Starting phenix.real_space_refine on Thu Sep 18 14:53:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gzr_51732/09_2025/9gzr_51732.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gzr_51732/09_2025/9gzr_51732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gzr_51732/09_2025/9gzr_51732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gzr_51732/09_2025/9gzr_51732.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gzr_51732/09_2025/9gzr_51732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gzr_51732/09_2025/9gzr_51732.map" } resolution = 2.45 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= 0.002 sd= 0.036 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 36 5.16 5 C 11124 2.51 5 N 3198 2.21 5 O 3396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17754 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1420 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 15, 'TRANS': 173} Chain breaks: 2 Chain: "B" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1539 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 15, 'TRANS': 188} Chain breaks: 1 Chain: "C" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1420 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 15, 'TRANS': 173} Chain breaks: 2 Chain: "D" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1539 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 15, 'TRANS': 188} Chain breaks: 1 Chain: "E" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1420 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 15, 'TRANS': 173} Chain breaks: 2 Chain: "F" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1539 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 15, 'TRANS': 188} Chain breaks: 1 Chain: "G" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1420 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 15, 'TRANS': 173} Chain breaks: 2 Chain: "H" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1539 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 15, 'TRANS': 188} Chain breaks: 1 Chain: "I" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1420 Classifications: {'peptide': 189} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 172} Chain breaks: 2 Chain: "J" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1539 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 15, 'TRANS': 188} Chain breaks: 1 Chain: "K" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1420 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 15, 'TRANS': 173} Chain breaks: 2 Chain: "L" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1539 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 15, 'TRANS': 188} Chain breaks: 1 Time building chain proxies: 4.37, per 1000 atoms: 0.25 Number of scatterers: 17754 At special positions: 0 Unit cell: (160.65, 157.25, 85, 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 36 16.00 O 3396 8.00 N 3198 7.00 C 11124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 661.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4308 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 48 sheets defined 23.9% alpha, 36.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 91 through 95 Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 216 through 227 removed outlier: 3.865A pdb=" N GLY A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 238 removed outlier: 3.635A pdb=" N GLU A 238 " --> pdb=" O SER A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 235 through 238' Processing helix chain 'A' and resid 239 through 245 removed outlier: 3.550A pdb=" N ARG A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'B' and resid 91 through 95 Processing helix chain 'B' and resid 111 through 116 removed outlier: 3.582A pdb=" N GLU B 116 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 Processing helix chain 'B' and resid 216 through 227 removed outlier: 3.916A pdb=" N GLY B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 238 removed outlier: 3.678A pdb=" N GLU B 238 " --> pdb=" O SER B 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 235 through 238' Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'C' and resid 91 through 96 removed outlier: 3.608A pdb=" N LEU C 96 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 141 through 145 Processing helix chain 'C' and resid 216 through 227 Processing helix chain 'C' and resid 235 through 238 removed outlier: 3.674A pdb=" N GLU C 238 " --> pdb=" O SER C 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 235 through 238' Processing helix chain 'C' and resid 239 through 245 removed outlier: 3.726A pdb=" N ARG C 243 " --> pdb=" O GLU C 239 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 91 through 96 removed outlier: 3.603A pdb=" N ALA D 94 " --> pdb=" O ARG D 91 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU D 96 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 removed outlier: 3.532A pdb=" N GLU D 116 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 216 through 227 removed outlier: 3.924A pdb=" N GLY D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 238 removed outlier: 3.632A pdb=" N GLU D 238 " --> pdb=" O SER D 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 235 through 238' Processing helix chain 'D' and resid 239 through 245 Processing helix chain 'D' and resid 263 through 267 Processing helix chain 'E' and resid 72 through 74 No H-bonds generated for 'chain 'E' and resid 72 through 74' Processing helix chain 'E' and resid 91 through 95 Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 141 through 145 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.885A pdb=" N GLY E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 245 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'F' and resid 91 through 96 removed outlier: 3.806A pdb=" N LEU F 96 " --> pdb=" O GLU F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 116 Processing helix chain 'F' and resid 121 through 125 removed outlier: 4.108A pdb=" N ILE F 125 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 145 Processing helix chain 'F' and resid 216 through 227 removed outlier: 3.670A pdb=" N GLY F 227 " --> pdb=" O ALA F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 238 removed outlier: 3.686A pdb=" N GLU F 238 " --> pdb=" O SER F 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 235 through 238' Processing helix chain 'F' and resid 239 through 245 Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'G' and resid 72 through 74 No H-bonds generated for 'chain 'G' and resid 72 through 74' Processing helix chain 'G' and resid 91 through 95 Processing helix chain 'G' and resid 120 through 124 Processing helix chain 'G' and resid 141 through 145 Processing helix chain 'G' and resid 161 through 165 removed outlier: 4.081A pdb=" N GLY G 164 " --> pdb=" O GLU G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 227 removed outlier: 3.988A pdb=" N GLY G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 238 removed outlier: 3.653A pdb=" N GLU G 238 " --> pdb=" O SER G 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 235 through 238' Processing helix chain 'G' and resid 239 through 245 removed outlier: 3.606A pdb=" N ARG G 243 " --> pdb=" O GLU G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 268 Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'H' and resid 91 through 95 Processing helix chain 'H' and resid 111 through 116 removed outlier: 3.524A pdb=" N GLU H 116 " --> pdb=" O ALA H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 125 removed outlier: 4.135A pdb=" N ILE H 125 " --> pdb=" O ALA H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 145 Processing helix chain 'H' and resid 216 through 227 removed outlier: 3.865A pdb=" N GLY H 227 " --> pdb=" O ALA H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 238 removed outlier: 3.637A pdb=" N GLU H 238 " --> pdb=" O SER H 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 235 through 238' Processing helix chain 'H' and resid 239 through 245 Processing helix chain 'H' and resid 263 through 267 Processing helix chain 'I' and resid 91 through 95 Processing helix chain 'I' and resid 120 through 124 Processing helix chain 'I' and resid 141 through 145 Processing helix chain 'I' and resid 216 through 227 removed outlier: 3.820A pdb=" N GLY I 227 " --> pdb=" O ALA I 223 " (cutoff:3.500A) Processing helix