Starting phenix.real_space_refine on Thu Oct 29 13:52:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wmj_66094/10_2026/9wmj_66094.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wmj_66094/10_2026/9wmj_66094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wmj_66094/10_2026/9wmj_66094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wmj_66094/10_2026/9wmj_66094.map" model { file = "/net/cci-nas-00/data/ceres_data/9wmj_66094/10_2026/9wmj_66094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wmj_66094/10_2026/9wmj_66094.cif" } resolution = 2.2 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= 0.054 sd= 0.799 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: 4 Type Number sf(0) Gaussians S 160 5.16 5 C 20672 2.51 5 N 5360 2.21 5 O 5888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32080 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1977 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "B" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1977 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "C" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1977 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "D" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1977 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "E" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1977 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "F" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1977 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "G" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1977 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "H" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1977 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "I" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1977 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "J" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1977 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "K" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1977 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "L" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1977 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "M" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1977 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "N" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1977 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "O" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1977 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "P" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1977 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.30, per 1000 atoms: 0.23 Number of scatterers: 32080 At special positions: 0 Unit cell: (173.58, 173.58, 119.928, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 160 16.00 O 5888 8.00 N 5360 7.00 C 20672 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: 2.41 Conformation dependent library (CDL) restraints added in 1.3 seconds 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7776 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 62 sheets defined 57.2% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 28 through 45 Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 128 through 135 Processing helix chain 'A' and resid 138 through 157 Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 166 through 183 removed outlier: 3.564A pdb=" N THR A 177 " --> pdb=" O ASN A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 208 removed outlier: 4.640A pdb=" N ARG A 205 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ALA A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 243 removed outlier: 4.650A pdb=" N ARG A 232 " --> pdb=" O MET A 228 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ALA A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A 243 " --> pdb=" O MET A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 260 removed outlier: 4.500A pdb=" N GLN A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 45 Processing helix chain 'B' and resid 45 through 53 removed outlier: 4.901A pdb=" N TRP B 51 " --> pdb=" O PRO B 47 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N MET B 52 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 135 Processing helix chain 'B' and resid 138 through 156 Processing helix chain 'B' and resid 159 through 166 Processing helix chain 'B' and resid 166 through 183 removed outlier: 3.539A pdb=" N THR B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.686A pdb=" N ARG B 205 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ALA B 206 " --> pdb=" O GLN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 230 Processing helix chain 'B' and resid 230 through 243 removed outlier: 3.713A pdb=" N GLU B 243 " --> pdb=" O MET B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 262 removed outlier: 3.962A pdb=" N GLN B 249 " --> pdb=" O PRO B 245 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 261 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'C' and resid 28 through 45 Processing helix chain 'C' and resid 45 through 53 removed outlier: 5.242A pdb=" N TRP C 51 " --> pdb=" O PRO C 47 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N MET C 52 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 135 Processing helix chain 'C' and resid 138 through 157 Processing helix chain 'C' and resid 159 through 166 Processing helix chain 'C' and resid 166 through 183 removed outlier: 3.522A pdb=" N THR C 177 " --> pdb=" O ASN C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 208 removed outlier: 4.609A pdb=" N ARG C 205 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ALA C 206 " --> pdb=" O GLN C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 230 Processing helix chain 'C' and resid 230 through 243 removed outlier: 3.785A pdb=" N GLU C 243 " --> pdb=" O MET C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 260 removed outlier: 4.547A pdb=" N GLN C 249 " --> pdb=" O PRO C 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 45 Processing helix chain 'D' and resid 45 through 53 removed outlier: 4.999A pdb=" N TRP D 51 " --> pdb=" O PRO D 47 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET D 52 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 135 Processing helix chain 'D' and resid 138 through 157 Processing helix chain 'D' and resid 159 through 166 Processing helix chain 'D' and resid 166 through 183 removed outlier: 3.549A pdb=" N THR D 177 " --> pdb=" O ASN D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 208 removed outlier: 4.680A pdb=" N ARG D 205 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ALA D 206 " --> pdb=" O GLN D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 244 removed outlier: 4.793A pdb=" N ARG D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ALA D 233 " --> pdb=" O ASN D 229 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU D 243 " --> pdb=" O MET D 239 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER D 244 " --> pdb=" O VAL D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 262 removed outlier: 3.922A pdb=" N GLN D 249 " --> pdb=" O PRO D 245 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA D 261 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 278 Processing helix chain 'E' and resid 28 through 45 Processing helix chain 'E' and resid 45 through 53 removed outlier: 5.116A pdb=" N TRP E 51 " --> pdb=" O PRO E 47 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N MET E 52 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 135 Processing helix chain 'E' and resid 138 through 157 Processing helix chain 'E' and resid 159 through 166 Processing helix chain 'E' and resid 166 through 183 removed outlier: 3.542A pdb=" N THR E 177 " --> pdb=" O ASN E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 208 removed outlier: 4.684A pdb=" N ARG E 205 " --> pdb=" O VAL E 201 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ALA E 206 " --> pdb=" O GLN E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 230 Processing helix chain 'E' and resid 230 through 243 removed outlier: 3.751A pdb=" N GLU E 243 " --> pdb=" O MET E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 260 removed outlier: 4.441A pdb=" N GLN E 249 " --> pdb=" O PRO E 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 45 Processing helix chain 'F' and resid 45 through 53 removed outlier: 3.692A pdb=" N ILE F 50 " --> pdb=" O PHE F 46 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TRP F 51 " --> pdb=" O PRO F 47 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N MET F 52 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 135 Processing helix chain 'F' and resid 138 through 157 Processing helix chain 'F' and resid 159 through 166 Processing helix chain 'F' and resid 166 through 183 removed outlier: 3.537A pdb=" N THR F 177 " --> pdb=" O ASN F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 208 removed outlier: 4.673A pdb=" N ARG F 205 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ALA F 206 " --> pdb=" O GLN F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 230 Processing helix chain 'F' and resid 230 through 242 Processing helix chain 'F' and resid 245 through 262 removed outlier: 3.925A pdb=" N GLN F 249 " --> pdb=" O PRO F 245 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR F 257 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA F 261 " --> pdb=" O THR F 257 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU F 262 " --> pdb=" O THR F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 280 removed outlier: 3.622A pdb=" N ILE F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 45 Processing helix chain 'G' and resid 45 through 53 removed outlier: 5.227A pdb=" N TRP G 51 " --> pdb=" O PRO G 47 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N MET G 52 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 135 Processing helix chain 'G' and resid 138 through 157 Processing helix chain 'G' and resid 159 through 166 Processing helix chain 'G' and resid 166 through 183 