Starting phenix.real_space_refine on Thu Mar 5 15:24:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lb5_23263/03_2026/7lb5_23263.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lb5_23263/03_2026/7lb5_23263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lb5_23263/03_2026/7lb5_23263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lb5_23263/03_2026/7lb5_23263.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lb5_23263/03_2026/7lb5_23263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lb5_23263/03_2026/7lb5_23263.map" } resolution = 3.16 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= 0.008 sd= 0.120 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 156 5.16 5 C 14772 2.51 5 N 4236 2.21 5 O 4452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23616 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1968 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Residues with excluded nonbonded symmetry interactions: 192 residue: pdb=" N PRO A 29 " occ=0.75 ... (5 atoms not shown) pdb=" CD PRO A 29 " occ=0.49 residue: pdb=" N PHE A 30 " occ=0.75 ... (9 atoms not shown) pdb=" CZ PHE A 30 " occ=0.49 residue: pdb=" N ALA A 60 " occ=0.90 ... (3 atoms not shown) pdb=" CB ALA A 60 " occ=0.90 residue: pdb=" N CYS A 63 " occ=0.86 ... (4 atoms not shown) pdb=" SG CYS A 63 " occ=0.65 residue: pdb=" N VAL A 71 " occ=0.89 ... (5 atoms not shown) pdb=" CG2 VAL A 71 " occ=0.89 residue: pdb=" N ARG A 72 " occ=0.89 ... (9 atoms not shown) pdb=" NH2 ARG A 72 " occ=0.56 residue: pdb=" N GLY A 75 " occ=0.89 ... (2 atoms not shown) pdb=" O GLY A 75 " occ=0.89 residue: pdb=" N GLY A 76 " occ=0.91 ... (2 atoms not shown) pdb=" O GLY A 76 " occ=0.91 residue: pdb=" N VAL A 77 " occ=0.91 ... (5 atoms not shown) pdb=" CG2 VAL A 77 " occ=0.89 residue: pdb=" N SER A 94 " occ=0.81 ... (4 atoms not shown) pdb=" OG SER A 94 " occ=0.83 residue: pdb=" N ARG A 141 " occ=0.91 ... (9 atoms not shown) pdb=" NH2 ARG A 141 " occ=0.54 residue: pdb=" N MET A 164 " occ=0.92 ... (6 atoms not shown) pdb=" CE MET A 164 " occ=0.92 ... (remaining 180 not shown) Time building chain proxies: 2.53, per 1000 atoms: 0.11 Number of scatterers: 23616 At special positions: 0 Unit cell: (119.163, 126.753, 107.019, 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 156 16.00 O 4452 8.00 N 4236 7.00 C 14772 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: 2.11 Conformation dependent library (CDL) restraints added in 1.1 seconds 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5760 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 12 sheets defined 54.6% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 29 through 38 removed outlier: 3.538A pdb=" N LYS A 33 " --> pdb=" O PRO A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 105 through 115 removed outlier: 3.575A pdb=" N ALA A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 177 through 197 removed outlier: 3.642A pdb=" N ASN A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 201 through 210 Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 237 through 247 Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.808A pdb=" N VAL A 258 " --> pdb=" O GLY A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 removed outlier: 3.574A pdb=" N LYS A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'B' and resid 30 through 38 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'B' and resid 105 through 115 removed outlier: 3.574A pdb=" N ALA B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 177 through 197 removed outlier: 3.642A pdb=" N ASN B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 201 through 210 Processing helix chain 'B' and resid 212 through 223 Processing helix chain 'B' and resid 237 through 247 Processing helix chain 'B' and resid 255 through 259 removed outlier: 3.808A pdb=" N VAL B 258 " --> pdb=" O GLY B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 removed outlier: 3.574A pdb=" N LYS B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 288 Processing helix chain 'C' and resid 30 through 38 Processing helix chain 'C' and resid 50 through 61 Processing helix chain 'C' and resid 82 through 93 Processing helix chain 'C' and resid 105 through 115 removed outlier: 3.573A pdb=" N ALA C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 177 through 197 removed outlier: 3.641A pdb=" N ASN C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 200 No H-bonds generated for 'chain 'C' and resid 198 through 200' Processing helix chain 'C' and resid 201 through 210 Processing helix chain 'C' and resid 212 through 223 Processing helix chain 'C' and resid 237 through 247 Processing helix chain 'C' and resid 255 through 259 removed outlier: 3.807A pdb=" N VAL C 258 " --> pdb=" O GLY C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 277 removed outlier: 3.575A pdb=" N LYS C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 288 Processing helix chain 'D' and resid 30 through 38 Processing helix chain 'D' and resid 50 through 61 Processing helix chain 'D' and resid 82 through 93 Processing helix chain 'D' and resid 105 through 115 removed outlier: 3.574A pdb=" N ALA D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 161 Processing helix chain 'D' and resid 177 through 197 removed outlier: 3.641A pdb=" N ASN D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'D' and resid 201 through 210 Processing helix chain 'D' and resid 212 through 223 Processing helix chain 'D' and resid 237 through 247 Processing helix chain 'D' and resid 255 through 259 removed outlier: 3.808A pdb=" N VAL D 258 " --> pdb=" O GLY D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 277 removed outlier: 3.574A pdb=" N LYS D 267 " --> pdb=" O ASP D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 288 Processing helix chain 'E' and resid 30 through 38 Processing helix chain 'E' and resid 50 through 61 Processing helix chain 'E' and resid 82 through 93 Processing helix chain 'E' and resid 105 through 115 removed outlier: 3.574A pdb=" N ALA E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 161 Processing helix chain 'E' and resid 177 through 197 removed outlier: 3.642A pdb=" N ASN E 196 " --> pdb=" O ARG E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 200 No H-bonds generated for 'chain 'E' and resid 198 through 200' Processing helix chain 'E' and resid 201 through 210 Processing helix chain 'E' and resid 212 through 223 Processing helix chain 'E' and resid 237 through 247 Processing helix chain 'E' and resid 255 through 259 removed outlier: 3.808A pdb=" N VAL E 258 " --> pdb=" O GLY E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 277 removed outlier: 3.573A pdb=" N LYS E 267 " --> pdb=" O ASP E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 288 Processing helix chain 'F' and resid 30 through 38 Processing helix chain 'F' and resid 50 through 61 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'F' and resid 105 through 115 removed outlier: 3.575A pdb=" N ALA F 109 " --> pdb=" O HIS F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 161 Processing helix chain 'F' and resid 177 through 197 removed outlier: 3.642A pdb=" N ASN F 196 " --> pdb=" O ARG F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 200 No H-bonds generated for 'chain 'F' and resid 198 through 200' Processing helix chain 'F' and resid 201 through 210 Processing helix chain 'F' and resid 212 through 223 Processing helix chain 'F' and resid 237 through 247 Processing helix chain 'F' and resid 255 through 259 removed outlier: 3.808A pdb=" N VAL F 258 " --> pdb=" O GLY F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 277 removed outlier: 3.573A pdb=" N LYS F 267 " --> pdb=" O ASP F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 288 Processing helix chain 'G' and resid 30 through 38 Processing helix chain 'G' and resid 50 through 61 Processing helix chain 'G' and resid 82 through 93 Processing helix chain 'G' and resid 105 through 115 removed outlier: 3.573A pdb=" N ALA