VAL 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 105 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 47 optimal weight: 0.3980 chunk 111 optimal weight: 10.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.140631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.095510 restraints weight = 30147.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.098841 restraints weight = 21247.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.098739 restraints weight = 14750.806| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12252 Z= 0.158 Angle : 0.762 13.566 16683 Z= 0.371 Chirality : 0.047 0.326 1917 Planarity : 0.004 0.050 2118 Dihedral : 9.002 55.586 2316 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.36 % Allowed : 17.22 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.20), residues: 1452 helix: 2.53 (0.25), residues: 414 sheet: 0.34 (0.39), residues: 162 loop : -2.51 (0.16), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 343 HIS 0.012 0.001 HIS C 17 PHE 0.008 0.001 PHE B 294 TYR 0.016 0.002 TYR C 105 ARG 0.003 0.000 ARG C 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 15) link_NAG-ASN : angle 3.55585 ( 45) link_BETA1-4 : bond 0.00686 ( 18) link_BETA1-4 : angle 1.80695 ( 54) hydrogen bonds : bond 0.03899 ( 474) hydrogen bonds : angle 4.98486 ( 1404) link_BETA1-6 : bond 0.00194 ( 3) link_BETA1-6 : angle 1.18719 ( 9) SS BOND : bond 0.00781 ( 18) SS BOND : angle 2.60135 ( 36) covalent geometry : bond 0.00354 (12198) covalent geometry : angle 0.72422 (16539) *********************** 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 137 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8830 (mtmm) cc_final: 0.8595 (mtmm) REVERT: A 85 ASP cc_start: 0.7949 (m-30) cc_final: 0.7498 (t70) REVERT: A 331 LEU cc_start: 0.7489 (mt) cc_final: 0.7058 (mt) REVERT: A 383 ARG cc_start: 0.8912 (mtt180) cc_final: 0.8454 (mpt-90) REVERT: A 399 PHE cc_start: 0.9355 (OUTLIER) cc_final: 0.9147 (m-80) REVERT: A 462 MET cc_start: 0.7219 (ptp) cc_final: 0.6983 (pmm) REVERT: B 399 PHE cc_start: 0.9319 (OUTLIER) cc_final: 0.8492 (t80) REVERT: B 462 MET cc_start: 0.7247 (ptp) cc_final: 0.7010 (pmm) REVERT: C 85 ASP cc_start: 0.8202 (m-30) cc_final: 0.7872 (t70) REVERT: C 383 ARG cc_start: 0.8783 (mtt180) cc_final: 0.8365 (mpt-90) REVERT: C 399 PHE cc_start: 0.9326 (OUTLIER) cc_final: 0.8611 (t80) outliers start: 30 outliers final: 9 residues processed: 132 average time/residue: 0.2684 time to fit residues: 50.5947 Evaluate side-chains 96 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 1.534 ------------------------------------------------------------------------------- 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 167 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 399 PHE 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 67 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 216 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN B 216 ASN B 246 ASN C 133 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.135980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.089776 restraints weight = 29816.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.091787 restraints weight = 20072.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093111 restraints weight = 16371.709| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 12252 Z= 0.351 Angle : 0.890 10.741 16683 Z= 0.442 Chirality : 0.051 0.410 1917 Planarity : 0.005 0.083 2118 Dihedral : 8.323 56.203 2316 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.46 % Allowed : 17.92 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.20), residues: 1452 helix: 2.05 (0.25), residues: 414 sheet: -0.26 (0.32), residues: 213 loop : -2.68 (0.16), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 180 HIS 0.004 0.001 HIS A 17 PHE 0.025 0.003 PHE A 87 TYR 0.026 0.003 TYR C 423 ARG 0.006 0.001 ARG A 329 Details of bonding type rmsd link_NAG-ASN : bond 0.00782 ( 15) link_NAG-ASN : angle 3.57421 ( 45) link_BETA1-4 : bond 0.00572 ( 18) link_BETA1-4 : angle 1.97924 ( 54) hydrogen bonds : bond 0.04689 ( 474) hydrogen bonds : angle 5.32654 ( 1404) link_BETA1-6 : bond 0.00089 ( 3) link_BETA1-6 : angle 1.34430 ( 9) SS BOND : bond 0.01321 ( 18) SS BOND : angle 2.20882 ( 36) covalent geometry : bond 0.00814 (12198) covalent geometry : angle 0.86002 (16539) *********************** 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 131 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 87 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8333 (m-30) cc_final: 0.8110 (t70) REVERT: A 226 LEU cc_start: 0.7844 (tp) cc_final: 0.7633 (tp) REVERT: A 383 ARG cc_start: 0.8918 (mtt180) cc_final: 0.8385 (mpt-90) REVERT: A 399 PHE cc_start: 0.9415 (OUTLIER) cc_final: 0.9208 (m-80) REVERT: B 68 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7704 (t0) REVERT: B 222 TRP cc_start: 0.8508 (m100) cc_final: 0.8154 (m100) REVERT: B 226 LEU cc_start: 0.7413 (tp) cc_final: 0.6230 (tp) REVERT: B 399 PHE cc_start: 0.9411 (OUTLIER) cc_final: 0.8658 (t80) REVERT: C 85 ASP cc_start: 0.8348 (m-30) cc_final: 0.8138 (t70) REVERT: C 222 TRP cc_start: 0.8626 (m100) cc_final: 0.8297 (m100) REVERT: C 226 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7000 (tp) REVERT: C 246 ASN cc_start: 0.8218 (m110) cc_final: 0.7933 (m110) REVERT: C 383 ARG cc_start: 0.8846 (mtt180) cc_final: 0.8428 (mpt-90) REVERT: C 399 PHE cc_start: 0.9412 (OUTLIER) cc_final: 0.8702 (t80) REVERT: C 462 MET cc_start: 0.7093 (pmm) cc_final: 0.6822 (pmm) outliers start: 44 outliers final: 20 residues processed: 121 average time/residue: 0.2251 time to fit residues: 41.4049 Evaluate side-chains 99 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 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 399 PHE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 399 PHE Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 166 VAL 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 399 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 141 optimal weight: 20.0000 chunk 139 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 142 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 C 17 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.138316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.091630 restraints weight = 29316.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.094319 restraints weight = 17891.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.095825 restraints weight = 13852.442| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12252 Z= 0.130 Angle : 0.698 11.577 16683 Z= 0.339 Chirality : 0.045 0.302 1917 Planarity : 0.004 0.057 2118 Dihedral : 7.687 58.802 2316 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.58 % Favored : 96.35 % Rotamer: Outliers : 2.75 % Allowed : 18.32 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.21), residues: 1452 helix: 2.43 (0.26), residues: 414 sheet: -0.12 (0.33), residues: 213 loop : -2.42 (0.17), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 343 HIS 0.004 0.001 HIS C 17 PHE 0.019 0.001 PHE C 467 TYR 0.016 0.001 TYR B 105 ARG 0.002 0.000 ARG B 90 Details of bonding type rmsd link_NAG-ASN : bond 0.00399 ( 15) link_NAG-ASN : angle 3.01283 ( 45) link_BETA1-4 : bond 0.00601 ( 18) link_BETA1-4 : angle 1.57677 ( 54) hydrogen bonds : bond 0.03667 ( 474) hydrogen bonds : angle 4.79266 ( 1404) link_BETA1-6 : bond 0.00316 ( 3) link_BETA1-6 : angle 1.14960 ( 9) SS BOND : bond 0.00817 ( 18) SS BOND : angle 2.27710 ( 36) covalent geometry : bond 0.00286 (12198) covalent geometry : angle 0.66791 (16539) *********************** 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 130 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8752 (mtmm) cc_final: 0.8516 (mtmm) REVERT: A 383 ARG cc_start: 0.8935 (mtt180) cc_final: 0.8392 (mpt-90) REVERT: B 217 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8890 (tp) REVERT: B 226 LEU cc_start: 0.7550 (tp) cc_final: 0.6397 (tp) REVERT: B 399 PHE cc_start: 0.9380 (OUTLIER) cc_final: 0.9073 (m-80) REVERT: C 85 ASP cc_start: 0.8268 (m-30) cc_final: 0.8032 (t70) REVERT: C 217 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8789 (tp) REVERT: C 222 TRP cc_start: 0.8519 (m100) cc_final: 0.8219 (m100) REVERT: C 226 LEU cc_start: 0.7847 (tp) cc_final: 0.6888 (tp) REVERT: C 246 ASN cc_start: 0.8146 (m110) cc_final: 0.7906 (m110) REVERT: C 383 ARG cc_start: 0.8836 (mtt180) cc_final: 0.8484 (mpt-90) REVERT: C 462 MET cc_start: 0.7083 (pmm) cc_final: 0.6741 (pmm) outliers start: 35 outliers final: 15 residues processed: 124 average time/residue: 0.2455 time to fit residues: 48.4486 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 : 1.368 ------------------------------------------------------------------------------- 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 167 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 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 399 PHE Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 217 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 113 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.135495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.090649 restraints weight = 30341.