Starting phenix.real_space_refine on Thu Feb 13 00:26:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c48_45177/02_2025/9c48_45177.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c48_45177/02_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_45177/02_2025/9c48_45177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c48_45177/02_2025/9c48_45177.map" model { file = "/net/cci-nas-00/data/ceres_data/9c48_45177/02_2025/9c48_45177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c48_45177/02_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-5592/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: 13.88, per 1000 atoms: 1.64 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: 2.53 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: 0.98 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: 2.36 Time building geometry restraints manager: 2.83 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: 23.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 32.620 Find NCS groups from input model: 0.470 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:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.220 ------------------------------------------------------------------------------- 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 8409 Z= 0.381 Angle : 0.901 18.729 11466 Z= 0.632 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 *********************** 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 : 0.943 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: 1.6915 time to fit residues: 145.9685 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 : 0.866 ------------------------------------------------------------------------------- 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 8409 Z= 0.286 Angle : 0.622 7.111 11466 Z= 0.328 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 *********************** 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 : 0.902 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: 1.6767 time to fit residues: 174.1883 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 : 0.860 ------------------------------------------------------------------------------- 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: 0.7980 chunk 51 optimal weight: 0.0980 chunk 18 optimal weight: 0.1980 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 90 optimal weight: 0.5980 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.122005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.083096 restraints weight = 37708.476| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 4.02 r_work: 0.2885 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 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 = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8409 Z= 0.184 Angle : 0.526 6.205 11466 Z= 0.279 Chirality : 0.047 0.223 1395 Planarity : 0.003 0.031 1404 Dihedral : 9.799 78.925 1800 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.83 % Allowed : 11.86 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 0.008 0.001 TRP B 259 HIS 0.002 0.001 HIS A 286 PHE 0.008 0.001 PHE B 294 TYR 0.013 0.001 TYR A 89 ARG 0.002 0.000 ARG B 203 *********************** 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 101 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7793 (mm-30) REVERT: A 95 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7691 (mt-10) REVERT: A 307 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7862 (mt-10) REVERT: B 51 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7736 (mm-30) REVERT: B 307 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7644 (mm-30) REVERT: B 308 GLN cc_start: 0.8468 (mt0) cc_final: 0.8238 (mt0) REVERT: B 326 LYS cc_start: 0.8682 (pttt) cc_final: 0.8136 (pptt) REVERT: C 51 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7719 (mm-30) REVERT: C 95 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7623 (mt-10) REVERT: C 326 LYS cc_start: 0.8585 (pttp) cc_final: 0.7970 (pptt) outliers start: 7 outliers final: 0 residues processed: 97 average time/residue: 1.6780 time to fit residues: 170.8696 Evaluate side-chains 94 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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: 0.5980 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 0.0980 chunk 55 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 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 = 0.3694 r_free = 0.3694 target = 0.120672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.081369 restraints weight = 30598.682| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.44 r_work: 0.2876 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 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 = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 8409 Z= 0.227 Angle : 0.546 5.415 11466 Z= 0.292 Chirality : 0.047 0.245 1395 Planarity : 0.004 0.033 1404 Dihedral : 9.512 77.137 1800 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.95 % Allowed : 12.10 % 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: 0.12 (0.26), residues: 996 helix: 0.83 (0.34), residues: 252 sheet: 0.27 (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 0.004 0.001 HIS A 286 PHE 0.010 0.002 PHE C 294 TYR 0.012 0.001 TYR C 89 ARG 0.002 0.000 ARG B 203 *********************** 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 101 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7873 (mm-30) REVERT: A 95 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7704 (mt-10) REVERT: A 307 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7839 (mt-10) REVERT: B 51 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7652 (mm-30) REVERT: B 307 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7640 (mm-30) REVERT: B 308 GLN cc_start: 0.8512 (mt0) cc_final: 0.8296 (mt0) REVERT: B 326 LYS cc_start: 0.8682 (pttt) cc_final: 0.8130 (pptt) REVERT: C 51 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7749 (mm-30) REVERT: C 95 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7618 (mt-10) REVERT: C 260 ASP cc_start: 0.8381 (t70) cc_final: 0.8137 (t0) REVERT: C 307 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7707 (mm-30) REVERT: C 308 GLN cc_start: 0.8497 (mt0) cc_final: 0.8286 (mt0) REVERT: C 326 LYS cc_start: 0.8551 (pttp) cc_final: 0.7966 (pptt) outliers start: 8 outliers final: 3 residues processed: 95 average time/residue: 1.7067 time to fit residues: 170.4413 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 : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 307 GLU 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: 0.1980 chunk 84 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 