G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 161 Processing helix chain 'G' and resid 177 through 197 removed outlier: 3.641A pdb=" N ASN G 196 " --> pdb=" O ARG G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 200 No H-bonds generated for 'chain 'G' and resid 198 through 200' Processing helix chain 'G' and resid 201 through 210 Processing helix chain 'G' and resid 212 through 223 Processing helix chain 'G' and resid 237 through 247 Processing helix chain 'G' and resid 255 through 259 removed outlier: 3.808A pdb=" N VAL G 258 " --> pdb=" O GLY G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 277 removed outlier: 3.574A pdb=" N LYS G 267 " --> pdb=" O ASP G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 288 Processing helix chain 'H' and resid 30 through 38 Processing helix chain 'H' and resid 50 through 61 Processing helix chain 'H' and resid 82 through 93 Processing helix chain 'H' and resid 105 through 115 removed outlier: 3.574A pdb=" N ALA H 109 " --> pdb=" O HIS H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 161 Processing helix chain 'H' and resid 177 through 197 removed outlier: 3.641A pdb=" N ASN H 196 " --> pdb=" O ARG H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'H' and resid 201 through 210 Processing helix chain 'H' and resid 212 through 223 Processing helix chain 'H' and resid 237 through 247 Processing helix chain 'H' and resid 255 through 259 removed outlier: 3.808A pdb=" N VAL H 258 " --> pdb=" O GLY H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 277 removed outlier: 3.574A pdb=" N LYS H 267 " --> pdb=" O ASP H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 288 Processing helix chain 'I' and resid 30 through 38 Processing helix chain 'I' and resid 50 through 61 Processing helix chain 'I' and resid 82 through 93 Processing helix chain 'I' and resid 105 through 115 removed outlier: 3.574A pdb=" N ALA I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 161 Processing helix chain 'I' and resid 177 through 197 removed outlier: 3.642A pdb=" N ASN I 196 " --> pdb=" O ARG I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 200 No H-bonds generated for 'chain 'I' and resid 198 through 200' Processing helix chain 'I' and resid 201 through 210 Processing helix chain 'I' and resid 212 through 223 Processing helix chain 'I' and resid 237 through 247 Processing helix chain 'I' and resid 255 through 259 removed outlier: 3.808A pdb=" N VAL I 258 " --> pdb=" O GLY I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 263 through 277 removed outlier: 3.574A pdb=" N LYS I 267 " --> pdb=" O ASP I 263 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 288 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 50 through 61 Processing helix chain 'J' and resid 82 through 93 Processing helix chain 'J' and resid 105 through 115 removed outlier: 3.574A pdb=" N ALA J 109 " --> pdb=" O HIS J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 161 Processing helix chain 'J' and resid 177 through 197 removed outlier: 3.642A pdb=" N ASN J 196 " --> pdb=" O ARG J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 200 No H-bonds generated for 'chain 'J' and resid 198 through 200' Processing helix chain 'J' and resid 201 through 210 Processing helix chain 'J' and resid 212 through 223 Processing helix chain 'J' and resid 237 through 247 Processing helix chain 'J' and resid 255 through 259 removed outlier: 3.807A pdb=" N VAL J 258 " --> pdb=" O GLY J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 263 through 277 removed outlier: 3.575A pdb=" N LYS J 267 " --> pdb=" O ASP J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 288 Processing helix chain 'K' and resid 30 through 38 Processing helix chain 'K' and resid 50 through 61 Processing helix chain 'K' and resid 82 through 93 Processing helix chain 'K' and resid 105 through 115 removed outlier: 3.574A pdb=" N ALA K 109 " --> pdb=" O HIS K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 161 Processing helix chain 'K' and resid 177 through 197 removed outlier: 3.642A pdb=" N ASN K 196 " --> pdb=" O ARG K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 200 No H-bonds generated for 'chain 'K' and resid 198 through 200' Processing helix chain 'K' and resid 201 through 210 Processing helix chain 'K' and resid 212 through 223 Processing helix chain 'K' and resid 237 through 247 Processing helix chain 'K' and resid 255 through 259 removed outlier: 3.809A pdb=" N VAL K 258 " --> pdb=" O GLY K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 263 through 277 removed outlier: 3.574A pdb=" N LYS K 267 " --> pdb=" O ASP K 263 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 288 Processing helix chain 'L' and resid 30 through 38 Processing helix chain 'L' and resid 50 through 61 Processing helix chain 'L' and resid 82 through 93 Processing helix chain 'L' and resid 105 through 115 removed outlier: 3.573A pdb=" N ALA L 109 " --> pdb=" O HIS L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 161 Processing helix chain 'L' and resid 177 through 197 removed outlier: 3.642A pdb=" N ASN L 196 " --> pdb=" O ARG L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 200 No H-bonds generated for 'chain 'L' and resid 198 through 200' Processing helix chain 'L' and resid 201 through 210 Processing helix chain 'L' and resid 212 through 223 Processing helix chain 'L' and resid 237 through 247 Processing helix chain 'L' and resid 255 through 259 removed outlier: 3.807A pdb=" N VAL L 258 " --> pdb=" O GLY L 255 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 277 removed outlier: 3.574A pdb=" N LYS L 267 " --> pdb=" O ASP L 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 280 through 288 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 48 removed outlier: 6.583A pdb=" N ALA A 44 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE A 66 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL A 46 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 65 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ARG A 100 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL A 67 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ARG A 102 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A 97 " --> pdb=" O TYR A 119 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP A 121 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA A 99 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER A 123 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA A 101 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 120 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLY A 147 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLU A 122 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE A 144 " --> pdb=" O MET A 164 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG A 166 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS A 146 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN A 168 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS A 148 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 251 " --> pdb=" O GLN A 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 43 through 48 removed outlier: 6.583A pdb=" N ALA B 44 " --> pdb=" O SER B 64 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE B 66 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL B 46 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL B 65 " --> pdb=" O MET B 98 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ARG B 100 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL B 67 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ARG B 102 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B 97 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ASP B 121 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA B 99 " --> pdb=" O ASP B 121 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER B 123 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA B 101 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE B 120 