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.091960 restraints weight = 21563.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.091638 restraints weight = 17619.713| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 12252 Z= 0.361 Angle : 0.872 12.288 16683 Z= 0.429 Chirality : 0.050 0.354 1917 Planarity : 0.005 0.076 2118 Dihedral : 7.777 55.395 2312 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.51 % Favored : 94.35 % Rotamer: Outliers : 3.07 % Allowed : 19.65 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.20), residues: 1452 helix: 2.00 (0.25), residues: 414 sheet: -0.27 (0.32), residues: 213 loop : -2.61 (0.16), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 222 HIS 0.008 0.002 HIS C 17 PHE 0.040 0.003 PHE A 467 TYR 0.026 0.003 TYR C 423 ARG 0.007 0.001 ARG B 224 Details of bonding type rmsd link_NAG-ASN : bond 0.00813 ( 15) link_NAG-ASN : angle 3.33737 ( 45) link_BETA1-4 : bond 0.00538 ( 18) link_BETA1-4 : angle 1.85844 ( 54) hydrogen bonds : bond 0.04568 ( 474) hydrogen bonds : angle 5.21756 ( 1404) link_BETA1-6 : bond 0.00071 ( 3) link_BETA1-6 : angle 1.40271 ( 9) SS BOND : bond 0.01079 ( 18) SS BOND : angle 3.16713 ( 36) covalent geometry : bond 0.00839 (12198) covalent geometry : angle 0.83791 (16539) *********************** 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 119 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 80 time to evaluate : 1.526 Fit side-chains REVERT: A 217 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8809 (tp) REVERT: A 222 TRP cc_start: 0.8787 (m100) cc_final: 0.8318 (m100) REVERT: A 226 LEU cc_start: 0.7934 (tp) cc_final: 0.6926 (tp) REVERT: A 383 ARG cc_start: 0.8957 (mtt180) cc_final: 0.8521 (mmt90) REVERT: A 462 MET cc_start: 0.7096 (pmm) cc_final: 0.6691 (pmm) REVERT: B 217 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8871 (tp) REVERT: B 222 TRP cc_start: 0.8446 (m100) cc_final: 0.7184 (t-100) REVERT: B 390 GLU cc_start: 0.8788 (pp20) cc_final: 0.8543 (pp20) REVERT: C 217 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8727 (tp) REVERT: C 222 TRP cc_start: 0.8800 (m100) cc_final: 0.8424 (m100) REVERT: C 226 LEU cc_start: 0.7999 (tp) cc_final: 0.7107 (tp) REVERT: C 246 ASN cc_start: 0.8141 (m110) cc_final: 0.7838 (m110) REVERT: C 383 ARG cc_start: 0.8864 (mtt180) cc_final: 0.8506 (mpt-90) REVERT: C 399 PHE cc_start: 0.9421 (OUTLIER) cc_final: 0.8680 (t80) REVERT: C 462 MET cc_start: 0.7484 (pmm) cc_final: 0.7277 (pmm) outliers start: 39 outliers final: 23 residues processed: 113 average time/residue: 0.2972 time to fit residues: 51.4826 Evaluate side-chains 98 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 1.861 ------------------------------------------------------------------------------- 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 130 VAL 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 217 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 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 268 MET Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 399 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 50 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** 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 = 0.4094 r_free = 0.4094 target = 0.138904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.093735 restraints weight = 30104.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.096225 restraints weight = 18942.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.097861 restraints weight = 14876.069| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12252 Z= 0.129 Angle : 0.704 13.729 16683 Z= 0.340 Chirality : 0.044 0.290 1917 Planarity : 0.004 0.058 2118 Dihedral : 7.080 54.620 2310 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.12 % Allowed : 20.13 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.21), residues: 1452 helix: 2.50 (0.26), residues: 411 sheet: -0.11 (0.32), residues: 213 loop : -2.38 (0.17), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 343 HIS 0.007 0.001 HIS C 17 PHE 0.026 0.001 PHE A 467 TYR 0.020 0.001 TYR C 302 ARG 0.003 0.000 ARG B 90 Details of bonding type rmsd link_NAG-ASN : bond 0.00361 ( 15) link_NAG-ASN : angle 2.80676 ( 45) link_BETA1-4 : bond 0.00598 ( 18) link_BETA1-4 : angle 1.50442 ( 54) hydrogen bonds : bond 0.03646 ( 474) hydrogen bonds : angle 4.68476 ( 1404) link_BETA1-6 : bond 0.00303 ( 3) link_BETA1-6 : angle 1.15169 ( 9) SS BOND : bond 0.00701 ( 18) SS BOND : angle 2.86440 ( 36) covalent geometry : bond 0.00287 (12198) covalent geometry : angle 0.67285 (16539) *********************** 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 120 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 1.527 Fit side-chains revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8772 (mtmm) cc_final: 0.8472 (mtmm) REVERT: A 217 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8785 (tp) REVERT: A 222 TRP cc_start: 0.8326 (m100) cc_final: 0.8110 (m100) REVERT: A 383 ARG cc_start: 0.8934 (mtt180) cc_final: 0.8375 (mpt-90) REVERT: A 462 MET cc_start: 0.6886 (pmm) cc_final: 0.6507 (pmm) REVERT: B 50 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8604 (mttp) REVERT: B 217 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8875 (tp) REVERT: B 222 TRP cc_start: 0.8134 (m100) cc_final: 0.6974 (t-100) REVERT: B 462 MET cc_start: 0.6996 (pmm) cc_final: 0.6700 (pmm) REVERT: C 217 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8820 (tp) REVERT: C 226 LEU cc_start: 0.7897 (tp) cc_final: 0.6974 (tp) REVERT: C 246 ASN cc_start: 0.8174 (m110) cc_final: 0.7889 (m110) REVERT: C 383 ARG cc_start: 0.8856 (mtt180) cc_final: 0.8502 (mpt-90) REVERT: C 462 MET cc_start: 0.7367 (pmm) cc_final: 0.6890 (pmm) outliers start: 27 outliers final: 21 residues processed: 115 average time/residue: 0.1987 time to fit residues: 35.0399 Evaluate side-chains 103 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 1.404 ------------------------------------------------------------------------------- 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 130 VAL 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 246 ASN Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 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 C residue 20 VAL Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 130 VAL 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 237 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 124 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 31 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 104 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.138341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.092841 restraints weight = 30200.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.095077 restraints weight = 19335.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.096599 restraints weight = 15322.829| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12252 Z= 0.161 Angle : 0.749 13.815 16683 Z= 0.362 Chirality : 0.045 0.292 1917 Planarity : 0.005 0.060 2118 Dihedral : 6.964 54.686 2310 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.41 % Favored : 95.45 % Rotamer: Outliers : 2.36 % Allowed : 20.83 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1452 helix: 2.45 (0.26), residues: 414 sheet: -0.10 (0.33), residues: 213 loop : -2.34 (0.17), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 222 HIS 0.007 0.001 HIS C 17 PHE 0.022 0.001 PHE A 467 TYR 0.015 0.002 TYR B 105 ARG 0.005 0.000 ARG C 224 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 15) link_NAG-ASN : angle 2.81701 ( 45) link_BETA1-4 : bond 0.00546 ( 18) link_BETA1-4 : angle 1.50970 ( 54) hydrogen bonds : bond 0.03679 ( 474) hydrogen bonds : angle 4.64048 ( 1404) link_BETA1-6 : bond 0.00324 ( 3) link_BETA1-6 : angle 1.15490 ( 9) SS BOND : bond 0.00746 ( 18) SS BOND : angle 4.33321 ( 36) covalent geometry : bond 0.00375 (12198) covalent geometry : angle 0.70368 (16539) *********************** 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 119 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 1.534 Fit side-chains revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8801 (mtmm) cc_final: 0.8498 (mtmm) REVERT: A 217 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8782 (tp) REVERT: A 222 TRP cc_start: 0.8432 (m100) cc_final: 0.8212 (m100) REVERT: A 383 ARG cc_start: 0.8961 (mtt180) cc_final: 0.8457 (mmt90) REVERT: A 462 MET cc_start: 0.6875 (pmm) cc_final: 0.6493 (pmm) REVERT: B 50 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8615 (mttp) REVERT: B 217 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8880 (tp) REVERT: B 222 TRP cc_start: 0.8261 (m100) cc_final: 0.7122 (t-100) REVERT: B 390 GLU cc_start: 0.8742 (pp20) cc_final: 0.8518 (pp20) REVERT: B 462 MET cc_start: 0.6917 (pmm) cc_final: 0.6601 (pmm) REVERT: C 217 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8787 (tp) REVERT: C 222 TRP