removed outlier: 3.564A pdb=" N THR G 177 " --> pdb=" O ASN G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 208 removed outlier: 4.613A pdb=" N ARG G 205 " --> pdb=" O VAL G 201 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ALA G 206 " --> pdb=" O GLN G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 230 Processing helix chain 'G' and resid 230 through 243 removed outlier: 3.798A pdb=" N GLU G 243 " --> pdb=" O MET G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 260 removed outlier: 4.522A pdb=" N GLN G 249 " --> pdb=" O PRO G 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 45 Processing helix chain 'H' and resid 45 through 53 removed outlier: 5.319A pdb=" N TRP H 51 " --> pdb=" O PRO H 47 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET H 52 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 135 Processing helix chain 'H' and resid 138 through 157 Processing helix chain 'H' and resid 159 through 166 Processing helix chain 'H' and resid 166 through 183 removed outlier: 3.581A pdb=" N THR H 177 " --> pdb=" O ASN H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 208 removed outlier: 4.677A pdb=" N ARG H 205 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ALA H 206 " --> pdb=" O GLN H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 230 Processing helix chain 'H' and resid 230 through 244 removed outlier: 3.769A pdb=" N GLU H 243 " --> pdb=" O MET H 239 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER H 244 " --> pdb=" O VAL H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 261 removed outlier: 3.890A pdb=" N GLN H 249 " --> pdb=" O PRO H 245 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR H 257 " --> pdb=" O LEU H 253 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA H 261 " --> pdb=" O THR H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 278 Processing helix chain 'I' and resid 28 through 45 Processing helix chain 'I' and resid 45 through 50 Processing helix chain 'I' and resid 128 through 135 Processing helix chain 'I' and resid 138 through 157 Processing helix chain 'I' and resid 159 through 166 Processing helix chain 'I' and resid 166 through 183 removed outlier: 3.543A pdb=" N THR I 177 " --> pdb=" O ASN I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 202 No H-bonds generated for 'chain 'I' and resid 200 through 202' Processing helix chain 'I' and resid 203 through 208 Processing helix chain 'I' and resid 208 through 243 removed outlier: 4.791A pdb=" N ARG I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ALA I 233 " --> pdb=" O ASN I 229 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU I 243 " --> pdb=" O MET I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 245 through 260 removed outlier: 4.534A pdb=" N GLN I 249 " --> pdb=" O PRO I 245 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 45 Processing helix chain 'J' and resid 45 through 53 removed outlier: 5.307A pdb=" N TRP J 51 " --> pdb=" O PRO J 47 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N MET J 52 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 135 Processing helix chain 'J' and resid 138 through 157 Processing helix chain 'J' and resid 159 through 166 Processing helix chain 'J' and resid 166 through 183 removed outlier: 3.567A pdb=" N THR J 177 " --> pdb=" O ASN J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 208 removed outlier: 4.655A pdb=" N ARG J 205 " --> pdb=" O VAL J 201 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ALA J 206 " --> pdb=" O GLN J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 243 removed outlier: 4.675A pdb=" N ARG J 232 " --> pdb=" O MET J 228 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ALA J 233 " --> pdb=" O ASN J 229 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU J 243 " --> pdb=" O MET J 239 " (cutoff:3.500A) Processing helix chain 'J' and resid 245 through 261 removed outlier: 3.939A pdb=" N GLN J 249 " --> pdb=" O PRO J 245 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR J 257 " --> pdb=" O LEU J 253 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA J 261 " --> pdb=" O THR J 257 " (cutoff:3.500A) Processing helix chain 'J' and resid 273 through 280 removed outlier: 3.530A pdb=" N ILE J 280 " --> pdb=" O LEU J 276 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 45 Processing helix chain 'K' and resid 45 through 53 removed outlier: 5.219A pdb=" N TRP K 51 " --> pdb=" O PRO K 47 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N MET K 52 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 135 removed outlier: 3.529A pdb=" N ASN K 135 " --> pdb=" O LEU K 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 157 Processing helix chain 'K' and resid 159 through 166 Processing helix chain 'K' and resid 166 through 183 removed outlier: 3.580A pdb=" N THR K 177 " --> pdb=" O ASN K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 208 removed outlier: 4.638A pdb=" N ARG K 205 " --> pdb=" O VAL K 201 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ALA K 206 " --> pdb=" O GLN K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 230 Processing helix chain 'K' and resid 230 through 243 removed outlier: 3.821A pdb=" N GLU K 243 " --> pdb=" O MET K 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 245 through 260 removed outlier: 4.561A pdb=" N GLN K 249 " --> pdb=" O PRO K 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 45 Processing helix chain 'L' and resid 45 through 53 removed outlier: 5.277A pdb=" N TRP L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N MET L 52 " --> pdb=" O ILE L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 135 Processing helix chain 'L' and resid 138 through 157 Processing helix chain 'L' and resid 159 through 166 Processing helix chain 'L' and resid 166 through 183 removed outlier: 3.631A pdb=" N THR L 177 " --> pdb=" O ASN L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 208 removed outlier: 4.672A pdb=" N ARG L 205 " --> pdb=" O VAL L 201 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ALA L 206 " --> pdb=" O GLN L 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 208 through 230 Processing helix chain 'L' and resid 230 through 244 removed outlier: 3.705A pdb=" N GLU L 243 " --> pdb=" O MET L 239 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER L 244 " --> pdb=" O VAL L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 245 through 261 removed outlier: 3.953A pdb=" N GLN L 249 " --> pdb=" O PRO L 245 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR L 257 " --> pdb=" O LEU L 253 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA L 261 " --> pdb=" O THR L 257 " (cutoff:3.500A) Processing helix chain 'L' and resid 273 through 280 removed outlier: 3.634A pdb=" N ILE L 279 " --> pdb=" O MET L 275 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE L 280 " --> pdb=" O LEU L 276 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 45 Processing helix chain 'M' and resid 45 through 50 Processing helix chain 'M' and resid 128 through 135 Processing helix chain 'M' and resid 138 through 157 Processing helix chain 'M' and resid 159 through 166 Processing helix chain 'M' and resid 166 through 183 removed outlier: 3.554A pdb=" N THR M 177 " --> pdb=" O ASN M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 208 removed outlier: 4.713A pdb=" N ARG M 205 " --> pdb=" O VAL M 201 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ALA M 206 " --> pdb=" O GLN M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 208 through 230 Processing helix chain 'M' and resid 230 through 243 removed outlier: 3.828A pdb=" N GLU M 243 " --> pdb=" O MET M 239 " (cutoff:3.500A) Processing helix chain 'M' and resid 245 through 260 removed outlier: 4.554A pdb=" N GLN M 249 " --> pdb=" O PRO M 245 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 45 Processing helix chain 'N' and resid 45 through 53 removed outlier: 5.255A pdb=" N TRP N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET N 52 " --> pdb=" O ILE N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 135 Processing helix chain 'N' and resid 138 through 156 Processing helix chain 'N' and resid 159 through 166 Processing helix chain 'N' and resid 166 through 183 removed outlier: 3.552A pdb=" N THR N 177 " --> pdb=" O ASN N 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 200 through 208 removed outlier: 4.654A pdb=" N ARG N 205 " --> pdb=" O VAL N 201 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ALA N 206 " --> pdb=" O GLN N 202 " (cutoff:3.500A) Processing helix chain 'N' and resid 208 through 243 removed outlier: 4.736A pdb=" N ARG N 232 " --> pdb=" O MET N 228 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ALA N 233 " --> pdb=" O ASN N 229 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU N 243 " --> pdb=" O MET N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 245 through 261 removed outlier: 3.962A pdb=" N GLN N 249 " --> pdb=" O PRO N 245 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR N 257 " --> pdb=" O LEU N 253 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA N 261 " --> pdb=" O THR N 257 " (cutoff:3.500A) Processing helix chain 'N' and resid 273 through 280 removed outlier: 3.530A pdb=" N ILE N 279 " --> pdb=" O MET N 275 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE N 280 " --> pdb=" O LEU N 276 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 45 Processing helix chain 'O' and resid 45 through 53 removed outlier: 4.923A pdb=" N TRP O 51 " --> pdb=" O PRO O 47 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N MET O 52 " --> pdb=" O ILE O 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 135 Processing helix chain 'O' and resid 138 through 157 Processing helix chain 'O' and resid 159 through 166 Processing helix chain 'O' and resid 166 through 183 removed outlier: 3.564A pdb=" N THR O 177 " --> pdb=" O ASN O 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 200 through 208 removed outlier: 4.640A pdb=" N ARG O 205 " --> pdb=" O VAL O 201 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ALA