Starting phenix.real_space_refine on Sun May 11 23:03:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c48_45177/05_2025/9c48_45177.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c48_45177/05_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_45177/05_2025/9c48_45177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c48_45177/05_2025/9c48_45177.map" model { file = "/net/cci-nas-00/data/ceres_data/9c48_45177/05_2025/9c48_45177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c48_45177/05_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 13.16, per 1000 atoms: 1.55 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: 2.41 Conformation dependent library (CDL) restraints added in 1.8 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: 0.95 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: 2.45 Time building geometry restraints manager: 2.76 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: 28.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 30.620 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.220 ------------------------------------------------------------------------------- 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 : 0.953 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: 1.6646 time to fit residues: 143.8215 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 : 0.848 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.081528 restraints weight = 29910.193| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.45 r_work: 0.2876 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 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 = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- 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 3.02509 ( 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 : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7747 (mm-30) REVERT: A 95 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7722 (mt-10) REVERT: A 326 LYS cc_start: 0.8018 (pptt) cc_final: 0.7818 (pttp) REVERT: B 51 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7727 (mm-30) REVERT: B 326 LYS cc_start: 0.8687 (pttt) cc_final: 0.8084 (pptt) REVERT: C 51 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7759 (mm-30) outliers start: 11 outliers final: 5 residues processed: 99 average time/residue: 1.6206 time to fit residues: 168.6177 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 : 0.859 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 50 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 18 optimal weight: 0.1980 chunk 56 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 90 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.121459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.082302 restraints weight = 37674.798| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 4.09 r_work: 0.2872 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 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 = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8451 Z= 0.139 Angle : 0.581 6.169 11580 Z= 0.296 Chirality : 0.047 0.207 1395 Planarity : 0.003 0.031 1404 Dihedral : 9.799 78.849 1800 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.95 % Allowed : 11.39 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.07 (0.26), residues: 996 helix: 0.72 (0.34), residues: 252 sheet: 0.26 (0.26), residues: 366 loop : -0.48 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 259 HIS 0.003 0.001 HIS A 286 PHE 0.009 0.002 PHE C 294 TYR 0.013 0.001 TYR A 89 ARG 0.002 0.000 ARG B 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 18) link_NAG-ASN : angle 2.58677 ( 54) link_BETA1-4 : bond 0.00426 ( 12) link_BETA1-4 : angle 2.24077 ( 36) hydrogen bonds : bond 0.04210 ( 349) hydrogen bonds : angle 5.03004 ( 1029) SS BOND : bond 0.00323 ( 12) SS BOND : angle 1.57999 ( 24) covalent geometry : bond 0.00317 ( 8409) covalent geometry : angle 0.53746 (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 : 0.863 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7780 (mm-30) REVERT: A 95 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7723 (mt-10) REVERT: A 307 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: B 51 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7726 (mm-30) REVERT: B 307 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7633 (mm-30) REVERT: B 308 GLN cc_start: 0.8490 (mt0) cc_final: 0.8261 (mt0) REVERT: B 326 LYS cc_start: 0.8688 (pttt) cc_final: 0.8121 (pptt) REVERT: C 51 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7705 (mm-30) REVERT: C 95 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7636 (mt-10) REVERT: C 326 LYS cc_start: 0.8567 (pttp) cc_final: 0.7922 (pptt) outliers start: 8 outliers final: 1 residues processed: 98 average time/residue: 1.6539 time to fit residues: 170.0941 Evaluate side-chains 94 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL 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: 0.5980 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 74 optimal weight: 0.3980 chunk 7 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 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 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 = 0.3695 r_free = 0.3695 target = 0.120682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.081593 restraints weight = 30618.241| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.38 r_work: 0.2883 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8451 Z= 0.146 Angle : 0.585 5.540 11580 Z= 0.299 Chirality : 0.047 0.246 1395 Planarity : 0.003 0.032 1404 Dihedral : 9.472 76.975 1800 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.07 % Allowed : 12.22 % 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: 0.15 (0.26), residues: 996 helix: 0.85 (0.34), residues: 252 sheet: 0.31 (0.26), residues: 366 loop : -0.49 (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 A 286 PHE 0.010 0.002 PHE C 294 TYR 0.012 0.001 TYR A 89 ARG 0.002 0.000 ARG B 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00410 ( 18) link_NAG-ASN : angle 2.55825 ( 54) link_BETA1-4 : bond 0.00432 ( 12) link_BETA1-4 : angle 2.11601 ( 36) hydrogen bonds : bond 0.04014 ( 349) hydrogen bonds : angle 4.92218 ( 1029) SS BOND : bond 0.00326 ( 12) SS BOND : angle 1.71588 ( 24) covalent geometry : bond 0.00343 ( 8409) covalent geometry : angle 0.54243 (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 102 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7892 (mm-30) REVERT: A 95 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7699 (mt-10) REVERT: B 51 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7680 (mm-30) REVERT: B 307 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7663 (mm-30) REVERT: B 308 GLN cc_start: 0.8494 (mt0) cc_final: 0.8293 (mt0) REVERT: B 326 LYS cc_start: 0.8716 (pttt) cc_final: 0.8191 (pptt) REVERT: C 51 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7772 (mm-30) REVERT: C 95 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7626 (mt-10) REVERT: C 260 ASP cc_start: 0.8367 (t70) cc_final: 0.8154 (t0) REVERT: C 307 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7734 (mm-30) REVERT: C 326 LYS cc_start: 0.8570 (pttp) cc_final: 0.8024 (pptt) outliers start: 9 outliers final: 4 residues processed: 96 average time/residue: 1.5797 time to fit residues: 159.4692 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 : 0.962 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 47 optimal weight: 0.4980 chunk 84 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 0.1980 chunk 25 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 94 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 0.1980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.121220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.082084 restraints weight = 38149.817| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 4.13 r_work: 0.2869 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 8451 Z= 0.127 Angle : 0.562 5.429 11580 Z= 0.287 Chirality : 0.047 0.257 1395 Planarity : 0.003 0.032 1404 Dihedral : 9.322 76.596 1800 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.07 % Allowed : 12.69 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.18 (0.26), residues: 996 helix: 0.91 (0.34), residues: 252 sheet: 0.31 (0.26), residues: 366 loop : -0.49 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 259 HIS 0.003 0.001 HIS A 286 PHE 0.009 0.001 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 0.00417 ( 18) link_NAG-ASN : angle 2.54612 ( 54) link_BETA1-4 : bond 0.00454 ( 12) link_BETA1-4 : angle 2.05776 ( 36) hydrogen bonds : bond 0.03793 ( 349) hydrogen bonds : angle 4.83445 ( 1029) SS BOND : bond 0.00331 ( 12) SS BOND : angle 1.58426 ( 24) covalent geometry : bond 0.00291 ( 8409) covalent geometry : angle 0.51920 (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: 9 poor density : 93 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7867 (mm-30) REVERT: A 95 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7710 (mt-10) REVERT: B 51 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7684 (mm-30) REVERT: B 307 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7694 (mm-30) REVERT: B 308 GLN cc_start: 0.8550 (mt0) cc_final: 0.8340 (mt0) REVERT: B 326 LYS cc_start: 0.8709 (pttt) cc_final: 0.8194 (pptt) REVERT: C 51 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7663 (mm-30) REVERT: C 95 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7613 (mt-10) REVERT: C 260 ASP cc_start: 0.8403 (t70) cc_final: 0.8178 (t0) REVERT: C 307 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7721 (mm-30) REVERT: C 326 LYS cc_start: 0.8573 (pttp) cc_final: 0.8027 (pptt) outliers start: 9 outliers final: 5 residues processed: 95 average time/residue: 1.6405 time to fit residues: 163.8135 Evaluate side-chains 99 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 109 MET Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 307 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 58 optimal weight: 0.0010 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 56 optimal weight: 0.0980 chunk 39 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 21 optimal weight: 0.0670 chunk 15 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.1924 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.123157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.085014 restraints weight = 28613.043| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.33 r_work: 0.2950 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8451 Z= 0.098 Angle : 0.515 6.372 11580 Z= 0.263 Chirality : 0.045 0.241 1395 Planarity : 0.003 0.030 1404 Dihedral : 8.923 77.438 1800 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.59 % Allowed : 13.29 % 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: 0.42 (0.26), residues: 996 helix: 1.21 (0.35), residues: 252 sheet: 0.47 (0.26), residues: 360 loop : -0.43 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 259 HIS 0.001 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 B 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 18) link_NAG-ASN : angle 2.21293 ( 54) link_BETA1-4 : bond 0.00485 ( 12) link_BETA1-4 : angle 1.87704 ( 36) hydrogen bonds : bond 0.03335 ( 349) hydrogen bonds : angle 4.62800 ( 1029) SS BOND : bond 0.00319 ( 12) SS BOND : angle 1.30032 ( 24) covalent geometry : bond 0.00208 ( 8409) covalent geometry : angle 0.47947 (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 100 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7716 (mm-30) REVERT: A 95 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7628 (mt-10) REVERT: A 307 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7769 (mm-30) REVERT: A 308 GLN cc_start: 0.8334 (mt0) cc_final: 0.8074 (mt0) REVERT: B 51 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7660 (mm-30) REVERT: B 307 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7675 (mm-30) REVERT: B 308 GLN cc_start: 0.8463 (mt0) cc_final: 0.8164 (mt0) REVERT: B 326 LYS cc_start: 0.8634 (pttt) cc_final: 0.8214 (pptt) REVERT: C 51 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7639 (mm-30) REVERT: C 95 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7598 (mt-10) REVERT: C 260 ASP cc_start: 0.8335 (t70) cc_final: 0.8132 (t0) REVERT: C 307 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7697 (mm-30) REVERT: C 308 GLN cc_start: 0.8388 (mt0) cc_final: 0.8112 (mt0) REVERT: C 326 LYS cc_start: 0.8508 (pttp) cc_final: 0.8029 (pptt) outliers start: 5 outliers final: 1 residues processed: 95 average time/residue: 1.6230 time to fit residues: 162.1636 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 : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET 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: 0.9980 chunk 38 optimal weight: 0.4980 chunk 75 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 59 optimal weight: 0.0980 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 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 = 0.3711 r_free = 0.3711 target = 0.120975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.082368 restraints weight = 39338.819| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 4.01 r_work: 0.2890 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8451 Z= 0.144 Angle : 0.569 6.406 11580 Z= 0.293 Chirality : 0.047 0.213 1395 Planarity : 0.003 0.031 1404 Dihedral : 9.210 76.198 1800 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.47 % Allowed : 13.76 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.26 (0.26), residues: 996 helix: 1.10 (0.35), residues: 252 sheet: 0.31 (0.26), residues: 366 loop : -0.48 (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 A 286 PHE 0.011 0.002 PHE C 294 TYR 0.012 0.001 TYR A 89 ARG 0.002 0.000 ARG B 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 18) link_NAG-ASN : angle 2.28602 ( 54) link_BETA1-4 : bond 0.00438 ( 12) link_BETA1-4 : angle 2.02560 ( 36) hydrogen bonds : bond 0.03808 ( 349) hydrogen bonds : angle 4.74632 ( 1029) SS BOND : bond 0.00315 ( 12) SS BOND : angle 1.65407 ( 