43 optimal weight: 0.0370 chunk 94 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 overall best weight: 0.3458 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.121609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.082435 restraints weight = 38138.919| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 4.19 r_work: 0.2872 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 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 = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 8409 Z= 0.178 Angle : 0.513 5.998 11466 Z= 0.273 Chirality : 0.046 0.251 1395 Planarity : 0.003 0.032 1404 Dihedral : 9.281 76.773 1800 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.95 % Allowed : 12.57 % Favored : 86.48 % 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: 0.23 (0.26), residues: 996 helix: 0.96 (0.34), residues: 252 sheet: 0.40 (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 0.003 0.001 HIS A 286 PHE 0.009 0.001 PHE C 294 TYR 0.012 0.001 TYR C 89 ARG 0.002 0.000 ARG B 203 *********************** 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 100 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7862 (mm-30) REVERT: A 95 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7704 (mt-10) REVERT: B 51 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7592 (mm-30) REVERT: B 307 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7678 (mm-30) REVERT: B 308 GLN cc_start: 0.8551 (mt0) cc_final: 0.8230 (mt0) REVERT: B 326 LYS cc_start: 0.8701 (pttt) cc_final: 0.8191 (pptt) REVERT: C 51 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7662 (mm-30) REVERT: C 95 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7612 (mt-10) REVERT: C 260 ASP cc_start: 0.8404 (t70) cc_final: 0.8158 (t0) REVERT: C 307 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7716 (mm-30) REVERT: C 308 GLN cc_start: 0.8548 (mt0) cc_final: 0.8305 (mt0) REVERT: C 326 LYS cc_start: 0.8575 (pttp) cc_final: 0.8010 (pptt) outliers start: 8 outliers final: 3 residues processed: 93 average time/residue: 1.7354 time to fit residues: 169.9088 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 : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 307 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 58 optimal weight: 0.0980 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 56 optimal weight: 0.0270 chunk 39 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.120769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.082322 restraints weight = 28542.268| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.29 r_work: 0.2908 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 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 = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8409 Z= 0.213 Angle : 0.532 5.432 11466 Z= 0.284 Chirality : 0.047 0.221 1395 Planarity : 0.003 0.033 1404 Dihedral : 9.321 76.095 1800 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.83 % Allowed : 12.93 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.96 (0.34), residues: 252 sheet: 0.30 (0.26), residues: 366 loop : -0.53 (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 A 286 PHE 0.011 0.002 PHE C 294 TYR 0.011 0.001 TYR C 89 ARG 0.002 0.000 ARG B 203 *********************** 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 105 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7702 (mm-30) REVERT: A 95 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7634 (mt-10) REVERT: B 51 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7632 (mm-30) REVERT: B 307 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7645 (mm-30) REVERT: B 308 GLN cc_start: 0.8547 (mt0) cc_final: 0.8225 (mt0) REVERT: B 326 LYS cc_start: 0.8686 (pttt) cc_final: 0.8238 (pptt) REVERT: C 51 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7669 (mm-30) REVERT: C 95 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7591 (mt-10) REVERT: C 260 ASP cc_start: 0.8317 (t70) cc_final: 0.8114 (t0) REVERT: C 307 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7702 (mm-30) REVERT: C 308 GLN cc_start: 0.8576 (mt0) cc_final: 0.8289 (mt0) REVERT: C 326 LYS cc_start: 0.8582 (pttp) cc_final: 0.8073 (pptt) outliers start: 7 outliers final: 4 residues processed: 101 average time/residue: 1.7439 time to fit residues: 184.9506 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 : 0.940 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 6 optimal weight: 0.0670 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.121220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.082349 restraints weight = 39322.627| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 4.21 r_work: 0.2878 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- 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 = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8409 Z= 0.192 Angle : 0.519 6.628 11466 Z= 0.276 Chirality : 0.046 0.219 1395 Planarity : 0.003 0.032 1404 Dihedral : 9.195 75.788 1800 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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: 0.23 (0.26), residues: 996 helix: 1.05 (0.35), residues: 252 sheet: 0.32 (0.26), residues: 366 loop : -0.51 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 A 89 ARG 0.002 0.000 ARG C 33 *********************** 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 : 0.710 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7923 (mm-30) REVERT: A 95 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7658 (mt-10) REVERT: B 51 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7636 (mm-30) REVERT: B 307 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7692 (mm-30) REVERT: B 308 GLN cc_start: 0.8606 (mt0) cc_final: 0.8289 (mt0) REVERT: B 326 LYS cc_start: 0.8697 (pttt) cc_final: 0.8207 (pptt) REVERT: C 51 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7620 (mm-30) REVERT: C 95 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7622 (mt-10) REVERT: C 260 ASP cc_start: 0.8381 (t70) cc_final: 0.8159 (t0) REVERT: C 307 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7771 (mm-30) REVERT: C 308 GLN cc_start: 0.8619 (mt0) cc_final: 0.8326 (mt0) REVERT: C 326 LYS cc_start: 0.8574 (pttp) cc_final: 0.8028 (pptt) outliers start: 6 outliers final: 3 residues processed: 97 average time/residue: 1.7274 time to fit residues: 175.4631 Evaluate side-chains 97 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.0970 chunk 56 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.120469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.081700 restraints weight = 37494.203| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 4.04 r_work: 0.2872 rms_B_bonded: 3.83 