Starting phenix.real_space_refine on Wed Sep 17 11:54:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c48_45177/09_2025/9c48_45177.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c48_45177/09_2025/9c48_45177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c48_45177/09_2025/9c48_45177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c48_45177/09_2025/9c48_45177.map" model { file = "/net/cci-nas-00/data/ceres_data/9c48_45177/09_2025/9c48_45177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c48_45177/09_2025/9c48_45177.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 60 5.16 5 C 5202 2.51 5 N 1341 2.21 5 O 1866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8481 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2575 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 331, 2566 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 331, 2566 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 2613 Chain: "B" Number of atoms: 2575 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 331, 2566 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 331, 2566 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 2613 Chain: "C" Number of atoms: 2575 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 331, 2566 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 331, 2566 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 2613 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: 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: "F" 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: "G" 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: "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: "I" 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: "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: "K" 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: "L" 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: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 74 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 74 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 74 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AGLN A 94 " occ=0.62 ... (16 atoms not shown) pdb=" NE2BGLN A 94 " occ=0.38 residue: pdb=" N AGLN B 94 " occ=0.62 ... (16 atoms not shown) pdb=" NE2BGLN B 94 " occ=0.38 residue: pdb=" N AGLN C 94 " occ=0.62 ... (16 atoms not shown) pdb=" NE2BGLN C 94 " occ=0.38 Time building chain proxies: 3.59, per 1000 atoms: 0.42 Number of scatterers: 8481 At special positions: 0 Unit cell: (87.48, 86.184, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 9 15.00 Mg 3 11.99 O 1866 8.00 N 1341 7.00 C 5202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 227 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 227 " distance=2.04 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 270 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " 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 L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A 402 " - " ASN A 75 " " NAG A 403 " - " ASN A 110 " " NAG A 404 " - " ASN A 153 " " NAG B 503 " - " ASN B 75 " " NAG B 504 " - " ASN B 110 " " NAG B 505 " - " ASN B 153 " " NAG C 503 " - " ASN C 75 " " NAG C 504 " - " ASN C 110 " " NAG C 505 " - " ASN C 153 " " NAG D 1 " - " ASN A 184 " " NAG E 1 " - " ASN A 199 " " NAG F 1 " - " ASN A 208 " " NAG G 1 " - " ASN B 184 " " NAG H 1 " - " ASN B 199 " " NAG I 1 " - " ASN B 208 " " NAG J 1 " - " ASN C 184 " " NAG K 1 " - " ASN C 199 " " NAG L 1 " - " ASN C 208 " Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 549.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1854 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 15 sheets defined 25.8% alpha, 47.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 31 through 46 Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.926A pdb=" N SER A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.865A pdb=" N VAL A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 331 through 361 removed outlier: 3.679A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 210 through 216 removed outlier: 3.927A pdb=" N SER B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.865A pdb=" N VAL B 248 " --> pdb=" O GLN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 331 through 361 removed outlier: 3.679A pdb=" N THR B 335 " --> pdb=" O ASP B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 210 through 216 removed outlier: 3.926A pdb=" N SER