Starting phenix.real_space_refine on Fri Aug 7 08:58:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zhh_74236/08_2026/9zhh_74236.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zhh_74236/08_2026/9zhh_74236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zhh_74236/08_2026/9zhh_74236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zhh_74236/08_2026/9zhh_74236.map" model { file = "/net/cci-nas-00/data/ceres_data/9zhh_74236/08_2026/9zhh_74236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zhh_74236/08_2026/9zhh_74236.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians S 24 5.16 5 C 6300 2.51 5 N 1764 2.21 5 O 1944 1.98 5 H 9924 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19956 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1663 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Chain: "G" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1663 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Chain: "B" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1663 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Chain: "H" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1663 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Chain: "C" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1663 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Chain: "I" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1663 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Chain: "D" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1663 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Chain: "J" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1663 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Chain: "E" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1663 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Chain: "K" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1663 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Chain: "F" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1663 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Chain: "L" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1663 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Time building chain proxies: 3.53, per 1000 atoms: 0.18 Number of scatterers: 19956 At special positions: 0 Unit cell: (134.638, 139.594, 60.298, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 O 1944 8.00 N 1764 7.00 C 6300 6.00 H 9924 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 181 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 181 " - pdb=" SG CYS G 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 181 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS H 181 " - pdb=" SG CYS H 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 181 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS I 181 " - pdb=" SG CYS I 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 181 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS J 181 " - pdb=" SG CYS J 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 181 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS K 181 " - pdb=" SG CYS K 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 181 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS L 181 " - pdb=" SG CYS L 248 " 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 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 604.7 milliseconds 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2376 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 24 sheets defined 7.6% alpha, 63.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 209 through 213 removed outlier: 3.595A pdb=" N ASP A 212 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A 213 " --> pdb=" O PRO A 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 209 through 213' Processing helix chain 'A' and resid 239 through 243 removed outlier: 3.719A pdb=" N ALA A 243 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 213 removed outlier: 4.095A pdb=" N ARG G 213 " --> pdb=" O PRO G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 243 removed outlier: 3.752A pdb=" N ALA G 243 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 removed outlier: 3.735A pdb=" N ALA B 243 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 213 removed outlier: 4.056A pdb=" N ARG H 213 " --> pdb=" O PRO H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 243 removed outlier: 3.762A pdb=" N ALA H 243 " --> pdb=" O LYS H 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 213 removed outlier: 3.582A pdb=" N ASP C 212 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG C 213 " --> pdb=" O PRO C 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 209 through 213' Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.727A pdb=" N ALA C 243 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 209 through 213 removed outlier: 4.059A pdb=" N ARG I 213 " --> pdb=" O PRO I 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 243 removed outlier: 3.753A pdb=" N ALA I 243 " --> pdb=" O LYS I 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 243 