chain 'I' and resid 235 through 238 removed outlier: 3.641A pdb=" N GLU I 238 " --> pdb=" O SER I 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 235 through 238' Processing helix chain 'I' and resid 239 through 246 removed outlier: 3.684A pdb=" N ARG I 243 " --> pdb=" O GLU I 239 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU I 244 " --> pdb=" O LEU I 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 263 through 268 Processing helix chain 'J' and resid 91 through 95 Processing helix chain 'J' and resid 112 through 116 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 216 through 227 removed outlier: 3.932A pdb=" N GLY J 227 " --> pdb=" O ALA J 223 " (cutoff:3.500A) Processing helix chain 'J' and resid 235 through 238 removed outlier: 3.674A pdb=" N GLU J 238 " --> pdb=" O SER J 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 235 through 238' Processing helix chain 'J' and resid 239 through 245 Processing helix chain 'J' and resid 263 through 267 Processing helix chain 'K' and resid 72 through 76 removed outlier: 3.854A pdb=" N LEU K 76 " --> pdb=" O ARG K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 95 Processing helix chain 'K' and resid 120 through 125 removed outlier: 4.151A pdb=" N ILE K 125 " --> pdb=" O ALA K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 145 Processing helix chain 'K' and resid 161 through 165 removed outlier: 4.065A pdb=" N GLY K 164 " --> pdb=" O GLU K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 216 through 227 Processing helix chain 'K' and resid 235 through 238 removed outlier: 3.707A pdb=" N GLU K 238 " --> pdb=" O SER K 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 235 through 238' Processing helix chain 'K' and resid 239 through 245 removed outlier: 3.609A pdb=" N ARG K 243 " --> pdb=" O GLU K 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 263 through 268 Processing helix chain 'L' and resid 91 through 96 removed outlier: 3.949A pdb=" N LEU L 96 " --> pdb=" O GLU L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 116 Processing helix chain 'L' and resid 141 through 145 Processing helix chain 'L' and resid 216 through 227 removed outlier: 3.686A pdb=" N GLY L 227 " --> pdb=" O ALA L 223 " (cutoff:3.500A) Processing helix chain 'L' and resid 235 through 238 removed outlier: 3.769A pdb=" N GLU L 238 " --> pdb=" O SER L 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 235 through 238' Processing helix chain 'L' and resid 239 through 245 Processing helix chain 'L' and resid 263 through 267 Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 61 Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 70 removed outlier: 3.721A pdb=" N ALA A 69 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 135 removed outlier: 6.705A pdb=" N ALA A 211 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL A 179 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 10.738A pdb=" N VAL A 177 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 154 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL A 152 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 186 Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 61 Processing sheet with id=AA6, first strand: chain 'B' and resid 69 through 70 removed outlier: 3.531A pdb=" N ALA B 69 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 129 through 135 removed outlier: 7.232A pdb=" N THR B 207 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TYR B 182 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL B 209 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG B 178 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N GLY B 176 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP B 160 " --> pdb=" O PRO B 168 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ALA B 170 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL B 158 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LEU B 172 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU B 156 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 174 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL B 152 " --> pdb=" O GLY B 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 185 through 186 removed outlier: 3.545A pdb=" N ARG B 185 " --> pdb=" O TYR B 182 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 57 through 61 Processing sheet with id=AB1, first strand: chain 'C' and resid 69 through 70 removed outlier: 3.667A pdb=" N ALA C 69 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 129 through 135 removed outlier: 6.469A pdb=" N ALA C 211 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL C 179 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 10.479A pdb=" N VAL C 177 " --> pdb=" O PRO C 213 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL C 154 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL C 152 " --> pdb=" O PRO C 175 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 185 through 186 Processing sheet with id=AB4, first strand: chain 'D' and resid 56 through 61 Processing sheet with id=AB5, first strand: chain 'D' and resid 69 through 70 removed outlier: 3.524A pdb=" N ALA D 69 " --> pdb=" O VAL D 100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 129 through 135 removed outlier: 7.441A pdb=" N THR D 207 " --> pdb=" O TYR D 182 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR D 182 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL D 209 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG D 178 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 12.117A pdb=" N GLY D 176 " --> pdb=" O PRO D 213 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASP D 160 " --> pdb=" O PRO D 168 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ALA D 170 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL D 158 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU D 172 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU D 156 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 174 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VAL D 152 " --> pdb=" O GLY D 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 185 through 186 removed outlier: 3.542A pdb=" N ARG D 185 " --> pdb=" O TYR D 182 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 57 through 61 Processing sheet with id=AB9, first strand: chain 'E' and resid 69 through 70 removed outlier: 3.649A pdb=" N ALA E 69 " --> pdb=" O VAL E 100 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 129 through 135 removed outlier: 6.569A pdb=" N ALA E 211 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL E 179 " --> pdb=" O ALA E 211 " (cutoff:3.500A) removed outlier: 10.716A pdb=" N VAL E 177 " --> pdb=" O PRO E 213 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASP E 160 " --> pdb=" O PRO E 168 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ALA E 170 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL E 158 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LEU E 172 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU E 156 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU E 174 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N VAL E 152 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 185 through 186 Processing sheet with id=AC3, first strand: chain 'F' and resid 56 through 61 Processing sheet with id=AC4, first strand: chain 'F' and resid 69 through 70 removed outlier: 3.561A pdb=" N ALA F 69 " --> pdb=" O VAL F 100 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 129 through 135 removed outlier: 6.457A pdb=" N ALA F 211 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL F 179 " --> pdb=" O ALA F 211 " (cutoff:3.500A) removed outlier: 10.790A pdb=" N VAL F 177 " --> pdb=" O PRO F 213 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL F 154 " --> pdb=" O VAL F 173 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL F 152 " --> pdb=" O PRO F 175 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 185 through 186 Processing sheet with id=AC7, first strand: chain 'G' and resid 57 through 61 Processing sheet with id=AC8, first strand: chain 'G' and resid 69 through 70 removed outlier: 3.677A pdb=" N ALA G 69 " --> pdb=" O VAL G 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 129 through 135 removed outlier: 7.261A pdb=" N THR G 207 " --> pdb=" O TYR G 182 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TYR