Starting phenix.real_space_refine on Tue Apr 29 08:22:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c48_45177/04_2025/9c48_45177.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c48_45177/04_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_45177/04_2025/9c48_45177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c48_45177/04_2025/9c48_45177.map" model { file = "/net/cci-nas-00/data/ceres_data/9c48_45177/04_2025/9c48_45177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c48_45177/04_2025/9c48_45177.cif" } resolution = 2.4 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= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 13.35, per 1000 atoms: 1.57 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: 2.42 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 0.92 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: 2.58 Time building geometry restraints manager: 2.81 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: 0.02 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: 228.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 32.480 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 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:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 275.080 ------------------------------------------------------------------------------- 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 (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: -0.49 (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 TRP 0.013 0.002 TRP B 164 HIS 0.001 0.000 HIS A 286 PHE 0.011 0.002 PHE B 198 TYR 0.008 0.001 TYR B 89 ARG 0.005 0.001 ARG B 265 Details of bonding type rmsd link_NAG-ASN : bond 0.00776 ( 18) link_NAG-ASN : angle 2.78258 ( 54) link_BETA1-4 : bond 0.00355 ( 12) link_BETA1-4 : angle 2.27571 ( 36) hydrogen bonds : bond 0.20042 ( 349) hydrogen bonds : angle 7.58264 ( 1029) SS BOND : bond 0.00234 ( 12) SS BOND : angle 1.40235 ( 24) covalent geometry : bond 0.00610 ( 8409) covalent geometry : angle 0.90076 (11466) *********************** 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 : 0.928 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: 1.7144 time to fit residues: 148.0346 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 : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 0.3980 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 175 GLN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 308 GLN B 338 ASN 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 = 0.3690 r_free = 0.3690 target = 0.120689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.081530 restraints weight = 29910.215| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.45 r_work: 0.2877 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- 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 = 0.2879 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: 0.8378 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8451 Z= 0.186 Angle : 0.670 8.920 11580 Z= 0.339 Chirality : 0.050 0.218 1395 Planarity : 0.004 0.032 1404 Dihedral : 12.158 79.639 1800 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.30 % Allowed : 11.74 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: -0.29 (0.25), residues: 996 helix: -0.10 (0.31), residues: 270 sheet: 0.22 (0.26), residues: 369 loop : -0.51 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 164 HIS 0.004 0.001 HIS A 286 PHE 0.011 0.002 PHE A 81 TYR 0.014 0.002 TYR C 89 ARG 0.004 0.001 ARG C 309 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 18) link_NAG-ASN : angle 3.02510 ( 54) link_BETA1-4 : bond 0.00386 ( 12) link_BETA1-4 : angle 2.17765 ( 36) hydrogen bonds : bond 0.04724 ( 349) hydrogen bonds : angle 5.43882 ( 1029) SS BOND : bond 0.00403 ( 12) SS BOND : angle 2.06642 ( 24) covalent geometry : bond 0.00444 ( 8409) covalent geometry : angle 0.62168 (11466) *********************** 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 104 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7725 (mm-30) REVERT: A 95 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7715 (mt-10) REVERT: B 51 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7708 (mm-30) REVERT: B 326 LYS cc_start: 0.8680 (pttt) cc_final: 0.8081 (pptt) REVERT: C 51 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7742 (mm-30) outliers start: 11 outliers final: 5 residues processed: 99 average time/residue: 1.6204 time to fit residues: 168.7650 Evaluate side-chains 93 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 156 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 93 