removed outlier: 3.695A pdb=" N ALA D 243 " --> pdb=" O LYS D 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 209 through 213 removed outlier: 4.030A pdb=" N ARG J 213 " --> pdb=" O PRO J 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 243 removed outlier: 3.735A pdb=" N ALA J 243 " --> pdb=" O LYS J 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 243 removed outlier: 3.732A pdb=" N ALA E 243 " --> pdb=" O LYS E 240 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 213 removed outlier: 4.052A pdb=" N ARG K 213 " --> pdb=" O PRO K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 243 removed outlier: 3.759A pdb=" N ALA K 243 " --> pdb=" O LYS K 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 243 removed outlier: 3.703A pdb=" N ALA F 243 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 209 through 213 removed outlier: 4.016A pdb=" N ARG L 213 " --> pdb=" O PRO L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 239 through 243 removed outlier: 3.698A pdb=" N ALA L 243 " --> pdb=" O LYS L 240 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 161 through 164 removed outlier: 6.719A pdb=" N GLU A 182 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU L 182 " --> pdb=" O VAL L 163 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ILE L 186 " --> pdb=" O GLY L 159 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY L 159 " --> pdb=" O ILE L 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 180 removed outlier: 3.533A pdb=" N LEU L 179 " --> pdb=" O VAL L 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 172 removed outlier: 6.591A pdb=" N ILE A 169 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL A 266 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASN A 171 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLU A 245 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 204 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 202 " --> pdb=" O GLY A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 158 through 164 removed outlier: 4.766A pdb=" N GLY G 159 " --> pdb=" O ILE G 186 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE G 186 " --> pdb=" O GLY G 159 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU G 182 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU B 182 " --> pdb=" O VAL B 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 177 through 180 Processing sheet with id=AA6, first strand: chain 'G' and resid 169 through 172 removed outlier: 6.592A pdb=" N ILE G 169 " --> pdb=" O THR G 264 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL G 266 " --> pdb=" O ILE G 169 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASN G 171 " --> pdb=" O VAL G 266 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU G 245 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN G 204 " --> pdb=" O LYS G 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 169 through 172 removed outlier: 6.559A pdb=" N ILE B 169 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL B 266 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASN B 171 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU B 245 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 197 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN B 204 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 202 " --> pdb=" O GLY B 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 158 through 164 removed outlier: 4.794A pdb=" N GLY H 159 " --> pdb=" O ILE H 186 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE H 186 " --> pdb=" O GLY H 159 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU H 182 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU C 182 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 177 through 180 Processing sheet with id=AB1, first strand: chain 'H' and resid 169 through 172 removed outlier: 6.593A pdb=" N ILE H 169 " --> pdb=" O THR H 264 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL H 266 " --> pdb=" O ILE H 169 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASN H 171 " --> pdb=" O VAL H 266 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU H 245 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN H 204 " --> pdb=" O LYS H 197 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 172 removed outlier: 6.557A pdb=" N ILE C 169 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL C 266 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASN C 171 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLU C 245 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 197 " --> pdb=" O GLN C 204 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN C 204 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY C 202 " --> pdb=" O GLY C 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 158 through 164 removed outlier: 4.767A pdb=" N GLY I 159 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ILE I 186 " --> pdb=" O GLY I 159 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLU I 182 " --> pdb=" O VAL I 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 158 