G 182 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL G 209 " --> pdb=" O LEU G 180 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG G 178 " --> pdb=" O ALA G 211 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N GLY G 176 " --> pdb=" O PRO G 213 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU G 169 " --> pdb=" O ASP G 160 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ASP G 160 " --> pdb=" O LEU G 169 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N GLN G 171 " --> pdb=" O VAL G 158 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL G 158 " --> pdb=" O GLN G 171 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL G 173 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU G 156 " --> pdb=" O VAL G 173 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL G 154 " --> pdb=" O PRO G 175 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 185 through 186 Processing sheet with id=AD2, first strand: chain 'H' and resid 56 through 61 Processing sheet with id=AD3, first strand: chain 'H' and resid 69 through 70 removed outlier: 3.543A pdb=" N ALA H 69 " --> pdb=" O VAL H 100 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 129 through 133 removed outlier: 6.313A pdb=" N ALA H 211 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL H 179 " --> pdb=" O ALA H 211 " (cutoff:3.500A) removed outlier: 10.742A pdb=" N VAL H 177 " --> pdb=" O PRO H 213 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ASP H 160 " --> pdb=" O PRO H 168 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ALA H 170 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL H 158 " --> pdb=" O ALA H 170 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU H 172 " --> pdb=" O LEU H 156 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU H 156 " --> pdb=" O LEU H 172 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU H 174 " --> pdb=" O VAL H 154 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N VAL H 152 " --> pdb=" O GLY H 176 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 185 through 186 removed outlier: 3.533A pdb=" N ARG H 185 " --> pdb=" O TYR H 182 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 57 through 61 Processing sheet with id=AD7, first strand: chain 'I' and resid 69 through 70 removed outlier: 3.804A pdb=" N ALA I 69 " --> pdb=" O VAL I 100 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 129 through 135 removed outlier: 7.166A pdb=" N THR I 207 " --> pdb=" O TYR I 182 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TYR I 182 " --> pdb=" O THR I 207 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL I 209 " --> pdb=" O LEU I 180 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG I 178 " --> pdb=" O ALA I 211 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N GLY I 176 " --> pdb=" O PRO I 213 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU I 169 " --> pdb=" O ASP I 160 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ASP I 160 " --> pdb=" O LEU I 169 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N GLN I 171 " --> pdb=" O VAL I 158 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N VAL I 158 " --> pdb=" O GLN I 171 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL I 173 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N LEU I 156 " --> pdb=" O VAL I 173 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL I 154 " --> pdb=" O PRO I 175 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 129 through 135 removed outlier: 7.166A pdb=" N THR I 207 " --> pdb=" O TYR I 182 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TYR I 182 " --> pdb=" O THR I 207 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL I 209 " --> pdb=" O LEU I 180 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG I 178 " --> pdb=" O ALA I 211 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N GLY I 176 " --> pdb=" O PRO I 213 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 56 through 61 Processing sheet with id=AE2, first strand: chain 'J' and resid 69 through 70 removed outlier: 3.506A pdb=" N ALA J 69 " --> pdb=" O VAL J 100 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 129 through 135 removed outlier: 6.501A pdb=" N ALA J 211 " --> pdb=" O VAL J 179 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL J 179 " --> pdb=" O ALA J 211 " (cutoff:3.500A) removed outlier: 10.845A pdb=" N VAL J 177 " --> pdb=" O PRO J 213 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N SER J 166 " --> pdb=" O ARG J 162 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ARG J 162 " --> pdb=" O SER J 166 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASP J 160 " --> pdb=" O PRO J 168 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ALA J 170 " --> pdb=" O VAL J 158 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL J 158 " --> pdb=" O ALA J 170 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU J 172 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU J 156 " --> pdb=" O LEU J 172 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU J 174 " --> pdb=" O VAL J 154 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL J 152 " --> pdb=" O GLY J 176 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 185 through 186 Processing sheet with id=AE5, first strand: chain 'K' and resid 57 through 60 Processing sheet with id=AE6, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.679A pdb=" N ALA K 69 " --> pdb=" O VAL K 100 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 129 through 135 removed outlier: 6.511A pdb=" N ALA K 211 " --> pdb=" O VAL K 179 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL K 179 " --> pdb=" O ALA K 211 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N VAL K 177 " --> pdb=" O PRO K 213 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL K 154 " --> pdb=" O VAL K 173 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL K 152 " --> pdb=" O PRO K 175 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 129 through 135 removed outlier: 6.511A pdb=" N ALA K 211 " --> pdb=" O VAL K 179 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL K 179 " --> pdb=" O ALA K 211 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N VAL K 177 " --> pdb=" O PRO K 213 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 56 through 61 Processing sheet with id=AF1, first strand: chain 'L' and resid 69 through 70 removed outlier: 3.595A pdb=" N ALA L 69 " --> pdb=" O VAL L 100 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 129 through 135 removed outlier: 7.423A pdb=" N THR L 207 " --> pdb=" O TYR L 182 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TYR L 182 " --> pdb=" O THR L 207 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL L 209 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG L 178 " --> pdb=" O ALA L 211 " (cutoff:3.500A) removed outlier: 11.995A pdb=" N GLY L 176 " --> pdb=" O PRO L 213 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL L 154 " --> pdb=" O VAL L 173 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL L 152 " --> pdb=" O PRO L 175 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 185 through 186 removed outlier: 3.502A pdb=" N ARG L 185 " --> pdb=" O TYR L 182 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 1.87 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: 6241 1.34 - 1.46: 2209 1.46 - 1.57: 9478 1.57 - 1.69: 0 1.69 - 1.80: 72 Bond restraints: 18000 Sorted by residual: bond pdb=" N LYS B 56 " pdb=" CA LYS B 56 " ideal model delta sigma weight residual 1.452 1.481 -0.029 1.46e-02 4.69e+03 3.98e+00 bond pdb=" C LYS I 56 " pdb=" N PRO I 57 " ideal model delta sigma weight residual 1.330 1.353 -0.023 1.23e-02 6.61e+03 3.54e+00 bond pdb=" C LYS B 56 " pdb=" N PRO B 57 " ideal model delta sigma weight residual 1.333 1.354 -0.021 1.20e-02 6.94e+03 3.02e+00 bond pdb=" N GLU B 54 " pdb=" CA GLU B 54 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.90e-02 2.77e+03 2.05e+00 bond pdb=" N ARG B 55 " pdb=" CA ARG B 55 " ideal model delta sigma weight residual 1.462 1.480 -0.019 1.35e-02 5.49e+03 1.88e+00 ... (remaining 17995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 22814 1.12 - 2.24: 1186 2.24 - 3.36: 362 3.36 - 4.48: 64 4.48 - 5.60: 24 Bond angle restraints: 24450 Sorted by residual: angle pdb=" N LYS B 56 " pdb=" CA LYS B 56 " pdb=" CB LYS B 56 " ideal model delta sigma weight