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 50 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 chunk 18 optimal weight: 0.1980 chunk 56 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 90 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 B 308 GLN 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 = 0.3706 r_free = 0.3706 target = 0.121829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.082853 restraints weight = 37664.420| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 4.02 r_work: 0.2883 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 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 = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 8451 Z= 0.134 Angle : 0.568 5.458 11580 Z= 0.289 Chirality : 0.047 0.263 1395 Planarity : 0.003 0.031 1404 Dihedral : 9.671 78.916 1800 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.95 % Allowed : 11.63 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 0.11 (0.26), residues: 996 helix: 0.78 (0.34), residues: 252 sheet: 0.26 (0.26), residues: 366 loop : -0.46 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 259 HIS 0.003 0.001 HIS A 286 PHE 0.008 0.002 PHE C 81 TYR 0.014 0.001 TYR A 89 ARG 0.002 0.000 ARG B 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 18) link_NAG-ASN : angle 2.55130 ( 54) link_BETA1-4 : bond 0.00445 ( 12) link_BETA1-4 : angle 2.23570 ( 36) hydrogen bonds : bond 0.04108 ( 349) hydrogen bonds : angle 4.99182 ( 1029) SS BOND : bond 0.00310 ( 12) SS BOND : angle 1.50460 ( 24) covalent geometry : bond 0.00306 ( 8409) covalent geometry : angle 0.52455 (11466) *********************** 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 102 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7820 (mm-30) REVERT: A 95 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7694 (mt-10) REVERT: A 307 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: A 326 LYS cc_start: 0.8556 (pttp) cc_final: 0.7946 (pptt) REVERT: B 51 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7767 (mm-30) REVERT: B 307 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7665 (mm-30) REVERT: B 308 GLN cc_start: 0.8477 (mt0) cc_final: 0.8244 (mt0) REVERT: B 326 LYS cc_start: 0.8695 (pttt) cc_final: 0.8161 (pptt) REVERT: C 51 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7760 (mm-30) REVERT: C 95 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7642 (mt-10) REVERT: C 326 LYS cc_start: 0.8591 (pttp) cc_final: 0.7982 (pptt) outliers start: 8 outliers final: 0 residues processed: 97 average time/residue: 1.6210 time to fit residues: 165.2982 Evaluate side-chains 93 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 73 optimal weight: 0.4980 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 74 optimal weight: 0.2980 chunk 7 optimal weight: 0.1980 chunk 31 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.120626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.081607 restraints weight = 30583.055| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.39 r_work: 0.2882 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 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 = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 8451 Z= 0.149 Angle : 0.587 5.491 11580 Z= 0.301 Chirality : 0.047 0.235 1395 Planarity : 0.004 0.033 1404 Dihedral : 9.498 76.878 1800 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.83 % Allowed : 12.46 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 0.14 (0.26), residues: 996 helix: 0.84 (0.34), residues: 252 sheet: 0.29 (0.26), residues: 366 loop : -0.48 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 164 HIS 0.004 0.001 HIS A 286 PHE 0.011 0.002 PHE C 294 TYR 0.012 0.001 TYR C 89 ARG 0.002 0.000 ARG B 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 18) link_NAG-ASN : angle 2.54240 ( 54) link_BETA1-4 : bond 0.00442 ( 12) link_BETA1-4 : angle 2.10801 ( 36) hydrogen bonds : bond 0.04040 ( 349) hydrogen bonds : angle 4.93347 ( 1029) SS BOND : bond 0.00346 ( 12) SS BOND : angle 1.78197 ( 24) covalent geometry : bond 0.00353 ( 8409) covalent geometry : angle 0.54481 (11466) *********************** 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 100 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7910 (mm-30) REVERT: A 95 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7711 (mt-10) REVERT: A 326 LYS cc_start: 0.8544 (pttp) cc_final: 0.7924 (pptt) REVERT: B 51 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7666 (mm-30) REVERT: B 307 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7659 (mm-30) REVERT: B 308 GLN cc_start: 0.8508 (mt0) cc_final: 0.8301 (mt0) REVERT: B 326 LYS cc_start: 0.8720 (pttt) cc_final: 0.8195 (pptt) REVERT: C 51 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7773 (mm-30) REVERT: C 95 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7650 (mt-10) REVERT: C 260 ASP cc_start: 0.8379 (t70) cc_final: 0.8160 (t0) REVERT: C 307 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7735 (mm-30) REVERT: C 326 LYS cc_start: 0.8563 (pttp) cc_final: 0.8019 (pptt) outliers start: 7 outliers final: 3 residues processed: 95 average time/residue: 1.6162 time to fit residues: 161.4565 Evaluate side-chains 97 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A 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 97 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 43 optimal weight: 0.0670 chunk 94 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 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 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 = 0.3692 r_free = 0.3692 target = 0.120681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.080936 restraints weight = 38111.115| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 4.19 r_work: 0.2848 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 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 = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 8451 Z= 0.153 Angle : 0.586 5.448 11580 Z= 0.299 Chirality : 0.047 0.266 1395 Planarity : 0.003 0.033 1404 Dihedral : 9.462 76.340 1800 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.83 % Allowed : 12.81 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 0.12 (0.26), residues: 996 helix: 0.85 (0.34), residues: 252 sheet: 0.31 (0.26), residues: 366 loop : -0.54 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 259 HIS 0.004 0.001 HIS A 286 PHE 0.010 0.002 PHE C 294 TYR 0.011 0.001 TYR C 89 ARG 0.002 0.000 ARG B 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 18) link_NAG-ASN : angle 2.58672 ( 54) link_BETA1-4 : bond 0.00456 ( 12) link_BETA1-4 : angle 2.12453 ( 36) hydrogen bonds : bond 0.03991 ( 349) hydrogen bonds : angle 4.89502 ( 1029) SS BOND : bond 0.00325 ( 12) SS BOND : angle 1.68625 ( 24) covalent geometry : bond 0.00363 ( 8409) covalent geometry : angle 0.54358 (11466) *********************** 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 102 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7644 (mm-30) REVERT: A 95 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7690 (mt-10) REVERT: A 326 LYS cc_start: 0.8566 (pttp) cc_final: 0.7930 (pptt) REVERT: B 51 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7659 (mm-30) REVERT: B 307 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7666 (mm-30) REVERT: B 308 GLN cc_start: 0.8597 (mt0) cc_final: 0.8238 (mt0) REVERT: B 326 LYS cc_start: 0.8711 (pttt) cc_final: 0.8164 (pptt) REVERT: C 51 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7655 (mm-30) REVERT: C 95 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7624 (mt-10) REVERT: C 260 ASP cc_start: 0.8401 (t70) cc_final: 0.8177 (t0) REVERT: C 307 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7731 (mm-30) REVERT: C 326 LYS cc_start: 0.8581 (pttp) cc_final: 0.8011 (pptt) outliers start: 7 outliers final: 4 residues processed: 98 average time/residue: 1.8704 time to fit residues: 192.6450 Evaluate side-chains 98 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 156 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 58 optimal weight: 0.0270 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 0.0670 chunk 86 optimal weight: 0.1980 chunk 56 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 overall best weight: 0.2776 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.121915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.083574 restraints weight = 28510.270| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.80 r_work: 0.2918 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 8451 Z= 0.108 Angle : 0.530 5.445 11580 Z= 0.271 Chirality : 0.046 0.250 1395 Planarity : 0.003 0.032 1404 Dihedral : 9.096 76.436 1800 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.71 % Allowed : 13.17 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 0.33 (0.26), residues: 996 helix: 1.12 (0.35), residues: 252 sheet: 0.45 (0.26), residues: 360 loop : -0.50 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 259 HIS 0.002 0.001 HIS A 286 PHE 0.008 0.001 PHE C 294 TYR 0.012 0.001 TYR C 89 ARG 0.001 0.000 ARG C 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 18) link_NAG-ASN : angle 