O 206 " --> pdb=" O GLN O 202 " (cutoff:3.500A) Processing helix chain 'O' and resid 208 through 230 Processing helix chain 'O' and resid 230 through 243 removed outlier: 3.791A pdb=" N GLU O 243 " --> pdb=" O MET O 239 " (cutoff:3.500A) Processing helix chain 'O' and resid 245 through 260 removed outlier: 4.518A pdb=" N GLN O 249 " --> pdb=" O PRO O 245 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 45 Processing helix chain 'P' and resid 45 through 53 removed outlier: 5.077A pdb=" N TRP P 51 " --> pdb=" O PRO P 47 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N MET P 52 " --> pdb=" O ILE P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 135 Processing helix chain 'P' and resid 138 through 157 Processing helix chain 'P' and resid 159 through 166 Processing helix chain 'P' and resid 166 through 183 removed outlier: 3.618A pdb=" N THR P 177 " --> pdb=" O ASN P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 200 through 208 removed outlier: 4.634A pdb=" N ARG P 205 " --> pdb=" O VAL P 201 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ALA P 206 " --> pdb=" O GLN P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 208 through 244 removed outlier: 4.669A pdb=" N ARG P 232 " --> pdb=" O MET P 228 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ALA P 233 " --> pdb=" O ASN P 229 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU P 243 " --> pdb=" O MET P 239 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER P 244 " --> pdb=" O VAL P 240 " (cutoff:3.500A) Processing helix chain 'P' and resid 245 through 262 removed outlier: 3.896A pdb=" N GLN P 249 " --> pdb=" O PRO P 245 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR P 257 " --> pdb=" O LEU P 253 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA P 261 " --> pdb=" O THR P 257 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU P 262 " --> pdb=" O THR P 258 " (cutoff:3.500A) Processing helix chain 'P' and resid 273 through 280 removed outlier: 3.722A pdb=" N ILE P 280 " --> pdb=" O LEU P 276 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 57 Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 102 Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 102 removed outlier: 6.432A pdb=" N SER A 117 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL A 197 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP A 119 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG A 125 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL A 189 " --> pdb=" O ARG A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 273 removed outlier: 6.244A pdb=" N THR B 266 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL C 268 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL B 268 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR D 266 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL E 268 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL D 268 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR F 266 " --> pdb=" O THR G 266 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL G 268 " --> pdb=" O THR F 266 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL F 268 " --> pdb=" O VAL G 268 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR H 266 " --> pdb=" O THR I 266 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL I 268 " --> pdb=" O THR H 266 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL H 268 " --> pdb=" O VAL I 268 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR J 266 " --> pdb=" O THR K 266 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL K 268 " --> pdb=" O THR J 266 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL J 268 " --> pdb=" O VAL K 268 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N THR L 266 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL M 268 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL L 268 " --> pdb=" O VAL M 268 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR N 266 " --> pdb=" O THR O 266 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL O 268 " --> pdb=" O THR N 266 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL N 268 " --> pdb=" O VAL O 268 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA8, first strand: chain 'B' and resid 99 through 102 Processing sheet with id=AA9, first strand: chain 'B' and resid 99 through 102 removed outlier: 6.432A pdb=" N SER B 117 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL B 197 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP B 119 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG B 125 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL B 189 " --> pdb=" O ARG B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 54 through 57 Processing sheet with id=AB2, first strand: chain 'C' and resid 70 through 71 Processing sheet with id=AB3, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=AB4, first strand: chain 'C' and resid 99 through 102 removed outlier: 7.026A pdb=" N THR C 115 " --> pdb=" O LYS C 198 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS C 198 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER C 117 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP C 196 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASP C 119 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE C 194 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL C 121 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL C 192 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR C 123 " --> pdb=" O GLU C 190 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 54 through 57 Processing sheet with id=AB6, first strand: chain 'D' and resid 70 through 71 Processing sheet with id=AB7, first strand: chain 'D' and resid 99 through 102 Processing sheet with id=AB8, first strand: chain 'D' and resid 99 through 102 removed outlier: 6.425A pdb=" N SER D 117 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL D 197 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASP D 119 " --> pdb=" O LYS D 195 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG D 191 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG D 125 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL D 189 " --> pdb=" O ARG D 125 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 54 through 57 Processing sheet with id=AC1, first strand: chain 'E' and resid 70 through 71 Processing sheet with id=AC2, first strand: chain 'E' and resid 99 through 102 Processing sheet with id=AC3, first strand: chain 'E' and resid 99 through 102 removed outlier: 6.442A pdb=" N SER E 117 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL E 197 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP E 119 " --> pdb=" O LYS E 195 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ARG E 125 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL E 189 " --> pdb=" O ARG E 125 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 54 through 57 Processing sheet with id=AC5, first strand: chain 'F' and resid 70 through 71 Processing sheet with id=AC6, first strand: chain 'F' and resid 99 through 102 Processing sheet with id=AC7, first strand: chain 'F' and resid 99 through 102 removed outlier: 6.423A pdb=" N SER F 117 " --> pdb=" O VAL F 197 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL F 197 " --> pdb=" O SER F 117 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASP F 119 " --> pdb=" O LYS F 195 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG F 191 " --> pdb=" O TYR F 123 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG F 125 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N VAL F 189 " --> pdb=" O ARG F 125 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 54 through 57 Processing sheet with id=AC9, first strand: chain 'G' and resid 70 through 71 Processing sheet with id=AD1, first strand: chain 'G' and resid 99 through 102 Processing sheet with id=AD2, first strand: chain 'G' and resid 99 through 102 removed outlier: 7.032A pdb=" N THR G 115 " --> pdb=" O LYS G 198 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LYS G 198 " --> pdb=" O THR G 115 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER G 117 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASP G 196 " --> pdb=" O SER G 117 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASP G 119 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE G 194 " --> pdb=" O ASP G 119 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL G 121 " --> pdb=" O VAL G 192 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL G 192 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR G 123 " --> pdb=" O GLU G 190 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 54 through 57 Processing sheet with id=AD4, first strand: chain 'H' and resid 70 through 71 Processing sheet with id=AD5, first strand: chain 'H' and resid 99 through 109 removed outlier: 4.253A pdb=" N GLY H 120 " --> pdb=" O ILE H 103 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL H 118 " --> pdb=" O PRO H 105 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU H 107 " --> pdb=" O ILE H 116 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE H 116 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR H 115 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LYS H 198 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER H 117 " --> pdb=" O ASP H 196 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASP H 196 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASP H 119 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE H 194 " --> pdb=" O ASP H 119 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL H 121 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL H 192 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TYR H 123 " --> pdb=" O GLU H 190 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 54 through 57 Processing sheet with id=AD7, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AD8, first strand: chain 'I' and resid 99 through 102 Processing sheet with id=AD9, first strand: chain 'I' and resid 99 through 102 removed