residual 109.78 104.61 5.17 1.38e+00 5.25e-01 1.40e+01 angle pdb=" C ARG F 162 " pdb=" N ASP F 163 " pdb=" CA ASP F 163 " ideal model delta sigma weight residual 121.54 127.14 -5.60 1.91e+00 2.74e-01 8.61e+00 angle pdb=" CA ARG B 55 " pdb=" C ARG B 55 " pdb=" O ARG B 55 " ideal model delta sigma weight residual 120.84 117.99 2.85 1.08e+00 8.57e-01 6.96e+00 angle pdb=" C GLN C 245 " pdb=" N GLU C 246 " pdb=" CA GLU C 246 " ideal model delta sigma weight residual 121.70 126.34 -4.64 1.80e+00 3.09e-01 6.65e+00 angle pdb=" C LEU B 172 " pdb=" N VAL B 173 " pdb=" CA VAL B 173 " ideal model delta sigma weight residual 122.66 120.33 2.33 9.70e-01 1.06e+00 5.75e+00 ... (remaining 24445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 9517 17.68 - 35.37: 1153 35.37 - 53.05: 421 53.05 - 70.74: 95 70.74 - 88.42: 34 Dihedral angle restraints: 11220 sinusoidal: 4536 harmonic: 6684 Sorted by residual: dihedral pdb=" CD ARG B 55 " pdb=" NE ARG B 55 " pdb=" CZ ARG B 55 " pdb=" NH1 ARG B 55 " ideal model delta sinusoidal sigma weight residual 0.00 87.10 -87.10 1 1.00e+01 1.00e-02 9.11e+01 dihedral pdb=" CA THR G 181 " pdb=" C THR G 181 " pdb=" N TYR G 182 " pdb=" CA TYR G 182 " ideal model delta harmonic sigma weight residual 180.00 154.00 26.00 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA THR A 181 " pdb=" C THR A 181 " pdb=" N TYR A 182 " pdb=" CA TYR A 182 " ideal model delta harmonic sigma weight residual 180.00 154.14 25.86 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 11217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1850 0.035 - 0.070: 689 0.070 - 0.105: 297 0.105 - 0.140: 49 0.140 - 0.175: 1 Chirality restraints: 2886 Sorted by residual: chirality pdb=" CA ASP L 163 " pdb=" N ASP L 163 " pdb=" C ASP L 163 " pdb=" CB ASP L 163 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA VAL F 212 " pdb=" N VAL F 212 " pdb=" C VAL F 212 " pdb=" CB VAL F 212 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA VAL L 212 " pdb=" N VAL L 212 " pdb=" C VAL L 212 " pdb=" CB VAL L 212 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 2883 not shown) Planarity restraints: 3246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 55 " 1.111 9.50e-02 1.11e+02 4.98e-01 1.49e+02 pdb=" NE ARG B 55 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG B 55 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 55 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG B 55 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 116 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 117 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 117 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 117 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 174 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO B 175 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 175 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 175 " -0.023 5.00e-02 4.00e+02 ... (remaining 3243 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1080 2.73 - 3.27: 15472 3.27 - 3.81: 26376 3.81 - 4.36: 32771 4.36 - 4.90: 57040 Nonbonded interactions: 132739 Sorted by model distance: nonbonded pdb=" OE2 GLU E 165 " pdb=" OG1 THR E 167 " model vdw 2.186 3.040 nonbonded pdb=" NH1 ARG D 126 " pdb=" OD1 ASP D 128 " model vdw 2.250 3.120 nonbonded pdb=" OD2 ASP A 160 " pdb=" NH1 ARG A 162 " model vdw 2.278 3.120 nonbonded pdb=" N ASP J 215 " pdb=" OD1 ASP J 215 " model vdw 2.293 3.120 nonbonded pdb=" NH2 ARG G 234 " pdb=" OE1 GLU G 238 " model vdw 2.295 3.120 ... (remaining 132734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 56 through 188 or resid 202 through 268)) selection = chain 'C' selection = (chain 'D' and (resid 56 through 188 or resid 202 through 268)) selection = chain 'E' selection = (chain 'F' and (resid 56 through 188 or resid 202 through 268)) selection = chain 'G' selection = (chain 'H' and (resid 56 through 188 or resid 202 through 268)) selection = chain 'I' selection = (chain 'J' and (resid 56 through 188 or resid 202 through 268)) selection = chain 'K' selection = (chain 'L' and (resid 56 through 188 or resid 202 through 268)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.050 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 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:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 0.038 18000 Z= 0.153 Angle : 0.653 5.605 24450 Z= 0.351 Chirality : 0.043 0.175 2886 Planarity : 0.011 0.498 3246 Dihedral : 18.441 88.422 6912 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.48 % Favored : 96.30 % Rotamer: Outliers : 3.83 % Allowed : 34.03 % Favored : 62.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 aren not related in a simple way. whole: -0.94 (0.16), residues: 2298 helix: -2.64 (0.23), residues: 312 sheet: -1.03 (0.18), residues: 618 loop : 0.26 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 203 TYR 0.014 0.001 TYR B 182 PHE 0.007 0.001 PHE F 145 TRP 0.013 0.002 TRP G 101 Details of bonding type rmsd covalent geometry : bond 0.00323 (18000) covalent geometry : angle 0.65328 (24450) hydrogen bonds : bond 0.22720 ( 534) hydrogen bonds : angle 7.61375 ( 1305) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 571 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 SER cc_start: 0.8677 (t) cc_final: 0.8477 (m) REVERT: C 239 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7759 (mp0) REVERT: D 82 ARG cc_start: 0.7741 (mtp85) cc_final: 0.7482 (mtp85) REVERT: E 74 ASP cc_start: 0.7606 (p0) cc_final: 0.7300 (p0) REVERT: G 60 VAL cc_start: 0.8463 (t) cc_final: 0.8237 (m) REVERT: G 161 GLU cc_start: 0.7602 (mp0) cc_final: 0.7237 (mp0) REVERT: J 82 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6879 (mtm-85) REVERT: J 161 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7393 (mt-10) REVERT: K 74 ASP cc_start: 0.7474 (p0) cc_final: 0.7249 (p0) REVERT: L 93 GLU cc_start: 0.7900 (mp0) cc_final: 0.7412 (mp0) outliers start: 72 outliers final: 61 residues processed: 603 average time/residue: 0.8416 time to fit residues: 548.0006 Evaluate side-chains 632 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 569 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 200 LYS Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 93 GLU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 268 GLU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 82 ARG Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 200 LYS Chi-restraints excluded: chain J residue 215 ASP Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 162 ARG Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain K residue 203 ARG Chi-restraints excluded: chain L residue 56 LYS Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 203 ARG Chi-restraints excluded: chain L residue 215 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 GLN F 171 GLN I 171 GLN I 225 GLN K 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.122867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.106540 restraints weight = 23000.363| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.87 r_work: 0.3365 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.103 18000 Z= 0.444 Angle : 0.814 7.626 24450 Z= 0.404 Chirality : 0.059 0.200 2886 Planarity : 0.008 0.052 3246 Dihedral : 8.854 63.782 2760 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.00 % Favored : 95.78 % Rotamer: Outliers : 7.08 % Allowed : 27.96 % Favored : 64.