cc_start: 0.8405 (m100) cc_final: 0.7322 (t-100) REVERT: C 246 ASN cc_start: 0.8159 (m110) cc_final: 0.7897 (m110) REVERT: C 383 ARG cc_start: 0.8871 (mtt180) cc_final: 0.8509 (mpt-90) REVERT: C 462 MET cc_start: 0.7240 (pmm) cc_final: 0.6754 (pmm) outliers start: 30 outliers final: 22 residues processed: 114 average time/residue: 0.2613 time to fit residues: 46.5696 Evaluate side-chains 110 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 1.634 ------------------------------------------------------------------------------- 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 130 VAL 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 B residue 20 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 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 C residue 17 HIS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 237 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 3 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.0970 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 89 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 33 GLN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.139552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.098107 restraints weight = 29868.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.098748 restraints weight = 19380.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.097962 restraints weight = 17130.549| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12252 Z= 0.123 Angle : 0.723 14.292 16683 Z= 0.349 Chirality : 0.044 0.282 1917 Planarity : 0.004 0.054 2118 Dihedral : 6.807 55.127 2310 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.28 % Allowed : 21.15 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.21), residues: 1452 helix: 2.61 (0.26), residues: 414 sheet: 0.08 (0.33), residues: 207 loop : -2.20 (0.18), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 180 HIS 0.006 0.001 HIS C 17 PHE 0.020 0.001 PHE A 467 TYR 0.016 0.001 TYR B 105 ARG 0.002 0.000 ARG B 90 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 15) link_NAG-ASN : angle 2.61891 ( 45) link_BETA1-4 : bond 0.00552 ( 18) link_BETA1-4 : angle 1.43193 ( 54) hydrogen bonds : bond 0.03406 ( 474) hydrogen bonds : angle 4.43646 ( 1404) link_BETA1-6 : bond 0.00379 ( 3) link_BETA1-6 : angle 1.11292 ( 9) SS BOND : bond 0.00497 ( 18) SS BOND : angle 4.45192 ( 36) covalent geometry : bond 0.00280 (12198) covalent geometry : angle 0.67693 (16539) *********************** 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 125 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8805 (mtmm) cc_final: 0.8507 (mtmm) REVERT: A 217 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8775 (tp) REVERT: A 222 TRP cc_start: 0.8553 (m100) cc_final: 0.8271 (m100) REVERT: A 383 ARG cc_start: 0.8944 (mtt180) cc_final: 0.8435 (mmt90) REVERT: A 462 MET cc_start: 0.6706 (pmm) cc_final: 0.6324 (pmm) REVERT: B 50 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8628 (mttp) REVERT: B 217 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8876 (tp) REVERT: B 222 TRP cc_start: 0.8348 (m100) cc_final: 0.7155 (t-100) REVERT: B 390 GLU cc_start: 0.8659 (pp20) cc_final: 0.8409 (pp20) REVERT: B 462 MET cc_start: 0.6784 (pmm) cc_final: 0.6490 (pmm) REVERT: C 217 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8824 (tp) REVERT: C 222 TRP cc_start: 0.8582 (m100) cc_final: 0.7275 (t-100) REVERT: C 246 ASN cc_start: 0.8234 (m110) cc_final: 0.7978 (m110) REVERT: C 383 ARG cc_start: 0.8831 (mtt180) cc_final: 0.8382 (mpt-90) REVERT: C 462 MET cc_start: 0.7030 (pmm) cc_final: 0.6647 (pmm) outliers start: 29 outliers final: 24 residues processed: 120 average time/residue: 0.1987 time to fit residues: 37.9043 Evaluate side-chains 115 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 130 VAL 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 B residue 20 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 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 C residue 17 HIS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 130 VAL 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 237 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 93 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 141 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 143 optimal weight: 20.0000 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 HIS B 246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.137946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.093641 restraints weight = 29924.