through 164 removed outlier: 4.767A pdb=" N GLY I 159 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ILE I 186 " --> pdb=" O GLY I 159 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLU I 182 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU D 182 " --> pdb=" O VAL D 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 169 through 172 removed outlier: 6.586A pdb=" N ILE I 169 " --> pdb=" O THR I 264 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL I 266 " --> pdb=" O ILE I 169 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASN I 171 " --> pdb=" O VAL I 266 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU I 245 " --> pdb=" O VAL I 196 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN I 204 " --> pdb=" O LYS I 197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 169 through 172 removed outlier: 6.541A pdb=" N ILE D 169 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL D 266 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASN D 171 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU D 245 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS D 197 " --> pdb=" O GLN D 204 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN D 204 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY D 202 " --> pdb=" O GLY D 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 158 through 164 removed outlier: 4.746A pdb=" N GLY J 159 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ILE J 186 " --> pdb=" O GLY J 159 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU J 182 " --> pdb=" O VAL J 163 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU E 182 " --> pdb=" O VAL E 163 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 177 through 180 removed outlier: 3.548A pdb=" N LEU J 179 " --> pdb=" O VAL J 233 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 169 through 172 removed outlier: 6.579A pdb=" N ILE J 169 " --> pdb=" O THR J 264 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL J 266 " --> pdb=" O ILE J 169 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN J 171 " --> pdb=" O VAL J 266 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU J 245 " --> pdb=" O VAL J 196 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN J 204 " --> pdb=" O LYS J 197 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 169 through 172 removed outlier: 6.553A pdb=" N ILE E 169 " --> pdb=" O THR E 264 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL E 266 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASN E 171 " --> pdb=" O VAL E 266 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU E 245 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS E 197 " --> pdb=" O GLN E 204 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN E 204 " --> pdb=" O LYS E 197 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY E 202 " --> pdb=" O GLY E 199 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 158 through 164 removed outlier: 4.795A pdb=" N GLY K 159 " --> pdb=" O ILE K 186 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE K 186 " --> pdb=" O GLY K 159 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU K 182 " --> pdb=" O VAL K 163 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLU F 182 " --> pdb=" O VAL F 163 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 177 through 180 Processing sheet with id=AC4, first strand: chain 'K' and resid 169 through 172 removed outlier: 6.581A pdb=" N ILE K 169 " --> pdb=" O THR K 264 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL K 266 " --> pdb=" O ILE K 169 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASN K 171 " --> pdb=" O VAL K 266 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU K 245 " --> pdb=" O VAL K 196 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN K 204 " --> pdb=" O LYS K 197 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 169 through 172 removed outlier: 6.550A pdb=" N ILE F 169 " --> pdb=" O THR F 264 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL F 266 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASN F 171 " --> pdb=" O VAL F 266 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU F 245 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN F 204 " --> pdb=" O LYS F 197 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY F 202 " --> pdb=" O GLY F 199 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 169 through 172 removed outlier: 6.579A pdb=" N ILE L 169 " --> pdb=" O THR L 264 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL L 266 " --> pdb=" O ILE L 169 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASN L 171 " --> pdb=" O VAL L 266 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU L 245 " --> pdb=" O VAL L 196 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN L 204 " --> pdb=" O LYS L 197 " (cutoff:3.500A) 535 hydrogen bonds defined for protein. 