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 aren not related in a simple way. whole: -0.92 (0.16), residues: 2298 helix: -1.82 (0.27), residues: 282 sheet: -0.92 (0.18), residues: 642 loop : -0.04 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 206 TYR 0.019 0.002 TYR B 182 PHE 0.012 0.004 PHE G 157 TRP 0.015 0.003 TRP G 101 Details of bonding type rmsd covalent geometry : bond 0.01139 (18000) covalent geometry : angle 0.81401 (24450) hydrogen bonds : bond 0.06709 ( 534) hydrogen bonds : angle 5.59789 ( 1305) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 597 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8766 (tt0) REVERT: A 234 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8564 (mtp180) REVERT: A 265 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7071 (mp10) REVERT: B 77 SER cc_start: 0.8759 (t) cc_final: 0.8557 (m) REVERT: C 239 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: D 82 ARG cc_start: 0.7996 (mtp85) cc_final: 0.7758 (mtp85) REVERT: D 155 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.7804 (mmm) REVERT: E 63 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7685 (ptt-90) REVERT: E 74 ASP cc_start: 0.7578 (p0) cc_final: 0.6455 (p0) REVERT: E 163 ASP cc_start: 0.7305 (p0) cc_final: 0.7056 (p0) REVERT: F 268 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7664 (pp20) REVERT: G 63 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7783 (ptt-90) REVERT: G 75 ASP cc_start: 0.7524 (m-30) cc_final: 0.7266 (m-30) REVERT: G 161 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: G 234 ARG cc_start: 0.8804 (mmm160) cc_final: 0.8591 (mtp180) REVERT: I 63 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7925 (ptt-90) REVERT: J 82 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7156 (mtm-85) REVERT: J 161 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7321 (mt-10) REVERT: K 74 ASP cc_start: 0.7454 (p0) cc_final: 0.7221 (p0) REVERT: L 93 GLU cc_start: 0.8048 (mp0) cc_final: 0.7447 (mp0) outliers start: 133 outliers final: 78 residues processed: 671 average time/residue: 0.7863 time to fit residues: 571.9454 Evaluate side-chains 676 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 587 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 234 ARG Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 82 ARG Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 162 ARG Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 200 LYS Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 126 ARG Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 268 GLU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 264 ASP Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 82 ARG Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 200 LYS Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 215 ASP Chi-restraints excluded: chain J residue 222 LEU Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 263 LEU Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 162 ARG Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain K residue 203 ARG Chi-restraints excluded: chain L residue 91 ARG Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain L residue 203 ARG Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 221 MET Chi-restraints excluded: chain L residue 222 LEU Chi-restraints excluded: chain L residue 228 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 181 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 195 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 GLN F 171 GLN G 171 GLN I 171 GLN K 171 GLN L 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.125669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.109321 restraints weight = 23052.675| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.90 r_work: 0.3408 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18000 Z= 0.124 Angle : 0.573 6.009 24450 Z= 0.286 Chirality : 0.043 0.165 2886 Planarity : 0.006 0.042 3246 Dihedral : 7.695 63.444 2708 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.66 % Favored : 96.08 % Rotamer: Outliers : 5.54 % Allowed : 29.39 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 aren not related in a simple way. whole: -0.75 (0.16), residues: 2298 helix: -1.02 (0.30), residues: 276 sheet: -0.93 (0.17), residues: 642 loop : -0.04 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 203 TYR 0.011 0.001 TYR B 182 PHE 0.006 0.001 PHE F 157 TRP 0.011 0.001 TRP I 101 Details of bonding type rmsd covalent geometry : bond 0.00297 (18000) covalent geometry : angle 0.57309 (24450) hydrogen bonds : bond 0.03929 ( 534) hydrogen bonds : angle 4.79306 ( 1305) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 582 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7614 (mtp85) REVERT: D 162 ARG cc_start: 0.6431 (OUTLIER) cc_final: 0.6206 (mtt-85) REVERT: D 178 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7831 (ttm170) REVERT: E 63 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7867 (ptt-90) REVERT: E 163 ASP cc_start: 0.7261 (p0) cc_final: 0.7008 (p0) REVERT: F 91 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7775 (mtm-85) REVERT: F 222 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7754 (tt) REVERT: G 161 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: G 238 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7940 (mt-10) REVERT: H 58 VAL cc_start: 0.8807 (t) cc_final: 0.8531 (p) REVERT: I 63 ARG cc_start: 0.8281 (mtp180) cc_final: 0.7816 (ptp-170) REVERT: J 82 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.7050 (mtm-85) REVERT: J 161 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7261 (mt-10) REVERT: L 82 ARG cc_start: 0.8185 (mmt90) cc_final: 0.7947 (mtt90) REVERT: L 93 GLU cc_start: 0.8041 (mp0) cc_final: 0.7520 (mp0) outliers start: 104 outliers final: 52 residues processed: 641 average time/residue: 0.7948 time to fit residues: 552.3544 Evaluate side-chains 634 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 576 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 162 ARG Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 162 ARG Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 200 LYS Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 126 ARG Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 268 GLU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 82 ARG Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 200 LYS Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 215 ASP Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain K residue 203 ARG Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 203 ARG Chi-restraints excluded: chain L residue 221 MET Chi-restraints excluded: chain L residue 222 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 66 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 79 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 chunk 203 optimal weight: 0.0060 chunk 43 optimal weight: 0.5980 chunk 223 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 171 GLN F 171 GLN G 225 GLN I 171 GLN I 225 GLN K 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.126705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.110385 restraints weight = 23104.924| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.90 r_work: 0.3423 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18000 Z= 0.099 Angle : 0.537 5.555 24450 Z= 0.265 Chirality : 0.043 0.161 2886 Planarity : 0.006 0.040 3246 Dihedral : 6.907 61.479 2691 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.52 % Favored : 96.21 % Rotamer: Outliers : 5.38 % Allowed : 29.71 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 aren not related in a simple way. whole: -0.55 (0.16), residues: 2298 helix: -0.55 (0.32), residues: 276 sheet: -0.90 (0.17), residues: 642 loop : 0.09 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 126 TYR 0.008 0.001 TYR B 182 PHE 0.005 0.001 PHE F 157 TRP 0.010 0.001 TRP I 101 Details of bonding type rmsd covalent geometry : bond 0.00244 (18000) covalent geometry : angle 0.53682 (24450) hydrogen bonds : bond 0.03187 ( 534) hydrogen bonds : angle 4.45043 ( 1305) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 587 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8494 (tp) REVERT: A 171 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8561 (tt0) REVERT: B 54 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6646 (pp20) REVERT: C 206 ARG cc_start: 0.8319 (mtm110) cc_final: 0.8077 (mtm180) REVERT: C 239 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: D 82 ARG cc_start: 0.7890 (mtp85) cc_final: 0.7629 (mtp85) REVERT: D 162 ARG cc_start: 0.6455 (OUTLIER) cc_final: 0.6230 (mtt-85) REVERT: D 178 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7813 (ttm170) REVERT: E 63 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7833 (ptt-90) REVERT: E 163 ASP cc_start: 0.7193 (p0) cc_final: 0.6951 (p0) REVERT: F 75 ASP cc_start: 0.8069 (m-30) cc_final: 0.7836 (m-30) REVERT: F 91 ARG cc_start: 0.7974 (mtm-85) cc_final: 0.7754 (mtm-85) REVERT: F 222 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7741 (tt) REVERT: F 268 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7635 (pp20) REVERT: G 161 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: H 58 VAL cc_start: 0.8748 (t) cc_final: 0.8464 (p) REVERT: I 63 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7884 (ptt-90) REVERT: I 171 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8846 (tt0) REVERT: J 82 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7030 (mtm-85) REVERT: J 161 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7212 (mt-10) REVERT: L 82 ARG cc_start: 0.8160 (mmt90) cc_final: 0.7955 (mtt90) REVERT: L 93 GLU cc_start: 0.8065 (mp0) cc_final: 0.7550 (mp0) REVERT: L 128 ASP cc_start: 0.8422 (p0) cc_final: 0.8182 (p0) outliers start: 101 outliers final: 56 residues processed: 640 average time/residue: 0.7713 time to fit residues: 536.4218 Evaluate side-chains 644 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 575 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 ARG Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain F residue 162 ARG Chi-restraints excluded: chain F residue 200 LYS Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain G residue 93 GLU Chi-restraints excluded: chain G residue 126 ARG Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 268 GLU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 171 GLN Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 82 ARG Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 200 LYS Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 215 ASP Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 162 ARG Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain K residue 203 ARG Chi-restraints excluded: chain L residue 56 LYS Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 203 ARG Chi-restraints excluded: chain L residue 221 MET Chi-restraints excluded: chain L residue 222 LEU Chi-restraints excluded: chain L residue 228 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 47 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 227 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 GLN E 171 GLN G 225 GLN I 225 GLN K 171 GLN L 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.125044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.108421 restraints weight = 23039.879| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.95 r_work: 0.3390 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18000 Z= 0.187 Angle : 0.598 5.781 24450 Z= 0.295 Chirality : 0.045 0.167 2886 Planarity : 0.006 0.043 3246 Dihedral : 6.909 59.968 2685 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.57 % Favored : 96.17 % Rotamer: Outliers : 5.96 % Allowed : 28.54 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 aren not related in a simple way. whole: -0.57 (0.17), residues: 2298 helix: -0.57 (0.32), residues: 276 sheet: -0.88 (0.18), residues: 642 loop : 0.06 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 126 TYR 0.011 0.001 TYR L 182 PHE 0.006 0.002 PHE C 157 TRP 0.008 0.002 TRP I 101 Details of bonding type rmsd covalent geometry : bond 0.00474 (18000) covalent geometry : angle 0.59779 (24450) hydrogen bonds : bond 0.04051 ( 534) hydrogen bonds : angle 4.64585 ( 1305) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 599 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6676 (pp20) REVERT: C 239 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7880 (mp0) REVERT: C 268 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6144 (mm-30) REVERT: D 82 ARG cc_start: 0.7957 (mtp85) cc_final: 0.7688 (mtp85) REVERT: D 162 ARG cc_start: 0.6446 (OUTLIER) cc_final: 0.6199 (mtt-85) REVERT: D 178 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7858 (ttm170) REVERT: E 63 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7890 (ptt-90) REVERT: E 163 ASP cc_start: 0.7292 (p0) cc_final: 0.7039 (p0) REVERT: F 91 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7826 (mtm-85) REVERT: F 222 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7805 (tt) REVERT: G 161 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: H 58 VAL cc_start: 0.8781 (t) cc_final: 0.8479 (p) REVERT: H 268 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7610 (pp20) REVERT: J 82 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.7102 (mtm-85) REVERT: J 161 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7275 (mt-10) REVERT: J 171 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8764 (tt0) REVERT: L 93 GLU cc_start: 0.8112 (mp0) cc_final: 0.7540 (mp0) outliers start: 112 outliers final: 74 residues processed: 662 average time/residue: 0.7927 time to fit residues: 569.8027 Evaluate side-chains 682 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 597 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 ARG Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain F residue 162 ARG Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 200 LYS Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain G residue 93 GLU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 268 GLU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 82 ARG Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 171 GLN Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 200 LYS Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 215 ASP Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 162 ARG Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain K residue 203 ARG Chi-restraints excluded: chain L residue 56 LYS Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 203 ARG Chi-restraints excluded: chain L residue 221 MET Chi-restraints excluded: chain L residue 222 LEU Chi-restraints excluded: chain L residue 228 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 92 optimal weight: 0.3980 chunk 74 optimal weight: 0.0970 chunk 120 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 123 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN E 171 GLN G 171 GLN G 225 GLN I 225 GLN K 171 GLN L 171 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.126153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.109672 restraints weight = 22995.358| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.91 r_work: 0.3418 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18000 Z= 0.096 Angle : 0.530 5.975 24450 Z= 0.262 Chirality : 0.042 0.161 2886 Planarity : 0.006 0.043 3246 Dihedral : 6.448 57.859 2681 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.57 % Favored : 96.17 % Rotamer: Outliers : 4.90 % Allowed : 29.77 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 aren not related in a simple way. whole: -0.40 (0.17), residues: 2298 helix: -0.03 (0.35), residues: 246 sheet: -0.85 (0.17), residues: 648 loop : 0.12 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 126 TYR 0.008 0.001 TYR B 182 PHE 0.004 0.001 PHE C 157 TRP 0.009 0.001 TRP I 101 Details of bonding type rmsd covalent geometry : bond 0.00239 (18000) covalent geometry : angle 0.52974 (24450) hydrogen bonds : bond 0.02993 ( 534) hydrogen bonds : angle 4.32992 ( 1305) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 595 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8491 (tp) REVERT: B 54 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6681 (pp20) REVERT: C 239 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: C 268 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6066 (mm-30) REVERT: D 82 ARG cc_start: 0.7872 (mtp85) cc_final: 0.7619 (mtp85) REVERT: D 162 ARG cc_start: 0.6339 (OUTLIER) cc_final: 0.6113 (mtt-85) REVERT: D 178 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7750 (ttm170) REVERT: E 63 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7856 (ptt-90) REVERT: E 163 ASP cc_start: 0.7197 (p0) cc_final: 0.6950 (p0) REVERT: F 91 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7750 (mtm-85) REVERT: F 222 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7758 (tt) REVERT: G 161 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: H 58 VAL cc_start: 0.8713 (t) cc_final: 0.8437 (p) REVERT: H 268 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7509 (pp20) REVERT: I 63 ARG cc_start: 0.8214 (mtp180) cc_final: 0.7896 (ptt-90) REVERT: J 82 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.7015 (mtm-85) REVERT: J 161 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7246 (mt-10) REVERT: J 171 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8647 (tt0) REVERT: L 93 GLU cc_start: 0.8042 (mp0) cc_final: 0.7524 (mp0) outliers start: 92 outliers final: 53 residues processed: 649 average time/residue: 0.7509 time to fit residues: 530.0927 Evaluate side-chains 653 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 