Starting phenix.real_space_refine on Fri Feb 6 01:48:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k8e_62170/02_2026/9k8e_62170.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k8e_62170/02_2026/9k8e_62170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k8e_62170/02_2026/9k8e_62170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k8e_62170/02_2026/9k8e_62170.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k8e_62170/02_2026/9k8e_62170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k8e_62170/02_2026/9k8e_62170.map" } resolution = 2.84 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= 0.003 sd= 0.210 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 Zn 24 6.06 5 S 72 5.16 5 C 14244 2.51 5 N 3576 2.21 5 O 4104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22020 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1833 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 1, 'TRANS': 226} Chain: "B" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1833 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 1, 'TRANS': 226} Chain: "C" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1833 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 1, 'TRANS': 226} Chain: "D" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1833 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 1, 'TRANS': 226} Chain: "G" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1833 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 1, 'TRANS': 226} Chain: "J" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1833 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 1, 'TRANS': 226} Chain: "E" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1833 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 1, 'TRANS': 226} Chain: "H" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1833 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 1, 'TRANS': 226} Chain: "K" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1833 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 1, 'TRANS': 226} Chain: "F" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1833 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 1, 'TRANS': 226} Chain: "I" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1833 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 1, 'TRANS': 226} Chain: "L" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1833 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 1, 'TRANS': 226} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.10, per 1000 atoms: 0.23 Number of scatterers: 22020 At special positions: 0 Unit cell: (151.899, 159.44, 133.585, 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) Zn 24 29.99 S 72 16.00 O 4104 8.00 N 3576 7.00 C 14244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.52 Conformation dependent library (CDL) restraints added in 751.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS B 36 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 47 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 195 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS L 175 " pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 36 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS C 47 " pdb=" ZN A 304 " pdb="ZN ZN A 304 " - pdb=" NE2 HIS A 175 " pdb="ZN ZN A 304 " - pdb=" NE2 HIS L 195 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS C 36 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 47 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 195 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS K 175 " pdb=" ZN B 303 " pdb="ZN ZN B 303 " - pdb=" NE2 HIS K 195 " pdb="ZN ZN B 303 " - pdb=" NE2 HIS B 175 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 195 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS G 175 " pdb=" ZN C 302 " pdb="ZN ZN C 302 " - pdb=" NE2 HIS G 195 " pdb="ZN ZN C 302 " - pdb=" NE2 HIS C 175 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS G 36 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 47 " pdb=" ZN D 302 " pdb="ZN ZN D 302 " - pdb=" NE2 HIS D 36 " pdb="ZN ZN D 302 " - pdb=" NE2 HIS J 47 " pdb=" ZN D 303 " pdb="ZN ZN D 303 " - pdb=" NE2 HIS F 195 " pdb="ZN ZN D 303 " - pdb=" NE2 HIS D 175 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS H 36 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 47 " pdb=" ZN E 302 " pdb="ZN ZN E 302 " - pdb=" NE2 HIS E 36 " pdb="ZN ZN E 302 " - pdb=" NE2 HIS K 47 " pdb=" ZN E 303 " pdb="ZN ZN E 303 " - pdb=" NE2 HIS I 195 " pdb="ZN ZN E 303 " - pdb=" NE2 HIS E 175 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS D 195 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS F 175 " pdb=" ZN F 302 " pdb="ZN ZN F 302 " - pdb=" NE2 HIS I 36 " pdb="ZN ZN F 302 " - pdb=" NE2 HIS F 47 " pdb=" ZN F 303 " pdb="ZN ZN F 303 " - pdb=" NE2 HIS F 36 " pdb="ZN ZN F 303 " - pdb=" NE2 HIS L 47 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" NE2 HIS J 36 " pdb="ZN ZN G 301 " - pdb=" NE2 HIS G 47 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS J 195 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS H 175 " pdb=" ZN H 302 " pdb="ZN ZN H 302 " - pdb=" NE2 HIS K 36 " pdb="ZN ZN H 302 " - pdb=" NE2 HIS H 47 " pdb=" ZN H 303 " pdb="ZN ZN H 303 " - pdb=" NE2 HIS H 195 " pdb="ZN ZN H 303 " - pdb=" NE2 HIS J 175 " pdb=" ZN I 301 " pdb="ZN ZN I 301 " - pdb=" NE2 HIS E 195 " pdb="ZN ZN I 301 " - pdb=" NE2 HIS I 175 " pdb=" ZN I 302 " pdb="ZN ZN I 302 " - pdb=" NE2 HIS L 36 " pdb="ZN ZN I 302 " - pdb=" NE2 HIS I 47 " 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5208 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 0 sheets defined 90.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 5 through 22 Processing helix chain 'A' and resid 26 through 41 Processing helix chain 'A' and resid 43 through 55 Processing helix chain 'A' and resid 59 through 75 Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 93 through 112 removed outlier: 3.711A pdb=" N LYS A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 138 removed outlier: 4.101A pdb=" N LYS A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 164 removed outlier: 3.825A pdb=" N VAL A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 188 Processing helix chain 'A' and resid 191 through 210 Processing helix chain 'A' and resid 214 through 231 removed outlier: 4.022A pdb=" N LEU A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 22 Processing helix chain 'B' and resid 26 through 41 Processing helix chain 'B' and resid 43 through 55 Processing helix chain 'B' and resid 59 through 75 Processing helix chain 'B' and resid 76 through 91 Processing helix chain 'B' and resid 93 through 112 removed outlier: 3.719A pdb=" N