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLY B 147 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N GLU B 122 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE B 144 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG B 166 " --> pdb=" O PHE B 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS B 146 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN B 168 " --> pdb=" O CYS B 146 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS B 148 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY B 251 " --> pdb=" O GLN B 229 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 48 removed outlier: 6.583A pdb=" N ALA C 44 " --> pdb=" O SER C 64 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE C 66 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL C 46 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL C 65 " --> pdb=" O MET C 98 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ARG C 100 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL C 67 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ARG C 102 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL C 97 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP C 121 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA C 99 " --> pdb=" O ASP C 121 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER C 123 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA C 101 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE C 120 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLY C 147 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLU C 122 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE C 144 " --> pdb=" O MET C 164 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG C 166 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS C 146 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN C 168 " --> pdb=" O CYS C 146 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS C 148 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY C 251 " --> pdb=" O GLN C 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 43 through 48 removed outlier: 6.584A pdb=" N ALA D 44 " --> pdb=" O SER D 64 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE D 66 " --> pdb=" O ALA D 44 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL D 46 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL D 65 " --> pdb=" O MET D 98 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ARG D 100 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL D 67 " --> pdb=" O ARG D 100 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ARG D 102 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL D 97 " --> pdb=" O TYR D 119 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP D 121 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA D 99 " --> pdb=" O ASP D 121 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER D 123 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA D 101 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE D 120 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLY D 147 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLU D 122 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE D 144 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG D 166 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS D 146 " --> pdb=" O ARG D 166 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN D 168 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS D 148 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY D 251 " --> pdb=" O GLN D 229 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 43 through 48 removed outlier: 6.583A pdb=" N ALA E 44 " --> pdb=" O SER E 64 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE E 66 " --> pdb=" O ALA E 44 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL E 46 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL E 65 " --> pdb=" O MET E 98 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ARG E 100 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL E 67 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 10.078A pdb=" N ARG E 102 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL E 97 " --> pdb=" O TYR E 119 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP E 121 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA E 99 " --> pdb=" O ASP E 121 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER E 123 " --> pdb=" O ALA E 99 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ALA E 101 " --> pdb=" O SER E 123 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE E 120 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLY E 147 " --> pdb=" O ILE E 120 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLU E 122 " --> pdb=" O GLY E 147 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE E 144 " --> pdb=" O MET E 164 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG E 166 " --> pdb=" O PHE E 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS E 146 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN E 168 " --> pdb=" O CYS E 146 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS E 148 " --> pdb=" O GLN E 168 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY E 251 " --> pdb=" O GLN E 229 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 43 through 48 removed outlier: 6.583A pdb=" N ALA F 44 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE F 66 " --> pdb=" O ALA F 44 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL F 46 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL F 65 " --> pdb=" O MET F 98 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ARG F 100 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL F 67 " --> pdb=" O ARG F 100 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ARG F 102 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL F 97 " --> pdb=" O TYR F 119 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP F 121 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA F 99 " --> pdb=" O ASP F 121 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER F 123 " --> pdb=" O ALA F 99 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA F 101 " --> pdb=" O SER F 123 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE F 120 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLY F 147 " --> pdb=" O ILE F 120 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLU F 122 " --> pdb=" O GLY F 147 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE F 144 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG F 166 " --> pdb=" O PHE F 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS F 146 " --> pdb=" O ARG F 166 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN F 168 " --> pdb=" O CYS F 146 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS F 148 " --> pdb=" O GLN F 168 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY F 251 " --> pdb=" O GLN F 229 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 43 through 48 removed outlier: 6.583A pdb=" N ALA G 44 " --> pdb=" O SER G 64 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE G 66 " --> pdb=" O ALA G 44 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL G 46 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL G 65 " --> pdb=" O MET G 98 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ARG G 100 " --> pdb=" O VAL G 65 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL G 67 " --> pdb=" O ARG G 100 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N ARG G 102 " --> pdb=" O VAL G 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL G 97 " --> pdb=" O TYR G 119 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP G 121 " --> pdb=" O VAL G 97 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA G 99 " --> pdb=" O ASP G 121 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER G 123 " --> pdb=" O ALA G 99 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA G 101 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE G 120 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLY G 147 " --> pdb=" O ILE G 120 