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.094764 restraints weight = 21030.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.094702 restraints weight = 16976.816| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12252 Z= 0.179 Angle : 0.724 13.889 16683 Z= 0.351 Chirality : 0.044 0.284 1917 Planarity : 0.005 0.060 2118 Dihedral : 6.819 54.694 2310 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.36 % Allowed : 21.23 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.21), residues: 1452 helix: 2.55 (0.26), residues: 414 sheet: -0.11 (0.33), residues: 213 loop : -2.25 (0.18), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 343 HIS 0.007 0.001 HIS C 17 PHE 0.020 0.001 PHE A 467 TYR 0.015 0.002 TYR B 423 ARG 0.003 0.000 ARG B 90 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 15) link_NAG-ASN : angle 2.70117 ( 45) link_BETA1-4 : bond 0.00511 ( 18) link_BETA1-4 : angle 1.50469 ( 54) hydrogen bonds : bond 0.03602 ( 474) hydrogen bonds : angle 4.50484 ( 1404) link_BETA1-6 : bond 0.00258 ( 3) link_BETA1-6 : angle 1.19533 ( 9) SS BOND : bond 0.00655 ( 18) SS BOND : angle 3.80181 ( 36) covalent geometry : bond 0.00418 (12198) covalent geometry : angle 0.68546 (16539) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 1.343 Fit side-chains revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8870 (mtmm) cc_final: 0.8579 (mtmm) REVERT: A 217 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8784 (tp) REVERT: A 222 TRP cc_start: 0.8706 (m100) cc_final: 0.8352 (m100) REVERT: A 383 ARG cc_start: 0.9011 (mtt180) cc_final: 0.8518 (mmt90) REVERT: A 462 MET cc_start: 0.6620 (pmm) cc_final: 0.6223 (pmm) REVERT: B 50 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8604 (mttp) REVERT: B 217 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8897 (tp) REVERT: B 222 TRP cc_start: 0.8553 (m100) cc_final: 0.7286 (t-100) REVERT: B 390 GLU cc_start: 0.8747 (pp20) cc_final: 0.8540 (pp20) REVERT: B 462 MET cc_start: 0.6915 (pmm) cc_final: 0.6612 (pmm) REVERT: C 217 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8742 (tp) REVERT: C 222 TRP cc_start: 0.8706 (m100) cc_final: 0.7376 (t-100) REVERT: C 246 ASN cc_start: 0.8217 (m110) cc_final: 0.7993 (m110) REVERT: C 383 ARG cc_start: 0.8876 (mtt180) cc_final: 0.8438 (mpt-90) REVERT: C 462 MET cc_start: 0.7026 (pmm) cc_final: 0.6576 (pmm) outliers start: 30 outliers final: 25 residues processed: 112 average time/residue: 0.1958 time to fit residues: 34.5047 Evaluate side-chains 115 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 130 VAL 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 B residue 20 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 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 C residue 17 HIS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 130 VAL 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 237 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 8.9990 chunk 89 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 ASN ** 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 = 0.4111 r_free = 0.4111 target = 0.139715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.094642 restraints weight = 30119.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.096191 restraints weight = 23536.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.096738 restraints weight = 18187.826| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12252 Z= 0.133 Angle : 0.684 11.909 16683 Z= 0.331 Chirality : 0.044 0.278 1917 Planarity : 0.005 0.056 2118 Dihedral : 6.743 54.916 2310 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.28 % Allowed : 21.46 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.21), residues: 1452 helix: 2.56 (0.26), residues: 414 sheet: 0.07 (0.34), residues: 207 loop : -2.15 (0.18), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 343 HIS 0.008 0.001 HIS C 17 PHE 0.019 0.001 PHE A 467 TYR 0.016 0.001 TYR B 105 ARG 0.002 0.000 ARG B 90 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 15) link_NAG-ASN : angle 2.55763 ( 45) link_BETA1-4 : bond 0.00528 ( 18) link_BETA1-4 : angle 1.45206 ( 54) hydrogen bonds : bond 0.03416 ( 474) hydrogen bonds : angle 4.40360 ( 1404) link_BETA1-6 : bond 0.00334 ( 3) link_BETA1-6 : angle 1.14091 ( 9) SS BOND : bond 0.00518 ( 18) SS BOND : angle 3.26282 ( 36) covalent geometry : bond 0.00307 (12198) covalent geometry : angle 0.65083 (16539) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4078.34 seconds wall clock time: 74 minutes 41.40 seconds (4481.40 seconds total)