LYS B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 138 removed outlier: 4.227A pdb=" N LYS B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 164 removed outlier: 3.863A pdb=" N VAL B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS B 146 " --> pdb=" O GLU B 142 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS B 164 " --> pdb=" O LYS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 188 Processing helix chain 'B' and resid 191 through 210 Processing helix chain 'B' and resid 214 through 231 removed outlier: 3.841A pdb=" N LEU B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 22 Processing helix chain 'C' and resid 26 through 41 Processing helix chain 'C' and resid 43 through 55 Processing helix chain 'C' and resid 59 through 75 Processing helix chain 'C' and resid 76 through 91 Processing helix chain 'C' and resid 93 through 112 removed outlier: 3.671A pdb=" N LYS C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 138 removed outlier: 4.057A pdb=" N LYS C 120 " --> pdb=" O GLU C 116 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 164 removed outlier: 3.906A pdb=" N VAL C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS C 145 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS C 146 " --> pdb=" O GLU C 142 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS C 164 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 188 Processing helix chain 'C' and resid 191 through 210 Processing helix chain 'C' and resid 214 through 231 removed outlier: 3.840A pdb=" N LEU C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 22 Processing helix chain 'D' and resid 26 through 41 Processing helix chain 'D' and resid 43 through 55 Processing helix chain 'D' and resid 59 through 75 Processing helix chain 'D' and resid 76 through 91 Processing helix chain 'D' and resid 93 through 112 removed outlier: 3.679A pdb=" N LYS D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 138 removed outlier: 3.983A pdb=" N LYS D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU D 121 " --> pdb=" O GLU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 164 removed outlier: 3.863A pdb=" N VAL D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS D 164 " --> pdb=" O LYS D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 188 Processing helix chain 'D' and resid 191 through 210 Processing helix chain 'D' and resid 214 through 231 removed outlier: 3.857A pdb=" N LEU D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 22 Processing helix chain 'G' and resid 26 through 41 Processing helix chain 'G' and resid 43 through 55 Processing helix chain 'G' and resid 59 through 75 Processing helix chain 'G' and resid 76 through 91 Processing helix chain 'G' and resid 93 through 112 removed outlier: 3.719A pdb=" N LYS G 112 " --> pdb=" O LYS G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 138 removed outlier: 4.079A pdb=" N LYS G 120 " --> pdb=" O GLU G 116 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 164 removed outlier: 3.903A pdb=" N VAL G 144 " --> pdb=" O ASP G 140 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS G 145 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS G 146 " --> pdb=" O GLU G 142 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS G 164 " --> pdb=" O LYS G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 188 Processing helix chain 'G' and resid 191 through 210 Processing helix chain 'G' and resid 214 through 231 removed outlier: 3.776A pdb=" N LEU G 218 " --> pdb=" O GLU G 214 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU G 231 " --> pdb=" O LYS G 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 22 Processing helix chain 'J' and resid 26 through 41 Processing helix chain 'J' and resid 43 through 55 Processing helix chain 'J' and resid 59 through 75 Processing helix chain 'J' and resid 76 through 91 Processing helix chain 'J' and resid 93 through 112 removed outlier: 3.740A pdb=" N LYS J 112 " --> pdb=" O LYS J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 138 removed outlier: 4.133A pdb=" N LYS J 120 " --> pdb=" O GLU J 116 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU J 121 " --> pdb=" O GLU J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 164 removed outlier: 3.935A pdb=" N VAL J 144 " --> pdb=" O ASP J 140 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS J 145 " --> pdb=" O LYS J 141 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS J 146 " --> pdb=" O GLU J 142 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS J 164 " --> pdb=" O LYS J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 188 Processing helix chain 'J' and resid 191 through 210 Processing helix chain 'J' and resid 214 through 231 removed outlier: 3.861A pdb=" N LEU J 218 " --> pdb=" O GLU J 214 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU J 231 " --> pdb=" O LYS J 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 22 Processing helix chain 'E' and resid 26 through 41 Processing helix chain 'E' and resid 43 through 55 Processing helix chain 'E' and resid 59 through 75 Processing helix chain 'E' and resid 76 through 91 Processing helix chain 'E' and resid 93 through 112 removed outlier: 3.718A pdb=" N LYS E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 138 removed outlier: 4.156A pdb=" N LYS E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 164 removed outlier: 3.952A pdb=" N VAL E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS E 146 " --> pdb=" O GLU E 142 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 188 Processing helix chain 'E' and resid 191 through 210 Processing helix chain 'E' and resid 214 through 231 removed outlier: 4.147A pdb=" N LEU E 218 " --> pdb=" O GLU E 214 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU E 231 " --> pdb=" O LYS E 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 22 Processing helix chain 'H' and resid 26 through 41 Processing helix chain 'H' and resid 43 through 55 Processing helix chain 'H' and resid 59 through 75 Processing helix chain 'H' and resid 76 through 91 Processing helix chain 'H' and resid 93 through 112 removed outlier: 3.682A pdb=" N LYS H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 138 removed outlier: 4.011A pdb=" N LYS H 120 " --> pdb=" O GLU H 116 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU H 121 " --> pdb=" O GLU H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 164 removed outlier: 3.871A pdb=" N VAL H 144 " --> pdb=" O ASP H 140 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS H 145 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS H 146 " --> pdb=" O GLU H 142 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS H 164 " --> pdb=" O