1371 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.38 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9924 1.03 - 1.23: 2 1.23 - 1.42: 4150 1.42 - 1.61: 6084 1.61 - 1.81: 24 Bond restraints: 20184 Sorted by residual: bond pdb=" CA VAL A 233 " pdb=" C VAL A 233 " ideal model delta sigma weight residual 1.527 1.519 0.008 8.50e-03 1.38e+04 8.86e-01 bond pdb=" CA VAL F 233 " pdb=" C VAL F 233 " ideal model delta sigma weight residual 1.527 1.519 0.008 8.50e-03 1.38e+04 8.67e-01 bond pdb=" CA VAL J 233 " pdb=" C VAL J 233 " ideal model delta sigma weight residual 1.527 1.519 0.008 8.50e-03 1.38e+04 8.37e-01 bond pdb=" CA VAL C 233 " pdb=" C VAL C 233 " ideal model delta sigma weight residual 1.527 1.520 0.007 8.50e-03 1.38e+04 7.36e-01 bond pdb=" CA VAL L 233 " pdb=" C VAL L 233 " ideal model delta sigma weight residual 1.527 1.520 0.007 8.50e-03 1.38e+04 7.04e-01 ... (remaining 20179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.82: 32929 0.82 - 1.64: 3455 1.64 - 2.47: 208 2.47 - 3.29: 60 3.29 - 4.11: 20 Bond angle restraints: 36672 Sorted by residual: angle pdb=" N GLY E 185 " pdb=" CA GLY E 185 " pdb=" C GLY E 185 " ideal model delta sigma weight residual 110.63 113.62 -2.99 1.45e+00 4.76e-01 4.25e+00 angle pdb=" N GLY G 185 " pdb=" CA GLY G 185 " pdb=" C GLY G 185 " ideal model delta sigma weight residual 110.63 113.57 -2.94 1.45e+00 4.76e-01 4.12e+00 angle pdb=" N GLY B 185 " pdb=" CA GLY B 185 " pdb=" C GLY B 185 " ideal model delta sigma weight residual 110.63 113.56 -2.93 1.45e+00 4.76e-01 4.10e+00 angle pdb=" CA GLY D 185 " pdb=" C GLY D 185 " pdb=" N ILE D 186 " ideal model delta sigma weight residual 114.53 116.90 -2.37 1.18e+00 7.18e-01 4.05e+00 angle pdb=" CA GLY F 185 " pdb=" C GLY F 185 " pdb=" N ILE F 186 " ideal model delta sigma weight residual 114.53 116.85 -2.32 1.18e+00 7.18e-01 3.86e+00 ... (remaining 36667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 8821 15.99 - 31.99: 417 31.99 - 47.98: 189 47.98 - 63.98: 95 63.98 - 79.97: 6 Dihedral angle restraints: 9528 sinusoidal: 5340 harmonic: 4188 Sorted by residual: dihedral pdb=" CA LYS D 226 " pdb=" CB LYS D 226 " pdb=" CG LYS D 226 " pdb=" CD LYS D 226 " ideal model delta sinusoidal sigma weight residual 60.00 114.69 -54.69 3 1.50e+01 4.44e-03 9.30e+00 dihedral pdb=" CA LYS F 226 " pdb=" CB LYS F 226 " pdb=" CG LYS F 226 " pdb=" CD LYS F 226 " ideal model delta sinusoidal sigma weight residual 60.00 114.51 -54.51 3 1.50e+01 4.44e-03 9.29e+00 dihedral pdb=" CA LYS B 226 " pdb=" CB LYS B 226 " pdb=" CG LYS B 226 " pdb=" CD LYS B 226 " ideal model delta sinusoidal sigma weight residual 60.00 111.58 -51.58 3 1.50e+01 4.44e-03 9.03e+00 ... (remaining 9525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 881 0.027 - 0.054: 423 0.054 - 0.082: 76 0.082 - 0.109: 99 0.109 - 0.136: 105 Chirality restraints: 1584 Sorted by residual: chirality pdb=" CA ILE D 192 " pdb=" N ILE D 192 " pdb=" C ILE D 192 " pdb=" CB ILE D 192 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE E 192 " pdb=" N ILE E 192 " pdb=" C ILE E 192 " pdb=" CB ILE E 192 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILE G 192 " pdb=" N ILE G 192 " pdb=" C ILE G 192 " pdb=" CB ILE G 192 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 1581 not shown) Planarity restraints: 3036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 186 " -0.014 5.00e-02 4.00e+02 2.05e-02 6.73e-01 pdb=" N PRO G 187 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO G 187 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO G 187 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 186 " 0.013 5.00e-02 4.00e+02 2.00e-02 6.37e-01 pdb=" N PRO F 187 " -0.035 5.00e-02 4.00e+02 pdb=" CA PRO F 187 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO F 187 " 0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 186 " 0.013 5.00e-02 4.00e+02 1.98e-02 6.26e-01 pdb=" N PRO A 187 " -0.034 5.00e-02 4.00e+02 pdb=" CA PRO A 187 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 187 " 0.010 5.00e-02 4.00e+02 ... (remaining 3033 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.43: 10407 2.43 - 2.97: 44443 2.97 - 3.51: 47656 3.51 - 4.06: 67698 4.06 - 4.60: 96540 Nonbonded interactions: 266744 Sorted by model distance: nonbonded pdb="HD21 ASN I 252 " pdb=" H GLN I 254 " model vdw 1.887 2.100 nonbonded pdb="HD21 ASN K 252 " pdb=" H GLN K 254 " model vdw 1.887 2.100 nonbonded pdb="HD21 ASN G 252 " pdb=" H GLN G 254 " model vdw 1.889 2.100 nonbonded pdb="HD21 ASN H 252 " pdb=" H GLN H 254 " model vdw 1.890 2.100 nonbonded pdb="HD21 ASN L 252 " pdb=" H GLN L 254 " model vdw 1.891 2.100 ... (remaining 266739 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' 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=1.00 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: 3.200 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: 0.130 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.520 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 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 : 0.003 0.018 10272 Z= 0.134 Angle : 0.527 4.109 14028 Z= 0.308 Chirality : 0.048 0.136 1584 Planarity : 0.003 0.021 1824 Dihedral : 10.281 79.972 3756 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.91 % Allowed : 4.62 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.25), residues: 1296 helix: None (None), residues: 0 sheet: 0.56 (0.20), residues: 780 loop : 0.33 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 198 TYR 0.002 0.000 TYR H 246 TRP 0.006 0.001 TRP K 232 HIS 0.003 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 (10260) covalent geometry : angle 0.52663 / 0.31 (14004) SS BOND : bond 0.00279 / 0.14 ( 12) SS BOND : angle 0.59399 / 0.36 ( 24) hydrogen bonds : bond 0.24980 / 16.63 ( 460) hydrogen bonds : angle 11.43039 / 8.03 ( 1371) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 369 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8582 (mmtt) cc_final: 0.8309 (mttp) REVERT: A 262 LYS cc_start: 0.8446 (mmmt) cc_final: 0.8174 (mmmm) REVERT: G 167 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8335 (mttp) REVERT: B 167 LYS cc_start: 0.8597 (mmtt) cc_final: 0.8389 (mttp) REVERT: B 245 GLU cc_start: 0.7720 (tt0) cc_final: 0.7460 (tm-30) REVERT: B 262 LYS cc_start: 0.8504 (mmmt) cc_final: 0.8180 (mmmm) REVERT: H 167 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8289 (mttm) REVERT: H 245 GLU cc_start: 0.7598 (tt0) cc_final: 0.7354 (tt0) REVERT: H 262 LYS cc_start: 0.8437 (mmmt) cc_final: 0.8202 (tppt) REVERT: C 167 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8348 (mttm) REVERT: C 262 LYS cc_start: 0.8474 (mmmt) cc_final: 0.8129 (mmmm) REVERT: I 167 LYS cc_start: 0.8561 (mmtt) cc_final: 0.8347 (mttm) REVERT: D 209 LEU cc_start: 0.8626 (mm) cc_final: 0.7929 (mm) REVERT: D 213 ARG cc_start: 0.7838 (tpt170) cc_final: 0.7578 (mmm160) REVERT: D 262 LYS cc_start: 0.8497 (mmmt) cc_final: 0.8267 (mmmm) REVERT: J 167 LYS cc_start: 0.8533 (mmtt) cc_final: 0.8307 (mttp) REVERT: J 254 GLN cc_start: 0.8847 (mm110) cc_final: 0.8641 (mm-40) REVERT: E 167 LYS cc_start: 0.8598 (mmtt) cc_final: 0.8392 (mttm) REVERT: E 245 GLU cc_start: 0.7706 (tt0) cc_final: 0.7449 (tm-30) REVERT: E 262 LYS cc_start: 0.8493 (mmmt) cc_final: 0.8135 (mmmm) REVERT: K 167 LYS cc_start: 0.8525 (mmtt) cc_final: 0.8296 (mttm) REVERT: K 262 LYS cc_start: 0.8512 (mmmt) cc_final: 0.8228 (mmmm) REVERT: F 167 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8271 (mttm) REVERT: F 195 LYS cc_start: 0.8838 (tppp) cc_final: 0.8636 (tptp) REVERT: F 209 LEU cc_start: 0.8597 (mm) cc_final: 0.8268 (mm) REVERT: F 262 LYS cc_start: 0.8464 (mmmt) cc_final: 0.8184 (mmmm) REVERT: L 157 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6884 (mt-10) REVERT: L 262 LYS cc_start: 0.8228 (mmmt) cc_final: 0.8005 (tppt) outliers start: 10 outliers final: 0 residues processed: 379 average time/residue: 0.2691 time to fit residues: 133.6337 Evaluate side-chains 280 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 227 HIS I 227 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.124346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.104578 restraints weight = 42001.083| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.31 r_work: 0.3290 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10272 Z= 0.133 Angle : 0.561 4.087 14028 Z= 0.297 Chirality : 0.049 0.147 1584 Planarity : 0.004 0.025 1824 Dihedral : 4.611 13.991 1392 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.18 % Allowed : 12.77 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.24), residues: 1296 helix: None (None), residues: 0 sheet: 0.58 (0.19), residues: 804 loop : 0.40 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 213 TYR 0.007 0.001 TYR C 246 TRP 0.010 0.001 TRP D 232 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (10260) covalent geometry : angle 0.56072 / 0.30 (14004) SS BOND : bond 0.00376 / 0.20 ( 12) SS BOND : angle 0.54101 / 0.34 ( 24) hydrogen bonds : bond 0.03762 / 2.40 ( 460) hydrogen bonds : angle 6.68104 / 4.74 ( 1371) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 300 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 240 LYS cc_start: 0.9319 (tppt) cc_final: 0.9110 (tptt) REVERT: D 167 LYS cc_start: 0.8576 (mmtt) cc_final: 0.8354 (mttp) outliers start: 13 outliers final: 12 residues processed: 308 average time/residue: 0.3019 time to fit residues: 118.4651 Evaluate side-chains 296 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 284 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain H residue 239 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain I residue 239 SER Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain J residue 239 SER Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain F residue 251 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.123538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.102875 restraints weight = 41825.016| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.46 r_work: 0.3276 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10272 Z= 0.136 Angle : 0.545 4.445 14028 Z= 0.284 Chirality : 0.049 0.141 1584 Planarity : 0.003 0.027 1824 Dihedral : 4.596 13.875 1392 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.08 % Allowed : 13.59 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.23), residues: 