C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.865A pdb=" N VAL C 248 " --> pdb=" O GLN C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 Processing helix chain 'C' and resid 331 through 361 removed outlier: 3.680A pdb=" N THR C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 59 removed outlier: 3.682A pdb=" N CYS A 261 " --> pdb=" O LYS A 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 151 removed outlier: 9.350A pdb=" N VAL A 144 " --> pdb=" O TRP A 164 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N TRP A 164 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N THR A 146 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ALA A 162 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ARG A 148 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR A 315 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL A 105 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS A 313 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU A 107 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU A 311 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N MET A 109 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ARG A 309 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLN A 111 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLU A 307 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 69 removed outlier: 3.757A pdb=" N PHE A 200 " --> pdb=" O TYR A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 69 Processing sheet with id=AA5, first strand: chain 'A' and resid 72 through 76 Processing sheet with id=AA6, first strand: chain 'B' and resid 55 through 59 removed outlier: 3.681A pdb=" N CYS B 261 " --> pdb=" O LYS B 326 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 144 through 151 removed outlier: 9.350A pdb=" N VAL B 144 " --> pdb=" O TRP B 164 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N TRP B 164 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N THR B 146 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ALA B 162 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ARG B 148 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TYR B 315 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B 105 " --> pdb=" O LYS B 313 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS B 313 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU B 107 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU B 311 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N MET B 109 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ARG B 309 " --> pdb=" O MET B 109 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLN B 111 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLU B 307 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 61 through 69 removed outlier: 3.757A pdb=" N PHE B 200 " --> pdb=" O TYR B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 61 through 69 Processing sheet with id=AB1, first strand: chain 'B' and resid 72 through 76 Processing sheet with id=AB2, first strand: chain 'C' and resid 55 through 59 removed outlier: 3.681A pdb=" N CYS C 261 " --> pdb=" O LYS C 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 151 removed outlier: 9.350A pdb=" N VAL C 144 " --> pdb=" O TRP C 164 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N TRP C 164 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N THR C 146 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ALA C 162 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ARG C 148 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR C 315 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL C 105 " --> pdb=" O LYS C 313 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS C 313 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU C 107 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU C 311 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N MET C 109 " --> pdb=" O ARG C 309 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ARG C 309 " --> pdb=" O MET C 109 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLN C 111 " --> pdb=" O GLU C 307 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLU C 307 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 61 through 69 removed outlier: 3.758A pdb=" N PHE C 200 " --> pdb=" O TYR C 195 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 61 through 69 Processing sheet with id=AB6, first strand: chain 'C' and resid 72 through 76 379 hydrogen bonds defined for protein. 