LYS H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 188 Processing helix chain 'H' and resid 191 through 210 Processing helix chain 'H' and resid 214 through 231 removed outlier: 3.866A pdb=" N LEU H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU H 231 " --> pdb=" O LYS H 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 22 Processing helix chain 'K' and resid 26 through 41 Processing helix chain 'K' and resid 43 through 55 Processing helix chain 'K' and resid 59 through 75 Processing helix chain 'K' and resid 76 through 91 Processing helix chain 'K' and resid 93 through 112 removed outlier: 3.686A pdb=" N LYS K 112 " --> pdb=" O LYS K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 138 removed outlier: 4.026A pdb=" N LYS K 120 " --> pdb=" O GLU K 116 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU K 121 " --> pdb=" O GLU K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 164 removed outlier: 3.909A pdb=" N VAL K 144 " --> pdb=" O ASP K 140 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS K 145 " --> pdb=" O LYS K 141 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS K 146 " --> pdb=" O GLU K 142 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS K 164 " --> pdb=" O LYS K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 188 Processing helix chain 'K' and resid 191 through 210 Processing helix chain 'K' and resid 214 through 231 removed outlier: 3.810A pdb=" N LEU K 218 " --> pdb=" O GLU K 214 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU K 231 " --> pdb=" O LYS K 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 22 Processing helix chain 'F' and resid 26 through 41 Processing helix chain 'F' and resid 43 through 55 Processing helix chain 'F' and resid 59 through 75 Processing helix chain 'F' and resid 76 through 91 Processing helix chain 'F' and resid 93 through 112 removed outlier: 3.673A pdb=" N LYS F 112 " --> pdb=" O LYS F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 138 removed outlier: 4.067A pdb=" N LYS F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU F 121 " --> pdb=" O GLU F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 164 removed outlier: 3.920A pdb=" N VAL F 144 " --> pdb=" O ASP F 140 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS F 146 " --> pdb=" O GLU F 142 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS F 164 " --> pdb=" O LYS F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 188 Processing helix chain 'F' and resid 191 through 210 Processing helix chain 'F' and resid 214 through 231 removed outlier: 3.860A pdb=" N LEU F 218 " --> pdb=" O GLU F 214 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU F 231 " --> pdb=" O LYS F 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 22 Processing helix chain 'I' and resid 26 through 41 Processing helix chain 'I' and resid 43 through 55 Processing helix chain 'I' and resid 59 through 75 Processing helix chain 'I' and resid 76 through 91 Processing helix chain 'I' and resid 93 through 112 removed outlier: 3.701A pdb=" N LYS I 112 " --> pdb=" O LYS I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 138 removed outlier: 4.117A pdb=" N LYS I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU I 121 " --> pdb=" O GLU I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 164 removed outlier: 3.891A pdb=" N VAL I 144 " --> pdb=" O ASP I 140 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS I 145 " --> pdb=" O LYS I 141 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS I 146 " --> pdb=" O GLU I 142 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 188 Processing helix chain 'I' and resid 191 through 210 Processing helix chain 'I' and resid 214 through 231 removed outlier: 3.894A pdb=" N LEU I 218 " --> pdb=" O GLU I 214 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU I 231 " --> pdb=" O LYS I 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 22 Processing helix chain 'L' and resid 26 through 41 Processing helix chain 'L' and resid 43 through 55 Processing helix chain 'L' and resid 59 through 75 Processing helix chain 'L' and resid 76 through 91 Processing helix chain 'L' and resid 93 through 112 removed outlier: 3.684A pdb=" N LYS L 112 " --> pdb=" O LYS L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 138 removed outlier: 4.053A pdb=" N LYS L 120 " --> pdb=" O GLU L 116 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU L 121 " --> pdb=" O GLU L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 164 removed outlier: 3.895A pdb=" N VAL L 144 " --> pdb=" O ASP L 140 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS L 145 " --> pdb=" O LYS L 141 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS L 146 " --> pdb=" O GLU L 142 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS L 164 " --> pdb=" O LYS L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 188 Processing helix chain 'L' and resid 191 through 210 Processing helix chain 'L' and resid 214 through 231 removed outlier: 3.779A pdb=" N LEU L 218 " --> pdb=" O GLU L 214 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU L 231 " --> pdb=" O LYS L 227 " (cutoff:3.500A) 1848 hydrogen bonds defined for protein. 5544 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: 3.65 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4252 1.33 - 1.45: 4164 1.45 - 1.57: 13628 1.57 - 1.69: 0 1.69 - 1.82: 144 Bond restraints: 22188 Sorted by residual: bond pdb=" CA LEU I 121 " pdb=" C LEU I 121 " ideal model delta sigma weight residual 1.524 1.467 0.057 1.24e-02 6.50e+03 2.12e+01 bond pdb=" C HIS G 47 " pdb=" O HIS G 47 " ideal model delta sigma weight residual 1.237 1.203 0.034 1.17e-02 7.31e+03 8.46e+00 bond pdb=" C HIS A 47 " pdb=" O HIS A 47 " ideal model delta sigma weight residual 1.236 1.206 0.031 1.15e-02 7.56e+03 7.21e+00 bond pdb=" N LEU I 122 " pdb=" CA LEU I 122 " ideal model delta sigma weight residual 1.458 1.424 0.033 1.29e-02 6.01e+03 6.64e+00 bond pdb=" C HIS B 47 " pdb=" O HIS B 47 " ideal model delta sigma weight residual 1.236 1.209 0.028 1.15e-02 7.56e+03 5.88e+00 ... (remaining 22183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 29201 1.78 - 3.56: 346 3.56 - 5.34: 79 5.34 - 7.12: 33 7.12 - 8.90: 5 Bond angle restraints: 29664 Sorted by residual: angle pdb=" N GLU K 220 " pdb=" CA GLU K 220 " pdb=" CB GLU K 220 " ideal model delta sigma weight residual 110.28 116.70 -6.42 1.55e+00 4.16e-01 1.71e+01 angle pdb=" N LEU I 121 " pdb=" CA LEU I 121 " pdb=" C LEU I 121 " ideal model delta sigma weight residual 111.03 106.85 4.18 1.11e+00 8.12e-01 1.42e+01 angle pdb=" CA GLU K 220 " pdb=" CB GLU K 220 " pdb=" CG GLU K 220 " ideal model delta sigma weight residual 114.10 