24) covalent geometry : bond 0.00339 ( 8409) covalent geometry : angle 0.53320 (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: 4 poor density : 97 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7951 (mm-30) REVERT: A 95 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7681 (mt-10) REVERT: B 51 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7695 (mm-30) REVERT: B 307 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7670 (mm-30) REVERT: B 308 GLN cc_start: 0.8556 (mt0) cc_final: 0.8238 (mt0) REVERT: B 326 LYS cc_start: 0.8694 (pttt) cc_final: 0.8249 (pptt) REVERT: C 51 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7636 (mm-30) REVERT: C 95 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7640 (mt-10) REVERT: C 307 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7746 (mm-30) REVERT: C 326 LYS cc_start: 0.8600 (pttp) cc_final: 0.8095 (pptt) outliers start: 4 outliers final: 1 residues processed: 97 average time/residue: 1.6635 time to fit residues: 169.4912 Evaluate side-chains 95 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 48 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 84 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 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 B 175 GLN C 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.119804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.081263 restraints weight = 37477.251| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.84 r_work: 0.2871 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8451 Z= 0.192 Angle : 0.637 6.776 11580 Z= 0.324 Chirality : 0.048 0.208 1395 Planarity : 0.004 0.033 1404 Dihedral : 9.648 75.660 1800 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % 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: 0.09 (0.26), residues: 996 helix: 0.88 (0.34), residues: 252 sheet: 0.30 (0.26), residues: 366 loop : -0.61 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 164 HIS 0.004 0.001 HIS B 286 PHE 0.011 0.002 PHE A 226 TYR 0.010 0.001 TYR A 89 ARG 0.003 0.000 ARG A 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 18) link_NAG-ASN : angle 2.48440 ( 54) link_BETA1-4 : bond 0.00438 ( 12) link_BETA1-4 : angle 2.23624 ( 36) hydrogen bonds : bond 0.04160 ( 349) hydrogen bonds : angle 4.94108 ( 1029) SS BOND : bond 0.00350 ( 12) SS BOND : angle 1.92317 ( 24) covalent geometry : bond 0.00466 ( 8409) covalent geometry : angle 0.59786 (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 98 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7965 (mm-30) REVERT: A 95 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7689 (mt-10) REVERT: B 51 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7717 (mm-30) REVERT: B 308 GLN cc_start: 0.8645 (mt0) cc_final: 0.8412 (mt0) REVERT: B 326 LYS cc_start: 0.8713 (pttt) cc_final: 0.8228 (pptt) REVERT: C 51 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7720 (mm-30) REVERT: C 326 LYS cc_start: 0.8617 (pttp) cc_final: 0.8071 (pptt) outliers start: 5 outliers final: 2 residues processed: 94 average time/residue: 1.5823 time to fit residues: 156.3555 Evaluate side-chains 94 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 MET 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: 0.5980 chunk 26 optimal weight: 0.3980 chunk 94 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 58 optimal weight: 0.0270 chunk 72 optimal weight: 0.9980 chunk 7 optimal weight: 0.0870 chunk 13 optimal weight: 0.0980 overall best weight: 0.2416 ------------------------------------------------------------------------------- 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 = 0.121939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.082550 restraints weight = 41341.235| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 4.23 r_work: 0.2882 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- 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 = 0.42 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: 0.8414 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8451 Z= 0.104 Angle : 0.543 7.016 11580 Z= 0.276 Chirality : 0.046 0.287 1395 Planarity : 0.003 0.031 1404 Dihedral : 9.117 76.121 1800 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.24 % Allowed : 14.35 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.32 (0.26), residues: 996 helix: 1.15 (0.35), residues: 252 sheet: 0.43 (0.26), residues: 360 loop : -0.54 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 259 HIS 0.002 0.001 HIS B 140 PHE 0.008 0.001 PHE C 294 TYR 0.012 0.001 TYR A 89 ARG 0.001 0.000 ARG B 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 18) link_NAG-ASN : angle 2.37895 ( 54) link_BETA1-4 : bond 0.00475 ( 12) link_BETA1-4 : angle 2.03113 ( 36) hydrogen bonds : bond 0.03469 ( 349) hydrogen bonds : angle 4.69086 ( 1029) SS BOND : bond 0.00311 ( 12) SS BOND : angle 1.38025 ( 24) covalent geometry : bond 0.00225 ( 8409) covalent geometry : angle 0.50449 (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 94 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7932 (mm-30) REVERT: A 95 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7707 (mt-10) REVERT: B 51 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7667 (mm-30) REVERT: B 326 LYS cc_start: 0.8691 (pttt) cc_final: 0.8242 (pptt) REVERT: C 51 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7733 (mm-30) REVERT: C 95 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7732 (mt-10) REVERT: C 307 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7791 (mm-30) REVERT: C 326 LYS cc_start: 0.8615 (pttp) cc_final: 0.8064 (pptt) outliers start: 2 outliers final: 2 residues processed: 93 average time/residue: 1.6029 time to fit residues: 156.6146 Evaluate side-chains 95 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 361 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 97 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 62 optimal weight: 0.1980 chunk 24 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN A 287 ASN B 175 GLN C 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.120447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.081265 restraints weight = 41845.342| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 4.34 r_work: 0.2851 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8451 Z= 0.175 Angle : 0.609 6.968 11580 Z= 0.311 Chirality : 0.048 0.226 1395 Planarity : 0.004 0.033 1404 Dihedral : 9.442 75.457 1800 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.24 % Allowed : 14.35 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.02 (0.34), residues: 252 sheet: 0.30 (0.26), residues: 366 loop : -0.57 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 164 HIS 0.003 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 0.00340 ( 18) link_NAG-ASN : angle 2.40397 ( 54) link_BETA1-4 : bond 0.00460 ( 12) link_BETA1-4 : angle 2.17820 ( 36) hydrogen bonds : bond 0.03933 ( 349) hydrogen bonds : angle 4.83590 ( 1029) SS BOND : bond 0.00324 ( 12) SS BOND : angle 1.77393 ( 24) covalent geometry : bond 0.00426 ( 8409) covalent geometry : angle 0.57109 (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 97 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7921 (mm-30) REVERT: A 95 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7713 (mt-10) REVERT: B 51 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7692 (mm-30) REVERT: B 326 LYS cc_start: 0.8728 (pttt) cc_final: 0.8232 (pptt) REVERT: C 51 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7740 (mm-30) REVERT: C 326 LYS cc_start: 0.8648 (pttp) cc_final: 0.8076 (pptt) outliers start: 2 outliers final: 2 residues processed: 96 average time/residue: 1.7067 time to fit residues: 172.0314 Evaluate side-chains 95 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 361 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 83 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 chunk 13 optimal weight: 0.0470 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 81 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.121383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.083025 restraints weight = 34653.728| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.76 r_work: 0.2903 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 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 = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8451 Z= 0.126 Angle : 0.565 6.976 11580 Z= 0.288 Chirality : 0.046 0.227 1395 Planarity : 0.003 0.032 1404 Dihedral : 9.218 75.395 1800 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.24 % Allowed : 14.35 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.15 (0.34), residues: 252 sheet: 0.28 (0.26), residues: 366 loop : -0.53 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 259 HIS 0.002 0.001 HIS C 286 PHE 0.009 0.001 PHE C 294 TYR 0.011 0.001 TYR A 89 ARG 0.001 0.000 ARG A 309 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 18) link_NAG-ASN : angle 2.28828 ( 54) link_BETA1-4 : bond 0.00470 ( 12) link_BETA1-4 : angle 2.08493 ( 36) hydrogen bonds : bond 0.03621 ( 349) hydrogen bonds : angle 4.73230 ( 1029) SS BOND : bond 0.00324 ( 12) SS BOND : angle 1.54673 ( 24) covalent geometry : bond 0.00293 ( 8409) covalent geometry : angle 0.52785 (11466) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7758.74 seconds wall clock time: 135 minutes 7.32 seconds (8107.32 seconds total)