1029 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2551 1.34 - 1.46: 1989 1.46 - 1.58: 3773 1.58 - 1.70: 12 1.70 - 1.82: 84 Bond restraints: 8409 Sorted by residual: bond pdb=" C4 ATP A 401 " pdb=" N9 ATP A 401 " ideal model delta sigma weight residual 1.374 1.329 0.045 1.00e-02 1.00e+04 2.06e+01 bond pdb=" C4 ATP B 502 " pdb=" N9 ATP B 502 " ideal model delta sigma weight residual 1.374 1.330 0.044 1.00e-02 1.00e+04 1.96e+01 bond pdb=" C4 ATP C 502 " pdb=" N9 ATP C 502 " ideal model delta sigma weight residual 1.374 1.330 0.044 1.00e-02 1.00e+04 1.94e+01 bond pdb=" C8 ATP C 502 " pdb=" N7 ATP C 502 " ideal model delta sigma weight residual 1.310 1.353 -0.043 1.00e-02 1.00e+04 1.87e+01 bond pdb=" C3' ATP A 401 " pdb=" C4' ATP A 401 " ideal model delta sigma weight residual 1.526 1.573 -0.047 1.10e-02 8.26e+03 1.83e+01 ... (remaining 8404 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 11397 3.75 - 7.49: 63 7.49 - 11.24: 0 11.24 - 14.98: 0 14.98 - 18.73: 6 Bond angle restraints: 11466 Sorted by residual: angle pdb=" PB ATP C 502 " pdb=" O3B ATP C 502 " pdb=" PG ATP C 502 " ideal model delta sigma weight residual 139.87 121.14 18.73 1.00e+00 1.00e+00 3.51e+02 angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 121.18 18.69 1.00e+00 1.00e+00 3.49e+02 angle pdb=" PB ATP B 502 " pdb=" O3B ATP B 502 " pdb=" PG ATP B 502 " ideal model delta sigma weight residual 139.87 121.19 18.68 1.00e+00 1.00e+00 3.49e+02 angle pdb=" PA ATP B 502 " pdb=" O3A ATP B 502 " pdb=" PB ATP B 502 " ideal model delta sigma weight residual 136.83 121.22 15.61 1.00e+00 1.00e+00 2.44e+02 angle pdb=" PA ATP C 502 " pdb=" O3A ATP C 502 " pdb=" PB ATP C 502 " ideal model delta sigma weight residual 136.83 121.22 15.61 1.00e+00 1.00e+00 2.44e+02 ... (remaining 11461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.20: 5010 21.20 - 42.41: 309 42.41 - 63.61: 63 63.61 - 84.82: 33 84.82 - 106.02: 12 Dihedral angle restraints: 5427 sinusoidal: 2541 harmonic: 2886 Sorted by residual: dihedral pdb=" CB CYS B 261 " pdb=" SG CYS B 261 " pdb=" SG CYS B 270 " pdb=" CB CYS B 270 " ideal model delta sinusoidal sigma weight residual 93.00 51.69 41.31 1 1.00e+01 1.00e-02 2.39e+01 dihedral pdb=" CB CYS C 261 " pdb=" SG CYS C 261 " pdb=" SG CYS C 270 " pdb=" CB CYS C 270 " ideal model delta sinusoidal sigma weight residual 93.00 51.69 41.31 1 1.00e+01 1.00e-02 2.39e+01 dihedral pdb=" CB CYS A 261 " pdb=" SG CYS A 261 " pdb=" SG CYS A 270 " pdb=" CB CYS A 270 " ideal model delta sinusoidal sigma weight residual 93.00 51.71 41.29 1 1.00e+01 1.00e-02 2.39e+01 ... (remaining 5424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1020 0.054 - 0.108: 256 0.108 - 0.162: 92 0.162 - 0.216: 21 0.216 - 0.269: 6 Chirality restraints: 1395 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1392 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 110 " 0.022 2.00e-02 2.50e+03 2.03e-02 5.16e+00 pdb=" CG ASN B 110 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN B 110 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 110 " -0.021 2.00e-02 2.50e+03 pdb=" C1 NAG B 504 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 110 " -0.022 2.00e-02 2.50e+03 2.01e-02 5.07e+00 pdb=" CG ASN A 110 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 110 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 110 " 0.020 2.00e-02 2.50e+03 pdb=" C1 NAG A 403 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 110 " 0.022 2.00e-02 2.50e+03 2.00e-02 5.00e+00 pdb=" CG ASN C 110 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN C 110 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 110 " -0.020 2.00e-02 2.50e+03 pdb=" C1 NAG C 504 " 0.022 2.00e-02 2.50e+03 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1341 2.77 - 3.30: 7791 3.30 - 3.83: 14313 3.83 - 4.37: 18443 4.37 - 4.90: 29492 Nonbonded interactions: 71380 Sorted by model distance: nonbonded pdb=" OE2 GLU A 95 " pdb=" O HOH A 501 " model vdw 2.232 3.040 nonbonded pdb=" OE2 GLU C 95 " pdb=" O HOH C 601 " model vdw 2.237 3.040 nonbonded pdb=" OE2 GLU B 95 " pdb=" O HOH B 601 " model vdw 2.244 3.040 nonbonded pdb=" OD1 ASP B 88 " pdb=" OH TYR C 299 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR A 299 " pdb=" OD1 ASP C 88 " model vdw 2.261 3.040 ... (remaining 71375 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 93 or resid 95 through 361 or resid 403 through \ 404)) selection = (chain 'B' and (resid 31 through 93 or resid 95 through 361 or resid 