121.48 -7.38 2.00e+00 2.50e-01 1.36e+01 angle pdb=" CB GLU B 224 " pdb=" CG GLU B 224 " pdb=" CD GLU B 224 " ideal model delta sigma weight residual 112.60 118.53 -5.93 1.70e+00 3.46e-01 1.22e+01 angle pdb=" CA GLU B 224 " pdb=" CB GLU B 224 " pdb=" CG GLU B 224 " ideal model delta sigma weight residual 114.10 121.01 -6.91 2.00e+00 2.50e-01 1.19e+01 ... (remaining 29659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 11322 17.91 - 35.82: 1870 35.82 - 53.73: 601 53.73 - 71.64: 147 71.64 - 89.54: 28 Dihedral angle restraints: 13968 sinusoidal: 5988 harmonic: 7980 Sorted by residual: dihedral pdb=" CB GLU K 183 " pdb=" CG GLU K 183 " pdb=" CD GLU K 183 " pdb=" OE1 GLU K 183 " ideal model delta sinusoidal sigma weight residual 0.00 89.54 -89.54 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU L 224 " pdb=" CG GLU L 224 " pdb=" CD GLU L 224 " pdb=" OE1 GLU L 224 " ideal model delta sinusoidal sigma weight residual 0.00 89.47 -89.47 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU D 187 " pdb=" CG GLU D 187 " pdb=" CD GLU D 187 " pdb=" OE1 GLU D 187 " ideal model delta sinusoidal sigma weight residual 0.00 89.44 -89.44 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 13965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2810 0.041 - 0.081: 657 0.081 - 0.122: 42 0.122 - 0.163: 14 0.163 - 0.204: 5 Chirality restraints: 3528 Sorted by residual: chirality pdb=" CA GLU D 220 " pdb=" N GLU D 220 " pdb=" C GLU D 220 " pdb=" CB GLU D 220 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA GLU H 220 " pdb=" N GLU H 220 " pdb=" C GLU H 220 " pdb=" CB GLU H 220 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA GLU F 220 " pdb=" N GLU F 220 " pdb=" C GLU F 220 " pdb=" CB GLU F 220 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 3525 not shown) Planarity restraints: 3708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 220 " 0.014 2.00e-02 2.50e+03 2.95e-02 8.70e+00 pdb=" CD GLU E 220 " -0.051 2.00e-02 2.50e+03 pdb=" OE1 GLU E 220 " 0.018 2.00e-02 2.50e+03 pdb=" OE2 GLU E 220 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 220 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.54e+00 pdb=" CD GLU A 220 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLU A 220 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU A 220 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 224 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" CD GLU A 224 " 0.038 2.00e-02 2.50e+03 pdb=" OE1 GLU A 224 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU A 224 " -0.013 2.00e-02 2.50e+03 ... (remaining 3705 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 136 2.57 - 3.16: 16905 3.16 - 3.74: 35817 3.74 - 4.32: 47522 4.32 - 4.90: 80945 Nonbonded interactions: 181325 Sorted by model distance: nonbonded pdb=" OD2 ASP B 40 " pdb="ZN ZN A 301 " model vdw 1.994 2.230 nonbonded pdb=" OD2 ASP I 51 " pdb="ZN ZN I 302 " model vdw 1.995 2.230 nonbonded pdb=" OD2 ASP D 51 " pdb="ZN ZN D 301 " model vdw 2.005 2.230 nonbonded pdb=" OD2 ASP H 51 " pdb="ZN ZN H 302 " model vdw 2.010 2.230 nonbonded pdb=" OD2 ASP A 51 " pdb="ZN ZN A 301 " model vdw 2.011 2.230 ... (remaining 181320 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' and resid 4 through 231) selection = (chain 'B' and resid 4 through 231) selection = (chain 'C' and resid 4 through 231) selection = (chain 'D' and resid 4 through 231) selection = (chain 'E' and resid 4 through 231) selection = (chain 'F' and resid 4 through 231) selection = (chain 'G' and resid 4 through 231) selection = (chain 'H' and resid 4 through 231) selection = (chain 'I' and resid 4 through 231) 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.540 Find NCS groups from input model: 0.540 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:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 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 : 0.008 0.243 22236 Z= 0.281 Angle : 0.548 8.896 29664 Z= 0.297 Chirality : 0.034 0.204 3528 Planarity : 0.002 0.029 3708 Dihedral : 19.972 89.545 8760 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 0.47 % Allowed : 26.89 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.28 (0.15), residues: 2712 helix: 2.71 (0.10), residues: 2400 sheet: None (None), residues: 0 loop : -2.57 (0.22), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 39 TYR 0.009 0.001 TYR L 68 PHE 0.014 0.001 PHE F 219 HIS 0.015 0.001 HIS G 47 Details of bonding type rmsd covalent geometry : bond 0.00317 (22188) covalent geometry : angle 0.54826 (29664) hydrogen bonds : bond 0.13149 ( 1848) hydrogen bonds : angle 4.31058 ( 5544) metal coordination : bond 0.15469 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 357 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 216 GLU cc_start: 0.6933 (mp0) cc_final: 0.6677 (mp0) REVERT: G 66 ARG cc_start: 0.7442 (mmp80) cc_final: 0.7195 (mmt180) REVERT: E 52 ARG cc_start: 0.7953 (mtp180) cc_final: 0.7584 (mpp-170) REVERT: H 63 MET cc_start: 0.7829 (ttp) cc_final: 0.7622 (ttp) REVERT: H 158 MET cc_start: 0.7578 (ttt) cc_final: 0.7331 (ttm) REVERT: F 104 GLU cc_start: 0.7592 (tt0) cc_final: 0.7345 (tt0) REVERT: F 228 GLU cc_start: 0.6028 (mm-30) cc_final: 0.5818 (mm-30) outliers start: 11 outliers final: 0 residues processed: 365 average time/residue: 0.8281 time to fit residues: 333.5196 Evaluate side-chains 313 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS B 47 HIS C 47 HIS G 47 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.202755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.178990 restraints weight = 23208.247| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 0.61 r_work: 0.3761 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.459 22236 Z= 0.240 Angle : 0.526 8.451 29664 Z= 0.269 Chirality : 0.034 0.175 3528 Planarity : 0.003 0.039 3708 Dihedral : 3.676 18.558 2892 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Rotamer: Outliers : 2.71 % Allowed : 27.28 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.64 (0.15), residues: 2712 helix: 2.80 (0.10), residues: 2460 sheet: None (None), residues: 0 loop : -2.03 (0.26), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 39 TYR 0.010 0.002 TYR L 68 PHE 0.009 0.001 PHE F 219 HIS 0.005 0.001 HIS G 175 Details of bonding type rmsd covalent geometry : bond 0.00378 (22188) covalent geometry : angle 0.52648 (29664) hydrogen bonds : bond 0.04658 ( 1848) hydrogen bonds : angle 3.54295 ( 5544) metal coordination : bond 0.11865 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 345 time to evaluate : 0.696 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 revert: symmetry clash REVERT: B 63 MET cc_start: 0.7900 (ttp) cc_final: 0.7696 (ttp) REVERT: D 96 