outlier: 6.995A pdb=" N THR I 115 " --> pdb=" O LYS I 198 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS I 198 " --> pdb=" O THR I 115 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N SER I 117 " --> pdb=" O ASP I 196 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP I 196 " --> pdb=" O SER I 117 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASP I 119 " --> pdb=" O ILE I 194 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE I 194 " --> pdb=" O ASP I 119 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL I 121 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL I 192 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR I 123 " --> pdb=" O GLU I 190 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 54 through 57 Processing sheet with id=AE2, first strand: chain 'J' and resid 70 through 71 Processing sheet with id=AE3, first strand: chain 'J' and resid 99 through 102 Processing sheet with id=AE4, first strand: chain 'J' and resid 99 through 102 removed outlier: 6.444A pdb=" N SER J 117 " --> pdb=" O VAL J 197 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL J 197 " --> pdb=" O SER J 117 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP J 119 " --> pdb=" O LYS J 195 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG J 125 " --> pdb=" O VAL J 189 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL J 189 " --> pdb=" O ARG J 125 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 54 through 57 Processing sheet with id=AE6, first strand: chain 'K' and resid 70 through 71 Processing sheet with id=AE7, first strand: chain 'K' and resid 99 through 102 Processing sheet with id=AE8, first strand: chain 'K' and resid 99 through 102 removed outlier: 6.996A pdb=" N THR K 115 " --> pdb=" O LYS K 198 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS K 198 " --> pdb=" O THR K 115 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N SER K 117 " --> pdb=" O ASP K 196 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASP K 196 " --> pdb=" O SER K 117 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP K 119 " --> pdb=" O ILE K 194 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE K 194 " --> pdb=" O ASP K 119 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL K 121 " --> pdb=" O VAL K 192 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL K 192 " --> pdb=" O VAL K 121 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TYR K 123 " --> pdb=" O GLU K 190 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 54 through 57 Processing sheet with id=AF1, first strand: chain 'L' and resid 70 through 71 Processing sheet with id=AF2, first strand: chain 'L' and resid 99 through 109 removed outlier: 4.225A pdb=" N GLY L 120 " --> pdb=" O ILE L 103 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL L 118 " --> pdb=" O PRO L 105 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLU L 107 " --> pdb=" O ILE L 116 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE L 116 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER L 117 " --> pdb=" O VAL L 197 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL L 197 " --> pdb=" O SER L 117 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ASP L 119 " --> pdb=" O LYS L 195 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG L 191 " --> pdb=" O TYR L 123 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG L 125 " --> pdb=" O VAL L 189 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL L 189 " --> pdb=" O ARG L 125 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 54 through 57 Processing sheet with id=AF4, first strand: chain 'M' and resid 70 through 71 Processing sheet with id=AF5, first strand: chain 'M' and resid 99 through 102 Processing sheet with id=AF6, first strand: chain 'M' and resid 99 through 102 removed outlier: 7.042A pdb=" N THR M 115 " --> pdb=" O LYS M 198 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS M 198 " --> pdb=" O THR M 115 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N SER M 117 " --> pdb=" O ASP M 196 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP M 196 " --> pdb=" O SER M 117 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASP M 119 " --> pdb=" O ILE M 194 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE M 194 " --> pdb=" O ASP M 119 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL M 121 " --> pdb=" O VAL M 192 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL M 192 " --> pdb=" O VAL M 121 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TYR M 123 " --> pdb=" O GLU M 190 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 54 through 57 Processing sheet with id=AF8, first strand: chain 'N' and resid 70 through 71 Processing sheet with id=AF9, first strand: chain 'N' and resid 99 through 102 Processing sheet with id=AG1, first strand: chain 'N' and resid 99 through 102 removed outlier: 6.429A pdb=" N SER N 117 " --> pdb=" O VAL N 197 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL N 197 " --> pdb=" O SER N 117 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASP N 119 " --> pdb=" O LYS N 195 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARG N 125 " --> pdb=" O VAL N 189 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N VAL N 189 " --> pdb=" O ARG N 125 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 54 through 57 Processing sheet with id=AG3, first strand: chain 'O' and resid 70 through 71 Processing sheet with id=AG4, first strand: chain 'O' and resid 99 through 102 Processing sheet with id=AG5, first strand: chain 'O' and resid 99 through 102 removed outlier: 7.048A pdb=" N THR O 115 " --> pdb=" O LYS O 198 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS O 198 " --> pdb=" O THR O 115 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER O 117 " --> pdb=" O ASP O 196 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASP O 196 " --> pdb=" O SER O 117 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ASP O 119 " --> pdb=" O ILE O 194 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE O 194 " --> pdb=" O ASP O 119 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL O 121 " --> pdb=" O VAL O 192 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL O 192 " --> pdb=" O VAL O 121 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR O 123 " --> pdb=" O GLU O 190 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 54 through 57 Processing sheet with id=AG7, first strand: chain 'P' and resid 70 through 71 Processing sheet with id=AG8, first strand: chain 'P' and resid 99 through 109 removed outlier: 4.233A pdb=" N GLY P 120 " --> pdb=" O ILE P 103 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL P 118 " --> pdb=" O PRO P 105 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU P 107 " --> pdb=" O ILE P 116 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE P 116 " --> pdb=" O GLU P 107 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N SER P 117 " --> pdb=" O VAL P 197 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL P 197 " --> pdb=" O SER P 117 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASP P 119 " --> pdb=" O LYS P 195 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG P 191 " --> pdb=" O TYR P 123 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG P 125 " --> pdb=" O VAL P 189 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VAL P 189 " --> pdb=" O ARG P 125 " (cutoff:3.500A) 2021 hydrogen bonds defined for protein. 5841 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: 6.54 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10352 1.34 - 1.46: 5926 1.46 - 1.58: 16058 1.58 - 1.69: 0 1.69 - 1.81: 272 Bond restraints: 32608 Sorted by residual: bond pdb=" C PHE B 46 " pdb=" N PRO B 47 " ideal model delta sigma weight residual 1.335 1.357 -0.021 1.30e-02 5.92e+03 2.69e+00 bond pdb=" C PHE H 46 " pdb=" N PRO H 47 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.36e-02 5.41e+03 2.63e+00 bond pdb=" C PHE J 46 " pdb=" N PRO J 47 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.36e-02 5.41e+03 2.59e+00 bond pdb=" C PHE D 46 " pdb=" N PRO D 47 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.38e-02 5.25e+03 2.46e+00 bond pdb=" C PHE G 46 " pdb=" N PRO G 47 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.38e+00 ... (remaining 32603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 42727 1.40 - 2.80: 1304 2.80 - 4.20: 222 4.20 - 5.60: 49 5.60 - 7.00: 18 Bond angle restraints: 44320 Sorted by residual: angle pdb=" N ILE M 279 " pdb=" CA ILE M 279 " pdb=" C ILE M 279 " ideal model delta sigma weight residual 112.29 106.15 6.14 9.40e-01 1.13e+00 4.26e+01 angle pdb=" N ILE G 279 " pdb=" CA ILE G 279 " pdb=" C ILE G 279 " ideal model delta sigma weight residual 111.91 107.46 4.45 8.90e-01 1.26e+00 2.50e+01 angle pdb=" N ILE O 279 " pdb=" CA ILE O 279 " pdb=" C ILE O 279 " ideal model delta sigma weight residual 111.91 107.47 4.44 8.90e-01 1.26e+00 2.49e+01 angle pdb=" N ILE I 279 " pdb=" CA ILE I 279 " pdb=" C ILE I 279 " ideal model delta sigma weight residual 111.91 107.56 4.35 8.90e-01 1.26e+00 2.39e+01 angle pdb=" N ILE C 279 " pdb=" CA ILE C 279 " pdb=" C ILE C 279 " ideal model delta sigma weight residual 111.91 107.60 4.31 8.90e-01 1.26e+00 2.35e+01 ... (remaining 44315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 18271 17.73 - 35.45: 1656 35.45 - 53.18: 634 53.18 - 70.90: 153 70.90 - 88.63: 38 Dihedral angle restraints: 20752 sinusoidal: 8832 harmonic: 11920 Sorted by residual: dihedral pdb=" CA ASP H 89 " pdb=" C ASP H 89 " pdb=" N SER H 90 " pdb=" CA SER H 90 " ideal model delta harmonic sigma weight residual 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CB GLU P 168 " pdb=" CG GLU P 168 " pdb=" CD GLU P 168 " pdb=" OE1 GLU P 168 " ideal model delta sinusoidal sigma weight residual 0.00 88.63 -88.63 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU K 227 " pdb=" CG GLU K 227 " pdb=" CD GLU K 227 " pdb=" OE1 GLU K 227 " ideal model delta sinusoidal sigma weight residual 0.00 88.16 -88.16 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 