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLU G 122 " --> pdb=" O GLY G 147 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE G 144 " --> pdb=" O MET G 164 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG G 166 " --> pdb=" O PHE G 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS G 146 " --> pdb=" O ARG G 166 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLN G 168 " --> pdb=" O CYS G 146 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS G 148 " --> pdb=" O GLN G 168 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY G 251 " --> pdb=" O GLN G 229 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 43 through 48 removed outlier: 6.583A pdb=" N ALA H 44 " --> pdb=" O SER H 64 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE H 66 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL H 46 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL H 65 " --> pdb=" O MET H 98 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ARG H 100 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL H 67 " --> pdb=" O ARG H 100 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ARG H 102 " --> pdb=" O VAL H 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL H 97 " --> pdb=" O TYR H 119 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP H 121 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA H 99 " --> pdb=" O ASP H 121 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER H 123 " --> pdb=" O ALA H 99 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA H 101 " --> pdb=" O SER H 123 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE H 120 " --> pdb=" O ILE H 145 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLY H 147 " --> pdb=" O ILE H 120 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N GLU H 122 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE H 144 " --> pdb=" O MET H 164 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG H 166 " --> pdb=" O PHE H 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS H 146 " --> pdb=" O ARG H 166 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN H 168 " --> pdb=" O CYS H 146 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS H 148 " --> pdb=" O GLN H 168 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY H 251 " --> pdb=" O GLN H 229 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 43 through 48 removed outlier: 6.584A pdb=" N ALA I 44 " --> pdb=" O SER I 64 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE I 66 " --> pdb=" O ALA I 44 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL I 46 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL I 65 " --> pdb=" O MET I 98 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ARG I 100 " --> pdb=" O VAL I 65 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL I 67 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ARG I 102 " --> pdb=" O VAL I 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL I 97 " --> pdb=" O TYR I 119 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ASP I 121 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA I 99 " --> pdb=" O ASP I 121 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER I 123 " --> pdb=" O ALA I 99 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ALA I 101 " --> pdb=" O SER I 123 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE I 120 " --> pdb=" O ILE I 145 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLY I 147 " --> pdb=" O ILE I 120 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLU I 122 " --> pdb=" O GLY I 147 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE I 144 " --> pdb=" O MET I 164 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ARG I 166 " --> pdb=" O PHE I 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS I 146 " --> pdb=" O ARG I 166 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLN I 168 " --> pdb=" O CYS I 146 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS I 148 " --> pdb=" O GLN I 168 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY I 251 " --> pdb=" O GLN I 229 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 43 through 48 removed outlier: 6.583A pdb=" N ALA J 44 " --> pdb=" O SER J 64 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE J 66 " --> pdb=" O ALA J 44 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL J 46 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL J 65 " --> pdb=" O MET J 98 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ARG J 100 " --> pdb=" O VAL J 65 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL J 67 " --> pdb=" O ARG J 100 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ARG J 102 " --> pdb=" O VAL J 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL J 97 " --> pdb=" O TYR J 119 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP J 121 " --> pdb=" O VAL J 97 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA J 99 " --> pdb=" O ASP J 121 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER J 123 " --> pdb=" O ALA J 99 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA J 101 " --> pdb=" O SER J 123 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE J 120 " --> pdb=" O ILE J 145 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLY J 147 " --> pdb=" O ILE J 120 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLU J 122 " --> pdb=" O GLY J 147 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE J 144 " --> pdb=" O MET J 164 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ARG J 166 " --> pdb=" O PHE J 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS J 146 " --> pdb=" O ARG J 166 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN J 168 " --> pdb=" O CYS J 146 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS J 148 " --> pdb=" O GLN J 168 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY J 251 " --> pdb=" O GLN J 229 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 43 through 48 removed outlier: 6.583A pdb=" N ALA K 44 " --> pdb=" O SER K 64 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE K 66 " --> pdb=" O ALA K 44 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL K 46 " --> pdb=" O ILE K 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL K 65 " --> pdb=" O MET K 98 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ARG K 100 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL K 67 " --> pdb=" O ARG K 100 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ARG K 102 " --> pdb=" O VAL K 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL K 97 " --> pdb=" O TYR K 119 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP K 121 " --> pdb=" O VAL K 97 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA K 99 " --> pdb=" O ASP K 121 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER K 123 " --> pdb=" O ALA K 99 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA K 101 " --> pdb=" O SER K 123 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE K 120 " --> pdb=" O ILE K 145 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLY K 147 " --> pdb=" O ILE K 120 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N GLU K 122 " --> pdb=" O GLY K 147 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE K 144 " --> pdb=" O MET K 164 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG K 166 " --> pdb=" O PHE K 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS K 146 " --> pdb=" O ARG K 166 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN K 168 " --> pdb=" O CYS K 146 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS K 148 " --> pdb=" O GLN K 168 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY K 251 " --> pdb=" O GLN K 229 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 43 through 48 removed outlier: 6.583A pdb=" N ALA L 44 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE L 66 " --> pdb=" O ALA L 44 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL L 46 " --> pdb=" O ILE L 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL L 65 " --> pdb=" O MET L 98 