MET cc_start: 0.8222 (mmm) cc_final: 0.8009 (mmm) REVERT: J 39 ARG cc_start: 0.8427 (ttm-80) cc_final: 0.7844 (ttp-110) REVERT: H 5 THR cc_start: 0.7656 (p) cc_final: 0.7397 (m) REVERT: H 11 ARG cc_start: 0.8155 (ttm170) cc_final: 0.7524 (ttp80) REVERT: H 63 MET cc_start: 0.7966 (ttp) cc_final: 0.7746 (ttp) REVERT: H 224 GLU cc_start: 0.7181 (tp30) cc_final: 0.6674 (tp30) REVERT: K 153 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8101 (mt) REVERT: K 230 ILE cc_start: 0.6833 (OUTLIER) cc_final: 0.6426 (tp) REVERT: F 230 ILE cc_start: 0.6684 (OUTLIER) cc_final: 0.6219 (tp) REVERT: I 39 ARG cc_start: 0.8435 (ttm-80) cc_final: 0.7939 (tpp-160) REVERT: I 98 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8163 (mtmt) REVERT: I 230 ILE cc_start: 0.6984 (OUTLIER) cc_final: 0.6706 (tp) REVERT: L 39 ARG cc_start: 0.8676 (ttm-80) cc_final: 0.8157 (tpp-160) outliers start: 63 outliers final: 18 residues processed: 391 average time/residue: 0.7802 time to fit residues: 338.4526 Evaluate side-chains 338 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 315 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 220 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 260 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.203045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.179505 restraints weight = 23301.656| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 0.61 r_work: 0.3762 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22236 Z= 0.141 Angle : 0.506 8.549 29664 Z= 0.255 Chirality : 0.033 0.157 3528 Planarity : 0.002 0.029 3708 Dihedral : 3.627 19.055 2892 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Rotamer: Outliers : 2.75 % Allowed : 27.49 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.86 (0.15), residues: 2712 helix: 2.94 (0.10), residues: 2460 sheet: None (None), residues: 0 loop : -2.02 (0.26), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 39 TYR 0.009 0.002 TYR L 68 PHE 0.008 0.001 PHE K 219 HIS 0.004 0.001 HIS J 175 Details of bonding type rmsd covalent geometry : bond 0.00344 (22188) covalent geometry : angle 0.50576 (29664) hydrogen bonds : bond 0.04293 ( 1848) hydrogen bonds : angle 3.41754 ( 5544) metal coordination : bond 0.00162 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 352 time to evaluate : 0.824 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 REVERT: A 230 ILE cc_start: 0.6679 (OUTLIER) cc_final: 0.6400 (tp) REVERT: B 63 MET cc_start: 0.7938 (ttp) cc_final: 0.7698 (ttp) REVERT: C 143 GLU cc_start: 0.7740 (tp30) cc_final: 0.7531 (tp30) REVERT: D 11 ARG cc_start: 0.7975 (ttp-110) cc_final: 0.7525 (ttp80) REVERT: D 39 ARG cc_start: 0.8333 (ttm-80) cc_final: 0.7503 (ttm110) REVERT: G 5 THR cc_start: 0.7742 (p) cc_final: 0.7368 (m) REVERT: J 39 ARG cc_start: 0.8427 (ttm-80) cc_final: 0.7850 (ttp-110) REVERT: E 5 THR cc_start: 0.7888 (p) cc_final: 0.7681 (m) REVERT: H 5 THR cc_start: 0.7754 (p) cc_final: 0.7361 (m) REVERT: H 11 ARG cc_start: 0.8106 (ttm170) cc_final: 0.7463 (ttp80) REVERT: H 63 MET cc_start: 0.7978 (ttp) cc_final: 0.7749 (ttp) REVERT: K 153 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8101 (mt) REVERT: K 230 ILE cc_start: 0.6762 (OUTLIER) cc_final: 0.6343 (tp) REVERT: F 230 ILE cc_start: 0.6572 (OUTLIER) cc_final: 0.6159 (tp) REVERT: I 5 THR cc_start: 0.7699 (p) cc_final: 0.7302 (m) REVERT: I 39 ARG cc_start: 0.8404 (ttm-80) cc_final: 0.7987 (tpp-160) REVERT: I 98 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8150 (mtmt) REVERT: I 230 ILE cc_start: 0.6937 (OUTLIER) cc_final: 0.6653 (tp) REVERT: L 39 ARG cc_start: 0.8707 (ttm-80) cc_final: 0.8199 (tpp-160) outliers start: 64 outliers final: 24 residues processed: 398 average time/residue: 0.8317 time to fit residues: 367.4859 Evaluate side-chains 346 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 316 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 78 ASP Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 220 GLU Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 220 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 205 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 185 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.203545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.178544 restraints weight = 23318.778| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 0.64 r_work: 0.3717 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22236 Z= 0.122 Angle : 0.499 8.852 29664 Z= 0.251 Chirality : 0.032 0.150 3528 Planarity : 0.002 0.029 3708 Dihedral : 3.558 18.726 2892 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 2.66 % Allowed : 28.31 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.02 (0.15), residues: 2712 helix: 3.04 (0.10), residues: 2460 sheet: None (None), residues: 0 loop : -1.94 (0.27), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 39 TYR 0.008 0.002 TYR L 68 PHE 0.005 0.001 PHE J 219 HIS 0.003 0.001 HIS E 175 Details of bonding type rmsd covalent geometry : bond 0.00288 (22188) covalent geometry : angle 0.49858 (29664) hydrogen bonds : bond 0.03850 ( 1848) hydrogen bonds : angle 3.33354 ( 5544) metal coordination : bond 0.00155 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 343 time to evaluate : 0.951 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 REVERT: B 63 MET cc_start: 0.7938 (ttp) cc_final: 0.7650 (ttp) REVERT: C 15 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7781 (ttt90) REVERT: C 181 ILE cc_start: 0.8946 (mt) cc_final: 0.8732 (mt) REVERT: D 11 ARG cc_start: 0.8115 (ttp-110) cc_final: 0.7594 (ttp80) REVERT: D 39 ARG cc_start: 0.8428 (ttm-80) cc_final: 0.8003 (tpp-160) REVERT: G 5 THR cc_start: 0.7679 (p) cc_final: 0.7275 (m) REVERT: G 11 ARG cc_start: 0.8099 (ttp-110) cc_final: 0.7670 (ttp80) REVERT: J 39 ARG cc_start: 0.8492 (ttm-80) cc_final: 0.7771 (ttm110) REVERT: H 11 ARG cc_start: 0.8245 (ttm170) cc_final: 0.7605 (ttp80) REVERT: H 63 MET cc_start: 0.8060 (ttp) cc_final: 0.7851 (ttp) REVERT: K 39 ARG cc_start: 0.8345 (ttm170) cc_final: 0.7566 (ttp80) REVERT: K 153 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8138 (mt) REVERT: K 230 ILE cc_start: 0.6956 (OUTLIER) cc_final: 0.6466 (tp) REVERT: F 158 MET cc_start: 0.7739 (ttm) cc_final: 0.7266 (ttm) REVERT: I 98 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8239 (mtmt) REVERT: I 230 ILE cc_start: 0.6990 (OUTLIER) cc_final: 0.6719 (tp) REVERT: L 6 MET cc_start: 0.7995 (mmp) cc_final: 0.7777 (mmp) REVERT: L 39 ARG cc_start: 0.8749 (ttm-80) cc_final: 0.8287 (tpp-160) outliers start: 62 outliers final: 23 residues processed: 392 average time/residue: 0.8374 time to fit residues: 364.5434 Evaluate side-chains 348 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 