20749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3021 0.032 - 0.063: 1563 0.063 - 0.095: 529 0.095 - 0.126: 287 0.126 - 0.158: 40 Chirality restraints: 5440 Sorted by residual: chirality pdb=" CB THR P 45 " pdb=" CA THR P 45 " pdb=" OG1 THR P 45 " pdb=" CG2 THR P 45 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA ILE C 273 " pdb=" N ILE C 273 " pdb=" C ILE C 273 " pdb=" CB ILE C 273 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" CA ILE M 279 " pdb=" N ILE M 279 " pdb=" C ILE M 279 " pdb=" CB ILE M 279 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 5437 not shown) Planarity restraints: 5488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU P 271 " 0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO P 272 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO P 272 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO P 272 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 271 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO H 272 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO H 272 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 272 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 271 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO B 272 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " 0.026 5.00e-02 4.00e+02 ... (remaining 5485 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 16815 3.00 - 3.48: 32409 3.48 - 3.95: 52883 3.95 - 4.43: 61857 4.43 - 4.90: 100577 Nonbonded interactions: 264541 Sorted by model distance: nonbonded pdb=" N ILE M 279 " pdb=" N ILE M 280 " model vdw 2.529 2.560 nonbonded pdb=" N ASP M 112 " pdb=" OD1 ASP M 112 " model vdw 2.544 3.120 nonbonded pdb=" N ASP A 112 " pdb=" OD1 ASP A 112 " model vdw 2.550 3.120 nonbonded pdb=" OD1 ASP O 274 " pdb=" OD2 ASP P 274 " model vdw 2.578 3.040 nonbonded pdb=" N ILE O 279 " pdb=" N ILE O 280 " model vdw 2.587 2.560 ... (remaining 264536 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 28.560 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9283 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32608 Z= 0.169 Angle : 0.628 6.995 44320 Z= 0.388 Chirality : 0.046 0.158 5440 Planarity : 0.005 0.049 5488 Dihedral : 16.506 88.625 12976 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.41 % Allowed : 24.13 % Favored : 73.46 % 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: 0.77 (0.12), residues: 4064 helix: 0.87 (0.11), residues: 2176 sheet: 1.27 (0.18), residues: 600 loop : -0.32 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 232 TYR 0.013 0.001 TYR E 252 PHE 0.011 0.001 PHE N 269 TRP 0.009 0.001 TRP H 51 HIS 0.003 0.002 HIS N 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (32608) covalent geometry : angle 0.62848 / 0.39 (44320) hydrogen bonds : bond 0.15173 / 10.22 ( 1969) hydrogen bonds : angle 6.19332 / 4.47 ( 5841) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 317 time to evaluate : 1.315 Fit side-chains REVERT: A 202 GLN cc_start: 0.9352 (OUTLIER) cc_final: 0.9032 (pm20) REVERT: C 48 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7675 (tp) REVERT: C 106 GLN cc_start: 0.9438 (OUTLIER) cc_final: 0.9218 (pt0) REVERT: D 46 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.7379 (m-10) REVERT: D 96 MET cc_start: 0.9459 (mmm) cc_final: 0.8960 (mmm) REVERT: E 207 MET cc_start: 0.9326 (mmm) cc_final: 0.9034 (mmt) REVERT: H 94 VAL cc_start: 0.9094 (OUTLIER) cc_final: 0.8876 (p) REVERT: H 96 MET cc_start: 0.9525 (mmm) cc_final: 0.9143 (mmm) REVERT: I 207 MET cc_start: 0.9370 (mmm) cc_final: 0.9155 (mmt) REVERT: J 46 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.6962 (m-80) REVERT: K 249 GLN cc_start: 0.8992 (mp10) cc_final: 0.8711 (mt0) REVERT: M 207 MET cc_start: 0.9369 (mmm) cc_final: 0.9150 (mmt) REVERT: O 191 ARG cc_start: 0.9374 (OUTLIER) cc_final: 0.9052 (ptp90) REVERT: P 96 MET cc_start: 0.9470 (mmm) cc_final: 0.8990 (mmm) outliers start: 83 outliers final: 49 residues processed: 378 average time/residue: 0.5758 time to fit residues: 263.8077 Evaluate side-chains 368 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 312 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 46 PHE Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 46 PHE Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 106 GLN Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 106 GLN Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain I residue 46 PHE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain J residue 46 PHE Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 280 ILE Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 256 LEU Chi-restraints excluded: chain M residue 46 PHE Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 106 GLN Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain N residue 46 PHE Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain O residue 46 PHE Chi-restraints excluded: chain O residue 191 ARG Chi-restraints excluded: chain P residue 46 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: [197, 388, 215, 20, 132, 261, 248, 207, 155, 244, 183] chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 73 GLN B 106 GLN F 106 GLN H 135 ASN H 264 ASN J 173 ASN K 106 GLN L 135 ASN O 73 GLN O 106 GLN P 135 ASN P 264 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.046940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.041099 restraints weight = 73179.227| |-----------------------------------------------------------------------------| r_work (start): 0.2525 rms_B_bonded: 1.07 r_work: 0.2438 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2361 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9302 moved from start: 0.0678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32608 Z= 0.178 Angle : 0.571 5.820 44320 Z= 0.318 Chirality : 0.046 0.145 5440 Planarity : 0.005 0.043 5488 Dihedral : 7.192 59.348 5503 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 5.03 % Allowed : 21.77 % Favored : 73.20 % 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: 1.12 (0.12), residues: 4064 helix: 1.25 (0.11), residues: 2168 sheet: 1.44 (0.18), residues: 600 loop : -0.35 (0.15), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 232 TYR 0.013 0.002 TYR E 252 PHE 0.016 0.002 PHE D 91 TRP 0.013 0.001 TRP L 51 HIS 0.004 0.002 HIS N 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (32608) covalent geometry : angle 0.57088 / 0.32 (44320) hydrogen bonds : bond 0.06314 / 4.19 ( 1969) hydrogen bonds : angle 4.74705 / 3.41 ( 5841) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 335 time to evaluate : 1.390 Fit side-chains REVERT: A 148 GLN cc_start: 0.9463 (OUTLIER) cc_final: 0.9262 (mt0) REVERT: B 46 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7551 (t80) REVERT: B 220 LYS cc_start: 0.9453 (OUTLIER) cc_final: 0.9030 (mttt) REVERT: C 106 GLN cc_start: 0.9448 (OUTLIER) cc_final: 0.9202 (pt0) REVERT: D 46 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.7289 (m-10) REVERT: D 96 MET cc_start: 0.9456 (mmm) cc_final: 0.9008 (mmm) REVERT: H 94 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8911 (p) REVERT: H 96 MET cc_start: 0.9524 (mmm) cc_final: 0.9165 (mmm) REVERT: I 34 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8639 (mt) REVERT: I 202 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8804 (pm20) REVERT: J 46 PHE cc_start: 0.7223 (OUTLIER) cc_final: 0.6823 (m-80) REVERT: L 46 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.7148 (m-80) REVERT: O 191 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.9146 (ptp90) REVERT: P 96 MET cc_start: 0.9472 (mmm) cc_final: 0.8916 (mmm) outliers start: 173 outliers final: 74 residues processed: 470 average time/residue: 0.5358 time to fit residues: 309.6208 Evaluate side-chains 406 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 321 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 46 PHE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 46 PHE Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 265 SER Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 46 PHE Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 202 GLN Chi-restraints excluded: chain I residue 241 ILE Chi-restraints excluded: chain J residue 46 PHE Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 265 SER Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain M residue 46 PHE Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 241 ILE Chi-restraints excluded: chain N residue 38 SER Chi-restraints excluded: chain N residue 46 PHE Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 265 SER Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 46 PHE Chi-restraints excluded: chain O residue 191 ARG Chi-restraints excluded: chain O residue 216 GLU Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 46 PHE Chi-restraints excluded: chain P residue 94 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: [386, 358, 308, 207, 363, 155, 197, 98, 238, 58, 314] chunk 386 optimal weight: 1.9990 chunk 358 optimal weight: 4.9990 chunk 308 optimal weight: 0.5980 chunk 207 optimal weight: 3.9990 chunk 363 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 197 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 238 optimal weight: 0.8980 chunk 58 optimal weight: 0.0370 chunk 314 optimal weight: 3.