1296 helix: None (None), residues: 0 sheet: 0.52 (0.19), residues: 696 loop : 0.40 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 213 TYR 0.008 0.001 TYR K 246 TRP 0.010 0.001 TRP K 232 HIS 0.003 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (10260) covalent geometry : angle 0.54551 / 0.28 (14004) SS BOND : bond 0.00263 / 0.14 ( 12) SS BOND : angle 0.46081 / 0.29 ( 24) hydrogen bonds : bond 0.03278 / 2.08 ( 460) hydrogen bonds : angle 5.80821 / 4.13 ( 1371) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 290 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 245 GLU cc_start: 0.7440 (tt0) cc_final: 0.7226 (tt0) REVERT: D 167 LYS cc_start: 0.8642 (mmtt) cc_final: 0.8435 (mttm) REVERT: E 245 GLU cc_start: 0.7436 (tt0) cc_final: 0.7231 (tt0) REVERT: L 195 LYS cc_start: 0.9056 (tptp) cc_final: 0.8817 (tttm) outliers start: 23 outliers final: 17 residues processed: 306 average time/residue: 0.3185 time to fit residues: 123.0057 Evaluate side-chains 293 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 276 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain H residue 239 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain I residue 239 SER Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 251 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 54 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 124 optimal weight: 0.2980 chunk 99 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.122591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.103242 restraints weight = 42071.991| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.23 r_work: 0.3298 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10272 Z= 0.157 Angle : 0.554 4.635 14028 Z= 0.288 Chirality : 0.049 0.140 1584 Planarity : 0.003 0.031 1824 Dihedral : 4.654 13.712 1392 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.45 % Allowed : 13.95 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.23), residues: 1296 helix: None (None), residues: 0 sheet: 0.52 (0.19), residues: 696 loop : 0.46 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 213 TYR 0.013 0.001 TYR H 246 TRP 0.011 0.001 TRP F 232 HIS 0.004 0.001 HIS B 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (10260) covalent geometry : angle 0.55443 / 0.29 (14004) SS BOND : bond 0.00262 / 0.14 ( 12) SS BOND : angle 0.19631 / 0.12 ( 24) hydrogen bonds : bond 0.03106 / 1.98 ( 460) hydrogen bonds : angle 5.50495 / 3.92 ( 1371) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 282 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 214 ASP cc_start: 0.7994 (p0) cc_final: 0.7716 (p0) REVERT: J 214 ASP cc_start: 0.7909 (p0) cc_final: 0.7635 (p0) outliers start: 27 outliers final: 18 residues processed: 303 average time/residue: 0.3200 time to fit residues: 122.5327 Evaluate side-chains 297 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 279 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain H residue 239 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain I residue 239 SER Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain J residue 212 ASP Chi-restraints excluded: chain J residue 239 SER Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 251 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 90 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 121 optimal weight: 0.2980 chunk 60 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.124196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.105208 restraints weight = 41936.406| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.19 r_work: 0.3326 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10272 Z= 0.113 Angle : 0.537 4.591 14028 Z= 0.277 Chirality : 0.049 0.138 1584 Planarity : 0.003 0.042 1824 Dihedral : 4.544 13.060 1392 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.27 % Allowed : 15.85 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.23), residues: 1296 helix: None (None), residues: 0 sheet: 0.57 (0.18), residues: 696 loop : 0.69 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 213 TYR 0.012 0.001 TYR H 246 TRP 0.010 0.001 TRP H 232 HIS 0.003 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.11 (10260) covalent geometry : angle 0.53761 / 0.28 (14004) SS BOND : bond 0.00308 / 0.17 ( 12) SS BOND : angle 0.17098 / 0.11 ( 24) hydrogen bonds : bond 0.02920 / 1.86 ( 460) hydrogen bonds : angle 5.23459 / 3.74 ( 1371) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 289 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 214 ASP cc_start: 0.7909 (p0) cc_final: 0.7621 (p0) REVERT: F 242 ASP cc_start: 0.8043 (m-30) cc_final: 0.7607 (m-30) outliers start: 14 outliers final: 11 residues processed: 300 average time/residue: 0.2990 time to fit residues: 114.2224 Evaluate side-chains 286 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 275 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain J residue 239 SER Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 216 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 124 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 