320 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 78 ASP Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 220 GLU Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 220 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 126 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 232 optimal weight: 0.8980 chunk 21 optimal weight: 0.0040 chunk 73 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 137 optimal weight: 0.4980 chunk 145 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 47 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.204314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.170729 restraints weight = 23366.124| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.08 r_work: 0.3733 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.401 22236 Z= 0.142 Angle : 0.492 9.161 29664 Z= 0.249 Chirality : 0.031 0.138 3528 Planarity : 0.002 0.032 3708 Dihedral : 3.475 17.698 2892 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 2.62 % Allowed : 29.55 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.18 (0.15), residues: 2712 helix: 3.14 (0.10), residues: 2460 sheet: None (None), residues: 0 loop : -1.85 (0.27), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 39 TYR 0.007 0.001 TYR L 68 PHE 0.009 0.001 PHE K 219 HIS 0.003 0.001 HIS E 175 Details of bonding type rmsd covalent geometry : bond 0.00254 (22188) covalent geometry : angle 0.49241 (29664) hydrogen bonds : bond 0.03498 ( 1848) hydrogen bonds : angle 3.26343 ( 5544) metal coordination : bond 0.05793 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 356 time to evaluate : 0.926 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 REVERT: A 230 ILE cc_start: 0.6507 (OUTLIER) cc_final: 0.6168 (tp) REVERT: B 11 ARG cc_start: 0.7948 (ttp-110) cc_final: 0.7744 (ttm-80) REVERT: B 63 MET cc_start: 0.7928 (ttp) cc_final: 0.7614 (ttp) REVERT: C 15 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7530 (ttt90) REVERT: C 181 ILE cc_start: 0.8857 (mt) cc_final: 0.8623 (mt) REVERT: D 11 ARG cc_start: 0.7930 (ttp-110) cc_final: 0.7321 (ttp80) REVERT: G 5 THR cc_start: 0.7411 (p) cc_final: 0.7169 (m) REVERT: J 39 ARG cc_start: 0.8319 (ttm-80) cc_final: 0.7636 (ttp-110) REVERT: K 39 ARG cc_start: 0.8221 (ttm170) cc_final: 0.7375 (ttp80) REVERT: K 230 ILE cc_start: 0.6696 (OUTLIER) cc_final: 0.6186 (tp) REVERT: I 39 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.7725 (ttp-110) REVERT: I 206 LEU cc_start: 0.6993 (mt) cc_final: 0.6747 (mt) REVERT: I 230 ILE cc_start: 0.6645 (OUTLIER) cc_final: 0.6358 (tp) REVERT: L 39 ARG cc_start: 0.8613 (ttm-80) cc_final: 0.8102 (tpp-160) outliers start: 61 outliers final: 18 residues processed: 404 average time/residue: 0.8062 time to fit residues: 361.0257 Evaluate side-chains 340 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 318 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 220 GLU Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 220 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 21 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 251 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 209 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 247 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.204695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.181980 restraints weight = 23366.133| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 0.66 r_work: 0.3780 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22236 Z= 0.124 Angle : 0.523 9.243 29664 Z= 0.263 Chirality : 0.032 0.144 3528 Planarity : 0.002 0.035 3708 Dihedral : 3.479 17.610 2892 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 2.71 % Allowed : 30.20 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.09 (0.15), residues: 2712 helix: 3.09 (0.10), residues: 2460 sheet: None (None), residues: 0 loop : -1.88 (0.28), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 39 TYR 0.008 0.002 TYR K 41 PHE 0.007 0.001 PHE J 219 HIS 0.003 0.001 HIS E 175 Details of bonding type rmsd covalent geometry : bond 0.00298 (22188) covalent geometry : angle 0.52259 (29664) hydrogen bonds : bond 0.03766 ( 1848) hydrogen bonds : angle 3.33765 ( 5544) metal coordination : bond 0.00150 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 322 time to evaluate : 0.875 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: A 230 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.6455 (tp) REVERT: B 63 MET cc_start: 0.7931 (ttp) cc_final: 0.7526 (ttp) REVERT: C 15 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7615 (ttt90) REVERT: C 181 ILE cc_start: 0.8884 (mt) cc_final: 0.8658 (mt) REVERT: D 8 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7376 (tm-30) REVERT: D 11 ARG cc_start: 0.7999 (ttp-110) cc_final: 0.7526 (ttp80) REVERT: D 39 ARG cc_start: 0.8313 (ttm-80) cc_final: 0.7665 (tpp-160) REVERT: G 158 MET cc_start: 0.7659 (ttm) cc_final: 0.7420 (ttt) REVERT: G 224 GLU cc_start: 0.7422 (tp30) cc_final: 0.7214 (tp30) REVERT: J 39 ARG cc_start: 0.8383 (ttm-80) cc_final: 0.7676 (ttm110) REVERT: H 8 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7005 (tm-30) REVERT: K 39 ARG cc_start: 0.8235 (ttm170) cc_final: 0.7485 (ttp80) REVERT: K 153 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8120 (mt) REVERT: K 230 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6370 (tp) REVERT: F 158 MET cc_start: 0.7695 (ttm) cc_final: 0.7245 (ttm) REVERT: F 216 GLU cc_start: 0.7646 (mp0) cc_final: 0.7145 (pm20) REVERT: I 39 ARG cc_start: 0.8530 (ttm-80) cc_final: 0.7822 (ttp-110) REVERT: I 206 LEU cc_start: 0.7192 (mt) cc_final: 0.6927 (mt) REVERT: L 39 ARG cc_start: 0.8685 (ttm-80) cc_final: 0.8256 (tpp-160) REVERT: L 153 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8100 (mt) outliers start: 63 outliers final: 23 residues processed: 374 average time/residue: 0.7331 time to fit residues: 306.2787 Evaluate side-chains 339 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 309 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 220 GLU Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 220 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 14 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 258 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 227 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.200295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.176490 restraints weight = 23029.699| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 0.66 r_work: 0.3683 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 22236 Z= 0.166 Angle : 0.583 9.511 29664 Z= 0.296 Chirality : 0.034 0.154 3528 Planarity : 0.003 0.033 3708 Dihedral : 3.622 18.966 2892 