2.28689 ( 54) link_BETA1-4 : bond 0.00470 ( 12) link_BETA1-4 : angle 1.98640 ( 36) hydrogen bonds : bond 0.03517 ( 349) hydrogen bonds : angle 4.69611 ( 1029) SS BOND : bond 0.00309 ( 12) SS BOND : angle 1.40341 ( 24) covalent geometry : bond 0.00240 ( 8409) covalent geometry : angle 0.49204 (11466) *********************** 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 98 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 1.431 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7884 (mm-30) REVERT: A 95 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7670 (mt-10) REVERT: A 307 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7744 (mm-30) REVERT: A 308 GLN cc_start: 0.8400 (mt0) cc_final: 0.8064 (tt0) REVERT: A 326 LYS cc_start: 0.8533 (pttp) cc_final: 0.7962 (pptt) REVERT: B 51 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7573 (mm-30) REVERT: B 307 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7643 (mm-30) REVERT: B 308 GLN cc_start: 0.8545 (mt0) cc_final: 0.8196 (mt0) REVERT: B 326 LYS cc_start: 0.8671 (pttt) cc_final: 0.8195 (pptt) REVERT: C 51 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7603 (mm-30) REVERT: C 260 ASP cc_start: 0.8345 (t70) cc_final: 0.8137 (t0) REVERT: C 307 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7701 (mm-30) REVERT: C 326 LYS cc_start: 0.8565 (pttp) cc_final: 0.8035 (pptt) outliers start: 6 outliers final: 1 residues processed: 93 average time/residue: 2.0900 time to fit residues: 205.0144 Evaluate side-chains 96 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain C residue 307 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 6 optimal weight: 0.5980 chunk 38 optimal weight: 0.2980 chunk 75 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 0.0870 chunk 59 optimal weight: 0.0570 overall best weight: 0.3076 ------------------------------------------------------------------------------- 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 C 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.121965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.083245 restraints weight = 39282.522| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 4.13 r_work: 0.2898 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 8451 Z= 0.113 Angle : 0.533 5.430 11580 Z= 0.273 Chirality : 0.046 0.217 1395 Planarity : 0.003 0.031 1404 Dihedral : 9.053 76.251 1800 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.71 % Allowed : 13.17 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 0.37 (0.26), residues: 996 helix: 1.19 (0.35), residues: 252 sheet: 0.46 (0.26), residues: 360 loop : -0.51 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 259 HIS 0.002 0.001 HIS A 286 PHE 0.009 0.001 PHE C 294 TYR 0.011 0.001 TYR A 89 ARG 0.001 0.000 ARG B 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 18) link_NAG-ASN : angle 2.18951 ( 54) link_BETA1-4 : bond 0.00465 ( 12) link_BETA1-4 : angle 1.96992 ( 36) hydrogen bonds : bond 0.03526 ( 349) hydrogen bonds : angle 4.67932 ( 1029) SS BOND : bond 0.00312 ( 12) SS BOND : angle 1.46300 ( 24) covalent geometry : bond 0.00253 ( 8409) covalent geometry : angle 0.49777 (11466) *********************** 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 101 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7902 (mm-30) REVERT: A 95 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7645 (mt-10) REVERT: A 307 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7791 (mm-30) REVERT: A 308 GLN cc_start: 0.8428 (mt0) cc_final: 0.8191 (mt0) REVERT: A 326 LYS cc_start: 0.8546 (pttp) cc_final: 0.7976 (pptt) REVERT: B 51 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7617 (mm-30) REVERT: B 307 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7681 (mm-30) REVERT: B 308 GLN cc_start: 0.8573 (mt0) cc_final: 0.8251 (mt0) REVERT: B 326 LYS cc_start: 0.8681 (pttt) cc_final: 0.8204 (pptt) REVERT: C 51 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7573 (mm-30) REVERT: C 95 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7624 (mt-10) REVERT: C 260 ASP cc_start: 0.8390 (t70) cc_final: 0.8170 (t0) REVERT: C 307 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7739 (mm-30) REVERT: C 308 GLN cc_start: 0.8481 (mt0) cc_final: 0.8198 (mt0) REVERT: C 326 LYS cc_start: 0.8557 (pttp) cc_final: 0.8021 (pptt) outliers start: 6 outliers final: 1 residues processed: 96 average time/residue: 1.7708 time to fit residues: 178.4606 Evaluate side-chains 95 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain C residue 307 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 