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ARG L 100 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL L 67 " --> pdb=" O ARG L 100 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ARG L 102 " --> pdb=" O VAL L 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL L 97 " --> pdb=" O TYR L 119 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ASP L 121 " --> pdb=" O VAL L 97 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA L 99 " --> pdb=" O ASP L 121 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER L 123 " --> pdb=" O ALA L 99 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA L 101 " --> pdb=" O SER L 123 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE L 120 " --> pdb=" O ILE L 145 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLY L 147 " --> pdb=" O ILE L 120 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N GLU L 122 " --> pdb=" O GLY L 147 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE L 144 " --> pdb=" O MET L 164 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG L 166 " --> pdb=" O PHE L 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS L 146 " --> pdb=" O ARG L 166 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN L 168 " --> pdb=" O CYS L 146 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS L 148 " --> pdb=" O GLN L 168 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY L 251 " --> pdb=" O GLN L 229 " (cutoff:3.500A) 1176 hydrogen bonds defined for protein. 3492 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 2.79 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: 8196 1.34 - 1.46: 3311 1.46 - 1.57: 12205 1.57 - 1.69: 0 1.69 - 1.80: 264 Bond restraints: 23976 Sorted by residual: bond pdb=" CB VAL I 181 " pdb=" CG1 VAL I 181 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.46e-01 bond pdb=" CB VAL C 181 " pdb=" CG1 VAL C 181 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.34e-01 bond pdb=" CB VAL J 181 " pdb=" CG1 VAL J 181 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.32e-01 bond pdb=" CB VAL H 181 " pdb=" CG1 VAL H 181 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.21e-01 bond pdb=" CB VAL F 181 " pdb=" CG1 VAL F 181 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 5.05e-01 ... (remaining 23971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 31011 1.12 - 2.23: 1186 2.23 - 3.35: 171 3.35 - 4.47: 32 4.47 - 5.58: 12 Bond angle restraints: 32412 Sorted by residual: angle pdb=" N THR E 172 " pdb=" CA THR E 172 " pdb=" C THR E 172 " ideal model delta sigma weight residual 113.38 110.56 2.82 1.17e+00 7.31e-01 5.83e+00 angle pdb=" N THR F 172 " pdb=" CA THR F 172 " pdb=" C THR F 172 " ideal model delta sigma weight residual 113.38 110.56 2.82 1.17e+00 7.31e-01 5.80e+00 angle pdb=" N THR C 172 " pdb=" CA THR C 172 " pdb=" C THR C 172 " ideal model delta sigma weight residual 113.38 110.57 2.81 1.17e+00 7.31e-01 5.77e+00 angle pdb=" N THR K 172 " pdb=" CA THR K 172 " pdb=" C THR K 172 " ideal model delta sigma weight residual 113.38 110.57 2.81 1.17e+00 7.31e-01 5.75e+00 angle pdb=" N THR I 172 " pdb=" CA THR I 172 " pdb=" C THR I 172 " ideal model delta sigma weight residual 113.38 110.58 2.80 1.17e+00 7.31e-01 5.73e+00 ... (remaining 32407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 13092 16.95 - 33.90: 1272 33.90 - 50.85: 300 50.85 - 67.80: 36 67.80 - 84.75: 24 Dihedral angle restraints: 14724 sinusoidal: 5820 harmonic: 8904 Sorted by residual: dihedral pdb=" CA GLU D 122 " pdb=" C GLU D 122 " pdb=" N SER D 123 " pdb=" CA SER D 123 " ideal model delta harmonic sigma weight residual -180.00 -163.99 -16.01 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA GLU H 122 " pdb=" C GLU H 122 " pdb=" N SER H 123 " pdb=" CA SER H 123 " ideal model delta harmonic sigma weight residual 180.00 -164.00 -16.00 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA GLU C 122 " pdb=" C GLU C 122 " pdb=" N SER C 123 " pdb=" CA SER C 123 " ideal model delta harmonic sigma weight residual -180.00 -164.01 -15.99 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 14721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2201 0.031 - 0.061: 1003 0.061 - 0.092: 342 0.092 - 0.122: 181 0.122 - 0.153: 29 Chirality restraints: 3756 Sorted by residual: chirality pdb=" CA ASP C 69 " pdb=" N ASP C 69 " pdb=" C ASP C 69 " pdb=" CB ASP C 69 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA ASP D 69 " pdb=" N ASP D 69 " pdb=" C ASP D 69 " pdb=" CB ASP D 69 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA ASP L 69 " pdb=" N ASP L 69 " pdb=" C ASP L 69 " pdb=" CB ASP L 69 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 3753 not shown) Planarity restraints: 4284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP H 82 " 0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO H 83 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO H 83 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 83 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 82 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO B 83 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 83 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 83 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP L 82 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.99e+00 pdb=" N PRO L 83 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO L 83 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO L 83 " 0.020 5.00e-02 4.00e+02 ... (remaining 4281 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 7465 2.84 - 3.35: 22202 3.35 - 3.87: 39180 3.87 - 4.38: 45440 4.38 - 4.90: 79182 Nonbonded interactions: 193469 Sorted by model distance: nonbonded pdb=" NH2 ARG A 224 " pdb=" OE1 GLN A 229 " model vdw 2.323 3.120 nonbonded pdb=" NH2 ARG D 224 " pdb=" OE1 GLN D 229 " model vdw 2.323 3.120 nonbonded pdb=" NH2 ARG J 224 " pdb=" OE1 GLN J 229 " model vdw 2.324 3.120 nonbonded pdb=" NH2 ARG H 224 " pdb=" OE1 GLN H 229 " model vdw 2.324 3.120 nonbonded pdb=" NH2 ARG E 224 " pdb=" OE1 GLN E 229 " model vdw 2.324 3.120 ... (remaining 193464 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=0.99 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: 6.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.440 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 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 0.024 23976 Z= 0.150 Angle : 0.515 5.585 32412 Z= 0.317 Chirality : 0.043 0.153 3756 Planarity : 0.004 0.035 4284 Dihedral : 14.285 84.754 8964 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.93 % Allowed : 1.87 % Favored : 97.20 % 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: -1.95 (0.13), residues: 3096 helix: -0.66 (0.11), residues: 1560 sheet: -0.95 (0.20), residues: 588 loop : -2.35 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 100 TYR 0.007 0.001 TYR C 213 PHE 0.008 0.001 PHE L 106 HIS 0.002 0.001 HIS L 105 Details of bonding type rmsd covalent geometry : bond 0.00338 (23976) covalent geometry : angle 0.51511 (32412) hydrogen bonds : bond 0.14409 ( 1176) hydrogen bonds : angle 4.62247 ( 3492) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 291 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.8255 (ttp) cc_final: 0.7989 (ttp) REVERT: D 80 MET cc_start: 0.8282 (ttp) cc_final: 0.8048 (ttp) REVERT: F 80 MET cc_start: 0.8207 (ttp) cc_final: 0.7965 (ttp) REVERT: H 80 MET cc_start: 0.8238 (ttp) cc_final: 0.8013 (ttp) REVERT: K 80 MET cc_start: 0.8196 (ttp) cc_final: 0.7990 (ttp) outliers start: 24 outliers final: 0 residues processed: 303 average time/residue: 0.1448 time to fit residues: 70.2724 Evaluate side-chains 232 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.0870 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN B 52 ASN C 52 ASN D 52 ASN E 38 GLN E 168 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 276 GLN F 52 ASN H 52 ASN I 52 ASN J 52 ASN J 168 GLN K 52 ASN L 52 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.074558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.060346 restraints