503 through \ 504)) selection = (chain 'C' and (resid 31 through 93 or resid 95 through 361 or resid 503 through \ 504)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'L' } 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 18.870 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.380 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 : 0.006 0.047 8451 Z= 0.405 Angle : 0.927 18.729 11580 Z= 0.634 Chirality : 0.060 0.269 1395 Planarity : 0.004 0.031 1404 Dihedral : 16.098 106.020 3537 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.26), residues: 996 helix: -1.00 (0.31), residues: 270 sheet: 0.44 (0.28), residues: 333 loop : -0.30 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 265 TYR 0.008 0.001 TYR B 89 PHE 0.011 0.002 PHE B 198 TRP 0.013 0.002 TRP B 164 HIS 0.001 0.000 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00610 ( 8409) covalent geometry : angle 0.90076 (11466) SS BOND : bond 0.00234 ( 12) SS BOND : angle 1.40235 ( 24) hydrogen bonds : bond 0.20042 ( 349) hydrogen bonds : angle 7.58264 ( 1029) link_BETA1-4 : bond 0.00355 ( 12) link_BETA1-4 : angle 2.27571 ( 36) link_NAG-ASN : bond 0.00776 ( 18) link_NAG-ASN : angle 2.78258 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.368 Fit side-chains REVERT: B 326 LYS cc_start: 0.8475 (pttt) cc_final: 0.8257 (pptt) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.8266 time to fit residues: 70.9955 Evaluate side-chains 81 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.0670 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 308 GLN B 175 GLN B 308 GLN B 338 ASN C 175 GLN C 308 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.120573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.082677 restraints weight = 33007.439| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.82 r_work: 0.2876 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8451 Z= 0.164 Angle : 0.644 8.821 11580 Z= 0.326 Chirality : 0.049 0.224 1395 Planarity : 0.004 0.031 1404 Dihedral : 12.269 80.065 1800 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.95 % Allowed : 11.74 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.25), residues: 996 helix: -0.03 (0.31), residues: 270 sheet: 0.29 (0.26), residues: 351 loop : -0.47 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 309 TYR 0.014 0.001 TYR B 89 PHE 0.011 0.002 PHE A 81 TRP 0.009 0.001 TRP A 164 HIS 0.004 0.001 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 8409) covalent geometry : angle 0.59574 (11466) SS BOND : bond 0.00402 ( 12) SS BOND : angle 1.92123 ( 24) hydrogen bonds : bond 0.04774 ( 349) hydrogen bonds : angle 5.43032 ( 1029) link_BETA1-4 : bond 0.00385 ( 12) link_BETA1-4 : angle 2.15584 ( 36) link_NAG-ASN : bond 0.00494 ( 18) link_NAG-ASN : angle 2.96611 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7689 (mm-30) REVERT: A 95 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7646 (mt-10) REVERT: A 307 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7771 (mm-30) REVERT: A 308 GLN cc_start: 0.8551 (mt0) cc_final: 0.8270 (mt0) REVERT: B 51 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7719 (mm-30) REVERT: B 307 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7606 (mm-30) REVERT: B 308 GLN cc_start: 0.8500 (mt0) cc_final: 0.8273 (mt0) REVERT: B 326 LYS cc_start: 0.8702 (pttt) cc_final: 0.8107 (pptt) REVERT: C 51 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7734 (mm-30) REVERT: C 82 ARG cc_start: 0.8188 (mmm-85) cc_final: 0.7982 (mmt90) outliers start: 8 outliers final: 3 residues processed: 96 average time/residue: 0.8156 time to fit residues: 81.8881 Evaluate side-chains 92 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain C residue 109 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 67 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 74 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 91 optimal weight: 0.0570 chunk 69 optimal weight: 0.9980 chunk 18 optimal weight: 0.0270 chunk 83 optimal weight: 0.5980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 244 GLN A 287 ASN B 175 GLN C 175 GLN C 308 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.122280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.083025 restraints weight = 31887.249| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.93 r_work: 0.2891 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8451 Z= 0.126 Angle : 0.572 7.656 11580 Z= 0.289 Chirality : 0.047 0.217 1395 Planarity : 0.003 0.030 1404 Dihedral : 9.782 79.425 1800 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.07 % Allowed : 11.27 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.26), residues: 996 helix: 0.82 (0.34), residues: 252 sheet: 0.27 (0.26), residues: 366 loop : -0.45 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 82 TYR 0.014 0.001 TYR A 89 PHE 0.008 0.002 PHE C 81 TRP 0.008 0.001 TRP B 259 HIS 0.003 0.001 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8409) covalent geometry : angle 0.52705 (11466) SS BOND : bond 0.00320 ( 12) SS BOND : angle 1.51405 ( 24) hydrogen bonds : bond 0.04038 ( 349) hydrogen bonds : angle 4.96182 ( 1029) link_BETA1-4 : bond 0.00461 ( 12) link_BETA1-4 : angle 2.19794 ( 36) link_NAG-ASN : bond 0.00425 ( 18) link_NAG-ASN : angle 2.65611 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7814 (mm-30) REVERT: A 95 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7636 (mt-10) REVERT: A 307 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7771 (mm-30) REVERT: A 308 GLN cc_start: 0.8576 (mt0) cc_final: 0.8297 (mt0) REVERT: A 326 LYS cc_start: 0.8492 (pttp) cc_final: 0.7884 (pptt) REVERT: B 51 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7755 (mm-30) REVERT: B 326 LYS cc_start: 0.8648 (pttt) cc_final: 0.8104 (pptt) REVERT: C 51 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7751 (mm-30) REVERT: C 95 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7622 (mt-10) outliers start: 9 outliers final: 2 residues processed: 101 average time/residue: 0.7833 time to fit residues: 83.0562 Evaluate side-chains 97 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 156 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 81 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 58 optimal weight: 0.0770 chunk 87 optimal weight: 0.6980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 244 GLN A 287 ASN B 175 GLN C 175 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.120856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.081656 restraints weight = 31037.293| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.90 r_work: 0.2873 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8451 Z= 0.148 Angle : 0.586 5.991 11580 Z= 0.299 Chirality : 0.047 0.253 1395 Planarity : 0.003 0.032 1404 Dihedral : 9.540 77.744 1800 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.07 % Allowed : 11.86 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.26), residues: 996 helix: 0.86 (0.34), residues: 252 sheet: 0.26 (0.26), residues: 366 loop : -0.47 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 203 TYR 0.012 0.001 TYR C 89 PHE 0.010 0.002 PHE C 294 TRP 0.009 0.002 TRP A 164 HIS 0.003 0.001 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8409) covalent geometry : angle 0.54196 (11466) SS BOND : bond 0.00331 ( 12) SS BOND : angle 1.72365 ( 24) hydrogen bonds : bond 0.04016 ( 349) hydrogen bonds : angle 4.92758 ( 1029) link_BETA1-4 : bond 0.00415 ( 12) link_BETA1-4 : angle 2.12982 ( 36) link_NAG-ASN : bond 0.00369 ( 18) link_NAG-ASN : angle 2.63700 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7843 (mm-30) REVERT: A 95 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7689 (mt-10) REVERT: A 326 LYS cc_start: 0.8511 (pttp) cc_final: 0.7912 (pptt) REVERT: B 51 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7636 (mm-30) REVERT: B 326 LYS cc_start: 0.8696 (pttt) cc_final: 0.8157 (pptt) REVERT: C 51 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7765 (mm-30) REVERT: C 95 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7624 (mt-10) REVERT: C 307 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7709 (mm-30) outliers start: 9 outliers final: 4 residues processed: 90 average time/residue: 0.7526 time to fit residues: 71.0699 Evaluate side-chains 95 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 307 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 22 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 0.0070 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 244 GLN A 287 ASN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN C 175 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.120761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.081388 restraints weight = 32911.371| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.93 r_work: 0.2868 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8451 Z= 0.147 Angle : 0.579 5.656 11580 Z= 0.296 Chirality : 