48 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 14 optimal weight: 0.0980 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 56 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 C 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.121097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.082720 restraints weight = 37464.653| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.92 r_work: 0.2893 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8451 Z= 0.140 Angle : 0.566 6.800 11580 Z= 0.291 Chirality : 0.046 0.206 1395 Planarity : 0.003 0.032 1404 Dihedral : 9.222 75.881 1800 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.71 % Allowed : 13.64 % 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 (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: 0.24 (0.26), residues: 996 helix: 1.10 (0.34), residues: 252 sheet: 0.31 (0.26), residues: 366 loop : -0.52 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 164 HIS 0.003 0.001 HIS C 286 PHE 0.010 0.002 PHE C 294 TYR 0.011 0.001 TYR A 89 ARG 0.002 0.000 ARG C 309 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 18) link_NAG-ASN : angle 2.23585 ( 54) link_BETA1-4 : bond 0.00448 ( 12) link_BETA1-4 : angle 2.05403 ( 36) hydrogen bonds : bond 0.03758 ( 349) hydrogen bonds : angle 4.76186 ( 1029) SS BOND : bond 0.00331 ( 12) SS BOND : angle 1.64745 ( 24) covalent geometry : bond 0.00330 ( 8409) covalent geometry : angle 0.53052 (11466) *********************** 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 101 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7932 (mm-30) REVERT: A 95 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7671 (mt-10) REVERT: A 326 LYS cc_start: 0.8560 (pttp) cc_final: 0.7986 (pptt) REVERT: B 51 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7646 (mm-30) REVERT: B 307 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7658 (mm-30) REVERT: B 308 GLN cc_start: 0.8599 (mt0) cc_final: 0.8182 (mt0) REVERT: B 326 LYS cc_start: 0.8694 (pttt) cc_final: 0.8207 (pptt) REVERT: C 51 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7615 (mm-30) REVERT: C 95 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7624 (mt-10) REVERT: C 260 ASP cc_start: 0.8382 (t70) cc_final: 0.8172 (t0) REVERT: C 307 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7751 (mm-30) REVERT: C 326 LYS cc_start: 0.8578 (pttp) cc_final: 0.8034 (pptt) outliers start: 6 outliers final: 2 residues processed: 97 average time/residue: 1.6934 time to fit residues: 172.5834 Evaluate side-chains 97 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain B residue 156 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 77 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 0.0770 chunk 13 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 C 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.120632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.081542 restraints weight = 41300.523| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 4.25 r_work: 0.2854 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1925 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= 0.160 Angle : 0.594 6.373 11580 Z= 0.303 Chirality : 0.047 0.243 1395 Planarity : 0.004 0.033 1404 Dihedral : 9.392 75.562 1800 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.59 % Allowed : 13.88 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 0.17 (0.26), residues: 996 helix: 1.03 (0.34), residues: 252 sheet: 0.29 (0.26), residues: 366 loop : -0.58 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 259 HIS 0.003 0.001 HIS B 286 PHE 0.011 0.002 PHE C 294 TYR 0.010 0.001 TYR A 89 ARG 0.003 0.000 ARG C 309 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 18) link_NAG-ASN : angle 2.44042 ( 54) link_BETA1-4 : bond 0.00453 ( 12) link_BETA1-4 : angle 2.13551 ( 36) hydrogen bonds : bond 0.03898 ( 349) hydrogen bonds : angle 4.83593 ( 1029) SS BOND : bond 0.00334 ( 12) SS BOND : angle 1.74217 ( 24) covalent geometry : bond 0.00384 ( 8409) covalent geometry : angle 0.55489 (11466) *********************** 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: 5 poor density : 93 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7958 (mm-30) REVERT: A 95 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7701 (mt-10) REVERT: A 326 LYS cc_start: 0.8590 (pttp) cc_final: 0.8035 (pptt) REVERT: B 51 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7682 (mm-30) REVERT: B 326 LYS cc_start: 0.8707 (pttt) cc_final: 0.8227 (pptt) REVERT: C 51 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7754 (mm-30) REVERT: C 95 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7677 (mt-10) REVERT: C 260 ASP cc_start: 0.8415 (t70) cc_final: 0.8214 (t0) REVERT: C 307 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7796 (mm-30) REVERT: C 326 LYS cc_start: 0.8605 (pttp) cc_final: 0.8071 (pptt) outliers start: 5 outliers final: 4 residues processed: 95 average time/residue: 1.6449 time to fit residues: 164.2546 Evaluate side-chains 97 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 348 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 97 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 75 optimal weight: 0.0770 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 C 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.120797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.082394 restraints weight = 41856.216| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 4.02 r_work: 0.2878 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1957 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= 0.153 Angle : 0.589 5.487 11580 Z= 0.301 Chirality : 0.047 0.262 1395 Planarity : 0.003 0.033 1404 Dihedral : 9.384 75.479 1800 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.47 % Allowed : 13.88 % 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 (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: 0.16 (0.26), residues: 996 helix: 1.05 (0.34), residues: 252 sheet: 0.26 (0.26), residues: 366 loop : -0.58 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 259 HIS 0.003 0.001 HIS C 286 PHE 0.010 0.002 PHE C 294 TYR 0.011 0.001 TYR A 89 ARG 0.003 0.000 ARG A 309 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 18) link_NAG-ASN : angle 2.44107 ( 54) link_BETA1-4 : bond 0.00459 ( 12) link_BETA1-4 : angle 2.14543 ( 36) hydrogen bonds : bond 0.03859 ( 349) hydrogen bonds : angle 4.79640 ( 1029) SS BOND : bond 0.00332 ( 12) SS BOND : angle 1.69071 ( 24) covalent geometry : bond 0.00364 ( 8409) covalent geometry : angle 0.54939 (11466) ********************** 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: 4 poor density : 94 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7938 (mm-30) REVERT: A 95 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7640 (mt-10) REVERT: A 326 LYS cc_start: 0.8584 (pttp) cc_final: 0.8043 (pptt) REVERT: B 51 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7697 (mm-30) REVERT: B 326 LYS cc_start: 0.8695 (pttt) cc_final: 0.8227 (pptt) REVERT: C 51 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7758 (mm-30) REVERT: C 95 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7634 (mt-10) REVERT: C 260 ASP cc_start: 0.8373 (t70) cc_final: 0.8169 (t0) REVERT: C 326 LYS cc_start: 0.8597 (pttp) cc_final: 0.8073 (pptt) outliers start: 4 outliers final: 3 residues processed: 95 average time/residue: 1.6311 time to fit residues: 162.9028 Evaluate side-chains 98 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain C residue 348 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 89 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 81 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 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 ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 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 = 0.3693 r_free = 0.3693 target = 0.120013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.081432 restraints weight = 34622.501| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.76 r_work: 0.2869 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8451 Z= 0.193 Angle : 0.634 5.515 11580 Z= 0.323 Chirality : 0.048 0.212 1395 Planarity : 0.004 0.034 1404 Dihedral : 9.673 75.384 1800 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.36 % Allowed : 14.12 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 0.06 (0.25), residues: 996 helix: 0.91 (0.34), residues: 252 sheet: 0.25 (0.26), residues: 366 loop : -0.65 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 164 HIS 0.004 0.001 HIS B 286 PHE 0.011 0.002 PHE C 294 TYR 0.011 0.001 TYR A 89 ARG 0.003 0.000 ARG C 309 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 18) link_NAG-ASN : angle 2.50421 ( 54) link_BETA1-4 : bond 0.00455 ( 12) link_BETA1-4 : angle 2.28559 ( 36) hydrogen bonds : bond 0.04135 ( 349) hydrogen bonds : angle 4.91656 ( 1029) SS BOND : bond 0.00353 ( 12) SS BOND : angle 1.91629 ( 24) covalent geometry : bond 0.00469 ( 8409) covalent geometry : angle 0.59345 (11466) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8816.51 seconds wall clock time: 153 minutes 49.44 seconds (9229.44 seconds total)