Starting phenix.real_space_refine on Sun Jun 15 18:21:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gzr_51732/06_2025/9gzr_51732.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gzr_51732/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9gzr_51732/06_2025/9gzr_51732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gzr_51732/06_2025/9gzr_51732.map" model { file = "/net/cci-nas-00/data/ceres_data/9gzr_51732/06_2025/9gzr_51732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gzr_51732/06_2025/9gzr_51732.cif" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.06, per 1000 atoms: 0.62 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: 4.31 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.63 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: 5.46 Time building geometry restraints manager: 5.02 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: 0.02 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: 1.850 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: 0.780 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 41.500 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.380 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.002 TRP G 101 PHE 0.007 0.001 PHE F 145 TYR 0.014 0.001 TYR B 182 ARG 0.015 0.001 ARG H 203 Details of bonding type rmsd hydrogen bonds : bond 0.22720 ( 534) hydrogen bonds : angle 7.61375 ( 1305) covalent geometry : bond 0.00323 (18000) covalent geometry : angle 0.65328 (24450) *********************** 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 : 1.907 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: 1.7874 time to fit residues: 1165.2076 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 : 2.313 ------------------------------------------------------------------------------- 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 192 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 59 optimal weight: 0.2980 chunk 116 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 108 optimal weight: 0.0770 chunk 133 optimal weight: 0.8980 chunk 207 optimal weight: 0.5980 overall best weight: 1.1740 ------------------------------------------------------------------------------- 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 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 = 0.3755 r_free = 0.3755 target = 0.125763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.109367 restraints weight = 22912.111| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.89 r_work: 0.3411 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18000 Z= 0.150 Angle : 0.602 5.733 24450 Z= 0.296 Chirality : 0.045 0.164 2886 Planarity : 0.006 0.045 3246 Dihedral : 8.164 62.348 2760 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.74 % Favored : 96.00 % Rotamer: Outliers : 5.64 % Allowed : 30.14 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.16), residues: 2298 helix: -1.21 (0.30), residues: 276 sheet: -0.92 (0.17), residues: 642 loop : 0.12 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 101 PHE 0.008 0.002 PHE F 145 TYR 0.012 0.001 TYR L 182 ARG 0.008 0.001 ARG F 206 Details of bonding type rmsd hydrogen bonds : bond 0.04347 ( 534) hydrogen bonds : angle 5.08494 ( 1305) covalent geometry : bond 0.00369 (18000) covalent geometry : angle 0.60244 (24450) *********************** 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 682 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 576 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8616 (tt0) REVERT: A 265 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7007 (mp10) REVERT: B 77 SER cc_start: 0.8708 (t) cc_final: 0.8507 (m) REVERT: C 239 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: D 82 ARG cc_start: 0.7812 (mtp85) cc_final: 0.7560 (mtp85) REVERT: E 63 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7823 (ptt-90) REVERT: G 161 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: H 58 VAL cc_start: 0.8793 (t) cc_final: 0.8511 (p) REVERT: J 82 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7052 (mtm-85) REVERT: J 161 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7296 (mt-10) REVERT: K 74 ASP cc_start: 0.7432 (p0) cc_final: 0.7224 (p0) REVERT: K 268 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.6129 (pp20) REVERT: L 93 GLU cc_start: 0.7996 (mp0) cc_final: 0.7394 (mp0) outliers start: 106 outliers final: 55 residues processed: 635 average time/residue: 1.6910 time to fit residues: 1165.8531 Evaluate side-chains 630 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 568 time to evaluate : 1.876 ------------------------------------------------------------------------------- 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 212 VAL 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 222 LEU 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 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 125 ILE Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 58 VAL 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 F residue 174 LEU Chi-restraints excluded: chain F residue 200 LYS Chi-restraints excluded: chain F residue 228 SER 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 222 LEU 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 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 222 LEU 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 K residue 268 GLU 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 228 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 71 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 171 GLN G 