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 2.53 % Allowed : 30.54 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.80 (0.15), residues: 2712 helix: 2.90 (0.10), residues: 2460 sheet: None (None), residues: 0 loop : -1.98 (0.28), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 39 TYR 0.010 0.002 TYR F 68 PHE 0.008 0.001 PHE A 38 HIS 0.004 0.001 HIS E 175 Details of bonding type rmsd covalent geometry : bond 0.00420 (22188) covalent geometry : angle 0.58275 (29664) hydrogen bonds : bond 0.04593 ( 1848) hydrogen bonds : angle 3.54729 ( 5544) metal coordination : bond 0.00171 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 323 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 MET cc_start: 0.7906 (ttp) cc_final: 0.7536 (ttp) REVERT: B 188 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7950 (mp) REVERT: B 216 GLU cc_start: 0.6985 (pm20) cc_final: 0.6716 (pm20) REVERT: C 15 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7561 (ttt90) REVERT: D 8 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7319 (tm-30) REVERT: D 11 ARG cc_start: 0.7998 (ttp-110) cc_final: 0.7551 (ttp80) REVERT: D 39 ARG cc_start: 0.8365 (ttm-80) cc_final: 0.7869 (tpp-160) REVERT: D 96 MET cc_start: 0.8059 (mmm) cc_final: 0.7746 (mmm) REVERT: J 39 ARG cc_start: 0.8435 (ttm-80) cc_final: 0.7833 (ttp-110) REVERT: K 98 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7993 (mtmm) REVERT: K 153 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8192 (mt) REVERT: K 230 ILE cc_start: 0.6852 (OUTLIER) cc_final: 0.6423 (tp) REVERT: I 39 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.8029 (tpp-160) REVERT: I 98 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8167 (mtmt) REVERT: L 39 ARG cc_start: 0.8702 (ttm-80) cc_final: 0.8254 (tpp-160) outliers start: 59 outliers final: 28 residues processed: 376 average time/residue: 0.6872 time to fit residues: 288.4348 Evaluate side-chains 343 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 308 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 78 ASP Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 98 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 220 GLU Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 220 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 129 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 31 optimal weight: 0.0980 chunk 88 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.202492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.170876 restraints weight = 23239.641| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 0.87 r_work: 0.3733 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 22236 Z= 0.131 Angle : 0.568 9.905 29664 Z= 0.286 Chirality : 0.033 0.164 3528 Planarity : 0.002 0.032 3708 Dihedral : 3.523 17.966 2892 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 2.62 % Allowed : 31.10 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.94 (0.15), residues: 2712 helix: 2.99 (0.10), residues: 2460 sheet: None (None), residues: 0 loop : -1.96 (0.28), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 39 TYR 0.009 0.001 TYR K 41 PHE 0.007 0.001 PHE J 219 HIS 0.003 0.001 HIS E 175 Details of bonding type rmsd covalent geometry : bond 0.00321 (22188) covalent geometry : angle 0.56840 (29664) hydrogen bonds : bond 0.03821 ( 1848) hydrogen bonds : angle 3.43277 ( 5544) metal coordination : bond 0.00141 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 322 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ILE cc_start: 0.6492 (OUTLIER) cc_final: 0.6100 (tp) REVERT: B 63 MET cc_start: 0.7928 (ttp) cc_final: 0.7582 (ttp) REVERT: B 188 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7888 (mp) REVERT: B 216 GLU cc_start: 0.6804 (pm20) cc_final: 0.6440 (pm20) REVERT: C 15 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8309 (ttt90) REVERT: D 8 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7368 (tm-30) REVERT: D 11 ARG cc_start: 0.7933 (ttp-110) cc_final: 0.7363 (ttp80) REVERT: D 18 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7442 (pt0) REVERT: D 39 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.7415 (ttm110) REVERT: J 39 ARG cc_start: 0.8451 (ttm-80) cc_final: 0.7658 (ttp-110) REVERT: K 39 ARG cc_start: 0.8188 (ttm170) cc_final: 0.7478 (ttp80) REVERT: K 98 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7755 (mtmm) REVERT: K 153 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7980 (mt) REVERT: K 216 GLU cc_start: 0.7680 (mp0) cc_final: 0.7272 (pm20) REVERT: K 230 ILE cc_start: 0.6693 (OUTLIER) cc_final: 0.6209 (tp) REVERT: F 216 GLU cc_start: 0.7467 (mp0) cc_final: 0.6839 (pm20) REVERT: I 39 ARG cc_start: 0.8538 (ttm-80) cc_final: 0.7691 (ttp-110) REVERT: I 98 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8044 (mtmt) REVERT: L 39 ARG cc_start: 0.8608 (ttm-80) cc_final: 0.8136 (tpp-160) REVERT: L 153 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7896 (mt) outliers start: 61 outliers final: 25 residues processed: 373 average time/residue: 0.7158 time to fit residues: 297.7067 Evaluate side-chains 335 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 301 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 98 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 220 GLU Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 220 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 50 optimal weight: 0.8980 chunk 159 optimal weight: 7.9990 chunk 55 optimal weight: 0.0050 chunk 182 optimal weight: 0.8980 chunk 207 optimal weight: 0.2980 chunk 41 optimal weight: 4.9990 chunk 209 optimal weight: 0.0770 chunk 213 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 0.4352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.206537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.184048 restraints weight = 23427.085| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 0.67 r_work: 0.3806 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 22236 Z= 0.118 Angle : 0.566 10.239 29664 Z= 0.288 Chirality : 0.033 0.207 3528 Planarity : 0.002 0.033 3708 Dihedral : 3.427 16.208 2892 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 2.32 % Allowed : 31.79 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.09 (0.15), residues: 2712 helix: 3.09 (0.10), residues: 2460 sheet: None (None), residues: 0 loop : -1.91 (0.28), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 39 TYR 0.006 0.001 TYR L 68 PHE 0.008 0.001 PHE C 219 HIS 0.003 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00281 (22188) covalent geometry : angle 0.56580 (29664) hydrogen bonds : bond 0.03395 ( 1848) hydrogen bonds : angle 3.36853 ( 5544) metal coordination : bond 0.00155 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 320 