weight = 58217.132| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 4.21 r_work: 0.2694 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 23976 Z= 0.106 Angle : 0.489 5.326 32412 Z= 0.258 Chirality : 0.043 0.140 3756 Planarity : 0.004 0.030 4284 Dihedral : 3.877 13.539 3360 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.39 % Allowed : 9.46 % Favored : 90.15 % 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: 0.04 (0.15), residues: 3096 helix: 1.24 (0.12), residues: 1584 sheet: -0.45 (0.22), residues: 588 loop : -1.74 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 149 TYR 0.015 0.002 TYR B 278 PHE 0.008 0.001 PHE J 205 HIS 0.002 0.000 HIS J 133 Details of bonding type rmsd covalent geometry : bond 0.00237 (23976) covalent geometry : angle 0.48924 (32412) hydrogen bonds : bond 0.03025 ( 1176) hydrogen bonds : angle 3.57354 ( 3492) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 251 time to evaluate : 0.743 Fit side-chains REVERT: B 229 GLN cc_start: 0.9127 (mt0) cc_final: 0.8903 (mp10) REVERT: B 279 ASN cc_start: 0.9447 (m110) cc_final: 0.9197 (m-40) REVERT: C 197 MET cc_start: 0.8754 (ttp) cc_final: 0.8329 (ttp) REVERT: D 279 ASN cc_start: 0.9438 (m110) cc_final: 0.9170 (m-40) REVERT: G 198 ASP cc_start: 0.8250 (t0) cc_final: 0.8043 (t0) REVERT: G 279 ASN cc_start: 0.9487 (m110) cc_final: 0.9263 (m-40) REVERT: H 198 ASP cc_start: 0.8140 (t0) cc_final: 0.7856 (t0) REVERT: J 279 ASN cc_start: 0.9474 (m110) cc_final: 0.9272 (m-40) REVERT: K 197 MET cc_start: 0.8756 (ttp) cc_final: 0.8383 (ttp) REVERT: K 198 ASP cc_start: 0.8432 (t0) cc_final: 0.7908 (t0) REVERT: L 222 MET cc_start: 0.9155 (ttm) cc_final: 0.8949 (mtm) REVERT: L 229 GLN cc_start: 0.9154 (mt0) cc_final: 0.8809 (mp10) outliers start: 10 outliers final: 7 residues processed: 251 average time/residue: 0.1212 time to fit residues: 52.4878 Evaluate side-chains 247 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 240 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain K residue 165 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 250 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 211 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 191 optimal weight: 0.4980 chunk 239 optimal weight: 0.9980 chunk 235 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN C 139 ASN I 38 GLN I 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.069002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.055981 restraints weight = 60699.642| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 4.04 r_work: 0.2648 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 23976 Z= 0.100 Angle : 0.472 5.340 32412 Z= 0.246 Chirality : 0.043 0.138 3756 Planarity : 0.003 0.026 4284 Dihedral : 3.677 15.087 3360 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.83 % Allowed : 8.57 % Favored : 89.60 % 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: 0.90 (0.15), residues: 3096 helix: 2.07 (0.13), residues: 1584 sheet: -0.26 (0.21), residues: 600 loop : -1.46 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 149 TYR 0.012 0.002 TYR L 278 PHE 0.007 0.001 PHE A 106 HIS 0.001 0.000 HIS E 133 Details of bonding type rmsd covalent geometry : bond 0.00231 (23976) covalent geometry : angle 0.47184 (32412) hydrogen bonds : bond 0.02738 ( 1176) hydrogen bonds : angle 3.47927 ( 3492) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 239 time to evaluate : 0.853 Fit side-chains REVERT: A 222 MET cc_start: 0.9200 (mtm) cc_final: 0.8958 (mtm) REVERT: B 229 GLN cc_start: 0.9037 (mt0) cc_final: 0.8760 (mp10) REVERT: B 279 ASN cc_start: 0.9489 (m110) cc_final: 0.9216 (m-40) REVERT: C 38 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8384 (tt0) REVERT: D 279 ASN cc_start: 0.9479 (m110) cc_final: 0.9200 (m-40) REVERT: E 197 MET cc_start: 0.8787 (ttt) cc_final: 0.8585 (ttp) REVERT: G 38 GLN cc_start: 0.8828 (pt0) cc_final: 0.8579 (tt0) REVERT: G 198 ASP cc_start: 0.8285 (t0) cc_final: 0.7979 (t0) REVERT: G 279 ASN cc_start: 0.9512 (m110) cc_final: 0.9255 (m-40) REVERT: H 38 GLN cc_start: 0.8837 (pt0) cc_final: 0.8555 (tt0) REVERT: H 197 MET cc_start: 0.8760 (ttp) cc_final: 0.8401 (ttp) REVERT: H 198 ASP cc_start: 0.8496 (t0) cc_final: 0.7938 (t0) REVERT: I 222 MET cc_start: 0.9235 (ttm) cc_final: 0.8970 (mtm) REVERT: I 244 MET cc_start: 0.9280 (mmp) cc_final: 0.9078 (mmp) REVERT: I 279 ASN cc_start: 0.9521 (m-40) cc_final: 0.9122 (m110) REVERT: J 38 GLN cc_start: 0.8867 (pt0) cc_final: 0.8633 (tt0) REVERT: J 222 MET cc_start: 0.9325 (tpp) cc_final: 0.8885 (mtp) REVERT: J 279 ASN cc_start: 0.9514 (m110) cc_final: 0.9290 (m-40) REVERT: K 38 GLN cc_start: 0.8845 (pt0) cc_final: 0.8581 (tt0) REVERT: K 198 ASP cc_start: 0.8472 (t0) cc_final: 0.7836 (t0) REVERT: L 198 ASP cc_start: 0.8213 (t0) cc_final: 0.7959 (t0) REVERT: L 222 MET cc_start: 0.9243 (ttm) cc_final: 0.9034 (mtm) outliers start: 47 outliers final: 44 residues processed: 264 average time/residue: 0.1220 time to fit residues: 55.2194 Evaluate side-chains 279 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 234 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 165 ILE Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 45 optimal weight: 0.9980 chunk 240 optimal weight: 7.9990 chunk 307 optimal weight: 1.9990 chunk 234 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 306 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 139 ASN B 139 ASN D 139 ASN E 139 ASN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 ASN G 139 ASN H 133 HIS H 139 ASN I 139 ASN J 139 ASN K 139 ASN L 139 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.063811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.050974 restraints weight = 62167.137| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 4.00 r_work: 0.2541 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2522 r_free = 0.2522 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 23976 Z= 0.251 Angle : 0.561 5.777 32412 Z= 0.292 Chirality : 0.046 0.145 3756 Planarity : 0.004 0.031 4284 Dihedral : 3.949 15.168 3360 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.14 % Allowed : 8.96 % Favored : 88.90 % 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: 1.22 (0.16), residues: 3096 helix: 2.38 (0.13), residues: 1584 sheet: -0.01 (0.22), residues: 588 loop : -1.51 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 74 TYR 0.010 0.002 TYR I 119 PHE 0.009 0.001 PHE E 259 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00578 (23976) covalent geometry : angle 0.56058 (32412) hydrogen bonds : bond 0.03615 ( 1176) hydrogen bonds : angle 3.81611 ( 3492) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 227 time to evaluate : 0.885 Fit side-chains REVERT: B 279 ASN cc_start: 0.9498 (m110) cc_final: 0.9216 (m-40) REVERT: D 279 ASN cc_start: 0.9495 (m110) cc_final: 0.9212 (m-40) REVERT: G 38 GLN cc_start: 0.8829 (pt0) cc_final: 0.8581 (tt0) REVERT: G 198 ASP cc_start: 0.8427 (t0) cc_final: 0.8107 (t0) REVERT: G 279 ASN cc_start: 0.9531 (m110) cc_final: 0.9250 (m-40) REVERT: H 198 ASP cc_start: 0.8578 (t0) cc_final: 0.8198 (t0) REVERT: H 221 GLN cc_start: 0.9518 (tm-30) cc_final: 0.9267 (tm-30) REVERT: H 222 MET cc_start: 0.9338 (mtp) cc_final: 0.9096 (mtp) REVERT: I 229 GLN cc_start: 0.9024 (mt0) cc_final: 0.8723 (mp10) REVERT: J 279 ASN cc_start: 0.9558 (m110) cc_final: 0.9341 (m110) REVERT: K 198 ASP cc_start: 0.8278 (t0) cc_final: 0.8006 (t0) REVERT: L 198 ASP cc_start: 0.8351 (t0) cc_final: 0.8075 (t0) REVERT: L 229 GLN cc_start: 0.9037 (mt0) cc_final: 0.8759 (mp10) outliers start: 55 outliers final: 42 residues processed: 262 average time/residue: 0.1209 time to fit residues: 53.7476 Evaluate side-chains 264 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 165 ILE Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 42 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 127 optimal weight: 0.0270 chunk 276 optimal weight: 4.9990 chunk 214 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.064469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.051653 