227 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.121174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.100668 restraints weight = 42060.959| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.44 r_work: 0.3246 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 10272 Z= 0.187 Angle : 0.570 4.399 14028 Z= 0.295 Chirality : 0.049 0.138 1584 Planarity : 0.003 0.046 1824 Dihedral : 4.733 14.275 1392 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.72 % Allowed : 15.76 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.23), residues: 1296 helix: None (None), residues: 0 sheet: 0.48 (0.19), residues: 696 loop : 0.67 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 213 TYR 0.010 0.001 TYR E 246 TRP 0.011 0.001 TRP F 232 HIS 0.004 0.002 HIS B 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (10260) covalent geometry : angle 0.57011 / 0.30 (14004) SS BOND : bond 0.00235 / 0.13 ( 12) SS BOND : angle 0.17809 / 0.10 ( 24) hydrogen bonds : bond 0.03060 / 1.97 ( 460) hydrogen bonds : angle 5.32310 / 3.81 ( 1371) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 277 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 214 ASP cc_start: 0.8056 (p0) cc_final: 0.7807 (p0) REVERT: J 214 ASP cc_start: 0.7993 (p0) cc_final: 0.7714 (p0) REVERT: K 241 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7908 (tm-30) outliers start: 19 outliers final: 17 residues processed: 292 average time/residue: 0.3141 time to fit residues: 116.0084 Evaluate side-chains 288 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 271 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain I residue 239 SER Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain J residue 212 ASP Chi-restraints excluded: chain J residue 239 SER Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 251 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 128 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 97 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 227 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.124121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.103880 restraints weight = 42060.794| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.39 r_work: 0.3298 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10272 Z= 0.110 Angle : 0.539 4.541 14028 Z= 0.277 Chirality : 0.049 0.140 1584 Planarity : 0.004 0.052 1824 Dihedral : 4.566 13.758 1392 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.45 % Allowed : 16.21 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.24), residues: 1296 helix: None (None), residues: 0 sheet: 0.52 (0.18), residues: 696 loop : 0.87 (0.28), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 213 TYR 0.008 0.001 TYR H 246 TRP 0.012 0.001 TRP K 232 HIS 0.003 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 (10260) covalent geometry : angle 0.53921 / 0.28 (14004) SS BOND : bond 0.00308 / 0.17 ( 12) SS BOND : angle 0.13209 / 0.08 ( 24) hydrogen bonds : bond 0.02734 / 1.73 ( 460) hydrogen bonds : angle 5.04479 / 3.61 ( 1371) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 275 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 214 ASP cc_start: 0.8008 (p0) cc_final: 0.7731 (p0) REVERT: K 241 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7835 (tm-30) REVERT: F 242 ASP cc_start: 0.7915 (m-30) cc_final: 0.7622 (m-30) outliers start: 16 outliers final: 15 residues processed: 287 average time/residue: 0.2828 time to fit residues: 103.8492 Evaluate side-chains 282 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 267 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 251 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 44 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 38 optimal weight: 0.1980 chunk 71 optimal weight: 0.3980 chunk 5 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.123468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.104364 restraints weight = 41999.648| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.20 r_work: 0.3311 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10272 Z= 0.130 Angle : 0.544 4.261 14028 Z= 0.280 Chirality : 0.049 0.137 1584 Planarity : 0.004 0.065 1824 Dihedral : 4.536 13.659 1392 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.63 % Allowed : 16.58 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.24), residues: 1296 helix: None (None), residues: 0 sheet: 0.39 (0.18), residues: 708 loop : 0.91 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 213 TYR 0.007 0.001 TYR E 246 TRP 0.010 0.001 TRP C 232 HIS 0.003 0.001 HIS J 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 (10260) covalent geometry : angle 0.54415 / 0.28 (14004) SS BOND : bond 0.00233 / 0.12 ( 12) SS BOND : angle 0.14950 / 0.09 ( 24) hydrogen bonds : bond 0.02746 / 1.74 ( 460) hydrogen bonds : angle 4.98513 / 3.56 ( 1371) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 269 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 214 ASP cc_start: 0.7906 (p0) cc_final: 0.7641 (p0) outliers start: 18 outliers final: 16 residues processed: 282 average