0.047 0.233 1395 Planarity : 0.003 0.033 1404 Dihedral : 9.410 76.289 1800 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.07 % Allowed : 12.34 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.26), residues: 996 helix: 0.88 (0.34), residues: 252 sheet: 0.27 (0.26), residues: 366 loop : -0.48 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 203 TYR 0.012 0.001 TYR C 89 PHE 0.010 0.002 PHE C 294 TRP 0.011 0.002 TRP B 259 HIS 0.003 0.001 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8409) covalent geometry : angle 0.53912 (11466) SS BOND : bond 0.00334 ( 12) SS BOND : angle 1.67214 ( 24) hydrogen bonds : bond 0.03919 ( 349) hydrogen bonds : angle 4.83949 ( 1029) link_BETA1-4 : bond 0.00451 ( 12) link_BETA1-4 : angle 2.08839 ( 36) link_NAG-ASN : bond 0.00373 ( 18) link_NAG-ASN : angle 2.44812 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7867 (mm-30) REVERT: A 95 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7673 (mt-10) REVERT: A 307 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7959 (mt-10) REVERT: A 326 LYS cc_start: 0.8540 (pttp) cc_final: 0.7930 (pptt) REVERT: B 51 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7632 (mm-30) REVERT: B 326 LYS cc_start: 0.8726 (pttt) cc_final: 0.8189 (pptt) REVERT: C 51 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7655 (mm-30) REVERT: C 95 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7617 (mt-10) REVERT: C 307 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7687 (mm-30) REVERT: C 308 GLN cc_start: 0.8499 (mt0) cc_final: 0.8294 (mt0) outliers start: 9 outliers final: 3 residues processed: 98 average time/residue: 0.7629 time to fit residues: 78.3671 Evaluate side-chains 101 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 307 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 77 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN A 287 ASN B 175 GLN B 308 GLN C 175 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.119900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.081203 restraints weight = 30812.881| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.80 r_work: 0.2869 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 8451 Z= 0.195 Angle : 0.635 5.881 11580 Z= 0.324 Chirality : 0.049 0.255 1395 Planarity : 0.004 0.035 1404 Dihedral : 9.731 75.823 1800 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.83 % Allowed : 12.93 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.26), residues: 996 helix: 0.74 (0.34), residues: 252 sheet: 0.28 (0.26), residues: 366 loop : -0.62 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 203 TYR 0.011 0.001 TYR C 89 PHE 0.011 0.002 PHE C 294 TRP 0.012 0.002 TRP A 164 HIS 0.004 0.001 HIS B 286 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 8409) covalent geometry : angle 0.59110 (11466) SS BOND : bond 0.00376 ( 12) SS BOND : angle 1.95708 ( 24) hydrogen bonds : bond 0.04234 ( 349) hydrogen bonds : angle 4.95858 ( 1029) link_BETA1-4 : bond 0.00441 ( 12) link_BETA1-4 : angle 2.26006 ( 36) link_NAG-ASN : bond 0.00336 ( 18) link_NAG-ASN : angle 2.68021 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7970 (mm-30) REVERT: A 95 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7695 (mt-10) REVERT: A 326 LYS cc_start: 0.8630 (pttp) cc_final: 0.8045 (pptt) REVERT: B 51 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7700 (mm-30) REVERT: B 326 LYS cc_start: 0.8755 (pttt) cc_final: 0.8252 (pptt) REVERT: C 51 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7674 (mm-30) outliers start: 7 outliers final: 4 residues processed: 98 average time/residue: 0.8018 time to fit residues: 82.1225 Evaluate side-chains 95 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 156 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 64 optimal weight: 4.9990 chunk 20 optimal weight: 0.0980 chunk 87 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN C 175 GLN C 244 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.120234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.080919 restraints weight = 36739.431| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 4.10 r_work: 0.2861 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8451 Z= 0.163 Angle : 0.602 6.427 11580 Z= 0.306 Chirality : 0.047 0.227 1395 Planarity : 0.004 0.035 1404 Dihedral : 9.572 75.608 1800 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.07 % Allowed : 13.29 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.26), residues: 