restraints weight = 61376.069| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 3.99 r_work: 0.2531 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23976 Z= 0.178 Angle : 0.510 5.914 32412 Z= 0.265 Chirality : 0.044 0.138 3756 Planarity : 0.004 0.033 4284 Dihedral : 3.821 14.937 3360 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.38 % Allowed : 9.70 % Favored : 87.93 % 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: 1.51 (0.16), residues: 3096 helix: 2.63 (0.13), residues: 1584 sheet: 0.07 (0.22), residues: 588 loop : -1.35 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 74 TYR 0.012 0.002 TYR A 278 PHE 0.007 0.001 PHE K 253 HIS 0.002 0.000 HIS H 105 Details of bonding type rmsd covalent geometry : bond 0.00415 (23976) covalent geometry : angle 0.51003 (32412) hydrogen bonds : bond 0.03103 ( 1176) hydrogen bonds : angle 3.61953 ( 3492) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 229 time to evaluate : 0.805 Fit side-chains REVERT: B 279 ASN cc_start: 0.9487 (m110) cc_final: 0.9191 (m-40) REVERT: D 279 ASN cc_start: 0.9468 (m110) cc_final: 0.9156 (m-40) REVERT: E 229 GLN cc_start: 0.8920 (mt0) cc_final: 0.8697 (mp10) REVERT: E 269 ARG cc_start: 0.8579 (tpt-90) cc_final: 0.8077 (tpp80) REVERT: G 38 GLN cc_start: 0.8842 (pt0) cc_final: 0.8606 (tt0) REVERT: G 198 ASP cc_start: 0.8400 (t0) cc_final: 0.8115 (t0) REVERT: G 279 ASN cc_start: 0.9525 (m110) cc_final: 0.9219 (m-40) REVERT: H 198 ASP cc_start: 0.8358 (t0) cc_final: 0.8108 (t0) REVERT: H 221 GLN cc_start: 0.9527 (tm-30) cc_final: 0.9267 (tm-30) REVERT: I 229 GLN cc_start: 0.9015 (mt0) cc_final: 0.8717 (mp10) REVERT: K 198 ASP cc_start: 0.8231 (t0) cc_final: 0.8004 (t0) REVERT: L 198 ASP cc_start: 0.8330 (t0) cc_final: 0.8037 (t0) REVERT: L 229 GLN cc_start: 0.9047 (mt0) cc_final: 0.8732 (mp10) outliers start: 61 outliers final: 43 residues processed: 270 average time/residue: 0.1195 time to fit residues: 55.4310 Evaluate side-chains 263 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 220 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 165 ILE Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 118 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 220 optimal weight: 1.9990 chunk 293 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 302 optimal weight: 5.9990 chunk 257 optimal weight: 0.0040 chunk 84 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.065288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.052558 restraints weight = 60962.209| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.98 r_work: 0.2587 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2566 r_free = 0.2566 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2566 r_free = 0.2566 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23976 Z= 0.127 Angle : 0.484 6.387 32412 Z= 0.250 Chirality : 0.043 0.135 3756 Planarity : 0.004 0.029 4284 Dihedral : 3.721 15.172 3360 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.79 % Allowed : 10.90 % Favored : 87.31 % 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: 1.81 (0.16), residues: 3096 helix: 2.77 (0.13), residues: 1584 sheet: 0.27 (0.22), residues: 576 loop : -1.02 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 74 TYR 0.013 0.002 TYR A 278 PHE 0.008 0.001 PHE G 205 HIS 0.001 0.000 HIS H 105 Details of bonding type rmsd covalent geometry : bond 0.00297 (23976) covalent geometry : angle 0.48382 (32412) hydrogen bonds : bond 0.02857 ( 1176) hydrogen bonds : angle 3.52574 ( 3492) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 232 time to evaluate : 0.817 Fit side-chains REVERT: D 279 ASN cc_start: 0.9454 (m110) cc_final: 0.9131 (m-40) REVERT: E 229 GLN cc_start: 0.8915 (mt0) cc_final: 0.8380 (mt0) REVERT: E 269 ARG cc_start: 0.8597 (tpt-90) cc_final: 0.8119 (tpp80) REVERT: G 198 ASP cc_start: 0.8627 (t0) cc_final: 0.8087 (t0) REVERT: H 198 ASP cc_start: 0.8317 (t0) cc_final: 0.8083 (t0) REVERT: H 221 GLN cc_start: 0.9546 (tm-30) cc_final: 0.9278 (tm-30) REVERT: I 279 ASN cc_start: 0.9495 (m110) cc_final: 0.9137 (m110) REVERT: J 279 ASN cc_start: 0.9503 (m110) cc_final: 0.9294 (m-40) REVERT: K 198 ASP cc_start: 0.8223 (t0) cc_final: 0.8007 (t0) REVERT: L 198 ASP cc_start: 0.8325 (t0) cc_final: 0.7993 (t0) REVERT: L 222 MET cc_start: 0.9254 (ttm) cc_final: 0.9042 (mtm) outliers start: 46 outliers final: 42 residues processed: 257 average time/residue: 0.1325 time to fit residues: 58.4860 Evaluate side-chains 270 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 228 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 165 ILE Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 301 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 53 optimal weight: 0.0470 chunk 80 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 chunk 284 optimal weight: 6.9990 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.065705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.052883 restraints weight = 60885.614| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 4.01 r_work: 0.2596 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23976 Z= 0.117 Angle : 0.478 6.983 32412 Z= 0.246 Chirality : 0.043 0.134 3756 Planarity : 0.003 0.029 4284 Dihedral : 3.632 15.277 3360 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.79 % Allowed : 11.41 % Favored : 86.80 % 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: 1.97 (0.16), residues: 3096 helix: 2.85 (0.13), residues: 1584 sheet: 0.31 (0.22), residues: 576 loop : -0.83 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 72 TYR 0.012 0.002 TYR A 278 PHE 0.006 0.001 PHE F 106 HIS 0.001 0.000 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00275 (23976) covalent geometry : angle 0.47764 (32412) hydrogen bonds : bond 0.02722 ( 1176) hydrogen bonds : angle 3.47442 ( 3492) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 0.904 Fit side-chains REVERT: B 222 MET cc_start: 0.9355 (tpp) cc_final: 0.8934 (mtt) REVERT: D 279 ASN cc_start: 0.9440 (m110) cc_final: 0.9121 (m-40) REVERT: E 229 GLN cc_start: 0.8938 (mt0) cc_final: 0.8438 (mt0) REVERT: E 269 ARG cc_start: 0.8597 (tpt-90) cc_final: 0.8081 (tpp80) REVERT: G 198 ASP cc_start: 0.8275 (t0) cc_final: 0.8009 (t0) REVERT: G 222 MET cc_start: 0.9367 (tpp) cc_final: 0.8930 (mtt) REVERT: H 198 ASP cc_start: 0.8305 (t0) cc_final: 0.8002 (t0) REVERT: H 221 GLN cc_start: 0.9552 (tm-30) cc_final: 0.9279 (tm-30) REVERT: I 222 MET cc_start: 0.9262 (ttm) cc_final: 0.8987 (mtm) REVERT: I 279 ASN cc_start: 0.9476 (m110) cc_final: 0.9111 (m110) REVERT: J 279 ASN cc_start: 0.9502 (m110) cc_final: 0.9280 (m-40) REVERT: K 198 ASP cc_start: 0.8224 (t0) cc_final: 0.7941 (t0) REVERT: L 198 ASP cc_start: 0.8315 (t0) cc_final: 0.7951 (t0) REVERT: L 222 MET cc_start: 0.9257 (ttm) cc_final: 0.9045 (mtm) outliers start: 46 outliers final: 42 residues processed: 256 average time/residue: 0.1198 time to fit residues: 52.5944 Evaluate side-chains 264 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 165 ILE Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 192 optimal weight: 0.0970 chunk 214 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 145 optimal weight: 0.6980 chunk 195 optimal weight: 0.9980 chunk 247 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 134 optimal weight: 0.0170 chunk 138 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.066981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.054379 restraints weight = 59849.207| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 3.99 r_work: 0.2609 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23976 Z= 0.087 Angle : 0.471 7.412 32412 Z= 0.242 Chirality : 0.042 0.131 3756 Planarity : 0.003 0.027 4284 Dihedral : 3.523 14.474 3360 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.67 % Allowed : 11.84 % Favored : 86.49 % 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: 2.00 (0.16), residues: 3096 helix: 2.84 (0.13), residues: 1596 sheet: 0.09 (0.22), residues: 600 loop : -0.62 