time/residue: 0.2947 time to fit residues: 105.7297 Evaluate side-chains 281 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 265 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain H residue 239 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 251 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 71 optimal weight: 0.0270 chunk 54 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 176 GLN L 227 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.123940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.103720 restraints weight = 41871.434| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.42 r_work: 0.3299 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10272 Z= 0.120 Angle : 0.542 4.198 14028 Z= 0.279 Chirality : 0.049 0.137 1584 Planarity : 0.004 0.063 1824 Dihedral : 4.490 13.685 1392 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.54 % Allowed : 16.67 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.24), residues: 1296 helix: None (None), residues: 0 sheet: 0.43 (0.18), residues: 708 loop : 0.93 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 213 TYR 0.008 0.001 TYR H 246 TRP 0.010 0.001 TRP G 232 HIS 0.003 0.001 HIS J 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 (10260) covalent geometry : angle 0.54221 / 0.28 (14004) SS BOND : bond 0.00243 / 0.13 ( 12) SS BOND : angle 0.14278 / 0.08 ( 24) hydrogen bonds : bond 0.02624 / 1.66 ( 460) hydrogen bonds : angle 4.90276 / 3.50 ( 1371) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 273 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 214 ASP cc_start: 0.8161 (p0) cc_final: 0.7863 (p0) outliers start: 17 outliers final: 15 residues processed: 286 average time/residue: 0.2747 time to fit residues: 100.5678 Evaluate side-chains 279 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 264 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain H residue 239 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 251 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 11 optimal weight: 0.0770 chunk 65 optimal weight: 5.9990 chunk 67 optimal weight: 0.0970 chunk 89 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.125024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.105067 restraints weight = 41704.861| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.38 r_work: 0.3318 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10272 Z= 0.104 Angle : 0.539 4.164 14028 Z= 0.276 Chirality : 0.049 0.136 1584 Planarity : 0.004 0.060 1824 Dihedral : 4.403 13.702 1392 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.45 % Allowed : 17.03 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.24), residues: 1296 helix: None (None), residues: 0 sheet: 0.46 (0.18), residues: 708 loop : 0.98 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 213 TYR 0.008 0.001 TYR H 246 TRP 0.010 0.001 TRP I 232 HIS 0.005 0.001 HIS J 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.10 (10260) covalent geometry : angle 0.53914 / 0.28 (14004) SS BOND : bond 0.00259 / 0.14 ( 12) SS BOND : angle 0.13725 / 0.08 ( 24) hydrogen bonds : bond 0.02506 / 1.58 ( 460) hydrogen bonds : angle 4.77885 / 3.42 ( 1371) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 275 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 16 residues processed: 286 average time/residue: 0.2895 time to fit residues: 105.9103 Evaluate side-chains 279 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 263 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain H residue 239 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 251 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 102 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 52 optimal weight: 0.0060 chunk 90 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 122 optimal weight: 0.1980 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 227 HIS E 227 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.123973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.103827 restraints weight = 42090.315| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.40 r_work: 0.3302 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10272 Z= 0.127 Angle : 0.546 4.198 14028 Z= 0.281 Chirality : 0.049 0.135 1584 Planarity : 0.004 0.056 1824 Dihedral : 4.427 13.972 1392 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.45 % Allowed : 17.57 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.24), residues: 1296 helix: None (None), residues: 0 sheet: 0.43 (0.18), residues: 708 loop : 0.95 (0.29), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 213 TYR 0.008 0.001 TYR H 246 TRP 0.009 0.001 TRP K 232 HIS 0.003 0.001 HIS J 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (10260) covalent geometry : angle 0.54635 / 0.28 (14004) SS BOND : bond 0.00227 / 0.12 ( 12) SS BOND : angle 0.18905 / 0.11 ( 24) hydrogen bonds : bond 0.02597 / 1.65 ( 460) hydrogen bonds : angle 4.81253 / 3.44 ( 1371) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4719.27 seconds wall clock time: 80 minutes 40.37 seconds (4840.37 seconds total)