588 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain F residue 162 ARG Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 200 LYS Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 93 GLU Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 268 GLU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 82 ARG Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 171 GLN Chi-restraints excluded: chain J residue 200 LYS Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 215 ASP Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain K residue 162 ARG Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain K residue 203 ARG Chi-restraints excluded: chain L residue 56 LYS Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 221 MET Chi-restraints excluded: chain L residue 222 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 63 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 180 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 191 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN E 171 GLN I 171 GLN K 171 GLN L 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.126029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.109440 restraints weight = 23037.609| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.94 r_work: 0.3409 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18000 Z= 0.128 Angle : 0.558 6.194 24450 Z= 0.274 Chirality : 0.043 0.163 2886 Planarity : 0.006 0.049 3246 Dihedral : 6.131 55.761 2674 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.39 % Favored : 96.39 % Rotamer: Outliers : 5.06 % Allowed : 29.98 % Favored : 64.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 aren not related in a simple way. whole: -0.38 (0.17), residues: 2298 helix: -0.03 (0.34), residues: 246 sheet: -0.83 (0.17), residues: 642 loop : 0.13 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 203 TYR 0.009 0.001 TYR L 182 PHE 0.004 0.001 PHE G 157 TRP 0.008 0.001 TRP I 101 Details of bonding type rmsd covalent geometry : bond 0.00323 (18000) covalent geometry : angle 0.55808 (24450) hydrogen bonds : bond 0.03379 ( 534) hydrogen bonds : angle 4.38390 ( 1305) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 594 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8514 (tp) REVERT: B 54 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6648 (pp20) REVERT: B 171 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8596 (tt0) REVERT: C 206 ARG cc_start: 0.8349 (mtm110) cc_final: 0.8080 (mtm180) REVERT: C 239 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: C 268 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6085 (mm-30) REVERT: D 82 ARG cc_start: 0.7943 (mtp85) cc_final: 0.7668 (mtp85) REVERT: D 162 ARG cc_start: 0.6382 (OUTLIER) cc_final: 0.6122 (mtt-85) REVERT: D 178 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7769 (ttm170) REVERT: E 63 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7925 (ptt-90) REVERT: E 163 ASP cc_start: 0.7249 (p0) cc_final: 0.7006 (p0) REVERT: F 222 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7792 (tt) REVERT: G 161 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: H 58 VAL cc_start: 0.8720 (t) cc_final: 0.8426 (p) REVERT: H 268 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7652 (pp20) REVERT: I 63 ARG cc_start: 0.8257 (mtp180) cc_final: 0.7879 (ptt-90) REVERT: J 82 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.7065 (mtm-85) REVERT: J 161 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7246 (mt-10) REVERT: J 171 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8703 (tt0) REVERT: L 93 GLU cc_start: 0.8099 (mp0) cc_final: 0.7544 (mp0) outliers start: 95 outliers final: 62 residues processed: 652 average time/residue: 0.7924 time to fit residues: 561.1949 Evaluate side-chains 666 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 591 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 162 ARG Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 200 LYS Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 93 GLU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 268 GLU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain I residue 56 LYS Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 82 ARG Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 171 GLN Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 200 LYS Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 215 ASP Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 162 ARG Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain K residue 203 ARG Chi-restraints excluded: chain L residue 56 LYS Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 221 MET Chi-restraints excluded: chain L residue 222 LEU Chi-restraints excluded: chain L residue 228 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 95 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 86 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 5 optimal weight: 0.0570 chunk 155 optimal weight: 0.3980 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 171 GLN I 171 GLN K 171 GLN L 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.127528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.110830 restraints weight = 23160.108| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.96 r_work: 0.3430 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18000 Z= 0.090 Angle : 0.530 7.450 24450 Z= 0.260 Chirality : 0.042 0.159 2886 Planarity : 0.005 0.045 3246 Dihedral : 5.761 54.333 2674 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.09 % Favored : 96.74 % Rotamer: Outliers : 4.47 % Allowed : 30.40 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 aren not related in a simple way. whole: -0.26 (0.17), residues: 2298 helix: 0.14 (0.35), residues: 246 sheet: -0.76 (0.17), residues: 642 loop : 0.21 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 203 TYR 0.007 0.001 TYR B 182 PHE 0.004 0.001 PHE K 157 TRP 0.009 0.001 TRP I 101 Details of bonding type rmsd covalent geometry : bond 0.00226 (18000) covalent geometry : angle 0.52957 (24450) hydrogen bonds : bond 0.02657 ( 534) hydrogen bonds : angle 4.16518 ( 1305) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 595 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8493 (tp) REVERT: A 171 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8635 (tt0) REVERT: B 54 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6611 (pp20) REVERT: C 206 ARG cc_start: 0.8358 (mtm110) cc_final: 0.8086 (mtm180) REVERT: C 239 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: C 268 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.5969 (mm-30) REVERT: D 162 ARG cc_start: 0.6411 (OUTLIER) cc_final: 0.6160 (mtt-85) REVERT: D 178 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7724 (ttm170) REVERT: E 63 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7881 (ptt-90) REVERT: E 163 ASP cc_start: 0.7180 (p0) cc_final: 0.6940 (p0) REVERT: F 222 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7701 (tt) REVERT: G 161 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: H 58 VAL cc_start: 0.8619 (t) cc_final: 0.8329 (p) REVERT: H 268 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7618 (pt0) REVERT: I 63 ARG cc_start: 0.8251 (mtp180) cc_final: 0.7905 (ptt-90) REVERT: J 82 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6949 (mtm-85) REVERT: J 115 LEU cc_start: 0.8675 (mt) cc_final: 0.8473 (mp) REVERT: J 161 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7281 (mt-10) REVERT: J 171 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8666 (tt0) REVERT: L 93 GLU cc_start: 0.8092 (mp0) cc_final: 0.7591 (mp0) outliers start: 84 outliers final: 48 residues processed: 648 average time/residue: 0.7413 time to fit residues: 522.9121 Evaluate side-chains 656 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 595 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain F residue 162 ARG Chi-restraints excluded: chain F residue 200 LYS Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 93 GLU Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 268 GLU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 82 ARG Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 171 GLN Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 200 LYS Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 215 ASP Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 221 MET Chi-restraints