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 73 GLN B 106 GLN F 106 GLN G 106 GLN J 73 GLN J 173 ASN K 106 GLN O 73 GLN O 106 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.047829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.042021 restraints weight = 72837.496| |-----------------------------------------------------------------------------| r_work (start): 0.2551 rms_B_bonded: 1.07 r_work: 0.2465 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2388 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9287 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32608 Z= 0.143 Angle : 0.520 5.735 44320 Z= 0.288 Chirality : 0.045 0.229 5440 Planarity : 0.004 0.041 5488 Dihedral : 6.730 59.713 5473 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.77 % Allowed : 22.15 % Favored : 73.08 % 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: 1.21 (0.12), residues: 4064 helix: 1.40 (0.11), residues: 2168 sheet: 1.49 (0.18), residues: 616 loop : -0.52 (0.15), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 232 TYR 0.012 0.001 TYR E 252 PHE 0.013 0.001 PHE P 91 TRP 0.009 0.001 TRP L 51 HIS 0.003 0.001 HIS N 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (32608) covalent geometry : angle 0.52022 / 0.29 (44320) hydrogen bonds : bond 0.05626 / 3.74 ( 1969) hydrogen bonds : angle 4.51070 / 3.26 ( 5841) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 344 time to evaluate : 1.263 Fit side-chains REVERT: B 46 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7540 (t80) REVERT: C 48 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7751 (tp) REVERT: D 46 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.7200 (m-80) REVERT: D 96 MET cc_start: 0.9450 (mmm) cc_final: 0.9034 (mmm) REVERT: H 94 VAL cc_start: 0.9098 (OUTLIER) cc_final: 0.8871 (p) REVERT: H 96 MET cc_start: 0.9523 (mmm) cc_final: 0.9126 (mmm) REVERT: I 34 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8630 (mt) REVERT: L 46 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.7035 (m-80) REVERT: O 191 ARG cc_start: 0.9342 (OUTLIER) cc_final: 0.9140 (ptp90) REVERT: P 96 MET cc_start: 0.9452 (mmm) cc_final: 0.8912 (mmm) outliers start: 164 outliers final: 69 residues processed: 472 average time/residue: 0.5092 time to fit residues: 295.2892 Evaluate side-chains 398 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 322 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 46 PHE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 46 PHE Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 46 PHE Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 241 ILE Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain M residue 46 PHE Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 241 ILE Chi-restraints excluded: chain N residue 38 SER Chi-restraints excluded: chain N residue 46 PHE Chi-restraints excluded: chain N residue 112 ASP Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 46 PHE Chi-restraints excluded: chain O residue 191 ARG Chi-restraints excluded: chain O residue 241 ILE Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 46 PHE Chi-restraints excluded: chain P residue 94 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: [357, 362, 191, 330, 69, 42, 280, 333, 207, 256, 345] chunk 357 optimal weight: 2.9990 chunk 362 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 330 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 chunk 333 optimal weight: 0.0980 chunk 207 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 345 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN A 249 GLN B 73 GLN B 106 GLN C 106 GLN F 106 GLN G 106 GLN G 153 ASN I 106 GLN ** I 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 ASN K 106 GLN K 153 ASN M 106 GLN O 73 GLN O 106 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.045173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2476 r_free = 0.2476 target = 0.039364 restraints weight = 72897.283| |-----------------------------------------------------------------------------| r_work (start): 0.2475 rms_B_bonded: 1.04 r_work: 0.2388 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2311 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9327 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 32608 Z= 0.241 Angle : 0.624 5.559 44320 Z= 0.345 Chirality : 0.050 0.215 5440 Planarity : 0.005 0.043 5488 Dihedral : 6.859 59.394 5456 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 5.87 % Allowed : 20.90 % Favored : 73.23 % 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: 0.97 (0.12), residues: 4064 helix: 1.18 (0.11), residues: 2168 sheet: 1.54 (0.18), residues: 616 loop : -0.66 (0.14), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 232 TYR 0.015 0.002 TYR O 60 PHE 0.018 0.002 PHE D 91 TRP 0.009 0.001 TRP H 51 HIS 0.005 0.002 HIS N 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.24 (32608) covalent geometry : angle 0.62431 / 0.35 (44320) hydrogen bonds : bond 0.06672 / 4.43 ( 1969) hydrogen bonds : angle 4.56276 / 3.28 ( 5841) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 321 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: B 46 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7665 (t80) REVERT: B 158 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.8408 (mmtm) REVERT: B 220 LYS cc_start: 0.9483 (OUTLIER) cc_final: 0.9032 (mttt) REVERT: C 48 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7776 (tp) REVERT: D 96 MET cc_start: 0.9423 (mmm) cc_final: 0.9062 (mmm) REVERT: E 227 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8869 (tt0) REVERT: F 158 LYS cc_start: 0.9432 (OUTLIER) cc_final: 0.9193 (mmtp) REVERT: H 96 MET cc_start: 0.9497 (mmm) cc_final: 0.9174 (mmm) REVERT: I 34 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8650 (mt) REVERT: I 202 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8694 (pm20) REVERT: I 215 ARG cc_start: 0.9581 (OUTLIER) cc_final: 0.7610 (mpt90) REVERT: K 48 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8273 (tp) REVERT: P 96 MET cc_start: 0.9474 (mmm) cc_final: 0.8971 (mmm) outliers start: 202 outliers final: 99 residues processed: 485 average time/residue: 0.4979 time to fit residues: 300.0010 Evaluate side-chains 422 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 313 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 46 PHE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 46 PHE Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 265 SER Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 46 PHE Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 202 GLN Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 241 ILE Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 265 SER Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain M residue 38 SER Chi-restraints excluded: chain M residue 46 PHE Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 241 ILE Chi-restraints excluded: chain N residue 38 SER Chi-restraints excluded: chain N residue 46 PHE Chi-restraints excluded: chain N residue 112 ASP Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 241 ILE Chi-restraints excluded: chain N residue 265 SER Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 38 SER Chi-restraints excluded: chain O residue 46 PHE Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 216 GLU Chi-restraints excluded: chain O residue 241 ILE Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 46 PHE Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain P residue 241 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: [130, 12, 109, 86, 224, 157, 125, 94, 112, 60, 271] chunk 130 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 224 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 125 optimal weight: 0.0970 chunk 94 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 271 optimal weight: 3.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 106 GLN F 106 GLN G 106 GLN ** I 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 ASN K 106 GLN O 73 GLN O 106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.048208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.042439 restraints weight = 72510.229| |-----------------------------------------------------------------------------| r_work (start): 0.2564 rms_B_bonded: 1.07 r_work: 0.2479 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2403 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9276 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 32608 Z= 0.125 Angle : 0.504 5.593 44320 Z= 0.277 Chirality : 0.045 0.198 5440 Planarity : 0.004 0.043 5488 Dihedral : 6.497 59.517 5450 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.87 % Allowed : 23.20 % Favored : 72.94 % 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: 1.33 (0.12), residues: 4064 helix: 1.48 (0.11), residues: 2168 sheet: 1.70 (0.18), residues: 608 loop : -0.52 (0.15), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 232 TYR 0.012 0.001 TYR E 252 PHE 0.012 0.001 PHE P 91 TRP 0.007 0.001 TRP L 51 HIS 0.003 0.001 HIS L 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (32608) covalent geometry : angle 0.50436 / 0.28 (44320) hydrogen bonds : bond 0.05220 / 3.46 ( 1969) hydrogen bonds : angle 4.38829 / 3.18 ( 5841) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 333 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: A 202 GLN cc_start: 0.9251 (OUTLIER) cc_final: 0.8788 (pt0) REVERT: B 220 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.8998 (mttt) REVERT: D 96 MET cc_start: 0.9418 (mmm) cc_final: 0.8970 (mmm) REVERT: D 275 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7897 (mmt) REVERT: G 27 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9122 (mp) REVERT: H 96 MET cc_start: 0.9514 (mmm) cc_final: 0.9150 (mmm) REVERT: H 202 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8820 (pm20) REVERT: I 34 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8640 (mt) REVERT: I 215 ARG cc_start: 0.9525 (OUTLIER) cc_final: 0.7664 (mpt90) REVERT: P 96 MET cc_start: 0.9439 (mmm) cc_final: 0.8926 (mmm) outliers start: 133 outliers final: 57 residues processed: 439 average time/residue: 0.5384 time to fit residues: 290.2550 Evaluate side-chains 390 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 326 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 46 PHE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 46 PHE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 215 ARG Chi-restraints excluded: chain J residue 265 SER Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain M residue 38 SER Chi-restraints excluded: chain M residue 46 PHE Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 241 ILE Chi-restraints excluded: chain N residue 38 SER Chi-restraints excluded: chain N residue 46 PHE Chi-restraints excluded: chain N residue 112 ASP Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 