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 = 0.3735 r_free = 0.3735 target = 0.124222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.107844 restraints weight = 23014.382| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.89 r_work: 0.3384 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 18000 Z= 0.268 Angle : 0.667 5.894 24450 Z= 0.330 Chirality : 0.049 0.171 2886 Planarity : 0.007 0.044 3246 Dihedral : 7.577 61.659 2698 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.66 % Favored : 96.08 % Rotamer: Outliers : 5.96 % Allowed : 28.75 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.16), residues: 2298 helix: -1.16 (0.30), residues: 276 sheet: -0.93 (0.18), residues: 642 loop : -0.01 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 101 PHE 0.008 0.002 PHE G 157 TYR 0.015 0.002 TYR B 182 ARG 0.010 0.001 ARG F 206 Details of bonding type rmsd hydrogen bonds : bond 0.05092 ( 534) hydrogen bonds : angle 5.08689 ( 1305) covalent geometry : bond 0.00681 (18000) covalent geometry : angle 0.66706 (24450) *********************** 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 704 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 592 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.8806 (mmm160) cc_final: 0.8554 (mtp180) REVERT: C 239 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: D 82 ARG cc_start: 0.7947 (mtp85) cc_final: 0.7702 (mtp85) REVERT: D 162 ARG cc_start: 0.6498 (OUTLIER) cc_final: 0.6280 (mtt-85) REVERT: D 178 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7909 (ttm170) REVERT: E 63 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7644 (ptt-90) REVERT: E 74 ASP cc_start: 0.7541 (p0) cc_final: 0.6393 (p0) REVERT: E 163 ASP cc_start: 0.7284 (p0) cc_final: 0.7035 (p0) REVERT: F 222 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7938 (tt) REVERT: G 161 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: I 56 LYS cc_start: 0.6516 (OUTLIER) cc_final: 0.6131 (ptpt) REVERT: J 82 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7111 (mtm-85) REVERT: J 161 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7293 (mt-10) REVERT: K 268 GLU cc_start: 0.6519 (OUTLIER) cc_final: 0.6148 (pp20) REVERT: L 89 TYR cc_start: 0.8963 (m-80) cc_final: 0.8740 (m-80) REVERT: L 93 GLU cc_start: 0.8046 (mp0) cc_final: 0.7514 (mp0) outliers start: 112 outliers final: 74 residues processed: 656 average time/residue: 1.7446 time to fit residues: 1242.6850 Evaluate side-chains 665 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 582 time to evaluate : 2.312 ------------------------------------------------------------------------------- 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 A residue 188 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 222 LEU 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 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 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 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 91 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 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 222 LEU Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 63 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 215 ASP Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 56 LYS 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 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 136 VAL Chi-restraints excluded: chain J residue 186 ILE 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 246 GLU Chi-restraints excluded: chain J residue 263 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 77 SER 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 K residue 268 GLU 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 221 MET Chi-restraints excluded: chain L residue 222 LEU Chi-restraints excluded: chain L residue 228 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 171 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 102 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 171 GLN I 225 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 = 0.3744 r_free = 0.3744 target = 0.124777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.108429 restraints weight = 22943.113| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.89 r_work: 0.3394 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18000 Z= 0.191 Angle : 0.608 6.000 24450 Z= 0.302 Chirality : 0.046 0.167 2886 Planarity : 0.006 0.044 3246 Dihedral : 7.360 61.818 2694 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.00 % Favored : 95.74 % Rotamer: Outliers : 5.96 % Allowed : 29.50 % Favored : 64.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.16), residues: 2298 helix: -0.86 (0.30), residues: 276 sheet: -0.92 (0.18), residues: 642 loop : -0.00 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 101 PHE 0.006 0.002 PHE F 145 TYR 0.013 0.001 TYR B 182 ARG 0.010 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 534) hydrogen bonds : angle 4.82225 ( 1305) covalent geometry : bond 0.00482 (18000) covalent geometry : angle 0.60767 (24450) *********************** 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 694 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 582 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8727 (tt0) REVERT: A 234 ARG cc_start: 0.8772 (mmm160) cc_final: 0.8555 (mtp180) REVERT: A 265 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.6862 (mp10) REVERT: B 54 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6702 (pp20) REVERT: B 98 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.7943 (mmmm) REVERT: D 82 ARG cc_start: 0.7939 (mtp85) cc_final: 0.7684 (mtp85) REVERT: D 162 ARG cc_start: 0.6554 (OUTLIER) cc_final: 0.6317 (mtt-85) REVERT: D 171 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8582 (tt0) REVERT: D 178 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7860 (ttm170) REVERT: E 63 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7859 (ptt-90) REVERT: E 163 ASP cc_start: 0.7260 (p0) cc_final: 0.6997 (p0) REVERT: F 222 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7895 (tt) REVERT: G 161 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: H 58 VAL cc_start: 0.8789 (t) cc_final: 0.8525 (p) REVERT: H 268 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7618 (pp20) REVERT: J 82 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.7084 (mtm-85) REVERT: J 161 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7292 (mt-10) REVERT: K 74 ASP cc_start: 0.7338 (p0) cc_final: 0.7131 (p0) REVERT: K 75 ASP cc_start: 0.7427 (m-30) cc_final: 0.7221 (m-30) REVERT: K 268 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6144 (pp20) REVERT: L 82 ARG cc_start: 0.8159 (mmt90) cc_final: 0.7920 (mtt90) REVERT: L 93 GLU cc_start: 0.8057 (mp0) cc_final: 0.7516 (mp0) outliers start: 112 outliers final: 71 residues processed: 647 average time/residue: 2.0927 time to fit residues: 1477.7486 Evaluate side-chains 673 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 589 time to evaluate : 2.616 ------------------------------------------------------------------------------- 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 171 GLN Chi-restraints excluded: chain A residue 212 VAL 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 83 THR Chi-restraints excluded: chain B residue 98 LYS 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 233 ILE 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 171 GLN 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 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 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 222 LEU 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 222 LEU Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain I residue 56 LYS 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 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 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 222 LEU Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 263 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 77 SER 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 K residue 268 GLU 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 207 THR Chi-restraints excluded: chain L residue 221 MET Chi-restraints excluded: chain L residue 222 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 24 optimal weight: 0.0070 chunk 23 optimal weight: 5.9990 chunk 221 optimal weight: 0.6980 chunk 168 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 132 optimal weight: 0.0170 chunk 93 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 171 GLN G 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 = 0.3773 r_free = 0.3773 target = 0.126880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.110509 restraints weight = 23275.855| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.92 r_work: 0.3425 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1331 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= 0.091 Angle : 0.530 5.723 24450 Z= 0.262 Chirality : 0.042 0.162 2886 Planarity : 0.005 0.041 3246 Dihedral : 6.752 62.384 2689 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.18 % Favored : 96.56 % Rotamer: Outliers : 4.79 % Allowed : 30.62 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.17), residues: 2298 helix: -0.35 (0.32), residues: 276 sheet: -0.88 (0.17), residues: 642 loop : 0.13 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 101 PHE 0.004 0.001 PHE F 157 TYR 0.008 0.001 TYR B 182 ARG 0.011 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.02951 ( 534) hydrogen bonds : angle 4.35420 ( 1305) covalent geometry : bond 0.00223 (18000) covalent geometry : angle 0.52966 (24450) *********************** 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 701 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 611 time to evaluate : 2.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8498 (tp) REVERT: B 54 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6687 (pp20) REVERT: C 239 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: C 268 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6131 (mm-30) REVERT: D 82 ARG cc_start: 0.7909 (mtp85) cc_final: 0.7653 (mtp85) REVERT: D 162 ARG cc_start: 0.6449 (OUTLIER) cc_final: 0.6212 (mtt-85) REVERT: D 178 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7769 (ttm170) REVERT: E 63 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7867 (ptt-90) REVERT: E 163 ASP cc_start: 0.7243 (p0) cc_final: 0.6998 (p0) REVERT: F 91 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7774 (mtm-85) REVERT: F 222 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7861 (tt) REVERT: G 161 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: H 58 VAL cc_start: 0.8691 (t) cc_final: 0.8449 (p) REVERT: I 63 ARG cc_start: 0.8283 (mtp180) cc_final: 0.7864 (ptp-170) REVERT: J 82 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.7027 (mtm-85) REVERT: J 161 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7216 (mt-10) REVERT: K 74 ASP cc_start: 0.7401 (p0) cc_final: 0.7190 (p0) REVERT: K 75 ASP cc_start: 0.7400 (m-30) cc_final: 0.7114 (m-30) REVERT: K 268 