excluded: chain L residue 222 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 113 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 42 optimal weight: 0.0570 chunk 74 optimal weight: 0.0060 chunk 192 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 207 optimal weight: 0.5980 chunk 143 optimal weight: 0.1980 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 GLN E 171 GLN I 171 GLN I 225 GLN K 171 GLN L 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.127654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.111030 restraints weight = 23028.391| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.95 r_work: 0.3434 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18000 Z= 0.092 Angle : 0.536 7.824 24450 Z= 0.261 Chirality : 0.042 0.160 2886 Planarity : 0.005 0.054 3246 Dihedral : 5.441 58.875 2665 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.00 % Favored : 96.82 % Rotamer: Outliers : 3.46 % Allowed : 31.79 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 aren not related in a simple way. whole: -0.18 (0.17), residues: 2298 helix: 0.26 (0.35), residues: 246 sheet: -0.71 (0.17), residues: 642 loop : 0.24 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 203 TYR 0.007 0.001 TYR L 182 PHE 0.004 0.001 PHE K 157 TRP 0.007 0.001 TRP E 101 Details of bonding type rmsd covalent geometry : bond 0.00231 (18000) covalent geometry : angle 0.53570 (24450) hydrogen bonds : bond 0.02669 ( 534) hydrogen bonds : angle 4.10957 ( 1305) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 596 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8602 (tt0) REVERT: B 54 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6604 (pp20) REVERT: C 239 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: C 268 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.5916 (mt-10) REVERT: D 162 ARG cc_start: 0.6412 (OUTLIER) cc_final: 0.6170 (mtt-85) REVERT: D 178 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7751 (ttm170) REVERT: E 63 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7868 (ptt-90) REVERT: E 163 ASP cc_start: 0.7166 (p0) cc_final: 0.6945 (p0) REVERT: F 222 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7686 (tt) REVERT: G 161 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: H 268 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7630 (pt0) REVERT: I 63 ARG cc_start: 0.8256 (mtp180) cc_final: 0.7906 (ptt-90) REVERT: J 82 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6655 (mtm-85) REVERT: J 115 LEU cc_start: 0.8649 (mt) cc_final: 0.8431 (mp) REVERT: J 161 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7268 (mt-10) REVERT: J 171 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8672 (tt0) REVERT: L 93 GLU cc_start: 0.8084 (mp0) cc_final: 0.7586 (mp0) outliers start: 65 outliers final: 44 residues processed: 637 average time/residue: 0.7610 time to fit residues: 526.8621 Evaluate side-chains 645 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 589 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain F residue 162 ARG Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 200 LYS Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 93 GLU Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 268 GLU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 82 ARG Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 171 GLN Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 200 LYS Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 215 ASP Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 222 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 32 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 190 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 171 GLN I 171 GLN K 171 GLN L 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.125232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.108518 restraints weight = 22937.847| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.95 r_work: 0.3397 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18000 Z= 0.178 Angle : 0.610 7.369 24450 Z= 0.298 Chirality : 0.045 0.163 2886 Planarity : 0.006 0.060 3246 Dihedral : 5.671 58.287 2662 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.66 % Favored : 96.17 % Rotamer: Outliers : 3.78 % Allowed : 31.47 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 aren not related in a simple way. whole: -0.31 (0.17), residues: 2298 helix: 0.02 (0.34), residues: 246 sheet: -0.76 (0.18), residues: 642 loop : 0.16 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 126 TYR 0.011 0.001 TYR L 182 PHE 0.005 0.001 PHE G 157 TRP 0.006 0.001 TRP G 101 Details of bonding type rmsd covalent geometry : bond 0.00452 (18000) covalent geometry : angle 0.61006 (24450) hydrogen bonds : bond 0.03810 ( 534) hydrogen bonds : angle 4.44993 ( 1305) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 602 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6615 (pp20) REVERT: C 239 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: C 268 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6135 (mm-30) REVERT: D 162 ARG cc_start: 0.6433 (OUTLIER) cc_final: 0.6174 (mtt-85) REVERT: D 178 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7824 (ttm170) REVERT: E 63 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7820 (ptt-90) REVERT: E 74 ASP cc_start: 0.7486 (p0) cc_final: 0.6365 (p0) REVERT: E 163 ASP cc_start: 0.7184 (p0) cc_final: 0.6949 (p0) REVERT: F 89 TYR cc_start: 0.8997 (m-80) cc_final: 0.8710 (m-80) REVERT: F 222 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7818 (tt) REVERT: G 161 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: H 58 VAL cc_start: 0.8642 (t) cc_final: 0.8441 (p) REVERT: I 63 ARG cc_start: 0.8250 (mtp180) cc_final: 0.7874 (ptt-90) REVERT: J 81 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7876 (mt) REVERT: J 82 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6904 (mtm-85) REVERT: J 115 LEU cc_start: 0.8692 (mt) cc_final: 0.8435 (mp) REVERT: J 161 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7241 (mt-10) REVERT: J 171 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8755 (tt0) REVERT: L 93 GLU cc_start: 0.8113 (mp0) cc_final: 0.7566 (mp0) outliers start: 71 outliers final: 47 residues processed: 644 average time/residue: 0.7716 time to fit residues: 540.7664 Evaluate side-chains 659 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 601 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain F residue 162 ARG Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 200 LYS Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 268 GLU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 82 ARG Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 171 GLN Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 200 LYS Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 215 ASP Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 222 LEU Chi-restraints excluded: chain L residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 116 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 112 optimal weight: 0.0980 chunk 64 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 GLN E 171 GLN I 171 GLN K 171 GLN L 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.124998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.108489 restraints weight = 23070.301| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.90 r_work: 0.3391 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18000 Z= 0.197 Angle : 0.629 7.293 24450 Z= 0.310 Chirality : 0.046 0.164 2886 Planarity : 0.006 0.061 3246 Dihedral : 5.691 58.424 2662 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.66 % Favored : 96.17 % Rotamer: Outliers : 3.41 % Allowed : 31.52 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 aren not related in a simple way. whole: -0.38 (0.17), residues: 2298 helix: -0.07 (0.34), residues: 246 sheet: -0.78 (0.18), residues: 642 loop : 0.10 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 91 TYR 0.013 0.001 TYR B 182 PHE 0.005 0.001 PHE G 157 TRP 0.009 0.001 TRP A 101 Details of bonding type rmsd covalent geometry : bond 0.00503 (18000) covalent geometry : angle 0.62906 (24450) hydrogen bonds : bond 0.03985 ( 534) hydrogen bonds : angle 4.52242 ( 1305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10300.64 seconds wall clock time: 174 minutes 36.03 seconds (10476.03 seconds total)