265 SER Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 38 SER Chi-restraints excluded: chain O residue 216 GLU Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 46 PHE Chi-restraints excluded: chain P residue 94 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: [52, 305, 371, 5, 97, 151, 370, 292, 359, 273, 63] chunk 52 optimal weight: 0.9980 chunk 305 optimal weight: 4.9990 chunk 371 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 chunk 370 optimal weight: 0.8980 chunk 292 optimal weight: 2.9990 chunk 359 optimal weight: 2.9990 chunk 273 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 106 GLN F 106 GLN G 106 GLN I 249 GLN J 173 ASN K 106 GLN O 73 GLN O 106 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.048017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.042226 restraints weight = 72748.745| |-----------------------------------------------------------------------------| r_work (start): 0.2557 rms_B_bonded: 1.07 r_work: 0.2473 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2397 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9283 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32608 Z= 0.137 Angle : 0.512 6.323 44320 Z= 0.281 Chirality : 0.045 0.151 5440 Planarity : 0.004 0.041 5488 Dihedral : 6.315 59.955 5444 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.92 % Allowed : 23.46 % Favored : 72.62 % 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: 1.39 (0.12), residues: 4064 helix: 1.54 (0.11), residues: 2168 sheet: 1.73 (0.18), residues: 608 loop : -0.52 (0.14), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 232 TYR 0.012 0.001 TYR E 252 PHE 0.012 0.001 PHE D 91 TRP 0.007 0.001 TRP D 51 HIS 0.003 0.001 HIS L 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (32608) covalent geometry : angle 0.51168 / 0.28 (44320) hydrogen bonds : bond 0.05312 / 3.53 ( 1969) hydrogen bonds : angle 4.34360 / 3.14 ( 5841) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 333 time to evaluate : 1.306 Fit side-chains revert: symmetry clash REVERT: A 202 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8768 (pt0) REVERT: B 220 LYS cc_start: 0.9410 (OUTLIER) cc_final: 0.8997 (mttt) REVERT: D 96 MET cc_start: 0.9419 (mmm) cc_final: 0.8977 (mmm) REVERT: F 158 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.9165 (mmtp) REVERT: G 27 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9126 (mp) REVERT: H 96 MET cc_start: 0.9510 (mmm) cc_final: 0.9176 (mmm) REVERT: I 34 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8631 (mt) REVERT: I 215 ARG cc_start: 0.9509 (OUTLIER) cc_final: 0.7672 (mpt90) REVERT: M 148 GLN cc_start: 0.9311 (OUTLIER) cc_final: 0.9049 (mt0) REVERT: P 96 MET cc_start: 0.9442 (mmm) cc_final: 0.8964 (mmm) outliers start: 135 outliers final: 79 residues processed: 442 average time/residue: 0.5219 time to fit residues: 284.5918 Evaluate side-chains 412 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 326 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 46 PHE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 225 GLU Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 46 PHE Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 215 ARG Chi-restraints excluded: chain J residue 265 SER Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain M residue 38 SER Chi-restraints excluded: chain M residue 46 PHE Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 148 GLN Chi-restraints excluded: chain M residue 241 ILE Chi-restraints excluded: chain N residue 38 SER Chi-restraints excluded: chain N residue 46 PHE Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 241 ILE Chi-restraints excluded: chain N residue 265 SER Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 38 SER Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 241 ILE Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 46 PHE Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain P residue 225 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: [371, 245, 329, 100, 179, 172, 163, 139, 15, 115, 218] chunk 371 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 329 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 179 optimal weight: 0.0670 chunk 172 optimal weight: 0.7980 chunk 163 optimal weight: 0.6980 chunk 139 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 218 optimal weight: 4.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 106 GLN G 106 GLN I 106 GLN I 249 GLN J 173 ASN K 106 GLN O 73 GLN O 106 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.048871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.043125 restraints weight = 72939.466| |-----------------------------------------------------------------------------| r_work (start): 0.2582 rms_B_bonded: 1.06 r_work: 0.2499 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2425 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9267 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 32608 Z= 0.123 Angle : 0.495 6.309 44320 Z= 0.270 Chirality : 0.045 0.146 5440 Planarity : 0.004 0.043 5488 Dihedral : 6.211 59.444 5444 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.37 % Allowed : 23.92 % Favored : 72.70 % 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: 1.48 (0.12), residues: 4064 helix: 1.64 (0.11), residues: 2168 sheet: 1.62 (0.18), residues: 624 loop : -0.46 (0.15), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 232 TYR 0.012 0.001 TYR E 252 PHE 0.012 0.001 PHE J 91 TRP 0.008 0.001 TRP D 51 HIS 0.003 0.001 HIS L 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (32608) covalent geometry : angle 0.49540 / 0.27 (44320) hydrogen bonds : bond 0.05020 / 3.33 ( 1969) hydrogen bonds : angle 4.29440 / 3.11 ( 5841) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 332 time to evaluate : 1.097 Fit side-chains REVERT: C 215 ARG cc_start: 0.9450 (OUTLIER) cc_final: 0.9159 (mpt180) REVERT: D 96 MET cc_start: 0.9404 (mmm) cc_final: 0.8969 (mmm) REVERT: E 148 GLN cc_start: 0.9307 (OUTLIER) cc_final: 0.9039 (mt0) REVERT: G 27 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9130 (mp) REVERT: H 96 MET cc_start: 0.9503 (mmm) cc_final: 0.9183 (mmm) REVERT: I 34 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8628 (mt) REVERT: I 215 ARG cc_start: 0.9496 (OUTLIER) cc_final: 0.7810 (mpt90) REVERT: L 96 MET cc_start: 0.9409 (mmm) cc_final: 0.8951 (mmm) REVERT: M 148 GLN cc_start: 0.9282 (OUTLIER) cc_final: 0.9023 (mt0) REVERT: P 96 MET cc_start: 0.9425 (mmm) cc_final: 0.8952 (mmm) outliers start: 116 outliers final: 66 residues processed: 423 average time/residue: 0.5352 time to fit residues: 278.4357 Evaluate side-chains 390 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 318 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 215 ARG Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 46 PHE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain H residue 37 PHE Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 46 PHE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 255 THR Chi-restraints excluded: chain J residue 265 SER Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain M residue 38 SER Chi-restraints excluded: chain M residue 46 PHE Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 148 GLN Chi-restraints excluded: chain N residue 38 SER Chi-restraints excluded: chain N residue 46 PHE Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 265 SER Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 216 GLU Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 46 PHE Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain P residue 225 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: [207, 295, 289, 338, 300, 144, 246, 45, 8, 323, 324] chunk 207 optimal weight: 2.9990 chunk 295 optimal weight: 0.7980 chunk 289 optimal weight: 0.7980 chunk 338 optimal weight: 0.2980 chunk 300 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 246 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 323 optimal weight: 0.8980 chunk 324 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 GLN F 106 GLN G 106 GLN I 106 GLN I 249 GLN J 73 GLN J 173 ASN K 106 GLN O 73 GLN O 106 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.048907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.043111 restraints weight = 72947.726| |-----------------------------------------------------------------------------| r_work (start): 0.2581 rms_B_bonded: 1.07 r_work: 0.2498 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2423 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9267 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32608 Z= 0.127 Angle : 0.498 6.589 44320 Z= 0.272 Chirality : 0.045 0.150 5440 Planarity : 0.004 0.044 5488 Dihedral : 6.031 59.924 5435 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.55 % Allowed : 23.92 % Favored : 72.53 % 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: 1.55 (0.12), residues: 4064 helix: 1.70 (0.11), residues: 2176 sheet: 1.65 (0.18), residues: 624 loop : -0.45 (0.15), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 232 TYR 0.012 0.001 TYR E 252 PHE 0.012 0.001 PHE F 269 TRP 0.012 0.001 TRP D 51 HIS 0.003 0.001 HIS L 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (32608) covalent geometry : angle 0.49844 / 0.27 (44320) hydrogen bonds : bond 0.05063 / 3.36 ( 1969) hydrogen bonds : angle 4.28522 / 3.10 ( 5841) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 329 time to evaluate : 1.197 Fit side-chains REVERT: B 220 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.8981 (mttt) REVERT: C 215 ARG cc_start: 0.9436 (OUTLIER) cc_final: 0.9150 (mpt180) REVERT: D 96 MET cc_start: 0.9400 (mmm) cc_final: 0.8977 (mmm) REVERT: E 148 GLN cc_start: 0.9322 (OUTLIER) cc_final: 0.9061 (mt0) REVERT: H 96 MET cc_start: 0.9512 (mmm) cc_final: 0.9198 (mmm) REVERT: I 34 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8612 (mt) REVERT: I 215 ARG cc_start: 0.9491 (OUTLIER) cc_final: 0.7799 (mpt90) REVERT: L 96 MET cc_start: 0.9395 (mmm) cc_final: 0.8959 (mmm) REVERT: M 148 GLN cc_start: 0.9282 (OUTLIER) cc_final: 0.9028 (mt0) REVERT: P 96 MET cc_start: 0.9405 (mmm) cc_final: 0.8930 (mmm) outliers start: 122 outliers final: 73 residues processed: 427 average time/residue: 0.5340 time to fit residues: 280.4330 Evaluate side-chains 401 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 322 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 215 ARG Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 46 PHE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 263 LYS Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 46 PHE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 255 THR Chi-restraints excluded: chain J residue 265 SER Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain M residue 38 SER Chi-restraints excluded: chain M residue 46 PHE Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 148 GLN Chi-restraints excluded: chain M residue 241 ILE Chi-restraints excluded: chain N residue 38 SER Chi-restraints excluded: chain N residue 46 PHE Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 241 ILE Chi-restraints excluded: chain N residue 265 SER Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 38 SER Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 216 GLU Chi-restraints excluded: chain O residue 241 ILE Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 46 PHE Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain P residue 225 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: [312, 109, 148, 95, 112, 214, 31, 126, 249, 101, 238] chunk 312 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 148 optimal weight: 0.0040 chunk 95 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 214 optimal weight: 0.0030 chunk 31 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 249 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 238 optimal weight: 0.9980 overall best weight: 0.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 106 GLN G 106 GLN I 249 GLN J 73 GLN J 173 ASN K 106 GLN O 73 GLN O 106 GLN O 277 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.050304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.044550 restraints weight = 72452.091| |-----------------------------------------------------------------------------| r_work (start): 0.2623 rms_B_bonded: 1.07 r_work: 0.2541 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9242 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 32608 Z= 0.112 Angle : 0.481 7.375 44320 Z= 0.261 Chirality : 0.044 0.155 5440 Planarity : 0.004 0.046 5488 Dihedral : 5.907 59.914 5435 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.56 % Allowed : 24.91 % Favored : 72.53 % 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: 1.66 (0.13), residues: 4064 helix: 1.80 (0.11), residues: 2176 sheet: 1.67 (0.18), residues: 624 loop : -0.41 (0.15), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 232 TYR 0.012 0.001 TYR A 252 PHE 0.016 0.001 PHE F 269 TRP 0.014 0.001 TRP D 51 HIS 0.003 0.001 HIS L 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (32608) covalent geometry : angle 0.48084 / 0.26 (44320) hydrogen bonds : bond 0.04653 / 3.09 ( 1969) hydrogen bonds : angle 4.24390 / 3.08 ( 5841) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 340 time to evaluate : 1.508 Fit side-chains REVERT: C 215 ARG cc_start: 0.9368 (OUTLIER) cc_final: 0.9119 (mpt180) REVERT: D 96 MET cc_start: 0.9394 (mmm) cc_final: 0.8978 (mmm) REVERT: E 215 ARG cc_start: 0.9482 (OUTLIER) cc_final: 0.7945 (mpt90) REVERT: H 96 MET cc_start: 0.9504 (mmm) cc_final: 0.9132 (mmm) REVERT: I 34 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8588 (mt) REVERT: L 96 MET cc_start: 0.9384 (mmm) cc_final: 0.8965 (mmm) REVERT: M 148 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8988 (mt0) REVERT: M 249 GLN cc_start: 0.9347 (mp10) cc_final: 0.9122 (mp10) REVERT: P 96 MET cc_start: 0.9386 (mmm) cc_final: 0.8909 (mmm) outliers start: 88 outliers final: 51 residues processed: 410 average time/residue: 0.5408 time to fit residues: 272.4744 Evaluate side-chains 385 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 330 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 215 ARG Chi-restraints excluded: chain D residue 46 PHE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 215 ARG Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 46 PHE Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 255 THR Chi-restraints excluded: chain J residue 265 SER Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain M residue 38 SER Chi-restraints excluded: chain M residue 46 PHE Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 148 GLN Chi-restraints excluded: chain N residue 46 PHE Chi-restraints excluded: chain N residue 241 ILE Chi-restraints excluded: chain N residue 265 SER Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 46 PHE Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain P residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: [262, 393, 121, 250, 229, 313, 231, 307, 164, 293, 108] chunk 262 optimal weight: 4.9990 chunk 393 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 250 optimal weight: 0.6980 chunk 229 optimal weight: 1.9990 chunk 313 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 307 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 293 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN B 106 GLN C 73 GLN C 106 GLN F 106 GLN G 106 GLN I 106 GLN ** I 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 73 GLN J 173 ASN K 106 GLN M 106 GLN O 73 GLN O 106 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.046392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.040515 restraints weight = 73122.463| |-----------------------------------------------------------------------------| r_work (start): 0.2509 rms_B_bonded: 1.07 r_work: 0.2423 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2346 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9309 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 32608 Z= 0.201 Angle : 0.590 7.069 44320 Z= 0.322 Chirality : 0.048 0.269 5440 Planarity : 0.005 0.044 5488 Dihedral : 6.275 59.817 5431 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.62 % Allowed : 25.00 % Favored : 72.38 % 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: 1.34 (0.12), residues: 4064 helix: 1.52 (0.11), residues: 2168 sheet: 1.61 (0.18), residues: 624 loop : -0.54 (0.14), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 232 TYR 0.014 0.002 TYR C 60 PHE 0.015 0.002 PHE A 269 TRP 0.016 0.001 TRP D 51 HIS 0.004 0.002 HIS N 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (32608) covalent geometry : angle 0.59007 / 0.32 (44320) hydrogen bonds : bond 0.06103 / 4.05 ( 1969) hydrogen bonds : angle 4.40753 / 3.18 ( 5841) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 329 time to evaluate : 1.306 Fit side-chains REVERT: A 215 ARG cc_start: 0.9515 (OUTLIER) cc_final: 0.7938 (mpt90) REVERT: D 96 MET cc_start: 0.9410 (mmm) cc_final: 0.8993 (mmm) REVERT: H 96 MET cc_start: 0.9504 (mmm) cc_final: 0.9159 (mmm) REVERT: I 34 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8644 (mt) REVERT: M 249 GLN cc_start: 0.9379 (mp10) cc_final: 0.9153 (mp10) REVERT: P 96 MET cc_start: 0.9453 (mmm) cc_final: 0.8992 (mmm) outliers start: 90 outliers final: 60 residues processed: 401 average time/residue: 0.5313 time to fit residues: 262.1649 Evaluate side-chains 382 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 320 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 46 PHE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 263 LYS Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 46 PHE Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 255 THR Chi-restraints excluded: chain J residue 265 SER Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain M residue 38 SER Chi-restraints excluded: chain M residue 46 PHE Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain N residue 46 PHE Chi-restraints excluded: chain N residue 241 ILE Chi-restraints excluded: chain N residue 265 SER Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 38 SER Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 46 PHE Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain P residue 241 ILE Chi-restraints excluded: chain P residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: [367, 340, 263, 292, 71, 2, 97, 237, 157, 300, 123] chunk 367 optimal weight: 1.9990 chunk 340 optimal weight: 3.9990 chunk 263 optimal weight: 0.3980 chunk 292 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 237 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 300 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 GLN C 106 GLN F 106 GLN G 73 GLN G 106 GLN I 106 GLN J 73 GLN J 173 ASN K 106 GLN M 106 GLN M 277 GLN O 73 GLN O 106 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.048599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.042844 restraints weight = 72893.526| |-----------------------------------------------------------------------------| r_work (start): 0.2576 rms_B_bonded: 1.05 r_work: 0.2492 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2417 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9271 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32608 Z= 0.132 Angle : 0.514 6.721 44320 Z= 0.279 Chirality : 0.045 0.179 5440 Planarity : 0.004 0.048 5488 Dihedral : 6.060 59.668 5431 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.33 % Allowed : 25.35 % Favored : 72.33 % 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: 1.52 (0.12), residues: 4064 helix: 1.67 (0.11), residues: 2168 sheet: 1.66 (0.18), residues: 624 loop : -0.46 (0.15), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 232 TYR 0.013 0.001 TYR A 252 PHE 0.012 0.001 PHE P 269 TRP 0.018 0.001 TRP D 51 HIS 0.003 0.001 HIS L 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (32608) covalent geometry : angle 0.51373 / 0.28 (44320) hydrogen bonds : bond 0.05139 / 3.41 ( 1969) hydrogen bonds : angle 4.32129 / 3.13 ( 5841) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10818.53 seconds wall clock time: 184 minutes 30.68 seconds (11070.68 seconds total)