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.6166 (pp20) REVERT: L 93 GLU cc_start: 0.8070 (mp0) cc_final: 0.7555 (mp0) outliers start: 90 outliers final: 43 residues processed: 659 average time/residue: 2.0291 time to fit residues: 1462.5794 Evaluate side-chains 655 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 601 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 162 ARG 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 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 215 ASP Chi-restraints excluded: chain E residue 63 ARG 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 114 THR Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain F residue 200 LYS Chi-restraints excluded: chain F residue 215 ASP 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 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 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 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 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 K residue 268 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 146 optimal weight: 0.3980 chunk 180 optimal weight: 2.9990 chunk 44 optimal weight: 0.0670 chunk 150 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 141 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 71 optimal weight: 0.0570 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN B 171 GLN D 171 GLN E 171 GLN I 171 GLN I 225 GLN K 171 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.126981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.110158 restraints weight = 23191.392| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.98 r_work: 0.3421 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1480 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= 0.091 Angle : 0.525 6.674 24450 Z= 0.258 Chirality : 0.042 0.161 2886 Planarity : 0.005 0.043 3246 Dihedral : 6.123 59.984 2678 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.39 % Favored : 96.39 % Rotamer: Outliers : 4.26 % Allowed : 31.58 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.17), residues: 2298 helix: 0.15 (0.35), residues: 246 sheet: -0.83 (0.17), residues: 642 loop : 0.21 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 101 PHE 0.008 0.001 PHE C 157 TYR 0.007 0.001 TYR B 182 ARG 0.011 0.000 ARG H 203 Details of bonding type rmsd hydrogen bonds : bond 0.02832 ( 534) hydrogen bonds : angle 4.22543 ( 1305) covalent geometry : bond 0.00227 (18000) covalent geometry : angle 0.52483 (24450) *********************** 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 680 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 600 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8532 (tp) REVERT: A 171 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8566 (tt0) REVERT: B 54 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6682 (pp20) REVERT: C 239 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: C 268 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6069 (mm-30) REVERT: D 82 ARG cc_start: 0.7904 (mtp85) cc_final: 0.7628 (mtp85) REVERT: D 178 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7721 (ttm170) REVERT: E 63 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7916 (ptt-90) REVERT: E 163 ASP cc_start: 0.7195 (p0) cc_final: 0.6939 (p0) REVERT: F 91 ARG cc_start: 0.7988 (mtm-85) cc_final: 0.7756 (mtm-85) REVERT: F 222 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7848 (tt) REVERT: G 161 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: H 58 VAL cc_start: 0.8638 (t) cc_final: 0.8378 (p) REVERT: I 63 ARG cc_start: 0.8291 (mtp180) cc_final: 0.7840 (ptp-170) REVERT: J 82 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7048 (mtm-85) REVERT: J 161 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7276 (mt-10) REVERT: K 74 ASP cc_start: 0.7393 (p0) cc_final: 0.7186 (p0) REVERT: K 75 ASP cc_start: 0.7402 (m-30) cc_final: 0.7094 (m-30) REVERT: K 268 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6154 (pp20) REVERT: L 93 GLU cc_start: 0.8111 (mp0) cc_final: 0.7548 (mp0) outliers start: 80 outliers final: 47 residues processed: 646 average time/residue: 1.7084 time to fit residues: 1200.6489 Evaluate side-chains 653 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 595 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 163 ASP Chi-restraints excluded: chain A residue 171 GLN 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 239 GLU Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain D residue 90 ASP 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 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 215 ASP Chi-restraints excluded: chain F residue 114 THR 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 215 ASP 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 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 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 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 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 203 ARG Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 221 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 222 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 197 optimal weight: 0.0870 chunk 163 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 GLN D 171 GLN E 171 GLN I 171 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 = 0.3759 r_free = 0.3759 target = 0.126000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.109259 restraints weight = 23101.411| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.95 r_work: 0.3409 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1498 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= 0.123 Angle : 0.553 6.874 24450 Z= 0.270 Chirality : 0.043 0.163 2886 Planarity : 0.006 0.049 3246 Dihedral : 6.105 59.768 2674 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.39 % Favored : 96.39 % Rotamer: Outliers : 4.63 % Allowed : 30.99 % Favored : 64.