996 helix: 0.82 (0.34), residues: 252 sheet: 0.28 (0.26), residues: 366 loop : -0.62 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 203 TYR 0.010 0.001 TYR A 89 PHE 0.010 0.002 PHE C 294 TRP 0.013 0.002 TRP B 259 HIS 0.003 0.001 HIS C 286 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8409) covalent geometry : angle 0.56110 (11466) SS BOND : bond 0.00340 ( 12) SS BOND : angle 1.74832 ( 24) hydrogen bonds : bond 0.03969 ( 349) hydrogen bonds : angle 4.89376 ( 1029) link_BETA1-4 : bond 0.00461 ( 12) link_BETA1-4 : angle 2.21697 ( 36) link_NAG-ASN : bond 0.00327 ( 18) link_NAG-ASN : angle 2.47985 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7959 (mm-30) REVERT: A 95 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7670 (mt-10) REVERT: A 326 LYS cc_start: 0.8633 (pttp) cc_final: 0.8045 (pptt) REVERT: B 51 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7669 (mm-30) REVERT: B 326 LYS cc_start: 0.8759 (pttt) cc_final: 0.8259 (pptt) REVERT: C 51 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7747 (mm-30) outliers start: 9 outliers final: 5 residues processed: 97 average time/residue: 0.8162 time to fit residues: 82.8851 Evaluate side-chains 95 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 156 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 85 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 18 optimal weight: 0.0370 chunk 78 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 84 optimal weight: 0.3980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN B 175 GLN C 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.120860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.082603 restraints weight = 38278.483| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.95 r_work: 0.2888 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8451 Z= 0.136 Angle : 0.571 5.482 11580 Z= 0.291 Chirality : 0.047 0.244 1395 Planarity : 0.003 0.034 1404 Dihedral : 9.387 75.449 1800 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.83 % Allowed : 13.40 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.26), residues: 996 helix: 0.96 (0.34), residues: 252 sheet: 0.29 (0.26), residues: 366 loop : -0.61 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 203 TYR 0.011 0.001 TYR A 89 PHE 0.009 0.002 PHE C 294 TRP 0.013 0.001 TRP B 259 HIS 0.003 0.001 HIS C 286 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8409) covalent geometry : angle 0.53044 (11466) SS BOND : bond 0.00318 ( 12) SS BOND : angle 1.60034 ( 24) hydrogen bonds : bond 0.03744 ( 349) hydrogen bonds : angle 4.78907 ( 1029) link_BETA1-4 : bond 0.00471 ( 12) link_BETA1-4 : angle 2.14950 ( 36) link_NAG-ASN : bond 0.00356 ( 18) link_NAG-ASN : angle 2.46183 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7936 (mm-30) REVERT: A 95 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7637 (mt-10) REVERT: A 326 LYS cc_start: 0.8603 (pttp) cc_final: 0.8034 (pptt) REVERT: B 51 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7658 (mm-30) REVERT: B 326 LYS cc_start: 0.8722 (pttt) cc_final: 0.8233 (pptt) REVERT: C 51 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7725 (mm-30) outliers start: 7 outliers final: 5 residues processed: 93 average time/residue: 0.7809 time to fit residues: 76.1093 Evaluate side-chains 95 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 156 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN B 175 GLN B 308 GLN C 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.120091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.081126 restraints weight = 31195.984| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.41 r_work: 0.2873 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8451 Z= 0.199 Angle : 0.644 7.121 11580 Z= 0.327 Chirality : 0.049 0.227 1395 Planarity : 0.004 0.035 1404 Dihedral : 9.718 75.623 1800 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.83 % Allowed : 13.52 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.25), residues: 996 helix: 0.77 (0.34), residues: 252 sheet: 0.29 (0.26), residues: 366 loop : -0.69 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 309 TYR 0.010 0.001 TYR A 89 PHE 0.012 0.002 PHE A 226 TRP 0.012 0.002 TRP A 164 HIS 0.004 0.001 HIS B 286 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 8409) covalent geometry : angle 0.60299 (11466) SS BOND : bond 0.00349 ( 12) SS BOND : angle 1.93164 ( 24) hydrogen bonds : bond 0.04167 ( 349) hydrogen bonds : angle 4.93556 ( 1029) link_BETA1-4 : bond 0.00456 ( 12) link_BETA1-4 : angle 2.30874 ( 36) link_NAG-ASN : bond 0.00325 ( 18) link_NAG-ASN : angle 2.57752 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7947 (mm-30) REVERT: A 95 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7679 (mt-10) REVERT: A 326 LYS cc_start: 0.8635 (pttp) cc_final: 0.8091 (pptt) REVERT: B 51 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7718 (mm-30) REVERT: B 326 LYS cc_start: 0.8749 (pttt) cc_final: 0.8318 (pptt) REVERT: C 51 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7768 (mm-30) outliers start: 7 outliers final: 5 residues processed: 94 average time/residue: 0.8578 time to fit residues: 84.4124 Evaluate side-chains 96 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 29 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 7 optimal weight: 0.1980 chunk 68 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN A 287 ASN B 175 GLN B 308 GLN C 175 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.119949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.081353 restraints weight = 37508.047| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.96 r_work: 0.2868 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8451 Z= 0.176 Angle : 0.619 5.524 11580 Z= 0.315 Chirality : 0.048 0.228 1395 Planarity : 0.004 0.035 1404 Dihedral : 9.662 75.706 1800 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.59 % Allowed : 13.76 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.25), residues: 996 helix: 0.82 (0.34), residues: 252 sheet: 0.27 (0.26), residues: 366 loop : -0.70 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 309 TYR 0.010 0.001 TYR A 89 PHE 0.011 0.002 PHE A 226 TRP 0.013 0.002 TRP B 259 HIS 0.003 0.001 HIS B 286 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 8409) covalent geometry : angle 0.57825 (11466) SS BOND : bond 0.00344 ( 12) SS BOND : angle 1.80046 ( 24) hydrogen bonds : bond 0.04032 ( 349) hydrogen bonds : angle 4.87366 ( 1029) link_BETA1-4 : bond 0.00461 ( 12) link_BETA1-4 : angle 2.30211 ( 36) link_NAG-ASN : bond 0.00318 ( 18) link_NAG-ASN : angle 2.49487 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7978 (mm-30) REVERT: A 95 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7691 (mt-10) REVERT: A 326 LYS cc_start: 0.8643 (pttp) cc_final: 0.8106 (pptt) REVERT: B 51 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7726 (mm-30) REVERT: B 326 LYS cc_start: 0.8763 (pttt) cc_final: 0.8317 (pptt) REVERT: C 51 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7779 (mm-30) outliers start: 5 outliers final: 5 residues processed: 96 average time/residue: 0.7957 time to fit residues: 79.9074 Evaluate side-chains 98 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 8 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 21 optimal weight: 0.0770 chunk 44 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 54 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 6 optimal weight: 0.0030 chunk 84 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 overall best weight: 0.2348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN B 175 GLN B 308 GLN C 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.121866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.083560 restraints weight = 29506.260| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.24 r_work: 0.2932 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8451 Z= 0.106 Angle : 0.545 5.647 11580 Z= 0.277 Chirality : 0.045 0.210 1395 Planarity : 0.003 0.033 1404 Dihedral : 9.158 76.206 1800 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.71 % Allowed : 13.88 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.26), residues: 996 helix: 1.14 (0.35), residues: 252 sheet: 0.41 (0.26), residues: 360 loop : -0.62 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 273 TYR 0.011 0.001 TYR B 89 PHE 0.009 0.001 PHE C 294 TRP 0.014 0.001 TRP B 259 HIS 0.002 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 8409) covalent geometry : angle 0.50920 (11466) SS BOND : bond 0.00327 ( 12) SS BOND : angle 1.39065 ( 24) hydrogen bonds : bond 0.03453 ( 349) hydrogen bonds : angle 4.65467 ( 1029) link_BETA1-4 : bond 0.00511 ( 12) link_BETA1-4 : angle 2.07588 ( 36) link_NAG-ASN : bond 0.00324 ( 18) link_NAG-ASN : angle 2.22254 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4000.08 seconds wall clock time: 68 minutes 48.30 seconds (4128.30 seconds total)