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: A 140 ASP cc_start: 0.7697 (t70) cc_final: 0.7372 (p0) REVERT: A 230 ILE cc_start: 0.6786 (OUTLIER) cc_final: 0.6351 (tp) REVERT: B 63 MET cc_start: 0.7955 (ttp) cc_final: 0.7527 (ttp) REVERT: B 216 GLU cc_start: 0.7055 (pm20) cc_final: 0.6705 (pm20) REVERT: C 15 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7580 (ttt90) REVERT: D 8 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: D 11 ARG cc_start: 0.7928 (ttp-110) cc_final: 0.7470 (ttp80) REVERT: D 39 ARG cc_start: 0.8312 (ttm-80) cc_final: 0.7692 (tpp-160) REVERT: D 216 GLU cc_start: 0.6799 (pm20) cc_final: 0.6484 (pm20) REVERT: G 7 GLU cc_start: 0.7658 (mp0) cc_final: 0.7405 (tp30) REVERT: G 158 MET cc_start: 0.7603 (ttm) cc_final: 0.7399 (ttt) REVERT: J 39 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.7752 (ttp-110) REVERT: E 5 THR cc_start: 0.7662 (t) cc_final: 0.7240 (m) REVERT: K 39 ARG cc_start: 0.8251 (ttm170) cc_final: 0.7589 (ttp80) REVERT: K 98 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7904 (mtmt) REVERT: K 216 GLU cc_start: 0.7696 (mp0) cc_final: 0.7298 (pm20) REVERT: K 230 ILE cc_start: 0.6850 (OUTLIER) cc_final: 0.6326 (tp) REVERT: F 158 MET cc_start: 0.7681 (ttm) cc_final: 0.7345 (ttm) REVERT: I 39 ARG cc_start: 0.8518 (ttm-80) cc_final: 0.7838 (ttp-110) REVERT: I 206 LEU cc_start: 0.7101 (mt) cc_final: 0.6857 (mt) REVERT: L 39 ARG cc_start: 0.8682 (ttm-80) cc_final: 0.8287 (tpp-160) REVERT: L 153 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8014 (mt) outliers start: 54 outliers final: 21 residues processed: 368 average time/residue: 0.7266 time to fit residues: 297.5894 Evaluate side-chains 323 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 295 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain K residue 98 LYS Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 220 GLU Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 220 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 162 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 172 optimal weight: 0.2980 chunk 231 optimal weight: 0.2980 chunk 109 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 237 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.205387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.182961 restraints weight = 23414.074| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 0.63 r_work: 0.3796 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 22236 Z= 0.129 Angle : 0.615 10.114 29664 Z= 0.310 Chirality : 0.033 0.219 3528 Planarity : 0.002 0.032 3708 Dihedral : 3.454 16.444 2892 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 1.80 % Allowed : 32.65 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.97 (0.15), residues: 2712 helix: 3.01 (0.10), residues: 2460 sheet: None (None), residues: 0 loop : -1.92 (0.28), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 39 TYR 0.008 0.001 TYR F 68 PHE 0.011 0.001 PHE K 219 HIS 0.003 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00313 (22188) covalent geometry : angle 0.61535 (29664) hydrogen bonds : bond 0.03663 ( 1848) hydrogen bonds : angle 3.43968 ( 5544) metal coordination : bond 0.00148 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 300 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: A 140 ASP cc_start: 0.7748 (t70) cc_final: 0.7393 (p0) REVERT: A 230 ILE cc_start: 0.6961 (OUTLIER) cc_final: 0.6493 (tp) REVERT: B 216 GLU cc_start: 0.6999 (pm20) cc_final: 0.6587 (pm20) REVERT: C 15 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7591 (ttt90) REVERT: D 8 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: D 11 ARG cc_start: 0.7955 (ttp-110) cc_final: 0.7541 (ttp80) REVERT: D 39 ARG cc_start: 0.8320 (ttm-80) cc_final: 0.7807 (tpp-160) REVERT: D 216 GLU cc_start: 0.6690 (pm20) cc_final: 0.6229 (pm20) REVERT: J 39 ARG cc_start: 0.8353 (ttm-80) cc_final: 0.7753 (ttp-110) REVERT: E 5 THR cc_start: 0.7646 (t) cc_final: 0.7277 (m) REVERT: H 24 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7704 (mt-10) REVERT: K 39 ARG cc_start: 0.8260 (ttm170) cc_final: 0.7580 (ttp80) REVERT: K 98 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7913 (mtmt) REVERT: K 216 GLU cc_start: 0.7698 (mp0) cc_final: 0.7406 (pm20) REVERT: K 230 ILE cc_start: 0.6790 (OUTLIER) cc_final: 0.6274 (tp) REVERT: F 39 ARG cc_start: 0.8632 (ttm-80) cc_final: 0.7803 (ttp-110) REVERT: F 158 MET cc_start: 0.7607 (ttm) cc_final: 0.7279 (ttm) REVERT: F 216 GLU cc_start: 0.7320 (mp0) cc_final: 0.6817 (pm20) REVERT: I 8 GLU cc_start: 0.7639 (tp30) cc_final: 0.7331 (tp30) REVERT: I 39 ARG cc_start: 0.8545 (ttm-80) cc_final: 0.7927 (ttp-110) REVERT: I 206 LEU cc_start: 0.7107 (mt) cc_final: 0.6876 (mt) REVERT: L 39 ARG cc_start: 0.8681 (ttm-80) cc_final: 0.8273 (tpp-160) REVERT: L 63 MET cc_start: 0.7643 (ttp) cc_final: 0.7252 (tmm) REVERT: L 153 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8052 (mt) outliers start: 42 outliers final: 25 residues processed: 340 average time/residue: 0.8304 time to fit residues: 313.1411 Evaluate side-chains 312 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 280 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain K residue 98 LYS Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 220 GLU Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 220 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 40 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 81 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 258 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 182 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.200122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.162156 restraints weight = 23110.440| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.44 r_work: 0.3639 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 22236 Z= 0.148 Angle : 0.626 9.719 29664 Z= 0.320 Chirality : 0.034 0.233 3528 Planarity : 0.003 0.031 3708 Dihedral : 3.553 17.339 2892 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 1.63 % Allowed : 32.56 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.81 (0.15), residues: 2712 helix: 2.90 (0.10), residues: 2460 sheet: None (None), residues: 0 loop : -2.00 (0.28), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 39 TYR 0.010 0.002 TYR F 68 PHE 0.014 0.001 PHE B 219 HIS 0.003 0.001 HIS E 175 Details of bonding type rmsd covalent geometry : bond 0.00369 (22188) covalent geometry : angle 0.62598 (29664) hydrogen bonds : bond 0.04121 ( 1848) hydrogen bonds : angle 3.54210 ( 5544) metal coordination : bond 0.00144 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8539.31 seconds wall clock time: 145 minutes 43.95 seconds (8743.95 seconds total)