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.17), residues: 2298 helix: 0.14 (0.34), residues: 246 sheet: -0.80 (0.17), residues: 642 loop : 0.21 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 101 PHE 0.004 0.001 PHE F 145 TYR 0.010 0.001 TYR B 182 ARG 0.012 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 534) hydrogen bonds : angle 4.31103 ( 1305) covalent geometry : bond 0.00310 (18000) covalent geometry : angle 0.55258 (24450) *********************** 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 682 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 595 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8564 (tp) REVERT: A 171 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8628 (tt0) REVERT: B 54 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6673 (pp20) REVERT: C 239 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: C 268 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6062 (mm-30) REVERT: D 82 ARG cc_start: 0.7913 (mtp85) cc_final: 0.7636 (mtp85) REVERT: D 178 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7786 (ttm170) REVERT: E 63 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7946 (ptt-90) REVERT: E 163 ASP cc_start: 0.7250 (p0) cc_final: 0.7004 (p0) REVERT: F 222 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7854 (tt) REVERT: G 161 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: H 58 VAL cc_start: 0.8667 (t) cc_final: 0.8405 (p) REVERT: I 63 ARG cc_start: 0.8274 (mtp180) cc_final: 0.7816 (ptp-170) REVERT: J 82 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.7056 (mtm-85) REVERT: J 161 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7260 (mt-10) REVERT: J 171 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8733 (tt0) REVERT: K 268 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.6142 (pp20) REVERT: L 93 GLU cc_start: 0.8112 (mp0) cc_final: 0.7548 (mp0) outliers start: 87 outliers final: 52 residues processed: 643 average time/residue: 1.6486 time to fit residues: 1152.6483 Evaluate side-chains 655 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 591 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 233 ILE Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain D residue 136 VAL 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 222 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 114 THR 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 215 ASP 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 116 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 222 LEU 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 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 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 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 268 GLU Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 207 THR 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 80 optimal weight: 1.9990 chunk 109 optimal weight: 0.0060 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 206 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 209 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 164 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 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 = 0.3759 r_free = 0.3759 target = 0.126180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.109351 restraints weight = 22948.942| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.97 r_work: 0.3407 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1545 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= 0.125 Angle : 0.558 6.939 24450 Z= 0.273 Chirality : 0.043 0.162 2886 Planarity : 0.006 0.056 3246 Dihedral : 5.786 59.294 2666 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.61 % Favored : 96.17 % Rotamer: Outliers : 4.63 % Allowed : 31.31 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.17), residues: 2298 helix: 0.18 (0.34), residues: 246 sheet: -0.80 (0.17), residues: 642 loop : 0.21 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 101 PHE 0.004 0.001 PHE G 157 TYR 0.010 0.001 TYR B 182 ARG 0.013 0.000 ARG H 203 Details of bonding type rmsd hydrogen bonds : bond 0.03240 ( 534) hydrogen bonds : angle 4.29250 ( 1305) covalent geometry : bond 0.00315 (18000) covalent geometry : angle 0.55776 (24450) *********************** 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 682 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 595 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8559 (tp) REVERT: A 171 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8624 (tt0) REVERT: B 54 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6665 (pp20) REVERT: B 171 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8597 (tt0) REVERT: C 239 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: C 268 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6061 (mm-30) REVERT: D 82 ARG cc_start: 0.7933 (mtp85) cc_final: 0.7663 (mtp85) REVERT: D 178 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7763 (ttm170) REVERT: E 63 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7943 (ptt-90) REVERT: E 163 ASP cc_start: 0.7220 (p0) cc_final: 0.6979 (p0) REVERT: F 222 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7867 (tt) REVERT: G 161 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: H 58 VAL cc_start: 0.8666 (t) cc_final: 0.8399 (p) REVERT: H 268 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7585 (pp20) REVERT: I 63 ARG cc_start: 0.8270 (mtp180) cc_final: 0.7823 (ptp-170) REVERT: J 82 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7069 (mtm-85) REVERT: J 161 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7263 (mt-10) REVERT: J 171 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8736 (tt0) REVERT: K 268 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.6041 (pp20) REVERT: L 93 GLU cc_start: 0.8123 (mp0) cc_final: 0.7565 (mp0) outliers start: 87 outliers final: 57 residues processed: 643 average time/residue: 1.6330 time to fit residues: 1142.7415 Evaluate side-chains 661 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 590 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 163 ASP Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 181 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 136 VAL 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 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 162 ARG Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 200 LYS Chi-restraints excluded: chain F residue 215 ASP 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 116 GLU 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 222 LEU Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain I residue 56 LYS 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 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 200 LYS Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 215 ASP Chi-restraints excluded: chain K residue 63 ARG 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 268 GLU Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 207 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 94 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 225 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN D 171 GLN E 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 = 0.3762 r_free = 0.3762 target = 0.126038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.109544 restraints weight = 22995.967| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.91 r_work: 0.3413 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1585 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= 0.134 Angle : 0.571 7.096 24450 Z= 0.279 Chirality : 0.044 0.161 2886 Planarity : 0.006 0.060 3246 Dihedral : 5.803 59.965 2666 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.52 % Favored : 96.30 % Rotamer: Outliers : 4.31 % Allowed : 31.79 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.17), residues: 2298 helix: 0.20 (0.34), residues: 246 sheet: -0.80 (0.17), residues: 642 loop : 0.20 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 101 PHE 0.004 0.001 PHE G 157 TYR 0.011 0.001 TYR B 182 ARG 0.014 0.000 ARG H 203 Details of bonding type rmsd hydrogen bonds : bond 0.03345 ( 534) hydrogen bonds : angle 4.32355 ( 1305) covalent geometry : bond 0.00340 (18000) covalent geometry : angle 0.57068 (24450) *********************** 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 680 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 599 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8571 (tp) REVERT: A 171 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8611 (tt0) REVERT: B 54 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6648 (pp20) REVERT: B 171 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8561 (tt0) REVERT: B 234 ARG cc_start: 0.8669 (mtp180) cc_final: 0.8394 (mtp180) REVERT: C 239 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: C 268 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6053 (mm-30) REVERT: D 178 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7821 (ttm170) REVERT: E 63 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7899 (ptt-90) REVERT: E 74 ASP cc_start: 0.7502 (p0) cc_final: 0.6816 (p0) REVERT: E 163 ASP cc_start: 0.7224 (p0) cc_final: 0.7008 (p0) REVERT: F 222 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7892 (tt) REVERT: G 161 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: H 58 VAL cc_start: 0.8680 (t) cc_final: 0.8440 (p) REVERT: I 63 ARG cc_start: 0.8238 (mtp180) cc_final: 0.7876 (ptp-170) REVERT: J 82 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7064 (mtm-85) REVERT: J 161 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7205 (mt-10) REVERT: J 171 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8709 (tt0) REVERT: K 268 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.6068 (pp20) REVERT: L 93 GLU cc_start: 0.8071 (mp0) cc_final: 0.7547 (mp0) outliers start: 81 outliers final: 62 residues processed: 643 average time/residue: 1.5941 time to fit residues: 1116.0269 Evaluate side-chains 672 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 597 time to evaluate : 1.915 ------------------------------------------------------------------------------- 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 171 GLN Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 181 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 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 81 LEU Chi-restraints excluded: chain D residue 136 VAL 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 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 162 ARG Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 200 LYS Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 93 GLU Chi-restraints excluded: chain