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 = 0.42 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 = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8409 Z= 0.247 Angle : 0.553 6.773 11466 Z= 0.293 Chirality : 0.047 0.218 1395 Planarity : 0.004 0.033 1404 Dihedral : 9.385 75.599 1800 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.59 % Allowed : 13.64 % 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: 0.15 (0.26), residues: 996 helix: 0.97 (0.34), residues: 252 sheet: 0.30 (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 0.002 0.000 ARG C 309 *********************** 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 102 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7949 (mm-30) REVERT: A 95 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7684 (mt-10) REVERT: B 51 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7681 (mm-30) REVERT: B 326 LYS cc_start: 0.8703 (pttt) cc_final: 0.8228 (pptt) REVERT: C 51 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7643 (mm-30) REVERT: C 95 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7652 (mt-10) REVERT: C 260 ASP cc_start: 0.8364 (t70) cc_final: 0.8158 (t0) REVERT: C 326 LYS cc_start: 0.8592 (pttp) cc_final: 0.8058 (pptt) outliers start: 5 outliers final: 3 residues processed: 100 average time/residue: 1.6404 time to fit residues: 172.4147 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 : 0.889 ------------------------------------------------------------------------------- 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 156 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 77 optimal weight: 0.4980 chunk 26 optimal weight: 0.3980 chunk 94 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 7 optimal weight: 0.0050 chunk 13 optimal weight: 0.6980 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.120860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.081779 restraints weight = 41354.354| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 4.44 r_work: 0.2859 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8409 Z= 0.217 Angle : 0.539 6.885 11466 Z= 0.285 Chirality : 0.046 0.212 1395 Planarity : 0.003 0.033 1404 Dihedral : 9.312 75.441 1800 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.71 % Allowed : 13.88 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.03 (0.34), residues: 252 sheet: 0.28 (0.26), residues: 366 loop : -0.57 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 0.002 0.000 ARG B 203 *********************** 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 99 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7929 (mm-30) REVERT: A 95 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7667 (mt-10) REVERT: B 51 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7649 (mm-30) REVERT: B 326 LYS cc_start: 0.8725 (pttt) cc_final: 0.8231 (pptt) REVERT: C 51 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7736 (mm-30) REVERT: C 95 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7631 (mt-10) REVERT: C 260 ASP cc_start: 0.8400 (t70) cc_final: 0.8183 (t0) REVERT: C 326 LYS cc_start: 0.8606 (pttp) cc_final: 0.8067 (pptt) outliers start: 6 outliers final: 5 residues processed: 96 average time/residue: 1.6534 time to fit residues: 166.9326 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 : 0.966 ------------------------------------------------------------------------------- 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 109 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 97 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 75 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 B 175 GLN C 175 GLN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.119940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.080759 restraints weight = 41846.713| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 4.44 r_work: 0.2839 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 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 = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 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 : 0.005 0.038 8409 Z= 0.290 Angle : 0.582 6.910 11466 Z= 0.308 Chirality : 0.048 0.203 1395 Planarity : 0.004 0.034 1404 Dihedral : 9.602 75.436 1800 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.71 % Allowed : 13.88 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.26), residues: 996 helix: 0.89 (0.34), residues: 252 sheet: 0.26 (0.26), residues: 366 loop : -0.64 (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 C 294 TYR 0.011 0.001 TYR A 89 ARG 0.003 0.000 ARG C 309 ********************** 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 99 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7924 (mm-30) REVERT: A 95 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7722 (mt-10) REVERT: B 51 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7670 (mm-30) REVERT: B 326 LYS cc_start: 0.8751 (pttt) cc_final: 0.8225 (pptt) REVERT: C 51 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7742 (mm-30) REVERT: C 95 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7700 (mt-10) REVERT: C 260 ASP cc_start: 0.8398 (t70) cc_final: 0.8180 (t0) REVERT: C 326 LYS cc_start: 0.8646 (pttp) cc_final: 0.8081 (pptt) outliers start: 6 outliers final: 5 residues processed: 96 average time/residue: 1.6593 time to fit residues: 167.7370 Evaluate side-chains 97 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 109 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 89 optimal weight: 0.0070 chunk 71 optimal weight: 0.5980 chunk 83 optimal weight: 0.2980 chunk 96 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN A 287 ASN B 175 GLN B 308 GLN C 175 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.120652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.082227 restraints weight = 34596.985| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.76 r_work: 0.2880 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 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 = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8409 Z= 0.238 Angle : 0.560 6.919 11466 Z= 0.296 Chirality : 0.047 0.240 1395 Planarity : 0.003 0.033 1404 Dihedral : 9.473 75.359 1800 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.83 % Allowed : 14.00 % Favored : 85.17 % 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: 0.10 (0.26), residues: 996 helix: 0.97 (0.34), residues: 252 sheet: 0.26 (0.26), residues: 366 loop : -0.63 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 259 HIS 0.003 0.001 HIS B 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7697.18 seconds wall clock time: 137 minutes 6.34 seconds (8226.34 seconds total)