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 72 TYR 0.012 0.001 TYR L 278 PHE 0.007 0.001 PHE J 230 HIS 0.001 0.000 HIS D 133 Details of bonding type rmsd covalent geometry : bond 0.00202 (23976) covalent geometry : angle 0.47053 (32412) hydrogen bonds : bond 0.02359 ( 1176) hydrogen bonds : angle 3.38493 ( 3492) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 244 time to evaluate : 0.822 Fit side-chains REVERT: A 245 MET cc_start: 0.9101 (mmm) cc_final: 0.8884 (mmm) REVERT: B 222 MET cc_start: 0.9346 (tpp) cc_final: 0.8921 (mtt) REVERT: D 279 ASN cc_start: 0.9413 (m110) cc_final: 0.9211 (m-40) REVERT: E 229 GLN cc_start: 0.8932 (mt0) cc_final: 0.8473 (mt0) REVERT: G 198 ASP cc_start: 0.8233 (t0) cc_final: 0.7991 (t0) REVERT: G 222 MET cc_start: 0.9361 (tpp) cc_final: 0.8949 (mtm) REVERT: H 198 ASP cc_start: 0.8270 (t0) cc_final: 0.7985 (t0) REVERT: H 221 GLN cc_start: 0.9561 (tm-30) cc_final: 0.9297 (tm-30) REVERT: I 188 MET cc_start: 0.9156 (mmt) cc_final: 0.8956 (mmt) REVERT: I 222 MET cc_start: 0.9228 (ttm) cc_final: 0.8952 (mtm) REVERT: I 279 ASN cc_start: 0.9464 (m110) cc_final: 0.9078 (m110) REVERT: J 222 MET cc_start: 0.9343 (tpp) cc_final: 0.8917 (mtm) REVERT: J 279 ASN cc_start: 0.9471 (m110) cc_final: 0.9238 (m-40) REVERT: K 198 ASP cc_start: 0.8165 (t0) cc_final: 0.7896 (t0) REVERT: L 188 MET cc_start: 0.9155 (mmt) cc_final: 0.8944 (mmt) REVERT: L 198 ASP cc_start: 0.8279 (t0) cc_final: 0.8034 (t0) REVERT: L 222 MET cc_start: 0.9251 (ttm) cc_final: 0.9044 (mtm) outliers start: 43 outliers final: 41 residues processed: 269 average time/residue: 0.1229 time to fit residues: 57.4282 Evaluate side-chains 270 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 229 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 165 ILE Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 294 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 203 optimal weight: 0.6980 chunk 289 optimal weight: 6.9990 chunk 256 optimal weight: 5.9990 chunk 307 optimal weight: 0.3980 chunk 159 optimal weight: 0.9990 chunk 265 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.066293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.053484 restraints weight = 60731.385| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 4.03 r_work: 0.2582 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23976 Z= 0.118 Angle : 0.487 8.639 32412 Z= 0.249 Chirality : 0.043 0.130 3756 Planarity : 0.003 0.029 4284 Dihedral : 3.535 13.280 3360 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.71 % Allowed : 12.58 % Favored : 85.71 % 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: 2.04 (0.16), residues: 3096 helix: 2.86 (0.13), residues: 1596 sheet: 0.24 (0.22), residues: 588 loop : -0.67 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 166 TYR 0.010 0.002 TYR A 278 PHE 0.006 0.001 PHE H 106 HIS 0.002 0.000 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00279 (23976) covalent geometry : angle 0.48699 (32412) hydrogen bonds : bond 0.02631 ( 1176) hydrogen bonds : angle 3.48683 ( 3492) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 230 time to evaluate : 0.632 Fit side-chains REVERT: B 222 MET cc_start: 0.9351 (tpp) cc_final: 0.8937 (mtt) REVERT: B 279 ASN cc_start: 0.9546 (m-40) cc_final: 0.9226 (m-40) REVERT: D 279 ASN cc_start: 0.9417 (m110) cc_final: 0.9090 (m-40) REVERT: E 229 GLN cc_start: 0.8939 (mt0) cc_final: 0.8471 (mt0) REVERT: G 198 ASP cc_start: 0.8252 (t0) cc_final: 0.8002 (t0) REVERT: G 222 MET cc_start: 0.9355 (tpp) cc_final: 0.8947 (mtt) REVERT: G 279 ASN cc_start: 0.9555 (m-40) cc_final: 0.9214 (m-40) REVERT: H 198 ASP cc_start: 0.8311 (t0) cc_final: 0.8022 (t0) REVERT: H 221 GLN cc_start: 0.9558 (tm-30) cc_final: 0.9279 (tm-30) REVERT: I 188 MET cc_start: 0.9179 (mmt) cc_final: 0.8978 (mmt) REVERT: J 222 MET cc_start: 0.9348 (tpp) cc_final: 0.8914 (mtt) REVERT: J 279 ASN cc_start: 0.9478 (m110) cc_final: 0.9244 (m-40) REVERT: K 198 ASP cc_start: 0.8188 (t0) cc_final: 0.7985 (t0) REVERT: L 198 ASP cc_start: 0.8512 (t0) cc_final: 0.7993 (t0) REVERT: L 222 MET cc_start: 0.9174 (ttm) cc_final: 0.8916 (mtm) outliers start: 44 outliers final: 39 residues processed: 255 average time/residue: 0.1146 time to fit residues: 50.6946 Evaluate side-chains 266 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 227 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 165 ILE Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 134 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 chunk 182 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 306 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.065369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.052582 restraints weight = 61206.801| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 4.03 r_work: 0.2590 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2584 r_free = 0.2584 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23976 Z= 0.147 Angle : 0.500 8.589 32412 Z= 0.257 Chirality : 0.043 0.130 3756 Planarity : 0.003 0.031 4284 Dihedral : 3.605 13.281 3360 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.52 % Allowed : 12.81 % Favored : 85.67 % 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: 2.06 (0.16), residues: 3096 helix: 2.85 (0.13), residues: 1596 sheet: 0.23 (0.22), residues: 588 loop : -0.61 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 72 TYR 0.010 0.002 TYR A 278 PHE 0.007 0.001 PHE F 253 HIS 0.002 0.000 HIS H 105 Details of bonding type rmsd covalent geometry : bond 0.00346 (23976) covalent geometry : angle 0.49965 (32412) hydrogen bonds : bond 0.02829 ( 1176) hydrogen bonds : angle 3.54534 ( 3492) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 0.671 Fit side-chains REVERT: B 222 MET cc_start: 0.9363 (tpp) cc_final: 0.8939 (mtt) REVERT: E 229 GLN cc_start: 0.8962 (mt0) cc_final: 0.8482 (mt0) REVERT: G 198 ASP cc_start: 0.8281 (t0) cc_final: 0.8033 (t0) REVERT: G 222 MET cc_start: 0.9373 (tpp) cc_final: 0.8951 (mtt) REVERT: G 279 ASN cc_start: 0.9561 (m-40) cc_final: 0.9228 (m110) REVERT: H 198 ASP cc_start: 0.8335 (t0) cc_final: 0.8119 (t0) REVERT: H 221 GLN cc_start: 0.9575 (tm-30) cc_final: 0.9299 (tm-30) REVERT: I 279 ASN cc_start: 0.9483 (m110) cc_final: 0.9114 (m110) REVERT: J 279 ASN cc_start: 0.9485 (m110) cc_final: 0.9252 (m-40) REVERT: L 198 ASP cc_start: 0.8317 (t0) cc_final: 0.7973 (t0) outliers start: 39 outliers final: 37 residues processed: 243 average time/residue: 0.1224 time to fit residues: 51.7998 Evaluate side-chains 251 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 214 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 165 ILE Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 269 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 309 optimal weight: 0.9990 chunk 190 optimal weight: 6.9990 chunk 186 optimal weight: 0.0970 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 145 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 173 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.066939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.054163 restraints weight = 60430.748| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 4.04 r_work: 0.2632 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 23976 Z= 0.097 Angle : 0.492 8.823 32412 Z= 0.252 Chirality : 0.042 0.129 3756 Planarity : 0.003 0.028 4284 Dihedral : 3.553 13.635 3360 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.48 % Allowed : 12.97 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.16), residues: 3096 helix: 2.89 (0.13), residues: 1596 sheet: 0.26 (0.22), residues: 588 loop : -0.52 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 72 TYR 0.010 0.001 TYR A 278 PHE 0.007 0.001 PHE K 253 HIS 0.001 0.000 HIS D 133 Details of bonding type rmsd covalent geometry : bond 0.00228 (23976) covalent geometry : angle 0.49201 (32412) hydrogen bonds : bond 0.02460 ( 1176) hydrogen bonds : angle 3.43583 ( 3492) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4054.01 seconds wall clock time: 70 minutes 35.28 seconds (4235.28 seconds total)