G residue 116 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 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 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 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 263 LEU Chi-restraints excluded: chain K residue 63 ARG 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 K residue 268 GLU Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 207 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 125 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN D 171 GLN E 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 = 0.3733 r_free = 0.3733 target = 0.124019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.107505 restraints weight = 22873.666| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.89 r_work: 0.3380 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 18000 Z= 0.271 Angle : 0.680 7.185 24450 Z= 0.333 Chirality : 0.049 0.167 2886 Planarity : 0.007 0.068 3246 Dihedral : 6.273 59.459 2666 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.96 % Favored : 95.87 % Rotamer: Outliers : 4.42 % Allowed : 31.58 % Favored : 64.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.16), residues: 2298 helix: -0.26 (0.33), residues: 246 sheet: -0.84 (0.18), residues: 642 loop : 0.04 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 101 PHE 0.007 0.002 PHE G 157 TYR 0.016 0.002 TYR B 182 ARG 0.016 0.001 ARG F 91 Details of bonding type rmsd hydrogen bonds : bond 0.04585 ( 534) hydrogen bonds : angle 4.72984 ( 1305) covalent geometry : bond 0.00692 (18000) covalent geometry : angle 0.68046 (24450) ********************** 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 684 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 601 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6686 (pp20) REVERT: B 171 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8588 (tt0) REVERT: B 234 ARG cc_start: 0.8706 (mtp180) cc_final: 0.8433 (mtp180) REVERT: C 239 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7898 (mt-10) REVERT: C 268 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6312 (mm-30) REVERT: D 178 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7867 (ttm170) REVERT: E 63 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7971 (ptt-90) REVERT: E 163 ASP cc_start: 0.7235 (p0) cc_final: 0.6996 (p0) REVERT: F 165 GLU cc_start: 0.7065 (mp0) cc_final: 0.6793 (mp0) REVERT: F 222 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7962 (tt) REVERT: G 161 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: H 58 VAL cc_start: 0.8777 (t) cc_final: 0.8538 (p) REVERT: I 63 ARG cc_start: 0.8281 (mtp180) cc_final: 0.7825 (ptp-170) REVERT: J 82 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.7126 (mtm-85) REVERT: J 161 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7252 (mt-10) REVERT: J 171 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8762 (tt0) REVERT: K 268 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6114 (pp20) REVERT: L 93 GLU cc_start: 0.8091 (mp0) cc_final: 0.7582 (mp0) outliers start: 83 outliers final: 57 residues processed: 647 average time/residue: 1.6114 time to fit residues: 1141.6130 Evaluate side-chains 668 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 600 time to evaluate : 1.924 ------------------------------------------------------------------------------- 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 235 SER 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 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 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 136 VAL 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 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 174 LEU Chi-restraints excluded: chain F residue 200 LYS Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 116 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 I residue 56 LYS 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 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 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 263 LEU Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain K residue 203 ARG Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain L residue 125 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 36 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 138 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 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 = 0.3759 r_free = 0.3759 target = 0.125890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.109089 restraints weight = 22986.967| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.96 r_work: 0.3401 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18000 Z= 0.122 Angle : 0.580 7.990 24450 Z= 0.286 Chirality : 0.043 0.160 2886 Planarity : 0.006 0.063 3246 Dihedral : 5.878 59.985 2664 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.70 % Favored : 96.13 % Rotamer: Outliers : 3.83 % Allowed : 32.48 % Favored : 63.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.17), residues: 2298 helix: 0.06 (0.34), residues: 246 sheet: -0.83 (0.18), residues: 642 loop : 0.10 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 101 PHE 0.008 0.001 PHE L 157 TYR 0.013 0.001 TYR B 182 ARG 0.015 0.001 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 534) hydrogen bonds : angle 4.39128 ( 1305) covalent geometry : bond 0.00304 (18000) covalent geometry : angle 0.58047 (24450) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23583.69 seconds wall clock time: 409 minutes 56.99 seconds (24596.99 seconds total)